SOX9-AS1

Summary

SOX9-AS1 (SOX9 antisense RNA 1, HGNC:49321) is a long non-coding RNA gene on chromosome 17q24.3.

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:49321
Approved symbol	SOX9-AS1
Name	SOX9 antisense RNA 1
Location	17q24.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	FLJ37644
Ensembl gene	ENSG00000234899
Ensembl biotype	lncRNA
Entrez	400618
RNAcentral	URS000075EE78 — lncRNA, 3033 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 36 lncRNA, 3 retained_intron

ENST00000414600, ENST00000434703, ENST00000440093, ENST00000443037, ENST00000446332, ENST00000529667, ENST00000532249, ENST00000533039, ENST00000533179, ENST00000533232, ENST00000533996, ENST00000588177, ENST00000623935, ENST00000653248, ENST00000653391, ENST00000655414, ENST00000655689, ENST00000656124, ENST00000656392, ENST00000657467, ENST00000659146, ENST00000659228, ENST00000659599, ENST00000662263, ENST00000662298, ENST00000663438, ENST00000664713, ENST00000666904, ENST00000668782, ENST00000668847, ENST00000668902, ENST00000670181, ENST00000671151, ENST00000715467, ENST00000715468, ENST00000715469, ENST00000715470, ENST00000715485, ENST00000715486

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000414600 — 2 exons

Exon	Start	End
ENSE00001662226	72141685	72141780
ENSE00001667916	72090459	72091104

Expression profiles

Bgee: expression breadth ubiquitous, 154 present calls, max score 91.77.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1178 / max 54.2742, expressed in 55 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
167850	0.1178	55

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
hindlimb stylopod muscle	UBERON:0004252	91.77	gold quality
ventricular zone	UBERON:0003053	87.13	gold quality
muscle of leg	UBERON:0001383	86.75	gold quality
gastrocnemius	UBERON:0001388	86.61	gold quality
apex of heart	UBERON:0002098	84.77	gold quality
body of pancreas	UBERON:0001150	83.93	gold quality
nucleus accumbens	UBERON:0001882	83.23	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	83.09	gold quality
putamen	UBERON:0001874	82.86	gold quality
heart left ventricle	UBERON:0002084	82.65	gold quality
amygdala	UBERON:0001876	82.53	gold quality
anterior cingulate cortex	UBERON:0009835	82.46	gold quality
caudate nucleus	UBERON:0001873	82.45	gold quality
hypothalamus	UBERON:0001898	82.05	gold quality
cardiac ventricle	UBERON:0002082	81.23	gold quality
minor salivary gland	UBERON:0001830	81.05	gold quality
right frontal lobe	UBERON:0002810	80.51	gold quality
ganglionic eminence	UBERON:0004023	80.49	gold quality
Brodmann (1909) area 9	UBERON:0013540	79.93	gold quality
spinal cord	UBERON:0002240	79.26	gold quality
right testis	UBERON:0004534	78.49	gold quality
left testis	UBERON:0004533	77.90	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.32	gold quality
pancreas	UBERON:0001264	76.81	gold quality
substantia nigra	UBERON:0002038	76.43	gold quality
heart	UBERON:0000948	76.10	gold quality
saliva-secreting gland	UBERON:0001044	76.08	gold quality
mouth mucosa	UBERON:0003729	75.82	gold quality
right atrium auricular region	UBERON:0006631	75.64	gold quality
testis	UBERON:0000473	74.92	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.84

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• SOX9-AS1 aggravates Hepatocellular carcinoma (HCC) progression and metastasis in vitro and in vivo. We demonstrated that SOX9-AS1 sponges miR-5590-3p to elevate SOX9 expression, and that SOX9 in turn transcriptionally activates SOX9-AS1. (PMID:31402556)
• Impact of lncRNA SOX9-AS1 overexpression on the prognosis and progression of intrahepatic cholangiocarcinoma. (PMID:35870795)
• LncRNA SOX9-AS1 triggers a transcriptional program involved in lipid metabolic reprogramming, cell migration and invasion in triple-negative breast cancer. (PMID:38233470)

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.