********************************************************************************
RefSeq-release214.txt       ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/

		NCBI Reference Sequence (RefSeq) Database

			Release 214
			September 12, 2022

		Distribution Release Notes

Release Size:	
   123394 organisms
   3197618853054 nucleotide bases
   93402053269 amino acids
   328588569 records
******************************************************************************

This document describes the format and content of the flat files that 
comprise releases of the NCBI Reference Sequence (RefSeq) database.

Additional information about RefSeq is available at:

1. NCBI Bookshelf:
   a) NCBI Handbook:  
   https://www.ncbi.nlm.nih.gov/books/NBK21091/
   b) RefSeq Help (FAQ)
   https://www.ncbi.nlm.nih.gov/books/NBK50680/
 
2. RefSeq Web Sites: 
   RefSeq Home:  https://www.ncbi.nlm.nih.gov/refseq/
   RefSeqGene Home: https://www.ncbi.nlm.nih.gov/refseq/rsg/

If you have any questions or comments about RefSeq, the RefSeq release files
or this document, please contact NCBI by email at:
   info@ncbi.nlm.nih.gov. 

To receive announcements of future RefSeq releases and large updates please
subscribe to NCBI's refseq-announce mail list:

   send email to refseq-announce-subscribe@ncbi.nlm.nih.gov
   with "subscribe" in the subject line (without quotes)
   and nothing in the email body

OR

subscribe using the web interface at:
   https://www.ncbi.nlm.nih.gov/mailman/listinfo/refseq-announce

=============================================================================
TABLE OF CONTENTS
=============================================================================
1. INTRODUCTION	
	1.1 This release
	1.2 Cutoff date
	1.3 RefSeq Project Background
		1.3.1 Sequence accessions, validation, and annotations
		1.3.2 Data assembly, curation, and collaboration 
		1.3.3 Biologically non-redundant data set
		1.3.4 RefSeq and DDBJ/EMBL/GenBank comparison
	1.4 Uses and applications of the RefSeq database
2. CONTENT
	2.1 Organisms included
	2.2 Molecule Types included
	2.3 Known Problems, Redundancies, and Inconsistencies
	2.4 Release Catalog
	2.5 Changes since the previous release 
3. ORGANIZATION OF DATA FILES
	3.1 FTP Site Organization
	3.2 Release Contents
	3.3 File Names and Formats
        3.4 File Sizes
        3.5 Statistics
	3.6 Release Catalog
	3.7 Removed Records
      	3.8 Accession Format
        3.9 Growth of RefSeq        
4. FLAT FILE ANNOTATION
	4.1 Main features of RefSeq Flat File
		4.1.1 LOCUS, DEFLINE, ACCESSION, KEYWORDS, SOURCE, ORGANISM
		4.1.2 REFERENCE, DIRECT SUBMISSION, COMMENT, PRIMARY
		4.1.3 NUCLEOTIDE FEATURE ANNOTATION (Gene, mRNA, CDS)
		4.1.4 PROTEIN FEATURE ANNOTATION
	4.2 Tracking Identifiers
		4.2.1 GeneID
		4.2.2 Transcript ID
		4.2.3 Protein ID
		4.2.4 Conserved Domain Database (CDD) ID
5. REFSEQ ADMINISTRATION
	5.1 Citing RefSeq
	5.2 RefSeq Distribution Formats
	5.3 Other Methods of Accessing RefSeq Data
	5.4 Request for Corrections and Comments
	5.5 Credits and Acknowledgements
	5.6 Disclaimer

=============================================================================
1. INTRODUCTION
=============================================================================
The NCBI Reference Sequence Project (RefSeq) is an effort to provide the 
best single collection of naturally occurring biomolecules, representative
of the central dogma, for each major organism. Ideally this would include 
one sequence record for each chromosome, organelle, or plasmid linked on a 
residue by residue basis to the expressed transcripts, to the translated 
proteins, and to each mature peptide product. Depending on the organism, we 
may have some, but not all, of this information at any given time. We 
pragmatically include the best view we can from available data.

Additional information about the RefSeq project is available from:
   a) RefSeq Web site  
      https://www.ncbi.nlm.nih.gov/refseq/
   b) Entrez Books, NCBI Handbook, RefSeq chapter
      https://www.ncbi.nlm.nih.gov/books/NBK21091/  

1.1 This Release 
----------------
The National Center for Biotechnology Information (NCBI) at the National
Library of Medicine (NLM), National Institutes of Health (NIH) is 
responsible for producing and distributing the RefSeq Sequence Database. 
Records are provided through a combination of collaboration and in-house 
processing including some curation by NCBI staff comprised of expert 
biologists.  

This is a full release of all NCBI RefSeq records.
The RefSeq project is an ongoing effort to provide a curated, non-redundant
collection of sequences. This release includes all of the sequence data
that we have collected at this time. Although the RefSeq collection is not yet 
complete, its value as a non-redundant dataset has reached a level that
justifies providing full releases.  

1.2 Cutoff date
---------------
This full release, Release 214, incorporates data available as of
September 12, 2022.

For more recent data, users are advised to:
	
   1. Download the RefSeq daily update files from the RefSeq FTP site
      ftp://ftp.ncbi.nlm.nih.gov/refseq/daily/

   2. Use NCBI's Entrez Programming Utilities to download records
      based on queries or lists of accessions
      https://www.ncbi.nlm.nih.gov/books/NBK25500/

   3. Use the interactive web query system to query based on date.
      https://www.ncbi.nlm.nih.gov/nucleotide/
      https://www.ncbi.nlm.nih.gov/protein/

1.3 RefSeq Project Background
-----------------------------

1.3.1 Sequence accessions, validation, and annotation
-----------------------------------------------------
Every sequence is assigned a stable accession and version, and 
all older versions remain available over time. RefSeq accessions
have a distinct format (see section 3.6); the underscore ("_") is the 
primary distinguishing feature of a RefSeq accession. 
DDBJ/EMBL/GenBank accessions never include an underscore.

Sequences are validated in several ways. For example, to confirm 
that genomic sequence from the region of the mRNA feature really 
does match the mRNA sequence itself, and that the annotated coding region 
features really can be translated into the protein sequences they refer to.
Validation also checks for valid ASN.1 format. Validation also ensures that
consistency is maintained in descriptive information (symbols, gene and 
protein names) between RefSeq and Gene records.

Each molecule is annotated as accurately as possible with the 
correct organism name, the correct gene symbol for that organism, 
and reasonable names for proteins where possible. When available, 
nomenclature provided by official nomenclature groups is used.  
Note that gene symbols are not required or expected to be unique 
either across species or within a species. 

1.3.2 Data assembly, curation, and collaboration 
------------------------------------------------
We welcome collaborations with authoritative groups outside NCBI 
who are willing to provide the sequences, annotations, or links 
to phenotypic or organism specific resources. Where such collaborations 
have not yet developed, NCBI staff have assembled the best view of 
the organism that we can put together ourselves. In some cases, as with the 
human genome, NCBI is an active participant in generating the 
genome assembly and in providing reference sequences to represent 
the annotated genome. For other genomes, we may compile the data 
ourselves from DDBJ/EMBL/GenBank or other public sources. For instance,  
we may simply select the "best" DDBJ/EMBL/GenBank record by automatic means, 
validate the data format (and correct if needed), and add an essentially 
unchanged copy to the RefSeq collection, attributed to the original 
DDBJ/EMBL/GenBank record. In other cases we may provide a record that is very 
similar to the DDBJ/EMBL/GenBank record, but to which experts at NCBI have added 
corrected or additional annotation. This latter process can range 
from minor technical repairs to a manually curated re-annotation of 
the sequence, often in collaboration with experts outside NCBI. 

Each record that has been curated, or that is in the pool for
future curation, is labeled with the level of curation it has received.  
Curation status information is provided primarily for transcript and 
protein records.  Curation is carried out on the whole genome level 
for some smaller genomes such as viral, organelle, and some microbial
genomes.  

Curation status codes are defined in the section 3.2 below.

