World Intellectual Property Organization

Administrative Instructions under the Patent Cooperation Treaty 

Annex C, Appendix 2

Nucleotide and Amino Acid Symbols and Feature Table

Table 5:  List of Feature Keys Related to Nucleotide Sequences

key description
allele 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
C_region 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 CAAT box; part of a conserved sequence located about 75 bp up-stream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG (C or T) CAATCT
CDS coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein (location includes stop codon); feature includes amino acid conceptual translation
conflict independent determinations of the “same” sequence differ at this site or region
D-loop displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein
D-segment diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain
enhancer a cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter
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 [  ]

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