SOX1-OT

Summary

SOX1-OT (SOX1 overlapping transcript, HGNC:42733) is a long non-coding RNA gene on chromosome 13q34.

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:42733
Approved symbol	SOX1-OT
Name	SOX1 overlapping transcript
Location	13q34
Locus type	RNA, long non-coding
Status	Approved
Aliases	uc.357
Ensembl gene	ENSG00000224243
Ensembl biotype	lncRNA
Entrez	100505996
RNAcentral	URS000075CA1A — lncRNA, 704 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 29 lncRNA

ENST00000421423, ENST00000653135, ENST00000657728, ENST00000658904, ENST00000662534, ENST00000663025, ENST00000666176, ENST00000671024, ENST00000732618, ENST00000732619, ENST00000732620, ENST00000732621, ENST00000732622, ENST00000732623, ENST00000732624, ENST00000732625, ENST00000732626, ENST00000732627, ENST00000732628, ENST00000732629, ENST00000732630, ENST00000732631, ENST00000732632, ENST00000732633, ENST00000732634, ENST00000732635, ENST00000732636, ENST00000732637, ENST00000732638

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000421423 — 2 exons

Exon	Start	End
ENSE00004063133	112105966	112107359
ENSE00004063156	112107712	112108154

Expression profiles

Bgee: expression breadth ubiquitous, 114 present calls, max score 93.33.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.9667 / max 109.2719, expressed in 104 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136128	0.7108	91
136126	0.1236	43
136127	0.0580	25
136125	0.0374	17
136124	0.0369	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	93.33	gold quality
nucleus accumbens	UBERON:0001882	92.91	gold quality
amygdala	UBERON:0001876	90.25	gold quality
temporal lobe	UBERON:0001871	90.12	gold quality
caudate nucleus	UBERON:0001873	89.91	gold quality
ganglionic eminence	UBERON:0004023	89.53	gold quality
anterior cingulate cortex	UBERON:0009835	88.28	gold quality
hypothalamus	UBERON:0001898	87.99	gold quality
putamen	UBERON:0001874	86.67	gold quality
superior frontal gyrus	UBERON:0002661	86.16	gold quality
right frontal lobe	UBERON:0002810	85.40	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	84.94	gold quality
cerebral cortex	UBERON:0000956	84.73	gold quality
Ammon’s horn	UBERON:0001954	84.15	gold quality
frontal cortex	UBERON:0001870	83.81	gold quality
substantia nigra	UBERON:0002038	83.55	gold quality
prefrontal cortex	UBERON:0000451	82.42	gold quality
Brodmann (1909) area 9	UBERON:0013540	82.23	gold quality
primary visual cortex	UBERON:0002436	82.16	gold quality
brain	UBERON:0000955	82.13	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.42	gold quality
sural nerve	UBERON:0015488	71.68	silver quality
C1 segment of cervical spinal cord	UBERON:0006469	70.68	gold quality
cortical plate	UBERON:0005343	70.55	gold quality
corpus callosum	UBERON:0002336	70.26	gold quality
pituitary gland	UBERON:0000007	70.09	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	69.41	gold quality
muscle layer of sigmoid colon	UBERON:0035805	68.48	gold quality
tonsil	UBERON:0002372	68.22	gold quality
adenohypophysis	UBERON:0002196	68.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.38

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• LncRNA SOX1-OT V1 acts as a decoy of HDAC10 to promote SOX1-dependent hESC neuronal differentiation. (PMID:34927789)

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.