Parsing the FEATURES Table

The full definition of the syntax of the FEATURES table can be found at http://www.ncbi.nlm.nih.gov/collab/FT/index.html. As an overview, you might first look over the NCBI gbrel.txt document mentioned earlier.

Features

The GenBank entries in the book are very simple, including only three features. The FEATURES table can support a great many more types, however, and these are listed here (and borrowed from Tisdall's book):

allele

Obsolete; see variation feature key

attenuator

Sequence related to transcription termination

C_region

Span of the C immunological feature

CAAT_signal

CAAT box in eukaryotic promoters

CDS

Sequence coding for amino acids in protein (includes stop codon)

conflict

Independent sequence determinations differ

D-loop

Displacement loop

D_segment

Span of the D immunological feature

enhancer

Cis-acting enhancer of promoter function

exon

Region that codes for part of spliced mRNA

gene

Region that defines a functional gene, possibly including upstream (promoter, enhancer, etc.) and downstream control elements, and for which a name has been assigned

GC_signal

GC box in eukaryotic promoters

iDNA

Intervening DNA eliminated by recombination

intron

Transcribed region excised by mRNA splicing

J_region

Span of the J immunological feature

LTR

Long terminal repeat

mat_peptide

Mature peptide coding region (doesn't include stop codon)

misc_binding

Miscellaneous binding site

misc_difference

Miscellaneous difference feature

misc_feature

Region of biological significance that can't be described by any other feature

misc_recomb

Miscellaneous recombination feature

misc_RNA

Miscellaneous transcript feature not defined by other RNA keys

misc_signal

Miscellaneous signal

misc_structure

Miscellaneous DNA or RNA structure

modified_base

The indicated base is a modified nucleotide

mRNA

Messenger RNA

mutation

Obsolete: see variation feature key

N_region

Span of the N immunological feature

old_sequence

Presented sequence revises a previous version

polyA_signal

Signal for cleavage and polyadenylation

polyA_site

Site at which polyadenine is added to mRNA

precursor_RNA

Any RNA species that isn't yet the mature RNA product

prim_transcript

Primary (unprocessed) transcript

primer

Primer binding region used with PCR

primer_bind

Noncovalent primer binding site

promoter

A region involved in transcription initiation

protein_bind

Noncovalent protein binding site on DNA or RNA

RBS

Ribosome binding site

rep_origin

Replication origin for duplex DNA

repeat_region

Sequence containing repeated subsequences

repeat_unit

One repeated unit of a repeat_region

rRNA

Ribosomal RNA

S_region

Span of the S immunological feature

satellite

Satellite repeated sequence

scRNA

Small cytoplasmic RNA

sig_peptide

Signal peptide coding region

snRNA

Small nuclear RNA

source

Biological source of the sequence data represented by a GenBank record; mandatory feature, one or more per record; for organisms that have been incorporated within the NCBI taxonomy database, an associated /db_xref="taxon:NNNN" qualifier will be present (where NNNNN is the numeric identifier assigned to the organism within the NCBI taxonomy database)

stem_loop

Hairpin loop structure in DNA or RNA

STS

Sequence Tagged Site: operationally unique sequence that identifies the combination of primer spans used in a PCR assay

TATA_signal

TATA box in eukaryotic promoters

terminator

Sequence causing transcription termination

transit_peptide

Transit peptide coding region

transposon

Transposable element (TN)

tRNA

Transfer RNA

unsure

Authors are unsure about the sequence in this region

V_region

Span of the V immunological feature

variation

A related population contains stable mutation

-

Placeholder (hyphen)

-10_signal

Pribnow box in prokaryotic promoters

-35_signal

-35 box in prokaryotic promoters

3'clip

3'-most region of a precursor transcript removed in processing

3'UTR

3' untranslated region (trailer)

5'clip

5'-most region of a precursor transcript removed in processing

5'UTR

5' untranslated region (leader)

Each of these features can have its own "sub-feature" keys, as well.