HCG9

Summary

HCG9 (HLA complex group 9, HGNC:21243) is a long non-coding RNA gene on chromosome 6p22.1.

This gene lies within the MHC class I region on chromosome 6p21.3. This gene is believed to be non-coding, but its function has not been determined.

Source: NCBI Gene 10255 — 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:21243
Approved symbol	HCG9
Name	HLA complex group 9
Location	6p22.1
Locus type	RNA, long non-coding
Status	Approved
Aliases	PERB11, HCGIX, HCGIX4, HCGIX-4
Ensembl gene	ENSG00000204625
Ensembl biotype	lncRNA
OMIM	615797
Entrez	10255
RNAcentral	URS000075AD1B — lncRNA, 670 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 lncRNA

ENST00000376800, ENST00000463275, ENST00000850532, ENST00000850533, ENST00000850534, ENST00000850535, ENST00000850536, ENST00000850537, ENST00000850538, ENST00000850539, ENST00000850540, ENST00000850541

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000376800 — 3 exons

Exon	Start	End
ENSE00001702072	29977654	29977717
ENSE00001862242	29975112	29975517
ENSE00001870821	29978218	29978410

Expression profiles

Bgee: expression breadth ubiquitous, 124 present calls, max score 79.00.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	79.00	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.29	silver quality
duodenum	UBERON:0002114	78.19	gold quality
rectum	UBERON:0001052	77.33	gold quality
apex of heart	UBERON:0002098	76.61	gold quality
body of pancreas	UBERON:0001150	76.49	gold quality
pituitary gland	UBERON:0000007	75.03	gold quality
pancreas	UBERON:0001264	73.58	gold quality
small intestine	UBERON:0002108	72.17	gold quality
metanephros cortex	UBERON:0010533	71.95	gold quality
small intestine Peyer’s patch	UBERON:0003454	71.78	gold quality
mucosa of transverse colon	UBERON:0004991	71.33	gold quality
left adrenal gland	UBERON:0001234	71.21	gold quality
transverse colon	UBERON:0001157	70.33	gold quality
adenohypophysis	UBERON:0002196	70.28	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	70.20	gold quality
right adrenal gland cortex	UBERON:0035827	69.83	gold quality
blood	UBERON:0000178	69.82	gold quality
left adrenal gland cortex	UBERON:0035825	69.65	gold quality
adrenal gland	UBERON:0002369	69.58	gold quality
endometrium	UBERON:0001295	69.27	gold quality
lower esophagus mucosa	UBERON:0035834	68.93	gold quality
right adrenal gland	UBERON:0001233	68.91	gold quality
right lung	UBERON:0002167	68.76	gold quality
monocyte	CL:0000576	68.42	gold quality
intestine	UBERON:0000160	68.12	gold quality
fundus of stomach	UBERON:0001160	67.83	gold quality
left lobe of thyroid gland	UBERON:0001120	67.79	gold quality
right atrium auricular region	UBERON:0006631	67.74	gold quality
islet of Langerhans	UBERON:0000006	67.68	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.56

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD. (PMID:21647149)
• Significant differences were detected in both CpG and CpH modifications in the brains of individuals affected with schizophrenia or bipolar disorder and unaffected controls (PMID:26078387)
• Long Noncoding RNA HCG9 Promotes Osteosarcoma Progression through RAD51 by Acting as a ceRNA of miR-34b-3p. (PMID:34456631)

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.