HOXC-AS3

Summary

HOXC-AS3 (HOXC cluster antisense RNA 3, HGNC:43751) 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:43751
Approved symbol	HOXC-AS3
Name	HOXC cluster antisense RNA 3
Location	12q13.13
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000251151
Ensembl biotype	lncRNA
Entrez	100874365
RNAcentral	URS0000207271 — ncRNA, 368 nt, 2 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 lncRNA, 1 retained_intron

ENST00000509870, ENST00000513165, ENST00000514702, ENST00000567780, ENST00000717839, ENST00000717840, ENST00000717841, ENST00000729786, ENST00000729787, ENST00000729788, ENST00000729789, ENST00000729790

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000509870 — 2 exons

Exon	Start	End
ENSE00004057688	53983185	53983864
ENSE00004057696	53984710	53984838

Expression profiles

Bgee: expression breadth broad, 98 present calls, max score 80.09.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1826 / max 12.0253, expressed in 84 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
131287	0.1171	52
131286	0.0655	31

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	80.09	gold quality
metanephros cortex	UBERON:0010533	75.88	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	71.41	gold quality
adult mammalian kidney	UBERON:0000082	70.64	gold quality
muscle of leg	UBERON:0001383	70.39	gold quality
cortex of kidney	UBERON:0001225	69.91	gold quality
tibial artery	UBERON:0007610	69.88	gold quality
popliteal artery	UBERON:0002250	69.86	gold quality
gastrocnemius	UBERON:0001388	69.43	gold quality
aorta	UBERON:0000947	67.84	gold quality
skin of leg	UBERON:0001511	67.69	gold quality
tendon	UBERON:0000043	66.31	gold quality
metanephros	UBERON:0000081	65.42	gold quality
skin of abdomen	UBERON:0001416	65.26	gold quality
hindlimb stylopod muscle	UBERON:0004252	64.78	gold quality
zone of skin	UBERON:0000014	63.51	gold quality
kidney	UBERON:0002113	63.02	gold quality
subcutaneous adipose tissue	UBERON:0002190	63.02	gold quality
buccal mucosa cell	CL:0002336	58.10	gold quality
sural nerve	UBERON:0015488	57.55	silver quality
right ovary	UBERON:0002118	56.19	gold quality
left uterine tube	UBERON:0001303	55.75	gold quality
adipose tissue	UBERON:0001013	54.94	gold quality
parotid gland	UBERON:0001831	53.22	gold quality
anatomical system	UBERON:0000467	51.78	gold quality
multicellular organism	UBERON:0000468	51.36	gold quality
material anatomical entity	UBERON:0000465	51.33	gold quality
lymph node	UBERON:0000029	50.34	gold quality
monocyte	CL:0000576	49.71	silver quality
left ovary	UBERON:0002119	49.29	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.64

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 8)

• YBX1 participates in HOXC-AS3-mediated gene transcriptional regulation in the tumorigenesis of gastric cancer. (PMID:30286788)
• HOXC-AS3 is aberrantly overexpressed in breast cancers especially the HER2+ type. High expression of HOXC-AS3 has a relationship with poor clinical outcomes of breast cancer. HOXC-AS3 regulates cell invasion and migration both in vitro and in vivo. Results demonstrated that miR-3922-5p was a direct target of HOXC-AS3, and PPP1R1A was a target of miR-3922-5p in breast cancer. (PMID:31797701)
• Long noncoding RNA HOXC-AS3 facilitates the progression of invasive mucinous adenocarcinomas of the lung via modulating FUS/FOXM1. (PMID:31925650)
• Long noncoding RNA HOXC-AS3 enhances the progression of cervical cancer via activating ErbB signaling pathway. (PMID:34387789)
• Low Glucose-Induced Overexpression of HOXC-AS3 Promotes Metabolic Reprogramming of Breast Cancer. (PMID:35031573)
• LncRNA HOXC-AS3 promotes non-small-cell lung cancer growth and metastasis through upregulation of YBX1. (PMID:35387975)
• LncRNA HOXC-AS3 overexpression inhibits TGF-beta2-induced colorectal cancer cell migration and invasion by sponging miR-1269. (PMID:35537198)
• LncRNA HOXC-AS3 accelerates malignant proliferation of cervical cancer cells via stabilizing KDM5B. (PMID:38842683)

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.