1.3.3 Biologically non-redundant data set
-----------------------------------------
RefSeq provides a biologically non-redundant set of sequences for database 
searching and gene characterization. It has the advantage of providing an 
objective and experimentally verifiable definition of "non-redundant" in 
supplying one example of each natural biomolecule per organism or sample.
The small amount of sequence redundancy introduced from close paralogs,
alternate splicing products, and genome assembly intermediates is compensated
for by the clarity of the model. RefSeq provides the substrate for a variety
of conclusions about non-redundancy based on clustering identical sequences, 
or families of related sequences, without confounding the database itself 
with these more subjective assessments.

1.3.4 RefSeq and DDBJ/EMBL/GenBank comparison
---------------------------------------------
RefSeq is unique in providing a large curated database across many 
organisms, which precisely and explicitly links genetic (chromosome), 
expression (mRNA), and functional (protein) sequence data into an 
integrated whole. 

DDBJ/EMBL/GenBank also integrates DNA and protein information, and RefSeq is 
substantially based on sequence records contributed to DDBJ/EMBL/GenBank. 
However, RefSeq is similar to a review article in that it represents 
a synthesis and summary of information by a particular group (NCBI or 
other RefSeq contributors) that is based on the primary data gathered 
by many others and made part of the scientific record. Also, like a 
review article, it has the advantage of organizing a large body of 
diverse data into a single consistent framework with a uniform set of 
conventions and standards.

Note that while based on DDBJ/EMBL/GenBank, RefSeq is distinct from 
DDBJ/EMBL/GenBank. DDBJ/EMBL/GenBank represents the sequence and annotations 
supplied by the original authors and is never changed by NCBI or RefSeq staff. 
DDBJ/EMBL/GenBank remains the primary sequence archive while RefSeq is a 
summary and synthesis based on that essential primary data.

1.4 Uses and applications of the RefSeq database
------------------------------------------------
A stable, consistent, comprehensive, non-redundant database of genomes
and their products provides a valuable sequence resource for similarity 
searching, gene identification, protein classification, comparative 
genomics, and selection of probes for gene expression. It also acts as 
molecular "white pages" by providing a single, uniform point of access 
for searching at the sequence level, and by connecting the results with 
a diversity of organism-specific databases or resources unique to that 
organism or field. 

=============================================================================
2. CONTENT
=============================================================================
2.1 Organisms included
----------------------
This number of organisms reported for the release (section 3.5 below) is 
determined by counting the number of distinct tax_ids included in the release.
Tax_ids are provided by the NCBI Taxonomy group. Tax_ids were historically 
provided for all species and strains having any amount of sequence data. In 2014
NCBI stopped assigning strain-level tax_ids. Strains are now being tracked by
the BioSample database.  

The release includes species ranging from viral to microbial to eukaryotic and 
includes organisms for which complete and incomplete genomic sequence data is 
available.  

The release does not include all species for which some sequence data is
available in DDBJ/EMBL/GenBank. The decision to generate RefSeq data for a 
species or strain depends in part on the amount of sequence data available.  
Additional species will be represented in the RefSeq collection as more
sequence data becomes available.

2.2 Molecule Types Included
---------------------------
The RefSeq release includes genomic, transcript, and protein sequence data; 
however, these molecule types are not provided for all organisms and the 
sequences provided may not be complete or comprehensive for some species.  

Transcript RefSeq records may represent protein-coding transcripts or 
non-coding RNA products; these records are currently only provided for 
eukaryotic species.

Genomic RefSeq records are provided when a sufficient quantity of genomic 
sequence data is available in DDBJ/EMBL/GenBank. Transcript and protein 
records may be provided for a species before genomic sequence data is available.

2.3 Known Problems, Redundancies, and Inconsistencies
------------------------------------------------------

Known Problems with RefSeq release 214:	
======================================

There are no known problems with RefSeq release 214. 

Known Redunancies and Inconsistencies:
======================================
The RefSeq collection is an ongoing project that is expected to grow
in scope and content over time.  Thus it is important to recognize that
it is not complete in that some genomes are not yet completely sequenced,
some incompletely sequenced genomes may not be included, or some gene 
products may not yet be represented. RefSeq records may be added, removed, 
or updated in future releases as new information becomes available and as 
a result of curation.

Known Data inconsistencies:

	[1] RefSeq status codes are not consistently provided for some species. 
	The goal is to consistently provide a status code for all RefSeq
	records. The release catalog indicates "UNKNOWN" if a status code
	was expected but not detected and "na" if a status code is not
	expected based on the original project plan for provision of this type
	of information. Status codes will be more consistently applied to all 
	records in the future.

	[2] The genomic, transcript, and protein collection is known to be 
	incomplete for many species. This is particularly true for those
	genomes for which a complete genome assembly is not yet available, 
	such as Sus scrofa (pig). As additional sequence data becomes available, 
	the RefSeq representation for this, and other, organisms will increase. 
	
	[3] Whole genome shotgun (WGS) assemblies of organelle, plastid, or viral 
        genomes are included in the complete node and in the taxonomic group that 
        the whole genome WGS project is reported in (e.g., fungi etc.). Our process 
	flow for WGS data provides a data extraction per WGS project with no 
	distinction by molecule (such as mitochondrial). Therefore, some nodes do 
        not include WGS data or may include WGS data for different taxa. For instance, 
        NZ_ACSJ01000000 includes contigs representing two tax_ids - a bacterium and a 
        phage.  The entire WGS project has been processed for the complete node and 
        the microbial node in this release.  Therefore, the microbial node includes 
        a small amount of viral sequence and the viral node omits this data. 
    	NZ_ACSJ01000001 to NZ_ACSJ01000011 microbial contigs
    	NZ_ACSJ01000012 to NZ_ACSJ01000019 viral contigs

	[4] Although the goal is to provide a non-redundant collection, some
	redundancy is included in this release as follows. 	

	Redundant Protein records:
	    Alternate Splicing		When additional transcripts are provided
					to represent alternate splicing products, 
					and the alternate splice site occurs in 
					the UTR, then the protein is redundantly 
					provided.

	    Paralogs (eukaryotes)	The goal is to provide a RefSeq record 
					for each naturally occurring molecule. 
					Therefore, records are provided for all 
					genes identified including those produced 
					by more recent gene duplication events in 
					which the genes are nearly identical.
	
	Redundant Genomic records:				
	   Intermediate records		For some species, intermediate genomic 
					records are provided to support the 
					assembly and/or annotation of the genome.
	
					For example, for human, a chromosome may 
					be represented by a chromosome RefSeq 
					record with a NC_ accession prefix.
					The chromosome record may consist of 
					many contigs, each represented as a 
					separate record with a NT_ accession
					prefix. In addition, some curated gene
					region records, with NG_ accession
					prefix, may also be provided to support
					annotation of complex regions.
					
	   Alternate assemblies		Genomic records are provided to represent 
					alternate assemblies of genomic sequence
					derived from different populations. These 
					records will have varying levels of 
					redundancy and represent polymorphic and
					haplotype differences in terms of the
					sequence and annotation.

					For example, alternate assemblies are
					provided for different mouse strains and
					for regions of the human major
					histocompatibility complex (MHC). The MHC
					is a highly variable region of chromosome
					6 which exhibits variation at the level 
					of both sequence polymorphism and gene 
					content. The alternate assemblies make it
					possible to represent this alternate gene
					content. 					

	Prokaryotic strains		Prokaryotic genome sequence data derived from 
		  			different strains may be represented as 
					additional RefSeq records. This introduces 
					redundancy but may also add representation for 
					some proteins that are unique to a strain.  
					RefSeq records for a specific strain can be 
					identified by the unique taxonomic ID for that 
					strain. The protein complement is non-redundant.

	[5] Note that for some organisms, most notably vertebrates, processing to update 
	    individual transcript and protein records may occur on a daily basis. Transcript 
	    and protein updates may include changes to descriptive information such as 
	    publications, names, or feature annotations. Updates can also include changes 
	    to the sequence or the addition of new sequence records. Thus information 
	    available on transcript and protein records may be more current than the 
	    annotated genome.  

2.4 Release Catalog
-------------------
The Release Catalog documents the full contents of the RefSeq Release.
The catalog can be used to identify data of interest.  See the format
description in section 3.6 for additional information.

