SNHG9

Summary

SNHG9 (small nucleolar RNA host gene 9, HGNC:33102) is a long non-coding RNA gene on chromosome 16p13.3.

Predicted to be involved in RNA processing. Predicted to be located in nucleolus.

Source: NCBI Gene 735301 — 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:33102
Approved symbol	SNHG9
Name	small nucleolar RNA host gene 9
Location	16p13.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	DKFZp686N06141, NCRNA00062
Ensembl gene	ENSG00000255198
Ensembl biotype	lncRNA
Entrez	735301
RNAcentral	URS000075D573 — lncRNA, 345 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 lncRNA

ENST00000531523, ENST00000564014, ENST00000731450

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000531523 — 2 exons

Exon	Start	End
ENSE00004060875	1965406	1965513
ENSE00004060879	1964526	1965129

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.1913 / max 285.5084, expressed in 1467 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152144	8.9901	1597
152143	7.5421	1702
152141	3.2816	1260
152145	1.2588	292
152142	0.6509	408

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
olfactory segment of nasal mucosa	UBERON:0005386	98.13	gold quality
granulocyte	CL:0000094	95.92	gold quality
putamen	UBERON:0001874	95.54	gold quality
adenohypophysis	UBERON:0002196	95.28	gold quality
pituitary gland	UBERON:0000007	94.64	gold quality
body of pancreas	UBERON:0001150	94.57	gold quality
nucleus accumbens	UBERON:0001882	94.49	gold quality
caudate nucleus	UBERON:0001873	94.45	gold quality
Ammon’s horn	UBERON:0001954	93.36	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.16	gold quality
left lobe of thyroid gland	UBERON:0001120	93.10	gold quality
amygdala	UBERON:0001876	92.85	gold quality
temporal lobe	UBERON:0001871	92.84	gold quality
substantia nigra	UBERON:0002038	92.74	gold quality
right lobe of thyroid gland	UBERON:0001119	92.53	gold quality
thyroid gland	UBERON:0002046	91.88	gold quality
left adrenal gland cortex	UBERON:0035825	91.81	gold quality
right lobe of liver	UBERON:0001114	91.70	gold quality
lower esophagus mucosa	UBERON:0035834	91.46	gold quality
hypothalamus	UBERON:0001898	91.27	gold quality
body of stomach	UBERON:0001161	91.17	gold quality
cortex of kidney	UBERON:0001225	90.97	gold quality
fundus of stomach	UBERON:0001160	90.92	gold quality
left ovary	UBERON:0002119	90.92	gold quality
left adrenal gland	UBERON:0001234	90.89	gold quality
apex of heart	UBERON:0002098	90.80	gold quality
prostate gland	UBERON:0002367	90.79	gold quality
right adrenal gland	UBERON:0001233	90.72	gold quality
saliva-secreting gland	UBERON:0001044	90.58	gold quality
omental fat pad	UBERON:0010414	90.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	20.88

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 8)

• The elevated SNHG9 expression was related to lower survival rate in patients with glioma. SNHG9 could downregulate miR-199a-5p and upregulate Wnt2 in glioblastoma cells. Overexpression of SNHG9 in glioblastoma cells promoted aerobic glycolysis and cell proliferation, which could be attenuated by miR-199a-5p. (PMID:31504670)
• SNHG9, delivered by adipocyte-derived exosomes, alleviates inflammation and apoptosis of endothelial cells through suppressing TRADD expression. (PMID:32007500)
• LncRNA SNHG9 is downregulated in osteoarthritis and inhibits chondrocyte apoptosis by downregulating miR-34a through methylation. (PMID:32738890)
• Knockdown of long non-coding RNA small nucleolar RNA host gene 9 or hexokinase 2 both suppress endometrial cancer cell proliferation and glycolysis. (PMID:33821518)
• A phosphatidic acid-binding lncRNA SNHG9 facilitates LATS1 liquid-liquid phase separation to promote oncogenic YAP signaling. (PMID:34267352)
• SNHG9/miR-214-5p/SOX4 feedback loop regulates osteosarcoma progression. (PMID:36004648)
• Up-regulated lncRNA SNHG9 mediates the pathogenesis of dilated cardiomyopathy via miR-326/EPHB3 axis. (PMID:37004604)
• lncRNA SNHG9 enhances liver cancer stem cell self-renewal and tumorigenicity by negatively regulating PTEN expression via recruiting EZH2. (PMID:37851112)

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.