a related individual or strain contains stable, alternative forms of the same gene which differs from the presented sequence at this location (and perhaps others)

attenuator

(1)  region of DNA at which regulation of termination of transcription occurs, which controls the expression of some bacterial operons;
(2)  sequence segment located between the promoter and the first structural gene that causes partial termination of transcription

constant region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; includes one or more exons depending on the particular chain

CAAT_signal

conflict

D-loop

D-segment

enhancer

exon

region of genome that codes for portion of spliced mRNA; may contain 5’UTR, all CDSs, and 3’UTR

GC_signal

GC box; a conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG

gene

region of biological interest identified as a gene and for which a name has been assigned

iDNA

intervening DNA; DNA which is eliminated through any of several kinds of recombination

intron

a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it

J_segment

joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains

LTR

long terminal repeat, a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses

mat_peptide

mature peptide or protein coding sequence; coding sequence for the mature or final peptide or protein product following post-translational modification; the location does not include the stop codon (unlike the corresponding CDS)

misc_binding

site in nucleic acid which covalently or non-covalently binds another moiety that cannot be described by any other Binding key (primer_bind or protein_bind)

misc_difference

feature sequence is different from that presented in the entry and cannot be described by any other Difference key (conflict, unsure, old_sequence, mutation, variation, allele, or modified_base)

misc_feature

region of biological interest which cannot be described by any other feature key; a new or rare feature

misc_recomb

site of any generalized, site-specific or replicative recombination event where there is a breakage and reunion of duplex DNA that cannot be described by other recombination keys (iDNA and virion) or qualifiers of source key (/insertion_seq, /transposon, /proviral)

misc_RNA

any transcript or RNA product that cannot be defined by other RNA keys (prim_transcript, precursor_RNA, mRNA, 5’clip, 3’clip, 5’UTR, 3’UTR, exon, CDS, sig_peptide, transit_peptide, mat_peptide, intron, polyA_site, rRNA, tRNA, scRNA, and snRNA)

misc_signal

any region containing a signal controlling or altering gene function or expression that cannot be described by other Signal keys (promoter, CAAT_signal, TATA_signal, -35_signal, -10_signal, GC_signal, RBS, polyA_signal, enhancer, attenuator, terminator, and rep_origin)

misc_structure

any secondary or tertiary structure or conformation that cannot be described by other Structure keys (stem_loop and D-loop)

modified_base

the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod_base qualifier value)

mRNA

messenger RNA; includes 5’ untranslated region (5’UTR), coding sequences (CDS, exon) and 3’ untranslated region (3’UTR)

mutation

a related strain has an abrupt, inheritable change in the sequence at this location

N_region

extra nucleotides inserted between rearranged immunoglobulin segments

old_sequence

the presented sequence revises a previous version of the sequence at this location

polyA_signal

recognition region necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA

polyA_site

site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation

precursor_RNA

any RNA species that is not yet the mature RNA product; may include 5’ clipped region (5’clip), 5’ untranslated region (5’UTR), coding sequences (CDS, exon), intervening sequences (intron), 3’ untranslated region (3’UTR), and 3’ clipped region (3’clip)

prim_transcript

primary (initial, unprocessed) transcript; includes 5’ clipped region (5’clip), 5’ untranslated region (5’UTR), coding sequences (CDS, exon), intervening sequences (intron), 3’ untranslated region (3’UTR), and 3’ clipped region (3’clip)

primer_bind

non-covalent primer binding site for initiation of replication, transcription, or reverse transcription; includes site(s) for synthetic, for example, PCR primer elements

promoter

region on a DNA molecule involved in RNA polymerase binding to initiate transcription

protein_bind

non-covalent protein binding site on nucleic acid

RBS

ribosome binding site

repeat_region

region of genome containing repeating units

repeat_unit

single repeat element

rep_origin

origin of replication; starting site for duplication of nucleic acid to give two identical copies

rRNA

mature ribosomal RNA; the RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins

S_region

switch region of immunoglobulin heavy chains; involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin class from the same B-cell

satellite

many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA

scRNA

small cytoplasmic RNA; any one of several small cytoplasmic RNA molecules present in the cytoplasm and (sometimes) nucleus of a eukaryote

sig_peptide

signal peptide coding sequence; coding sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane; leader sequence

snRNA

small nuclear RNA; any one of many small RNA species confined to the nucleus; several of the snRNAs are involved in splicing or other RNA processing reactions

source

identifies the biological source of the specified span of the sequence; this key is mandatory; every entry will have, as a minimum, a single source key spanning the entire sequence; more than one source key per sequence is permissable

stem_loop

hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA

STS

Sequence Tagged Site; short, single-copy DNA sequence that characterizes a mapping landmark on the genome and can be detected by PCR; a region of the genome can be mapped by determining the order of a series of STSs

TATA_signal

TATA box; Goldberg-Hogness box; a conserved AT-rich septamer found about 25 bp before the start point of each eukaryotic RNA polymerase II transcript unit which may be involved in positioning the enzyme for correct initiation; consensus=TATA(A or T)A(A or T)

terminator

sequence of DNA located either at the end of the transcript or adjacent to a promoter region that causes RNA polymerase to terminate transcription; may also be site of binding of repressor protein

transit_peptide

transit peptide coding sequence; coding sequence for an N-terminal domain of a nuclear-encoded organellar protein; this domain is involved in post-translational import of the protein into the organelle

tRNA

mature transfer RNA, a small RNA molecule (75-85 bases long) that mediates the translation of a nucleic acid sequence into an amino acid sequence

unsure

author is unsure of exact sequence in this region

V_region

variable region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; codes for the variable amino terminal portion; can be made up from V_segments, D_segments, N_regions, and J_segments

V_segment

variable segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; codes for most of the variable region (V_region) and the last few amino acids of the leader peptide

variation

a related strain contains stable mutations from the same gene (for example, RFLPs, polymorphisms, etc.) which differ from the presented sequence at this location (and possibly others)

3’clip

3’-most region of a precursor transcript that is clipped off during processing

3’UTR

region at the 3’ end of a mature transcript (following the stop codon) that is not translated into a protein

5’clip

5’-most region of a precursor transcript that is clipped off during processing

5’UTR

region at the 5’ end of a mature transcript (preceding the initiation codon) that is not translated into a protein

-10_signal

pribnow box; a conserved region about 10 bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT

-35_signal

a conserved hexamer about 35 bp upstream of the start point of bacterial transcription units; consensus=TTGACa [  ] or TGTTGACA [  ]