The release catalog is available at:
  ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/RefSeq-release#.catalog

The catalog for previous releases is available in the archive directory:
  ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/archive/

2.5 Changes since the previous release:	
--------------------------------------
[1] Foreign contamination screening
    Introducing the new Foreign Contamination Screen (FCS) tool! You can run this tool yourself,
    to improve your genome assemblies, and facilitate high-quality data submissions to GenBank.
    FCS is part of the NIH Comparative Genomics Resource (CGR), an NLM project to establish an
    ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms.
      https://www.ncbi.nlm.nih.gov/comparative-genomics-resource/
    Learn more about the enhanced contaminant detection sensitivity of FCS here:
      https://ncbiinsights.ncbi.nlm.nih.gov/2022/07/28/fcs-beta-tool/

[2] New eukaryotic genome annotations
    This release includes new annotations generated by NCBI's eukaryotic genome annotation 
    pipeline for 43 species, including
      Asiatic elephant annotation release 100, based on new assembly mEleMax1_primary_haplotype
      (GCF_024166365.1)
      Gray wolf (dingo) annotation release 102, based on updated assembly ASM325472v2
      (GCF_003254725.2)
      Reed vole annotation release 100, based on updated assembly M_Fortis_MF-2015_v1.1
      (GCF_014885135.2)
      Mexican tetra annotation release 103, based on new assembly AstMex3_surface (GCF_023375975.1)
      Quercus robur (English oak) annotation release 100, based on new assembly dhQueRobu3.1
      (GCF_932294415.1)
      Schistocerca gregaria (desert locust) annotation release 100, based on new assembly
      iqSchGreg1.2 (GCF_023897955.1) 
      Boll weevil annotation release 100, based on new assembly icAntGran1.3 (GCF_022605725.1) 

Previous Announcement:
----------------------
[1] Foreign contamination screening
    A new foreign contamination screen (FCS) tool is coming soon - watch NCBI Insights for more
    details! We have been using the new FCS-GX tool to identify contamination in RefSeq eukaryote
    genomes, and work with the genome submitters to suppress the contaminant sequences, or upgrade
    to a better assembly for the species. To date we have removed over 120 Mbp of contamination
    from RefSeq genomes, with more cleanup planned.
    
[2] New eukaryotic genome annotations
    This release includes new annotations generated by NCBI's eukaryotic genome annotation 
    pipeline for 30 species, including
      Brown bear annotation release 102, based on new assembly UrsArc1.0
      (GCF_023065955.1)
      Bank vole annotation release 100, based on new assembly Bank_vole1_10x
      (GCF_902806735.1)
      Hawaiian crow annotation release 100, based on new assembly bCorHaw1.pri.cur
      (GCF_020740725.1)
      Loggerhead turtle annotation release 100, based on new assembly GSC_CCare_1.0
      (GCF_023653815.1)
      Leguminivora glycinivorella annotation release 100, based on new assembly LegGlyc_1.1
      (GCF_023078275.1)
      Castor bean annotation release 102, based on new assembly ASM1957865v1
      (GCF_019578655.1)

Announcing Future Changes:   			      
--------------------------
[1] We will continue to update the human genome annotation on a more frequent basis to more quickly 
    incorporate ongoing curation work as part of the MANE project and other curation activities. 
    Further details are available at:
      https://ncbiinsights.ncbi.nlm.nih.gov/2019/03/26/human-genome-annotation-bimonthly-update/
    The last annotation release was in April 2022.
      https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Homo_sapiens/110/
      
[2] RefSeq assembly information
    We are considering adding information to the RefSeq FTP release catalog about the RefSeq assembly
    for each sequence. We welcome your comments on information that would be useful to you.

[3] Plasmid sequences
    We are  looking at revising the set of sequences included in the plasmid bin to add in plasmids
    from WGS sequences.

=============================================================================
3. ORGANIZATION OF DATA FILES
=============================================================================
3.1 FTP Site Organization
-------------------------
RefSeq releases are available on the NCBI FTP site at:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/
            

Documentation Directories and Files:
------------------------------------
  release-catalog/
     archive/						--subdirectory, archive of previous 
	  				       		  catalogs
     RefSeq-release#.catalog  		     		--file, comprehensive list of sequence 
	  				       		  records included in the current release
     release#.files.installed 		     		--file, list of sequence data files installed 
     release#.removed-records 		     		--file, list of removed records that were  
                                     	       		  included the previous release
     release#.taxon.new       		       		--file, list of organisms that have been
                                     	       		   added to the release since the previous 
					       		   release
     release#.taxon.update				--file, list of organisms for which there has
                                               		  been a change in either the NCBI Tax ID or
                                     	       		  the organism name.
     release#.AutonomousProtein2Genomic.gz     	   	--file, list of genomic accessions that 
     							  non-redundant WP protein accessions are
							  annotated on 
     release#.MultispeciesAutonomousProtein2taxname.gz  --file, list of NCBI TaxID and species name  
	  				       		  for the subset of non-redundant WP protein 
							  accessions that are annotated on genomic 
							  records from more than one species. 
     release#.accession2geneid.gz	     		--file, list of GeneIDs included in the 
     							  current release
	  				       		  
                                          
  release-notes/
     archive/		   --subdirectory, archive of previous documentation
     RefSeq-release#.txt   --file, this Release notes document

  release-statistics/
     archive/				 --subdirectory, archive of previous documentation
     RefSeq-release#.MMDDYYYY.stats.txt  --file, detailed release statistics
     *.acc_taxid_growth.txt   		 --growth file, where '*' is archaea, bacteria etc.
                                     	   first row identifies column content 
     RefSeq.taxid_growth.txt  		 --organism growth file, release nodes are columns
                                     	   first row identifies column content
                       
Sequence Data Directories and Files:
------------------------------------
The RefSeq collection is provided in a redundant fashion to best meet the needs
of those who want the full collection as well as those who want a specific
sub-set of the collection.  Therefore the collection is provided as: 
   1) the complete collection, and
   2) sections as defined by major taxonomic or other logical groupings. 

A subdirectory exists for each sub-section as follows:
   archaea
   bacteria
   fungi						
   invertebrate	
   mitochondrion
   other	
   plant
   plasmid		
   plastid		
   protozoa	
   vertebrate_mammalian	
   vertebrate_other	
   viral			

In addition, the complete collection is available without these
sub-groupings in the subdirectory:
   complete

Note that this directory structure intentionally provides the release 
data in a redundant fashion. We gave considerable thought to how to
package the release to meet the needs of different user groups. 
For instance, some groups may be interested in retrieving the complete
protein set, while other groups may be interested in retrieving data 
for a more limited number of organisms.  We decided to provide
logical groupings based on general taxonomic node (viral, mammalian etc.)
as well as logical molecule type compartmentalization (e.g., plastid).
Thus, all records are provided at least twice, once in the "complete" 
directory, and a second time in one of the other directories. 
Some sequences may be provided three times when it is logical to 
include the record in more than one additional directory. For example, 
a sequence may be provided in the "complete", "mitochondrion", and 
"vertebrate_mammalian" directories.

We are interested in hearing if you find this structure useful or if
you would like information grouped in a different manner.

Send suggestions or comments to the NCBI Help Desk at:
	info@ncbi.nlm.nih.gov

3.2 Release Contents
--------------------
A comprehensive list of sequence files provided for the current release
is available in:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/release#.files.installed

A comprehensive list of sequence records included in the current release is 
available in:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/release#.catalog

File name format indicates the directory node, molecule type, and format type. 

Name format:

 complete.10.1.bna.gz
|--------|--|-|---|--|
   1      2  3  4   5

   1. directory location 
   2. numerical increment 
       -to provide a set of unique file names
   3. optional: sub-part number 
       -to provide a unique file name for genomic FASTA files which may be split 
        based on size
   4. format type 
   5. compression

Multiple files may be provided for any given molecule and format type, indicated 
by a numerical increment in the file names. Files of the same molecule type and 
increment are related by content. Files of different molecule type and the same 
increment may or may not have related content. For example:

    complete.1006.bna.gz
    complete.1006.1.genomic.fna.gz
    complete.1006.2.genomic.fna.gz  -- genomic FASTA split into two sub-parts 
                                       due to size 
    complete.1006.genomic.gbff.gz  --  content related to the two 
                                       1006.#.genomic.fna.gz files 
    complete.1006.protein.faa.gz 
    complete.1006.protein.gpff.gz  -- contains proteins found in either genomic 
                                      or rna files of this increment 
    complete.1006.rna.fna.gz
    complete.1006.rna.gbff.gz  -- unrelated to the contents of the genomic files 
                                  of this increment

If you are interested in a complete set of genomic, protein, and rna files for a given 
tax_id, you must scan all files from the directory. You may also want to consider using 
the per-assembly files provided at ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/ instead. 
More information is available at:
    https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/

Note that for some molecule and format types, a number increment is skipped.
This is not an error. It is also not an error if a filename provided with one
release is not provided with a different release.  
For example:
   complete.281.genomic.gbff.gz
   complete.282.genomic.gbff.gz
   complete.284.genomic.gbff.gz
   complete.285.genomic.gbff.gz  
   complete.287.genomic.gbff.gz --release 70 did not include files named as
                               complete.283.genomic or complete.286.genomic
                               because complete.283.bna & complete.286.bna 
                               did not include genomic data.

