GenBank Submissions Annotation Examples

GenBank Annotation Examples

GENERAL REQUIREMENTS

Examples

mRNA sequence

Prokaryotic gene

Eukaryotic gene

rRNA and/or ITS

Promoter region

Viral sequence

HIV-1

Transposon or insertion sequence

Microsatellite

Repeat regions

Pseudogene

Translocation and/or fusion protein

Cloning vector

Gapped Sequence

Phylogenetic or population studies

EST submissions

STS submissions

GSS submissions

HTGs

FLICs

Gapped Sequence

A gapped sequence includes both known, directly sequenced data and unknown data. The unknown sections of sequence are represented by strings of 'nnn' between the known, directly sequenced, contiguous data. All pieces of a gapped sequence must be from the same source and be in the same orientation and in the correct order.

Relevant feature information for a gapped sequence:

if a gap length is estimated, insert the equivalent number of nnns between the directly determined, contiguous sections of sequence
if the gap length is unknown, insert a string of 100 nnns to represent the gap between the sections of sequence
add a misc_feature for each gap with a /note qualifier to describe it as either 'gap of unknown length' or 'gap of estimated length, # nts'
add all other appropriate features (exons, introns, CDS, gene, etc)

We strongly suggest that you provide as much of the above information as possible to ensure the most complete annotation of your sequence. If any of this information is not known, please inform us.

Example:

Homo sapiens MHC class I antigen (HLA-B) gene, HLA-B_458_01445 allele, exons 2, 3 and partial cds.
    FEATURES             Location/Qualifiers
     source          1..788
                     /organism="Homo sapiens"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:9606"

     gene            <1..>788
                     /gene="HLA-B"
                     /allele="HLA-B_458_01445"

     mRNA            join(<1..270,513..>788)
                     /gene="HLA-B"
                     /allele="HLA-B_458_01445"
                     /product="MHC class I antigen"

     CDS             join(<1..270,513..>788)
                     /gene="HLA-B"
                     /allele="HLA-B_458_01445"
                     /codon_start=3
                     /product="MHC class I antigen"
                     /protein_id="ACR38915.1"
                     /db_xref="GI:238055051"
                     /translation="SHSMRYFDTAMSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRE
                     EPRAPWIEQEGPEYWDRNTQIFKTNTQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDV
                     GPDGRLLRGHDQSAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAARVAEQDRAYLE
                     GTCVEWLRRYLENGKDTLERA"

     exon            1..270
                     /gene="HLA-B"
                     /allele="HLA-B_458_01445"
                     /number=2

     gap             271..512
                     /estimated_length=242

     exon            513..788
                     /gene="HLA-B"
                     /allele="HLA-B_458_01445"
                     /number=3

Revised June 2, 2009