NCBI Home GenBank Annotation Examples

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GENERAL REQUIREMENTS
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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

 Segmented set of exons/introns

 Phylogenetic or population studies

 EST submissions

 STS submissions

 GSS submissions

 HTGs

 FLICs

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  HIV-1 Sequence

Relevant feature information for an HIV-1 sequence:
  • name of the country from which the virus was isolated
  • clone and isolate information

    AND

  • coding region intervals, including start and stop codons, if present
  • protein names
  • gene names, if known
  • amino acid sequences, if known

    OR

  • if no coding region is present, other description of the sequence

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:

HIV-1 isolate X clone 5601 from USA, complete genome.

FEATURES             Location/Qualifiers

     source          1..9720
                     /organism="Human immunodeficiency virus type 1"
                     /clone="5601"
                     /isolate="X"
                     /country="USA"

     LTR             1..634

     gene            789..2291
                     /gene="gag"

     CDS             789..2291
                     /gene="gag"
                     /product="gag protein"

     gene            2084..5095
                     /gene="pol"
                     
     CDS             2084..5095
                     /gene="pol"
                     /product="pol protein"

     gene             5040..5618
                     /gene="vif"
                     
     CDS             5040..5618
                     /gene="vif"
                     /product="vif protein"

     gene             5558..5848
                     /gene="vpr"

     CDS             5558..5848
                     /gene="vpr"
                     /product="vpr protein"

     gene             5829..8476
                     /gene="tat"

     CDS             join(5829..6043,8386..8476)
                     /gene="tat"
                     /product="tat protein"

     gene             5968..8660
                     /gene="rev"

     CDS             join(5968..6043,8386..8660)
                     /gene="rev"
                     /product="rev protein"

     gene             6060..6305
                     /gene="vpu"
                     
     CDS             6060..6305
                     /gene="vpu"
                     /product="vpu protein"

     gene            6223..8802
                     /gene="env"
                     /pseudo
                     
     gene             8804..9070
                     /gene="nef"
                     
     CDS             8804..9070
                     /gene="nef"
                     /product="nef protein"

     LTR             9086..9719
     
     polyA_signal    9612..9617


 

Revised November 28, 2000