The RefSeq release processing first produces a comprehensive set of ASN.1 files, 
ordered by tax_id, and limited by a size constraint.  These initial files
are further processed to export the records by molecule and format type.
If the initial ASN.1 file does not include any records for a given molecule type, 
such as genomic sequence data, then the corresponding 'genomic' fasta and 
flatfile records will not be found.

The installed release includes a comprehensive report of all files installed
for a given release. Please refer to /release-catalog/release#.files.installed
(where # is the release number).

3.3 File Names and Formats 
--------------------------
File names are informative, and indicate the content, molecule type,
and file format of each RefSeq release data file. Most filenames
utilize this structure:

	directory.filenumber.subpart.molecule.format.gz
	1         2	     3       4        5	  

File Name Key:

	1. directory		directory level the file is provided in 
				(e.g.,complete, viral etc)
	2. file	number:		large data sets are provided as incrementally 
				numbered files 
        3. sub-part number:     large genomic fasta files may be split to facilitate transfer
	4. molecule		type of molecule (genomic, rna, or protein); 
				not relevant for ASN.1 format files provided 
				in the "complete" sub-directory
	5. format		the data format provided in the file; see below

For example:
	complete1.genomic.bna.gz
        vertebrate_mammalian2.protein.gpff.gz

The filenames for RefSeq non-redundant proteins use a slightly different 
structure:
	directory.nonredundant_protein.filenumber.molecule.format.gz

For example:
	complete.nonredundant_protein.20.protein.faa.gz
	bacteria.nonredundant_protein.105.protein.gpff.gz

The term "non-redundant protein" refers to the representation of identical 
proteins in the prokaryotic RefSeq protein dataset using a single non-redundant 
protein accession number (with the prefix 'WP_'). Non-redundant RefSeq protein 
records, which are currently provided for archaeal and bacterial RefSeq genomes, 
may be found in RefSeq genomes from multiple species. More information about this 
type of RefSeq protein record can be be found here:
     	https://www.ncbi.nlm.nih.gov/refseq/about/nonredundantproteins/ 
        ftp://ftp.ncbi.nlm.nih.gov/refseq/release/announcements/WP-proteins-06.10.2013.pdf
	

All RefSeq release files have been compressed with the gzip utility;
therefore, an invariant ".gz" suffix is present for all release files.

The data that comprises a RefSeq release are available in several
file formats, as indicated by the format component in the file name:
  bna	binary ASN.1 format; includes nucleotide and protein 
  gbff	GenBank flat file format; nucleotide records
  gpff	GenPept flat file format; protein records
  fna	FASTA format; nucleotide records
  faa	FASTA format; protein records

The comprehensive full release is deposited in the "complete"
directory and is available in all file types.

Binary ASN.1 format is only provided in the complete directory. The remaining
directories include all of the remaining file types.

The DDBJ/EMBL/GenBank and GenPept flat file format provided in this release 
matches that seen when accessing the records using the NCBI web site. 
Notably, some RefSeq record are in the CON division and do not instantiate 
the sequence on the flat file display, instead a 'join' statement is provided 
to indicate the assembly instructions.  The FASTA files do include the 
assembled sequences for these CON division RefSeq records.  

For example, see NC_000022.11

Suggestions regarding the structure of the RefSeq release product 
and the available formats may be sent to the NCBI Help Desk:
    info@ncbi.nlm.nih.gov

3.4 File Sizes	
--------------
RefSeq release files are provided in a range of sizes. Most are
limited to several hundred megabytes (MB) and uncompressed ASN.1 file
size will not exceed 500 MB. Nucleotide FASTA files are split when 
they reach 1 gigabyte (GB).

Files are compressed to reduce file size and facilitate FTP retrieval.

The total size of release 214 is as follows:

         Extension    Size (GB)          Type
         -----------------------------------------------------------
         bna          2780.75             ASN.1
         gbff         4051.97             GenBank flat file
         gpff         1224.72             GenPept flat file
         fna          6501.92             FASTA, nucleotide
         faa          227.02              FASTA, protein

Notes: 
 [A] The complete directory provides all file types. The ASN.1 format is only 
     available in the complete directory; the file sizes reported for the 
     remaining file formats represents the redundant total found in the complete 
     plus other directories.

3.5 Statistics
---------------
RefSeq release 214 includes sequences from 123394 different organisms.

The number of species represented in each Release sub-directory, 
determined by counting distinct tax IDs, is as follows: 

        archaea                 1489
        bacteria                69958
        complete                123394
        fungi                   17097
        invertebrate            5932
        mitochondrion           14005
        other                   4
        plant                   9674
        plasmid                 6193
        plastid                 9937
        protozoa                757
        vertebrate_mammalian    1561
        vertebrate_other        5285
        viral                   11618

Counts of accessions and basepairs/residues per molecule type:	

                 Accessions      Basepairs/Residues 
  Genomic:       41364448        3070737201648 
  RNA:           47387931        126881651406 
  Protein:       239609016       93402053269 
  Wgs master:    227174          0 
  
Complete RefSeq release statistics for each directory are provided 
in a separate document. Please see:

   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-statistics/
   
   file: RefSeq-release#.MMDDYYYY.stats.txt
         #: indicates release number
         MMDDYY: indicates release date as month,day,year
 
Statistics for previous releases are available in the archive subdirectory:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-statistics/archive/

3.6 Release Catalog Format
--------------------------
The full non-redundant contents of the release are documented in the 
release catalog. 

Available at:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/

The catalog includes the following columns:
  1. tax_id
  2. Taxon name
  3. RefSeq accession.version
  4. FTP directories data is provided in, '|' separated
  5. RefSeq status code
  6. sequence length

Note: the molecule type for each catalog entry can be inferred from 
the accession prefix (see below).

RefSeq Status Codes are documented on the RefSeq web site. The catalog includes 
the following terms:

  na			Not Applicable; 
			status codes are not provided for some records

  UNKNOWN		The status code has not yet been applied or status is not
  			applicable to the type of record. 

  REVIEWED		The RefSeq record has been the reviewed by NCBI  
			staff or by a collaborator. Some RefSeq records 
			may incorporate expanded sequence and annotation 
			information including additional publications 
			and features. This indicates a curated record.

  VALIDATED		The RefSeq record has undergone an initial review 
			to provide the preferred sequence standard. The  
			record has not yet been subject to final review 
			at which time additional functional information 
			may be provided. This indicates a curated record.	
			
  PROVISIONAL		The RefSeq record has not yet been subject to 
			individual review and is thought to be well 
			supported and to represent a valid transcript 
			and protein. This record is not curated.
			
  PREDICTED		The RefSeq transcript may represent an ab initio 
			prediction or may be weakly supported by transcripts
			or protein homology. This record is not curated.
			
  INFERRED		The RefSeq record is inferred by genome sequence 
			analysis. This record is not curated.

  MODEL			RefSeq records provided via automated processing 
  			and are not subject to individual review or revision 
			between builds. This record is not curated.

3.7 Removed Records
-------------------
This is a report of accessions that were included in the
previous release but are no longer included in the current release.

Available at:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/
   release#.removed-records file format

The file includes the following columns:

  1. tax_id
  2. species name
  3. RefSeq accession.version
  4. FTP directories data was provided in, in last release
  5. RefSeq status code
  6. sequence length
  7. type of removal
	type options include:
	   dead protein
	   replaced by accession  [original accession is not secondary]
           permanently suppressed
           temporarily suppressed [record may become available again in the future]

3.8 RefSeq Accession Format
---------------------------
RefSeq accessions are formatted as a two letter prefix, followed by 
an underscore, followed by six or nine digits, or 4 letters plus eight digits. 
For example, NM_020236, NP_001107345, and NZ_AABC02000001.  

