Submission of Annotation Using a Table
Introduction
The five-column, tab-delimited feature table format allows different kinds of features (e.g., gene, mRNA, coding region, tRNA) and qualifiers (e.g., /product, /note) to be annotated. The valid features and qualifiers are restricted to those approved by the International Nucleotide Sequence Database Collaboration. The entire process can be automated with the utility tbl2asn, which is a command line program that automates parts of the submission process and is available via ftp. tbl2asn reads a template, along with the sequence and table files, and outputs ASN.1 for submission to GenBank.
When submitting an annotated prokaryotic or eukaryotic genome, please review the genome guidelines and appropriate annotation details for prokaryotes or eukaryotes.
Table Layout
The five-column, tab-delimited feature table specifies the location and type of each feature. The first line of the table contains the following basic information:
›Feature SeqId table_name
The sequence identifier (SeqId) must be the same as that used on the sequence. The table_name is optional. Subsequent lines of the table list the features. Each feature is on a separate line. Qualifiers describing that feature are on the line below. Columns are separated by tabs.
Column 1: Start location of feature
Column 2: Stop location of feature
Column 3: Feature key
Line2:
Column 4: Qualifier key
Column 5: Qualifier value
Figure 1 shows a sample table and illustrates a number of points about the table format. The GenBank flatfile corresponding to this table is shown in Figure 2.
- Features that are on the complementary strand, such as the gene YPR027C and tRNA-Phe, are indicated by reversing the interval locations.
- Locations of partial (incomplete) features are indicated with a ">" or "<" in front of the nucleotide location. The “<” symbol always appears in column 1 and “>” always appears in column 2, regardless of the strandedness of the feature. In this example, the first gene, CDS, and mRNA all begin upstream of the start of the nucleotide sequence. The "<" symbol indicates that they are 5' partial features.
- For the protein of a CDS that is partial at its 5’ end to translate correctly, the first nucleotide of the CDS that is the first base of the first complete codon must be indicated with the qualifier "codon_start". This is not the reading frame of the entire sequence; it is just the nucleotide position within the CDS. In the example, nucleotide 2 begins the first complete codon of the acid trehalase CDS. The default situation is that the codon_start is 1. There is no need to indicate the codon_start on complete CDSs, as the translation always begins at the first nucleotide of the interval.
- If a feature contains multiple intervals, like the spliced tRNA-Phe or the Yip2p CDS, each interval is listed on a separate line by its start and stop position before subsequent qualifier lines.
- Gene features are always a single interval, and their location should cover the intervals of all the relevant features. For example, the gene YIP2 is as long as its mRNA, and is thus longer than its CDS.
- If the gene feature spans the intervals of the CDS or mRNA features for that gene, there is no need to include gene qualifiers on those features in the table, because they will be picked up by overlap. For example, in the flatfile, the gene names ATH1 and YPR027C are present as /gene on the overlapping CDS, even though they are not explicitly listed as gene qualifiers on those CDSs in the table. This option can be suppressed by adding a gene qualifier with the value '-' to the feature. Suppressing the overlapping /gene is important when, for example, a tRNA is encoded within an intron of a housekeeping gene.
- If a protein has more than one name, each can be listed in the table as a separate product qualifier on the CDS in the table. The value of the first product qualifier will become the /product on the CDS in the flatfile, and any additional product qualifiers will be shown as a /note on the CDS in the flatfile. See the first CDS, which has two product qualifiers, acid trehalase and Ath1p. All CDS features must have at least one product.
- A flatfile /note can be added to any feature using the qualifier note in the table. A note has been added to the second CDS.
- Published citations are added using the REFERENCE feature. For most publications, the start and stop of the feature are the first and last nucleotides of the sequence. The qualifier key is PubMed, and the value is the PubMed Identifier (PMID), which can be found in PubMed.
- The [offset] is used to add a specified number to all subsequent nucleotide intervals. In this example, the record was annotated in two pieces, each piece starting from residue number 1. The sequences themselves were joined together in the FASTA file. The [offset=2000] adds 2000 nt to the location of all features that follow it, sparing the submitter the need to recalculate the location of each feature. This option could be used if the feature intervals for two arms of a chromosome or adjacent contigs are stored separately, but needs to be joined for the final submission.
Figure 1 : Feature Table Format
>Feature Sc_16
1 7000 REFERENCE
PubMed 8849441
<1 1050 gene
gene ATH1
<1 1009 CDS
product acid trehalase
product Ath1p
codon_start 2
<1 1050 mRNA
product acid trehalase
[offset=2000]
1253 420 gene
gene YPR027C
1253 420 CDS
product Ypr027cp
note hypothetical protein
1253 420 mRNA
product Ypr027cp
2626 2535 gene
gene trnF
2626 2590 tRNA
2570 2535
product tRNA-Phe
2626 2590 exon
number 1
2570 2535 exon
number 2
3450 4536 gene
gene YIP2
3522 3572 CDS
3706 4197
product Yip2p
prot_desc similar to human polyposis locus protein 1 (YPD)
3450 3572 mRNA
3706 4536
product Yip2p
Figure 2 : GenBank Flatfile
LOCUS Sc_16 7000 bp DNA PLN 08-MAY-2000
DEFINITION Saccharomyces cerevisiae strain S288C chromosome XVI, partial sequence.
