CA3-AS1

Summary

CA3-AS1 (CA3 antisense RNA 1, HGNC:51657) is a long non-coding RNA gene on chromosome 8q21.2.

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:51657
Approved symbol	CA3-AS1
Name	CA3 antisense RNA 1
Location	8q21.2
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000253549
Ensembl biotype	lncRNA
Entrez	100996348
RNAcentral	URS000075D522 — lncRNA, 832 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 17 lncRNA

ENST00000517697, ENST00000521761, ENST00000524052, ENST00000654303, ENST00000660134, ENST00000660227, ENST00000666645, ENST00000671294, ENST00000754488, ENST00000754489, ENST00000754490, ENST00000754491, ENST00000754492, ENST00000754493, ENST00000754494, ENST00000754495, ENST00000754496

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000517697 — 3 exons

Exon	Start	End
ENSE00002123140	85462736	85462801
ENSE00004102580	85440537	85442237
ENSE00004102589	85464228	85464420

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 93.10.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3435 / max 25.0981, expressed in 181 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
93804	0.3435	181

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	93.10	gold quality
mucosa of transverse colon	UBERON:0004991	82.40	gold quality
putamen	UBERON:0001874	77.68	gold quality
substantia nigra	UBERON:0002038	77.60	gold quality
amygdala	UBERON:0001876	77.23	gold quality
temporal lobe	UBERON:0001871	76.93	gold quality
skeletal muscle tissue	UBERON:0001134	76.62	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	76.40	gold quality
Ammon’s horn	UBERON:0001954	75.27	gold quality
caudate nucleus	UBERON:0001873	75.07	gold quality
hindlimb stylopod muscle	UBERON:0004252	74.76	gold quality
hypothalamus	UBERON:0001898	73.98	gold quality
cortex of kidney	UBERON:0001225	73.57	gold quality
bone marrow cell	CL:0002092	73.49	gold quality
nucleus accumbens	UBERON:0001882	73.46	gold quality
right lobe of liver	UBERON:0001114	73.36	gold quality
muscle of leg	UBERON:0001383	73.10	gold quality
rectum	UBERON:0001052	72.87	gold quality
monocyte	CL:0000576	72.71	gold quality
adult mammalian kidney	UBERON:0000082	72.49	gold quality
leukocyte	CL:0000738	72.27	gold quality
gastrocnemius	UBERON:0001388	72.21	gold quality
corpus callosum	UBERON:0002336	72.16	gold quality
muscle tissue	UBERON:0002385	71.21	gold quality
kidney	UBERON:0002113	71.07	gold quality
liver	UBERON:0002107	70.92	gold quality
blood	UBERON:0000178	70.71	gold quality
prefrontal cortex	UBERON:0000451	70.60	gold quality
cerebral cortex	UBERON:0000956	70.44	gold quality
anterior cingulate cortex	UBERON:0009835	70.30	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.94

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• Low CA3-AS1 expression is associated with colorectal cancer progression. (PMID:30415006)
• Long noncoding RNA CA3-AS1 suppresses gastric cancer migration and invasion by sponging miR-93-5p and targeting BTG3. (PMID:33051589)

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.