The underscore ("_") is the primary distinguishing feature of a RefSeq 
accession; DDBJ/EMBL/GenBank accessions never include an underscore.

RefSeq accession prefixes
Prefix	Molecule    Use context				Complete accession format
	type	

NC_	DNA	    Chromosomes;			Prefix followed by 6 numbers, followed
		    Linkage Groups			by the sequence version number
							    
AC_	DNA	    Chromosomes;			Prefix followed by 6 numbers, followed 		
		    Linkage Groups			by the sequence version number
							   							
NZ_	DNA	    Chromosomes;			Prefix followed by the INSDC accession
		    Scaffolds;			   	number that the RefSeq record is based 
		    Used predominantly for 		on, followed by the RefSeq sequence 	   
		    prokaryotic genomes		   	version number

NT_	DNA	    Scaffolds   			Prefix followed by 6 or 9 numbers, 
		    					followed by the sequence version number  		   

NW_	DNA	    Scaffolds			   	Prefix followed by 6 or 9 numbers,
							followed by the sequence version number

NG_	DNA	    Genomic regions;		   	Prefix followed by 6 numbers, followed
		    A genomic region record may	   	by the sequence version number	
		    represent a single or multiple 
		    genetic loci (e.g., rRNA 
		    targeted locus, RefSeqGene, 
		    non-transcribed pseudogene)			

NM_	mRNA	    protein-coding transcripts	        Prefix followed by 6 or 9 numbers,
				       			followed by the sequence version number;
							curated by NCBI staff or a model organism 
							database; these records are referred to 
							as the 'known' RefSeq dataset
							   
XM_	mRNA	    protein-coding transcripts	   	Prefix followed by 6 or 9 numbers,
				       			followed by the sequence version number; 
							generated through either the eukaryotic 
							genome annotation pipeline, or the small 
							eukaryotic genome annotation pipeline; 
							records generated via the first method are
							referred to as the 'model' RefSeq dataset.
							
NR_	RNA	    non-protein-coding transcripts 	Prefix followed by 6 or 9 numbers,
		    including lncRNAs, structural 	followed by the sequence version number;
		    RNAs, transcribed pseudogenes, 	curated by NCBI staff or a model organism
		    and transcripts with unlikely	database; these records are referred to as      
		    protein-coding potential from 	the 'known' RefSeq dataset	
		    protein-coding genes

XR_	RNA	    non-protein-coding transcripts,	Prefix followed by 6 or 9 numbers,	
		    as above	   		        followed by the sequence version number
		       					generated through either the eukaryotic 
							genome annotation pipeline, or the small
							eukaryotic genome annotation pipeline; 
							records generated via the first method are
							referred to as the 'model' RefSeq dataset.

NP_	protein	    Proteins annotated on NM_ 	        Prefix followed by 6 or 9 numbers,
		    transcript accessions or 	        followed by the sequence version number;
		    annotated on genomic molecules 	curated by NCBI staff or a model organism
		    without an instantiated 		database; these records are referred to as 	
		    transcript (e.g. some 		the 'known' RefSeq dataset
		    mitochondrial genomes, viral 
		    genomes, and reference 
		    bacterial genomes

AP_	protein	    Proteins annotated on AC_	        Prefix followed by 6 or 9 numbers,
		    genomic accessions or annotated 	followed by the sequence version number
		    on genomic molecules without 
		    an instantiated transcript 
		    record

XP_	protein	    Proteins annotated on XM_		Prefix followed by 6 or 9 numbers,
		    transcript accessions or		followed by the sequence version number
		    annotated on genomic molecules 	generated through either the eukaryotic
		    without an instantiated 		genome annotation pipeline, or the small
		    transcript record			eukaryotic genome annotation pipeline; 
		    	       				records generated via the first method are
							referred to as the 'model' RefSeq dataset.

YP_	protein	    Proteins annotated on genomic 	Prefix followed by 6 or 9 numbers,
		    molecules without an		followed by the sequence version number
		    instantiated transcript 
		    record

WP_	protein	    Proteins that are non-redundant	Prefix followed by 9 numbers, followed
		    across multiple strains and 	by the version number, which is 
		    species. A single protein of 	always '.1' as these records are
		    this type may be annotated		not subject to update 	 
		    on more than one prokaryotic 
		    genome

See online documentation for additional information on WP_ accessions:
    https://www.ncbi.nlm.nih.gov/refseq/about/nonredundantproteins/

As needed, accession series will be expanded by adding 3 digits, with existing accessions 
remaining stable.

