SNHG3

Summary

SNHG3 (small nucleolar RNA host gene 3, HGNC:10118) is a long non-coding RNA gene on chromosome 1p35.3.

Predicted to be active in nucleus.

Source: NCBI Gene 8420 — 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:10118
Approved symbol	SNHG3
Name	small nucleolar RNA host gene 3
Location	1p35.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	U17HG, U17HG-A, NCRNA00014
Ensembl gene	ENSG00000242125
Ensembl biotype	lncRNA
OMIM	603238
Entrez	8420
RNAcentral	URS0000035204 — lncRNA, 2201 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 retained_intron, 1 lncRNA

ENST00000413987, ENST00000437681, ENST00000447507

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000413987 — 3 exons

Exon	Start	End
ENSE00001727037	28505980	28506084
ENSE00001756047	28508830	28510892
ENSE00003570048	28508128	28508160

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 97.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 194.0813 / max 3774.5380, expressed in 1818 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
1801	194.0813	1818
1802	7.8056	1459
1803	1.7574	545
1804	1.6557	579
1805	0.4395	205

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	97.01	gold quality
lower esophagus mucosa	UBERON:0035834	96.98	gold quality
right uterine tube	UBERON:0001302	93.75	gold quality
esophagus mucosa	UBERON:0002469	93.60	gold quality
right ovary	UBERON:0002118	93.09	gold quality
left ovary	UBERON:0002119	92.90	gold quality
adrenal tissue	UBERON:0018303	92.74	gold quality
right lobe of thyroid gland	UBERON:0001119	92.39	gold quality
mucosa of transverse colon	UBERON:0004991	92.24	gold quality
left lobe of thyroid gland	UBERON:0001120	92.09	gold quality
granulocyte	CL:0000094	92.01	gold quality
ectocervix	UBERON:0012249	91.77	gold quality
left uterine tube	UBERON:0001303	91.50	gold quality
spleen	UBERON:0002106	91.15	gold quality
endocervix	UBERON:0000458	90.88	gold quality
esophagus	UBERON:0001043	90.79	gold quality
upper lobe of left lung	UBERON:0008952	90.75	gold quality
rectum	UBERON:0001052	90.71	gold quality
monocyte	CL:0000576	90.63	gold quality
mononuclear cell	CL:0000842	90.44	gold quality
minor salivary gland	UBERON:0001830	90.31	gold quality
transverse colon	UBERON:0001157	90.10	gold quality
small intestine Peyer’s patch	UBERON:0003454	89.97	gold quality
leukocyte	CL:0000738	89.83	gold quality
thyroid gland	UBERON:0002046	89.83	gold quality
right lung	UBERON:0002167	89.42	gold quality
skin of abdomen	UBERON:0001416	89.18	gold quality
body of stomach	UBERON:0001161	88.78	gold quality
upper lobe of lung	UBERON:0008948	88.77	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	88.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 40)

