COLCA1

Summary

COLCA1 (colorectal cancer associated 1, HGNC:33789) is a long non-coding RNA gene on chromosome 11q23.1.

This gene encodes a transmembrane protein that localizes to granular structures, including crystalloid eosinophilic granules and other granular organelles. This gene, along with an overlapping opposite strand gene, has been implicated as a susceptibility locus for colorectal cancer. Alternative splicing of this gene results in multiple transcript variants.

Source: NCBI Gene 399948 — RefSeq curated summary.

At a glance

• Gene type: non-coding (lncRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33789
Approved symbol	COLCA1
Name	colorectal cancer associated 1
Location	11q23.1
Locus type	RNA, long non-coding
Status	Approved
Aliases	FLJ45803, CASC12
Ensembl gene	ENSG00000196167
Ensembl biotype	lncRNA
OMIM	615693
Entrez	399948
RNAcentral	URS0001BBE368 — lncRNA, 5499 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 lncRNA

ENST00000355430, ENST00000526150, ENST00000532918, ENST00000540738, ENST00000620864, ENST00000669257, ENST00000846569

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000355430 — 2 exons

Exon	Start	End
ENSE00004274461	111293446	111298666
ENSE00004274462	111299594	111299913

Expression profiles

Bgee: expression breadth ubiquitous, 191 present calls, max score 90.23.

FANTOM5 (CAGE): breadth broad, TPM avg 0.9069 / max 56.0513, expressed in 277 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
122214	0.5818	249
122215	0.1052	53
122222	0.0612	23
122216	0.0461	23
122218	0.0334	13
122217	0.0311	18
122219	0.0183	8
122221	0.0155	7
122220	0.0144	7

Top tissues by expression

252 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	90.23	gold quality
corpus epididymis	UBERON:0004359	89.87	gold quality
epithelium of nasopharynx	UBERON:0001951	88.96	gold quality
bronchus	UBERON:0002185	88.91	gold quality
epithelial cell of pancreas	CL:0000083	86.01	gold quality
mucosa of paranasal sinus	UBERON:0005030	85.32	gold quality
caput epididymis	UBERON:0004358	85.06	gold quality
parotid gland	UBERON:0001831	84.40	gold quality
seminal vesicle	UBERON:0000998	84.16	gold quality
right uterine tube	UBERON:0001302	84.14	gold quality
body of stomach	UBERON:0001161	84.06	gold quality
pancreatic ductal cell	CL:0002079	83.86	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	83.85	gold quality
stomach	UBERON:0000945	83.77	gold quality
prostate gland	UBERON:0002367	82.79	gold quality
tonsil	UBERON:0002372	82.67	gold quality
nasal cavity epithelium	UBERON:0005384	82.67	gold quality
saliva-secreting gland	UBERON:0001044	80.31	gold quality
fundus of stomach	UBERON:0001160	80.26	gold quality
minor salivary gland	UBERON:0001830	78.77	gold quality
urinary bladder	UBERON:0001255	78.28	gold quality
cardiac muscle of right atrium	UBERON:0003379	78.23	gold quality
left ventricle myocardium	UBERON:0006566	77.85	gold quality
myocardium	UBERON:0002349	77.50	gold quality
kidney epithelium	UBERON:0004819	77.04	gold quality
nasal cavity mucosa	UBERON:0001826	77.01	gold quality
palpebral conjunctiva	UBERON:0001812	76.91	gold quality
mouth mucosa	UBERON:0003729	76.45	gold quality
urethra	UBERON:0000057	76.35	gold quality
gall bladder	UBERON:0002110	76.14	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.76

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• We found PLCE1, C11orf92-C11orf93, and NOC3L associated with colorectal cancer susceptibility (PMID:24146276)
• Data implicate COLCA1 and COLCA2 in the pathogenesis of colon cancer. (PMID:24154973)
• rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis. (PMID:33633225)

Cross-species orthologs

0 orthologs

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.