3.9 Growth of RefSeq	
--------------------
Release	Date		Taxons	Nucleotides	 Amino Acids	 Records
1	Jun 30, 2003	2005	4672871949	 263588685	 1061675
2	Oct 21, 2003	2124	7745398573	 286957682	 1097404
3	Jan 13, 2004    2218	7992741222	 294647847	 1101244
4	Mar 24, 2004    2358	8175128887	 318253841	 1193457
5	May  3, 2004    2395    8325515623	 337229387	 1255613
6	Jul 5, 2004	2467	8696371716	 365446682	 1367206 
7       Sep 10, 2004    2558	21072808460	 405233619	 1579579
8       Oct 31, 2004    2645	26814386658	 430300369	 1709723 
9	Jan  9, 2005    2780	36786975473	 470534907	 1843944
10	Mar  6, 2005    2827    36893741150      482862858       1893478 
11	May  8, 2005    2928    39731702362      507980644       2477893
12      Jul 10,2005	2969    43043256058      608493108       2869675
13	Sep 11, 2005    3060    44727484853      686768902       3400773
14	Nov 20, 2005    3198	47364955367	 763761075	 3272776
15      Jan 1, 2006     3244    52645441913      810009733       3436263
16      Mar 11, 2006    3397    56175443059      887509001       3715260 
17	May 1, 2006	3497	62130037371	 927587669	 3999859 
18      Jul 11, 2006   3695	70474041999	 974374765	 4186692
19	Sep 10, 2006    3774    70694879544      1012985077      4311543 
20	Nov 5, 2006	3919	72679681505      1061797276	 4567569 
21	Jan 6, 2007	4079	73864990566      1144795927	 4742335
22	Mar 5, 2007	4187	82441128546      1215085694	 5207865
23	May 8, 2007	4300	83148327110      1291050995	 5503385
24	Jul 10, 2007	4511	89856995521      1365916222	 6073814
25	Sep 11, 2007	4646	91265840843      1470475398	 6515132 
26	Nov 4, 2007	4737	99105705485      1495032507 	 6698250 
27	Jan 6, 2008	4926    101059552113     1556356987	 7025715
28	Mar 9, 2008	5059	102051350525     1770627427	 7914560
29	May 4, 2008	5168	104671101150     1870214220	 8376141
30	Jul 7,2008	5395	105074486709     1913447691	 8572852 
31	Aug 30, 2008	5513	109214348591     2026768719	 9145702 
32	Nov 10, 2008	5726	111122203221     2089596746	 9501764
33	Jan 16, 2009	7773	116001583818     2204073443      10325282
34	Mar 6, 2009	8054	111792574830     2299682138      10021870
35	May 4, 2009	8393	113210655336     2565199170      10993891
36	Jul 2, 2009	8665	117013741530     2756884219      12141825
37	Sep 3, 2009    9005	119151229820     2965450333      12941750
38	Nov 7, 2009     9166	119196622435     3115246540      13436447
39	Jan 23, 2010    10171	118502856500     3221054793      13656433
40	Mar 7, 2010 	10291	118645985035     3280528951      13853798
41	May 9, 2010	10567	125500880884     3427514220      14472060
42	Jul 13, 2010	10728	143311839055     3553178673      15038858
43	Sep 5, 2010	10854	148706971456     3761205880      15934055
44	Nov 7, 2010	11354	152241490865     3899827321      16421261
45      Jan 7, 2011     11536	152787094873     3989526325      16748646
46	Mar 8, 2011	11734	153220856222     4064052954      16998463
47	May 7, 2011	12000	162001966044     4226432170      17631876
48	Jul 10, 2011	12235	163771272903     4381572480      18162534
49	Sep 7, 2011	16248	162286146420     4401462131      18236994
50 	Nov 8, 2011	16392	168702162406     4529303978      18815153
51	Jan 9, 2012	16609	172751347778     4727472575      19580946
52	Mar 5, 2012	16923	173705194347     4929467422      20235247
53	May 7, 2012	17339	175345433862     5247723883      21286080
54	Jul 9, 2012	17605	176492228688     5456992181      21889466
55	Sep 17, 2012	17994	194971374545     5803694332      23207572
56	Nov 8, 2012	18512	207200464965     6003283860      23892460
57	Jan 8, 2013	21415	227639108990     8895153979      34158511
58	Mar 11,2013 	22460	233247214400     9699076220      36938203
59	Apr 29, 2013	24656	256547643663     10081118607     39040745
60 	Jul 19, 2013	28560	304686151670     10968281809     40913699
61	Sep 9, 2013	29414	319551394177     11248966865     41958567
62	Nov 10, 2013	31646	361097812819     12364402476     45971929
63  	Jan 12, 2014	33485	380736496721     12898823816     48358066 
64	Mar 10, 2014	33693	407131829420     13126329523     49538213
65	May 12, 2014 	36335	430613954268     13544443640     51770174
66	Jul 7, 2014	41263	464958653006     15380643722     58334707 
67	Sep 8, 2014 	41913	490800792583     15984799771     61277203 
68	Nov 3, 2014	49312	551290496427     16790850066     66078114
69	Jan 2, 2015 	51661	594452675642     18690872100     74127019
70	Apr 30, 2015	54118	643051675415     18556381492     74720563
71	Jul 6, 2015 	55267	669786114584     19394398061     77730891
72	Aug 27, 2015	54937	705514040682     19748515407     79189847
73	Nov 2, 2015	55966	738575306673     20847187904     83881439
74	Jan 11, 2016	57993	780562546593     22359312327     89458499
75	Mar 7, 2016	58776	807349580822     23386816845     92936289
76	May 9, 2016 	59995	859358759387     24586044092     97792976
77 	Jun 29, 2016	60892	872938972710     25449517637     100678438
78	Sep 6, 2016	62739	904423741786     27105909174     107045797
79 	Oct 31, 2016	64277	941153466527     28214340731     111024999
80	Jan 9, 2017	66224 	988758901224     30073388355     118059547
81	Mar 6, 2017     68165	1022393849190    31208765769     121954847
82	May 8, 2017	69035	1066355456886	 32674281195	 127098389
83	Jul 17, 2017	71356	1121562831367	 34113050666	 132052465
84      Sep 11, 2017    72965   1158748173657    36673975257     140627690
85	Nov 6, 2017	73996	1204502588476	 38371950939	 146710309
86	Jan 8, 2018	75218	1224147155468	 39198368659	 149493466
87      Mar 5, 2018	77225	1266924789413	 40799318419	 155118991
88	May 14, 2018	79448	1281457514351	 42356891903	 160224355
89	Jul 9, 2018	81345	1310406641373	 43546263891	 163859625
90	Sep 10, 2018	84276	1391082745897	 46448327052	 173956003
91	Nov 5, 2018	85308	1430969078377	 48133151229	 179672083
92	Jan 4, 2019	86867	1487640446350	 50022196212	 185738687
93	Mar 13, 2019	88816	1538401021292	 52033004779	 192722653
94 	May 13, 2019	91873	1604159550977	 54355271806	 200311267
95	Jul 8, 2019	93618	1663456288307	 56131094433	 206416381
96	Sep 9, 2019	94946	1731968697055	 58596894789	 213863503
97	Nov 4, 2019	97407	1775844555056	 60395267362	 219407891
98	Jan 6, 2020	98406	1811879348292	 61751602519	 223560051
99	Mar 2, 2020	99842	1865535232080	 64046042055	 231402293
200	May 4, 2020	100605	1935188461619	 65917036726	 237381664
201	Jul 6, 2020	103293	2011499231032	 68531730058	 246016651
202	Sep 8, 2020	104969	2062903159398	 71660941848	 255571455
203	Nov 2, 2020	105349	2120884152245	 71914251558	 256340911
204	Jan 4, 2021	106581	2219687944618	 73969071608	 262714372
205 	Mar 1, 2021	108257	2293291152174	 76233183903	 269975565
206	May 17, 2021	111743	2403475808345	 79078139531	 279425850
207	Jul 12, 2021	112462	2452064583574	 80920690233	 285425070
208	Sep 7, 2021	113002	2512362022380	 81791867275	 288903207
209	Nov 1, 2021	114396	2714890725865	 83861496486	 296293486
210	Jan 3, 2022	115929	2775270855148	 85704927012	 302482881
211     Mar 7, 2022     117030  2858986635659    87327984938     308229655
212	May 2, 2022	119373  2968684923393    89276136473     314915153
213	Jul 11, 2022	121461	3045465416031	 91290623940	 321282996
214	Sep 12, 2022	123394  3197618853054    93402053269     328588569

Note: Date refers to the data cut-off date, i.e., the release incorporates 
data available as of the listed date.

=============================================================================
4. FLAT FILE ANNOTATION
=============================================================================

4.1 Main features of RefSeq Flat File
-------------------------------------
Also see the RefSeq web site and the NCBI Handbook, RefSeq chapter.

   https://www.ncbi.nlm.nih.gov/refseq/
   https://www.ncbi.nlm.nih.gov/books/NBK21091/

4.1.1 LOCUS, DEFLINE, ACCESSION, KEYWORDS, SOURCE, ORGANISM 
--------------------------------------------------------------------
The beginning of each RefSeq record provides information about the accession,
length, molecule type, division, and last update date. This is followed by the 
descriptive DEFINITION line, then by the Accession and version, followed by
detailed information about the organism and taxomonic lineage.

//
LOCUS       NC_004916             384502 bp    DNA     linear   CON 18-JUN-2017
DEFINITION  Leishmania major strain Friedlin complete genome, chromosome 3.
ACCESSION   NC_004916 AC125735
VERSION     NC_004916.2
DBLINK      BioProject: PRJNA15564
            BioSample: SAMEA3138173
            Assembly: GCF_000002725.2
KEYWORDS    RefSeq; complete genome.
SOURCE      Leishmania major strain Friedlin
  ORGANISM  Leishmania major strain Friedlin
            Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
            Leishmaniinae; Leishmania.
//

Note: The VERSION number increments when a sequence is updated, 
while the ACCESSION remains the same.  The "ACCESSION.VERSION" 
identifier provides the finest resolution reference to a sequence.

4.1.2 REFERENCE, DIRECT SUBMISSION, COMMENT, PRIMARY
-------------------------------------------
REFERENCE: 
While the majority of RefSeq records do include REFERENCE
data, this data is not required and some records do not include any
citations. Publications are propagated from the GenBank record(s) from which
the RefSeq is derived, provided by collaborating groups and NCBI staff
during the curation process, and provided by the National Library of
Medicine (NLM) PubMed MeSH indexing staff as they add new articles to PubMed.

Functionally relevant citations are added by individual scientists using
the Entrez Gene GeneRIF submission form, and a significant volume of citation
connections are supplied by the NLM MeSH indexing staff for human, 
mouse, rat, zebrafish,and cow. This functionality is expected to increase 
in the future to treat all organisms represented in the RefSeq collection.  
Citations supplied by the MeSH indexers and individual scientists can be 
identified by the presence of a REMARK beginning with the text string "GeneRIF".
This represents a significant method to keep sequence connections to the
literature up-to-date; GeneRIFs add considerable value to the RefSeq 
collection.

For more information on GeneRIFs please see:

   https://www.ncbi.nlm.nih.gov/gene/about-generif 

For example, several GeneRIFs have been added to NM_000173.7, including:

//

REFERENCE   2  (bases 1 to 2514)
  AUTHORS   Xu M, Li J, Neves MAD, Zhu G, Carrim N, Yu R, Gupta S, Marshall J,
            Rotstein O, Peng J, Hou M, Kunishima S, Ware J, Branch DR, Lazarus
            AH, Ruggeri ZM, Freedman J and Ni H.
  TITLE     GPIbalpha is required for platelet-mediated hepatic thrombopoietin
            generation
  JOURNAL   Blood 132 (6), 622-634 (2018)
   PUBMED   29794068
  REMARK    GeneRIF: In GPIbalpha-deficient human Bernard-Soulier syndrome
            patients, a decrease occurred in circulating TPO.
	    