• SNHG3 was higher expression in ovarian cancer tissues and cells. Higher SNHG3 predicted a poor prognosis of ovarian cancer. (PMID:29758922)
• TCGA analysis showed lncRNA SNHG3 was not only related to ovarian cancer survival, but also energy metabolism. Analysis of the results of GSEA analysis and Starbase 2.0 found that SNHG3 was related to energy metabolism by regulating miRNAs and EIF4AIII, and those molecules had target sites with PKM, PDHB, IDH2, and UQCRH in the glycolysis, Kreb’s cycle, and oxidative phosphorylation (OXPHOS) pathways. (PMID:29921511)
• forced expression of SNHG3 promoted cell invasion, epithelial-mesenchymal transition (EMT), and sorafenib resistance in HCC. Moreover, SNHG3 overexpression induced HCC cells EMT via miR-128/CD151 cascade activation. (PMID:30132868)
• Results found that the lncRNA SNHG3 was significantly upregulated in lung adenocarcinoma. Also, SNHG3 promoted proliferation, cell cycle, and suppressed cell apoptosis of lung adenocarcinoma, suggesting that SNHG3 acted as an oncogene in lung adenocarcinoma (PMID:30154938)
• SNHG3 is highly expressed in osteosarcoma and promotes the invasive and migratory potentials of osteosarcoma cells by absorbing MIRN151a to up-regulate RAB22A expression. (PMID:30797154)
• Knockdown of SNHG3 upregulated miR-384 expression and that overexpression of miR-384 decreased SNHG3. Inhibition of miR-384 markedly increased WEE1 expression. (PMID:31238052)
• lncRNA SNHG3 facilitates acute myeloid leukemia cell growth via the regulation of miR-758-3p/SRGN axis. (PMID:31452272)
• The SNHG3/miR-139-5p/TOP2A axis plays an important role in the proliferation. (PMID:31505165)
• SNHG3 promotes hepatocellular cancer progression via the miR-326/SMAD3/ZEB1 signaling pathway. (PMID:31548493)
• LncRNA SNHG3 is activated by E2F1 and promotes proliferation and migration of non-small-cell lung cancer cells through activating TGF-beta pathway and IL-6/JAK2/STAT3 pathway. (PMID:31602642)
• Snhg3 acted as the sponge of miR-196 in the hippocampal cells by regulating the expression of miR-196 target genes, XIAP and CAAP1. Moreover, Snhg3 overexpression decreased brain infarct size and ameliorated hypoxic-ischemic neonatal brain damage (PMID:31751562)
• Small nucleolar RNA host gene 3 facilitates cell proliferation and migration in oral squamous cell carcinoma via targeting nuclear transcription factor Y subunit gamma. (PMID:31762107)
• SNHG3 Functions as miRNA Sponge to Promote Breast Cancer Cells Growth Through the Metabolic Reprogramming. (PMID:31956955)
• LncRNA SNHG3 sponges miR-577 to up-regulate SMURF1 expression in prostate cancer. (PMID:32248648)
• SNHG3 silencing suppresses the malignant development of triple-negative breast cancer cells by regulating miRNA-326/integrin alpha5 axis and inactivating Vav2/Rac1 signaling pathway. (PMID:32495883)
• The knockdown of SNHG3 inhibits the progression of laryngeal squamous cell carcinoma by miR-340-5p/YAP1 axis and Wnt/beta-catenin pathway. (PMID:32538668)
• LncRNA SNHG3 promotes bladder cancer proliferation and metastasis through miR-515-5p/GINS2 axis. (PMID:32596993)
• Overexpression of lncRNA SNGH3 Predicts Unfavorable Prognosis and Clinical Outcomes in Human Cancers: Evidence from a Meta-Analysis. (PMID:32802874)
• Long non-coding RNA SNHG3 promotes breast cancer cell proliferation and metastasis by binding to microRNA-154-3p and activating the notch signaling pathway. (PMID:32883233)
• SNHG3/miR-2682-5p/HOXB8 promotes cell proliferation and migration in oral squamous cell carcinoma. (PMID:32989886)
• lncRNA SNHG3 accelerates the proliferation and invasion of non-small cell lung cancer by downregulating miR-340-5p. (PMID:33225676)
• LncRNA SNHG3 Promotes Proliferation and Metastasis of Non-Small-Cell Lung Cancer Cells Through miR-515-5p/SUMO2 Axis. (PMID:34032148)
• [Role of long noncoding RNA SNHG3 in regulating proliferation, migration and invasion of cervical cancer SiHa cells]. (PMID:34238747)
• LncRNA SNHG3 Facilitates the Malignant Phenotype of Cholangiocarcinoma Cells via the miR-3173-5p/ERG Axis. (PMID:34647226)
• LncRNA SNHG3 is responsible for the deterioration of colorectal carcinoma through regulating the miR-370-5p/EZH1 axis. (PMID:34661273)
• Long noncoding RNA SNHG3 promotes malignant phenotypes in cervical cancer cells via association with YAP1. (PMID:34816392)
• LncRNA SNHG3 promotes gastric cancer cell proliferation and metastasis by regulating the miR-139-5p/MYB axis. (PMID:34898477)
• High expression of small nucleolar RNA host gene 3 predicts poor prognosis and promotes bone metastasis in prostate cancer by activating transforming growth factor-beta signaling. (PMID:35030969)
• LncRNA SNHG3 regulates the BMSC osteogenic differentiation in bone metastasis of breast cancer by modulating the miR-1273g-3p/BMP3 axis. (PMID:35081500)
• SNHG3 could promote prostate cancer progression through reducing methionine dependence of PCa cells. (PMID:35123415)
• Potential diagnostic and prognostic value of the long non-coding RNA SNHG3 in human cancers: A systematic review and meta-analysis. (PMID:35130083)
• SNHG3 regulates NEIL3 via transcription factor E2F1 to mediate malignant proliferation of hepatocellular carcinoma. (PMID:36114381)
• LncRNA SNHG3 enhances BMI1 mRNA stability by binding and regulating c-MYC: Implications for the carcinogenic role of SNHG3 in bladder cancer. (PMID:36208024)
• BMP9 promotes autophagy and inhibits migration and invasion in breast cancer cells through the c-Myc/SNHG3/mTOR signaling axis. (PMID:36963166)
• SNHG3/hsa-miR-455-5p Axis-mediated High Expression of MTHFD2 Correlates with Tumor Immune Infiltration and Endometrial Carcinoma Progression. (PMID:37484807)
• METTL3-mediated m[6]A modification of lncRNA SNHG3 accelerates gastric cancer progression by modulating miR-186-5p/cyclinD2 axis. (PMID:37823387)
• SNHG3/WISP2 Axis Promotes Hela Cell Migration and Invasion via Activating Wnt/beta-Catenin Signaling. (PMID:38035707)
• Long noncoding RNA SNHG3 interacts with microRNA-502-3p to mediate ITGA6 expression in liver hepatocellular carcinoma. (PMID:38680094)
• Cancer-derived exosomal lncRNA SNHG3 promotes the metastasis of colorectal cancer through hnRNPC-mediating RNA stability of beta-catenin. (PMID:38725844)
• Investigating SNHG3 and BCYRN1 lncRnas expression in the peripheral blood cells of multiple sclerosis patients. (PMID:38832630)

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.