ACCESSION Sc_16
VERSION
KEYWORDS .
SOURCE baker's yeast.
ORGANISM Saccharomyces cerevisiae
Eukaryota; Fungi; Ascomycota; Hemiascomycetes; Saccharomycetales;
Saccharomycetaceae; Saccharomyces.
REFERENCE 1 (bases 1 to 7000)
AUTHORS Goffeau,A., Barrell,B.G., Bussey,H., Davis,R.W., Dujon,B.,
Feldmann,H., Galibert,F., Hoheisel,J.D., Jacq,C., Johnston,M.,
Louis,E.J., Mewes,H.W., Murakami,Y., Philippsen,P., Tettelin,H. and
Oliver,S.G.
TITLE Life with 6000 genes
JOURNAL Science 274 (5287), 546 (1996)
PUBMED 8849441
REFERENCE 2 (bases 1 to 7000)
AUTHORS Ouellette,B.F.F.
TITLE Direct Submission
JOURNAL Submitted (08-MAY-2000) NCBI/NLM, National Institutes of Health,
Building 38A, Room 8N805, Bethesda, MD 20894, USA
FEATURES Location/Qualifiers
source 1..7000
/organism="Saccharomyces cerevisiae"
/strain="S288C"
/chromosome="XVI"
mRNA <1..1050
/gene="ATH1"
/product="acid trehalase"
gene <1..1050
/gene="ATH1"
CDS <1..1009
/gene="ATH1"
/note="Ath1p"
/codon_start=2
/product="acid trehalase"
/translation="DHNGTIVHKSGDVPIHIKIPNRSLIHDQDINFYNGSENERKPNL
ERRDVDRVGDPMRMDRYGTYYLLKPKQELTVQLFKPGLNARNNIAENKQITNLTAGVP
GDVAFSALDGNNYTHWQPLDKIHRAKLLIDLGEYNEKEITKGMILWGQRPAKNISISI
LPHSEKVENLFANVTEIMQNSGNDQLLNETIGQLLDNAGIPVENVIDFDGIEQEDDES
LDDVQALLHWKKEDLAKLIEQIPRLNFLKRKFVKILDNVPVSPSEPYYEASRNQSLIE
ILPSNRTTFTIDYDKLQVGDKGNTDWRKTRYIVVAVQGVYDDYDDDNKGATIKEIVLN
D"
mRNA complement(2420..3253)
/gene="YPR027C"
/product="Ypr027cp"
gene complement(2420..3253)
/gene="YPR027C"
CDS complement(2420..3253)
/gene="YPR027C"
/note="hypothetical protein"
/codon_start=1
/product="Ypr027cp"
/translation="MVGIYRILASFVPLLGLLFAFHDDDMIDTVTIIKTVYETVTSTS
TAPAPAATKSVSEKKLDDTKLTLQVIQTMVSCFSVGENPANMISCGLGVVILMFSLII
ELINKLENDGINEPQRLYDLIKPKYVELPSNYVNEKIKTTFEPLDLYLGVNMNTSGSE
LNQNCLILKLGEKTALPFPGLAQQICYTKGASNEFTNYKLSDIQGNLNENSQGIANGV
FQKISNIRKISGNFKSQLYQISEKITDENWDGSAVGFTAHGREKGPNKSQISVSFYRD
N"
gene complement(4535..4626)
/gene="trnF"
tRNA complement(join(4535..4570,4590..4626))
/product="tRNA-Phe"
/gene="trnF"
exon complement(4535..4570)
/number=1
exon complement(4590..4626)
/number=2
mRNA join(5450..5572,5706..6536)
/gene="YIP2"
/product="Yip2p"
gene 5450..6536
/gene="YIP2"
CDS join(5522..5572,5706..6197)
/gene="YIP2"
/note="similar to human polyposis locus protein 1 (YPD)"
/codon_start=1
/product="Yip2p"
/translation="MSEYASSIHSQMKQFDTKYSGNRILQQLENKTNLPKSYLVAGLG
FAYLLLIFINVGGVGEILSNFAGFVLPAYLSLVALKTPTSTDDTQLLTYWIVFSFLSV
IEFWSKAILYLIPFYWFLKTVFLIYIALPQTGGARMIYQKIVAPLTDRYILRDVSKTE
KDEIRASVNEASKATGASVH"
BASE COUNT 2201 a 1276 c 1255 g 2268 t
ORIGIN
1 cgaccacaat ggtacgattg ttcataaatc aggagatgtt cctattcata taaagatacc
61 aaacagatct ctaatacatg accaggatat caacttctat aatggttccg aaaacgaaag
121 aaaaccaaat ctagagcgta gagacgtcga ccgtgttggt gatccaatga ggatggatag [etc.]