//

DIRECT SUBMISSION: 
A Direct Submission field is provided on some RefSeq records but not all. It
is propagated from the underlying GenBank record from which the RefSeq is 
derived or provided on submissions from collaborating groups. Transcript
and protein RefSeqs for human, mouse, rat, zebrafish, and cow do not provide
this field as records often include additional data and are not necessarily
direct copies of the GenBank submission.

COMMENT: 
A COMMENT is provided for the majority of RefSeq records. We are working to supply 
a COMMENT more comprehensively in the future. A COMMENT is always provided if 
the version number has  changed. 

COMMENT sections may include information on:	 
    RefSeq Status (PROVISIONAL, INFERRED, VALIDATED REVIEWED, etc.)
    Information on collaborating groups (e.g. RefSeqGene project)
    GenBank records(s) from which the RefSeq is derived. 
    Version changes
    A summary about sequence function
    Description of transcript variants
    Sequence note to describe the components of the RefSeq transcript
    Evidence data describing transcript and RNA-Seq support for the RefSeq transcript
    Attributes: examples - 'non-AUG initiation codon', 'Protein has antimicrobial activity',
                           'RefSeq Select criteria'
    5' and/or 3' completeness of the RefSeq transcript			   
	
Example: COMMENT section of NM_004323.6 
//
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL356472.17 and AL161445.10.
            On Nov 23, 2018 this sequence version replaced NM_004323.5.
            
            Summary: The oncogene BCL2 is a membrane protein that blocks a step
            in a pathway leading to apoptosis or programmed cell death. The
            protein encoded by this gene binds to BCL2 and is referred to as
            BCL2-associated athanogene. It enhances the anti-apoptotic effects
            of BCL2 and represents a link between growth factor receptors and
            anti-apoptotic mechanisms. Multiple protein isoforms are encoded by
            this mRNA through the use of a non-AUG (CUG) initiation codon, and
            three alternative downstream AUG initiation codons. A related
            pseudogene has been defined on chromosome X. [provided by RefSeq,
            Feb 2010].
            
            Transcript Variant: This transcript (1) encodes multiple isoforms
            due to the use of alternative translation initiation codons. The
            longest isoform (BAG-1L or p50) is derived from an upstream non-AUG
            (CUG) start codon, while three shorter isoforms are derived from
            downstream AUG start codons. The longest isoform (BAG-1L) is
            represented in this RefSeq.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            CCDS Note: This CCDS ID represents the longest human BAG1 isoform,
            known as BAG-1L or p50, as described in the literature, including
            PMIDs 9396724, 9679980, 9747877 and 17662274. This isoform
            initiates translation at a non-AUG (CUG) start codon that is
            well-conserved and present in a strong Kozak signal context.
            Alternative translation initiation at downstream AUG start codons
            produces three additional isoforms with shorter N-termini, known as
            BAG-1M or p46, BAG-1S or p36 (also known as p33), and p29. The most
            abundant of the shorter isoforms, BAG-1S, is represented by CCDS
            55301.1. Evidence in PMIDs 9747877 and 17662274 indicates that
            these isoforms have distinct subcellular distributions, which may
            contribute to the multifunctionality of the protein.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK222749.1, SRR3476690.264741.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2147975, SAMEA2149876
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
	    MANE Ensembl match       :: ENST00000634734.3/ ENSP00000489189.2
            non-AUG initiation codon :: PMID: 9679980, 9396724
            RefSeq Select criteria   :: based on conservation, expression,
                                        longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
//

PRIMARY:
This section contains the coordinates of the transcript and/or genomic components 
of the RefSeq. The 'c' in the COMP column indicates that the coordinates are on 
the complementary strand.    
Example: NM_004006.3

//
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-37                AL031643.1         20726-20762         c
            38-2881             M18533.1           9-2852
            2882-2882           AL031542.1         65972-65972         c
            2883-4642           M18533.1           2854-4613
            4643-4643           AL109609.5         79506-79506         c
            4644-5766           M18533.1           4615-5737
            5767-5767           AL109609.5         35892-35892         c
            5768-7332           M18533.1           5739-7303
            7333-7333           AC079864.22        141601-141601       c
            7334-9046           M18533.1           7305-9017
            9047-9047           AC079177.21        132735-132735       c
            9048-12741          M18533.1           9019-12712
            12742-13992         BC028720.1         3398-4648
//	    

4.1.3 NUCLEOTIDE FEATURE ANNOTATION
-----------------------------------
Gene, mRNA, CDS:
Every effort is made to consistently provide the Gene and coding sequence (CDS)
feature (when relevant). If a RefSeq is based on a GenBank record that is only 
annotated with the CDS, then a Gene feature is created.  mRNA features are 
provided for most eukaryotic records; this is not yet comprehensively provided
and will improve in future releases.

Gene Names: 
Gene symbols and names are provided by external official 
nomenclature groups for some organisms.  If official nomenclature is 
not available we may use a systemic name provided by the data submittor 
or apply a more functional name during curation. When official nomenclature 
is available we may provide additional alternate names for some organisms.

Variation:
Variation is computed by the dbSNP database staff and added via post-processing
to RefSeq records.

Miscellaneous:
For some records, additional annotation may be provided when identified by the 
curation staff or provided by a collaborating group. For example, the location 
of polyA signal and sites may be included.

4.1.4 PROTEIN FEATURE ANNOTATION
--------------------------------
Protein Names: 
Protein names may be provided by a collaborating group, may be based on the 
Gene Name, or for some records, the curation process may identify the 
preferred protein name based on that associated with a specific EC number 
or based on the literature.

Protein Products:
Signal peptide and mature peptide annotation is provided by propagation from 
the GenBank submission that the RefSeq is based on, when provided by a 
collaborating group, or when determined by the curation process.

Domains:
Domains are computed by alignment to the NCBI Conserved Domain Database 
database for  human, mouse, rat, zebrafish, nematode, and cow.  The best 
hits are annotated on the RefSeq. For some records, additional functionally 
significant regions of the protein may be annotated by the curation staff.
Domain annotation is not provided comprehensively at this time.

4.2 Tracking Identifiers
------------------------
Several identifiers are provided on RefSeq records that can be used to track 
relationships between annotated features, relationships between RefSeq records, 
and changes to RefSeq records over time. 

The GeneID identifies the related Gene, mRNA, and CDS features. 
Transcript IDs (RefSeq accessions) provide an explicit connection between a 
transcript feature annotated on a genomic RefSeq record, and the RefSeq 
transcript record itself. Likewise, the Protein ID (RefSeq accessions) provides 
the association between the annotated CDS feature on a genomic or transcript 
RefSeq record, and the protein record itself.

Changes to a RefSeq sequence over time can be identified by changes to the version
number.
	
4.2.1 GeneID
------------
A gene feature database cross-reference qualifier (dbxref), the GeneID, 
is provided on many RefSeq records to support access to the Entrez Gene
database. 

Entrez Gene provides gene-oriented information for a sub-set of the
RefSeq collection. Gene includes data for all Eukaryotic genomes, viral genomes,
and a representative Prokaryotic genomes. 

The GeneID  provides a distinct tracking identifier for a gene
or locus and is provided on the gene, mRNA, and CDS features. The GeneID 
can be used to identify a set of related features; this is especially useful 
when multiple products are provided to represent alternate splicing events.
	
For example:

NC_000003.12	Homo sapiens chromosome 3, GRCh38.p14 Primary Assembly.

//

     gene            38039208..38124025
                     /gene="DLEC1"
                     /gene_synonym="CFAP81; DLC-1; DLC1; F56; FAP81"
                     /note="DLEC1 cilia and flagella associated protein;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefSeq,Gnomon."
                     /db_xref="GeneID:9940"	<<<--- GeneID
                     /db_xref="HGNC:HGNC:2899"
                     /db_xref="MIM:604050"

//
	

When viewing RefSeq records via the internet, the GeneID is hot-linked to Entrez
Gene. 

