FxnSet
Defined in file docsum.asn
C++ class: CFxnSet
FxnSet ::= SEQUENCE {
attlist SET {
geneId INTEGER OPTIONAL, --gene-id of gene as aligned to contig
--symbol (official if present in Entrez Gene) of
-- gene
symbol VisibleString OPTIONAL,
mrnaAcc VisibleString OPTIONAL, --mRNA accession if variation in transcript
--mRNA sequence version if variation is in
-- transcripot
mrnaVer INTEGER OPTIONAL,
protAcc VisibleString OPTIONAL, --protein accession if variation in protein
--protein version if variation is in
-- protein
protVer INTEGER OPTIONAL,
--variation in region of gene, but not in
-- transcript - deprecated
fxnClass ENUMERATED {
locus-region (1),
coding-unknown (2),
synonymous-codon (3),
non-synonymous-codon (4),
mrna-utr (5),
intron-variant (6),
splice-region-variant (7),
reference (8),
coding-exception (9),
coding-sequence-variant (10),
nc-transcript-variant (11),
downstream-variant-500B (12),
upstream-variant-2KB (13),
nonsense (14),
missense (15),
frameshift-variant (16),
utr-variant-3-prime (17),
utr-variant-5-prime (18),
splice-acceptor-variant (19),
splice-donor-variant (20),
cds-indel (21),
stop-gained (22),
stop-lost (23),
complex-change-in-transcript (24),
incomplete-terminal-codon-variant (25),
nmd-transcript-variant (26),
mature-miRNA-variant (27),
upstream-variant-5KB (28),
downstream-variant-5KB (29),
intergenic (30)
} OPTIONAL,
readingFrame INTEGER OPTIONAL,
--variation allele: * suffix indicates allele of contig at this
-- location
allele VisibleString OPTIONAL,
residue VisibleString OPTIONAL, --translated amino acid residue for allele
--position of the variant residue in peptide
-- sequence
aaPosition INTEGER OPTIONAL,
mrnaPosition INTEGER OPTIONAL,
soTerm VisibleString OPTIONAL
},
--functional relationship of SNP (and possibly alleles) to genes at
-- contig location as defined in organism-specific bxxx_SNPContigLocusId_xxx
-- tables.
fxnSet NULL
}