SCN1A-AS1

Summary

SCN1A-AS1 (SCN1A and SCN9A antisense RNA 1, HGNC:54069) is a long non-coding RNA gene on chromosome 2q24.3.

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:54069
Approved symbol	SCN1A-AS1
Name	SCN1A and SCN9A antisense RNA 1
Location	2q24.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	SCN1ANAT, SCN1A-NAT
Ensembl gene	ENSG00000236107
Ensembl biotype	lncRNA
Entrez	101929680
RNAcentral	URS0000086FDD — lncRNA, 2305 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 32 lncRNA

ENST00000447809, ENST00000595268, ENST00000595647, ENST00000597623, ENST00000599041, ENST00000625775, ENST00000627027, ENST00000628608, ENST00000628933, ENST00000629609, ENST00000629804, ENST00000630020, ENST00000630226, ENST00000651013, ENST00000651562, ENST00000651574, ENST00000651673, ENST00000651782, ENST00000657189, ENST00000658447, ENST00000660239, ENST00000660342, ENST00000668514, ENST00000668610, ENST00000670867, ENST00000671220, ENST00000671284, ENST00000714451, ENST00000727524, ENST00000834712, ENST00000834713, ENST00000834714

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000447809 — 12 exons

Exon	Start	End
ENSE00001595034	166300931	166301784
ENSE00001617748	166298690	166298841
ENSE00001628603	166277088	166277247
ENSE00001676173	166248195	166248276
ENSE00001689957	166251779	166251912
ENSE00001699709	166294565	166294727
ENSE00001724512	166092553	166092663
ENSE00001736129	166199639	166199818
ENSE00001751017	166296023	166296129
ENSE00001762115	166081531	166081678
ENSE00001776452	166249343	166249384
ENSE00001783027	166171387	166171558

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 80.81.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7088 / max 153.9752, expressed in 147 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
23444	0.4118	78
23446	0.2167	56
23445	0.0620	25
23443	0.0184	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	80.81	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.05	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.11	gold quality
left testis	UBERON:0004533	73.88	gold quality
testis	UBERON:0000473	73.66	gold quality
corpus callosum	UBERON:0002336	72.75	gold quality
primary visual cortex	UBERON:0002436	71.12	gold quality
right uterine tube	UBERON:0001302	68.89	gold quality
right testis	UBERON:0004534	68.05	gold quality
colonic epithelium	UBERON:0000397	68.01	silver quality
superior frontal gyrus	UBERON:0002661	64.82	gold quality
adrenal tissue	UBERON:0018303	64.59	gold quality
prefrontal cortex	UBERON:0000451	63.19	gold quality
calcaneal tendon	UBERON:0003701	62.55	gold quality
frontal cortex	UBERON:0001870	61.51	gold quality
ventricular zone	UBERON:0003053	60.99	gold quality
skeletal muscle tissue	UBERON:0001134	60.68	gold quality
ganglionic eminence	UBERON:0004023	60.44	gold quality
hindlimb stylopod muscle	UBERON:0004252	60.23	gold quality
liver	UBERON:0002107	59.51	gold quality
cerebral cortex	UBERON:0000956	58.84	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	58.82	gold quality
Brodmann (1909) area 9	UBERON:0013540	58.68	gold quality
right frontal lobe	UBERON:0002810	58.14	gold quality
lung	UBERON:0002048	58.13	gold quality
lymph node	UBERON:0000029	57.57	gold quality
monocyte	CL:0000576	56.81	gold quality
upper lobe of left lung	UBERON:0008952	56.77	gold quality
cortex of kidney	UBERON:0001225	56.58	gold quality
endometrium	UBERON:0001295	56.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.03

Regulation

Is transcription factor: no

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.