4.2.2 Transcript ID
-------------------
The transcript_id qualifier found on a mRNA or other RNA feature annotation
provides an explicit correspondence between a feature annotation on a genomic 
record and the RefSeq transcript record.

For example:

NC_000022.11	Homo sapiens chromosome 22, GRCh38.p14 Primary Assembly.   

//

     mRNA            complement(46255663..46263343)
                     /gene="PKDREJ"
                     /product="polycystin family receptor for egg jelly"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefSeq."
                     /transcript_id="NM_006071.2"	<<<--- linked RefSeq transcript
		     /db_xref="Ensembl:ENST00000253255.7"
                     /db_xref="GeneID:10343"
                     /db_xref="HGNC:HGNC:9015"
                     /db_xref="MIM:604670"

//

		
4.2.3 Protein ID
----------------
The protein_id qualifier found on a coding region (CDS) feature provides an 
explicit correspondance between feature annotation on a genomic or transcript 
RefSeq record and the RefSeq transcript record.

For example:

NC_001144.5 	Saccharomyces cerevisiae S288C chromosome XII, complete sequence. 

//

     CDS             complement(16639..17613)
                     /gene="MHT1"
                     /locus_tag="YLL062C"
                     /EC_number="2.1.1.10"
                     /experiment="EXISTENCE:direct assay:GO:0005737 cytoplasm
                     [PMID:14562095]"
                     /experiment="EXISTENCE:direct assay:GO:0008898
                     S-adenosylmethionine-homocysteine S-methyltransferase
                     activity [PMID:11013242]"
                     /experiment="EXISTENCE:mutant phenotype:GO:0000096 sulfur
                     amino acid metabolic process [PMID:11013242]"
                     /note="S-methylmethionine-homocysteine methyltransferase;
                     functions along with Sam4p in the conversion of
                     S-adenosylmethionine (AdoMet) to methionine to control the
                     methionine/AdoMet ratio"
                     /codon_start=1
                     /product="S-adenosylmethionine-homocysteine
                     S-methyltransferase MHT1"
                     /protein_id="NP_013038.1"      <<<--- linked RefSeq protein
                     /db_xref="GeneID:850664"
                     /db_xref="SGD:S000003985"
                     /translation="MKRIPIKELIVEHPGKVLILDGGQGTELENRGININSPVWSAAP
                     FTSESFWEPSSQERKVVEEMYRDFMIAGANILMTITYQANFQSISENTSIKTLAAYKR
                     FLDKIVSFTREFIGEERYLIGSIGPWAAHVSCEYTGDYGPHPENIDYYGFFKPQLENF
                     NQNRDIDLIGFETIPNFHELKAILSWDEDIISKPFYIGLSVDDNSLLRDGTTLEEISV
                     HIKGLGNKINKNLLLMGVNCVSFNQSALILKMLHEHLPGMPLLVYPNSGEIYNPKEKT
                     WHRPTNKLDDWETTVKKFVDNGARIIGGCCRTSPKDIAEIASAVDKYS"		     
    
 //

4.2.4 Conserved Domain Database (CDD) ID
----------------------------------------
Protein domain annotation is calculated by the Conserved Domain Database
and is included in RefSeq protein records processed for the FTP site. Domain
annotation appears as a Region feature on protein records and is propagated to
associated transcript features (if available) as a misc_feat. The feature
annotation includes a dbxref cross-reference to the CDD database that may change
over time.  The dbxref retrieves a domain model as calculated at a point in time;
recalculation of domains by the CDD group may result in a new CDD identifier value.
The CDD dbxref values that are available in the RefSeq release, although not 
stable, will continue to retrieve data from the CDD database where a newer 
identifier value may be found.

For example:

NP_000550.2	 hemoglobin subunit gamma-1 [Homo sapiens].        

//

     Region          8..146
                     /region_name="Hb-beta-like"
                     /note="Hemoglobin beta, gamma, delta, epsilon, and related
                     Hb subunits; cd08925"
                     /db_xref="CDD:381262"      <<<--- CDD identifier

//

=============================================================================
5. REFSEQ ADMINISTRATION
=============================================================================
The National Center for Biotechnology Information (NCBI), National Library
of Medicine, National Institutes of Health, is responsible for the production
and distribution of the NIH RefSeq Sequence Database. NCBI distributes
RefSeq sequence data by anonymous FTP. For more information, you may contact 
NCBI by email at info@ncbi.nlm.nih.gov or by phone at 301-496-2475.

5.1 Citing RefSeq
-----------------
When citing data in RefSeq, it is appropriate to to give the sequence name,
and primary accession and version number. Note, the most accurate citation
of the sequence is provided by including the combined accession plus version number.

It is also appropriate to list a reference for the RefSeq project. Please
refer to the RefSeq web site for the most recent publication.
  https://www.ncbi.nlm.nih.gov/refseq/publications/

5.2 RefSeq Release Schedule and Distribution Formats
-------------------------------
RefSeq releases occur in the first two weeks of odd-numbered months:
January, March, May, July, September, November

Complete flat file releases of the RefSeq database are available via
NCBI's anonymous ftp server:
	ftp://ftp.ncbi.nlm.nih.gov/refseq/release/

Each release is cumulative, incorporating previous data plus new data.
Records that have been suppressed are not included in the release.

Incremental updates that become available between RefSeq releases
are available at:

ftp://ftp.ncbi.nlm.nih.gov/refseq/daily
ftp://ftp.ncbi.nlm.nih.gov/refseq/cumulative

Please refer to the README for additional information:
ftp://ftp.ncbi.nlm.nih.gov/refseq/README

5.3 Other Methods of Accessing RefSeq Data
------------------------------------------
Entrez is a molecular biology database system that presents an integrated
view of DNA and protein sequence data, structure data, genome data, 
publications, and other data fields.  The Entrez query and retrieval
system is produced by the National Center for Biotechnology Information
(NCBI) and is available only via the internet.

Entrez is accessed at:

	https://www.ncbi.nlm.nih.gov/Entrez/

RefSeq entries are indexed for retrieval in the Entrez system. The web-based
filter restrictions can be used to restrict your query to RefSeq data or to 
specific subsets of the RefSeq database.

Additional specific property restrictions are provided to support querying
for RefSeq records with specific STATUS codes. Queries are defined on the
RefSeq web site at:

	https://www.ncbi.nlm.nih.gov/RefSeq/

5.4 Request for Corrections and Comments
----------------------------------------
We welcome your suggestions to improve the RefSeq collection; we invite 
groups interested in contributing toward the collection and curation 
of the RefSeq database to improve the representation of single genes, 
gene families, or complete genomes to contact us.

Please refer to RefSeq accession and version numbers (or GI) and the RefSeq
Release number to which your comments apply; it is useful if you
indicate the source of data that you found to be problematic (e.g., data on
the FTP site, data retrieved on the web site), the entry DEFLINE, and the 
specific annotation field for which you are suggesting a change.

Suggestions and corrections can be sent to:

	info@ncbi.nlm.nih.gov

5.5 Credits and Acknowledgements
--------------------------------
This RefSeq release would not be possible without the support of numerous
collaborators and the primary sequence data that is submitted by thousands
of laboratories and available in GenBank.

The RefSeq project is ambitious in scope and we actively welcome opportunities
to work with other groups to provide this collection. We value all of our 
collaborators; they contribute information with a large range in scope and 
volume such as completely annotated genomes, advice to improve the sequence 
or annotation of individual RefSeq records, information about official 
nomenclature, and information about function.

In addition to the significant information collected by collaboration, 
numerous NCBI staff are involved in infrastructure support, programmatic 
support, and curation. RefSeq is supported by 3 primary work groups that 
are associated with Entrez Gene, Entrez Genomes, and the Genome Annotation 
Pipeline. 

5.6 Disclaimer
--------------
The United States Government makes no representations or warranties
regarding the content or accuracy of the information.  The United States
Government also makes no representations or warranties of merchantability
or fitness for a particular purpose or that the use of the sequences will
not infringe any patent, copyright, trademark, or other rights.  The
United States Government accepts no responsibility for any consequence
of the receipt or use of the information.

For additional information about RefSeq releases, please contact
NCBI by e-mail at info@ncbi.nlm.nih.gov or by phone at (301) 496-2475.