HOXC-AS1

Summary

HOXC-AS1 (HOXC cluster antisense RNA 1, HGNC:43749) is a long non-coding RNA gene on chromosome 12q13.13.

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:43749
Approved symbol	HOXC-AS1
Name	HOXC cluster antisense RNA 1
Location	12q13.13
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000250451
Ensembl biotype	lncRNA
Entrez	100874363
RNAcentral	URS000048B8CE — lncRNA, 548 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 lncRNA

ENST00000505700, ENST00000512427, ENST00000809710

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000505700 — 2 exons

Exon	Start	End
ENSE00004205785	53999020	53999267
ENSE00004205787	53999709	54000011

Expression profiles

Bgee: expression breadth ubiquitous, 104 present calls, max score 89.16.

FANTOM5 (CAGE): breadth broad, TPM avg 0.8779 / max 22.1103, expressed in 455 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
131291	0.6638	364
131290	0.2141	109

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.16	gold quality
skeletal muscle tissue	UBERON:0001134	87.46	gold quality
muscle of leg	UBERON:0001383	86.04	gold quality
gastrocnemius	UBERON:0001388	86.02	gold quality
popliteal artery	UBERON:0002250	84.24	gold quality
tibial artery	UBERON:0007610	84.23	gold quality
skin of leg	UBERON:0001511	83.56	gold quality
subcutaneous adipose tissue	UBERON:0002190	83.40	gold quality
tibial nerve	UBERON:0001323	82.91	gold quality
zone of skin	UBERON:0000014	82.86	gold quality
skin of abdomen	UBERON:0001416	82.24	gold quality
sural nerve	UBERON:0015488	80.29	gold quality
hindlimb stylopod muscle	UBERON:0004252	79.34	gold quality
metanephros cortex	UBERON:0010533	78.52	gold quality
thoracic mammary gland	UBERON:0005200	77.82	gold quality
cortex of kidney	UBERON:0001225	77.58	gold quality
calcaneal tendon	UBERON:0003701	77.58	gold quality
kidney	UBERON:0002113	76.76	gold quality
adult mammalian kidney	UBERON:0000082	76.53	gold quality
left uterine tube	UBERON:0001303	76.31	gold quality
right ovary	UBERON:0002118	73.37	gold quality
adipose tissue	UBERON:0001013	73.06	gold quality
small intestine Peyer’s patch	UBERON:0003454	72.92	gold quality
small intestine	UBERON:0002108	71.97	gold quality
colonic epithelium	UBERON:0000397	70.61	silver quality
ovary	UBERON:0000992	69.76	gold quality
left ovary	UBERON:0002119	69.02	gold quality
bone marrow cell	CL:0002092	68.76	silver quality
multicellular organism	UBERON:0000468	66.63	gold quality
fallopian tube	UBERON:0003889	65.75	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.35

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 5)

• oxidized low-density lipoprotein (Ox-LDL) decreased expression of HOXC-AS1 and HOXC6 in a time-dependent manner (PMID:27574949)
• Our research illustrated a feedback loop of HOXC-AS1-MYC in aggravating GC cell growth and metastasis, highlighting HOXC-AS1 as a promising target for GC diagnosis and treatment. (PMID:31870402)
• lncRNA HOXC-AS1 promotes gastric cancer via binding eIF4AIII by activating Wnt/beta-catenin signaling. (PMID:32307743)
• Identification of long non-coding RNAs in advanced prostate cancer associated with androgen receptor splicing factors. (PMID:32704143)
• Long non-coding RNA HOXC-AS1 exerts its oncogenic effects in esophageal squamous cell carcinoma by interaction with IGF2BP2 to stabilize SIRT1 expression. (PMID:36510377)

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.