SLC12A2-DT

Summary

SLC12A2-DT (SLC12A2 divergent transcript, HGNC:49565) is a long non-coding RNA gene on chromosome 5q23.3.

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:49565
Approved symbol	SLC12A2-DT
Name	SLC12A2 divergent transcript
Location	5q23.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	FLJ33630
Ensembl gene	ENSG00000245937
Ensembl biotype	lncRNA
Entrez	644873
RNAcentral	URS0000CCDFD9 — lncRNA, 3078 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 52 — 52 lncRNA

ENST00000499346, ENST00000501173, ENST00000501652, ENST00000501702, ENST00000508353, ENST00000508878, ENST00000512185, ENST00000514409, ENST00000514573, ENST00000606251, ENST00000606855, ENST00000654888, ENST00000655628, ENST00000656154, ENST00000656563, ENST00000657475, ENST00000657683, ENST00000659415, ENST00000659990, ENST00000660180, ENST00000660408, ENST00000661296, ENST00000661552, ENST00000663841, ENST00000663976, ENST00000664006, ENST00000665302, ENST00000665599, ENST00000668265, ENST00000668567, ENST00000687795, ENST00000689029, ENST00000702397, ENST00000702468, ENST00000826857, ENST00000826858, ENST00000826859, ENST00000826860, ENST00000826861, ENST00000826862, ENST00000826863, ENST00000826864, ENST00000826865, ENST00000826866, ENST00000826867, ENST00000826868, ENST00000826869, ENST00000826870, ENST00000826871, ENST00000826872, ENST00000826873, ENST00000826874

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000499346 — 4 exons

Exon	Start	End
ENSE00001986176	128061144	128061244
ENSE00003868882	127939152	127941220
ENSE00004238145	128082735	128083104
ENSE00004238163	127956804	127956921

Expression profiles

Bgee: expression breadth ubiquitous, 245 present calls, max score 92.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.0825 / max 162.8225, expressed in 1790 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
63219	15.2759	1786
63218	0.7315	442
63216	0.0750	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	92.82	gold quality
colonic epithelium	UBERON:0000397	92.18	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.44	gold quality
cardia of stomach	UBERON:0001162	90.04	gold quality
calcaneal tendon	UBERON:0003701	90.02	gold quality
spinal cord	UBERON:0002240	89.76	gold quality
prefrontal cortex	UBERON:0000451	89.37	gold quality
pylorus	UBERON:0001166	88.83	gold quality
Brodmann (1909) area 9	UBERON:0013540	88.66	gold quality
anterior cingulate cortex	UBERON:0009835	88.52	gold quality
right frontal lobe	UBERON:0002810	88.47	gold quality
cerebellar hemisphere	UBERON:0002245	88.44	gold quality
cerebellar cortex	UBERON:0002129	88.34	gold quality
hypothalamus	UBERON:0001898	88.20	gold quality
right hemisphere of cerebellum	UBERON:0014890	88.15	gold quality
amygdala	UBERON:0001876	87.84	gold quality
putamen	UBERON:0001874	87.81	gold quality
fundus of stomach	UBERON:0001160	87.69	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.58	gold quality
stomach	UBERON:0000945	87.23	gold quality
cerebellum	UBERON:0002037	87.22	gold quality
sural nerve	UBERON:0015488	87.17	gold quality
tendon	UBERON:0000043	87.16	gold quality
oviduct epithelium	UBERON:0004804	87.15	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.87	gold quality
body of stomach	UBERON:0001161	86.71	gold quality
right atrium auricular region	UBERON:0006631	86.62	gold quality
nucleus accumbens	UBERON:0001882	86.55	gold quality
medial globus pallidus	UBERON:0002477	86.50	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.17

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 4)

• six novel lncRNAs (CDKN2B-AS1, MIR22HG, GABPB1-AS1, FLJ33630, LINC00152, and LINC0541471_v2) that respond to model chemical stresses (cycloheximide, hydrogen peroxide, cadmium, or arsenic) in hiPSCs. (PMID:25171338)
• We also discovered and replicated three genome-wide significant variants in previously unreported loci for RDW (SLC12A2 rs17764730, PSMB5 rs941718), and hematocrit (PROX1 rs3754140) and an upstream anti-sense long-noncoding RNA, LINC01184, as the likely causal variant (PMID:28453575)
• The Role, Function, and Mechanism of Long Intergenic Noncoding RNA1184 (linc01184) in Colorectal Cancer. (PMID:33564344)
• GWAS Identifies LINC01184/SLC12A2 as a Risk Locus for Skin and Soft Tissue Infections. (PMID:33662382)

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.