CSMD2-AS1

Summary

CSMD2-AS1 (CSMD2 antisense RNA 1, HGNC:40882) is a long non-coding RNA gene on chromosome 1p35.1.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• Sense gene: antisense to CSMD2 — the sense gene carries 20 GWAS associations, 566 ClinVar variants (the sense gene’s biology, not this transcript’s)
• GTEx eGene: eQTL in 1 tissue, sQTL in 1 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40882
Approved symbol	CSMD2-AS1
Name	CSMD2 antisense RNA 1
Location	1p35.1
Locus type	RNA, long non-coding
Status	Approved
Aliases	ENST00000434181
Ensembl gene	ENSG00000231163
Ensembl biotype	lncRNA
Entrez	402779
RNAcentral	URS000075D4C3 — lncRNA, 1379 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 26 lncRNA

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 3, TSL 3: 2

ENST00000414868, ENST00000425631, ENST00000431046, ENST00000432447, ENST00000434181, ENST00000438719, ENST00000653656, ENST00000653768, ENST00000654712, ENST00000659019, ENST00000659870, ENST00000660205, ENST00000661122, ENST00000661540, ENST00000662460, ENST00000663192, ENST00000663471, ENST00000664189, ENST00000665318, ENST00000667628, ENST00000668264, ENST00000802551, ENST00000802552, ENST00000802553, ENST00000802554, ENST00000802555

RefSeq mRNA: 0

Canonical transcript exons

ENST00000414868 — 3 exons

Exon	Start	End
ENSE00001631384	33873602	33873811
ENSE00001640076	33870226	33870424
ENSE00001653048	33870872	33871008

Expression profiles

Bgee: expression breadth broad, 82 present calls, max score 96.72.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0714 / max 73.5269, expressed in 3 samples.

Highest expression (Bgee): sperm, testis, male germ line stem cell (sensu Vertebrata) in testis, cerebellar vermis, skeletal muscle tissue of rectus abdominis.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CSMD2-AS1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 1 tissue and its splicing (sQTL) in 1 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

2 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	eqtl	2.7e-23	-0.21	1:33870384:T:A
Testis	sqtl	3.2e-05	+0.94	1:33870384:T:A

FANTOM5 promoters

3 alternative TSS:

Promoter ID	TPM avg	Samples expressed
2062	0.0510	3
2063	0.0157	3
2061	0.0047	2

Top tissues by expression

showing 100 of 177 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	96.72	gold quality
left testis	UBERON:0004533	96.06	gold quality
right testis	UBERON:0004534	95.32	gold quality
testis	UBERON:0000473	92.38	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.15	gold quality
cerebellar vermis	UBERON:0004720	76.88	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	75.77	gold quality
oocyte	CL:0000023	71.65	gold quality
secondary oocyte	CL:0000655	70.60	silver quality
vena cava	UBERON:0004087	68.86	gold quality
epithelium of nasopharynx	UBERON:0001951	68.74	gold quality
cardia of stomach	UBERON:0001162	66.99	gold quality
tongue	UBERON:0001723	66.87	gold quality
body of tongue	UBERON:0011876	66.87	gold quality
ventral tegmental area	UBERON:0002691	66.73	gold quality
superior surface of tongue	UBERON:0007371	66.68	gold quality
bone marrow	UBERON:0002371	66.51	gold quality
myocardium	UBERON:0002349	66.29	gold quality
subthalamic nucleus	UBERON:0001906	66.25	gold quality
saphenous vein	UBERON:0007318	66.10	gold quality
inferior vagus X ganglion	UBERON:0005363	66.01	gold quality
dorsal plus ventral thalamus	UBERON:0001897	65.99	gold quality
mucosa of paranasal sinus	UBERON:0005030	65.92	gold quality
nipple	UBERON:0002030	65.87	gold quality
pericardium	UBERON:0002407	65.87	gold quality
lower lobe of lung	UBERON:0008949	65.60	silver quality
trachea	UBERON:0003126	65.57	gold quality
substantia nigra pars reticulata	UBERON:0001966	65.48	gold quality
vastus lateralis	UBERON:0001379	65.39	gold quality
dorsal root ganglion	UBERON:0000044	65.37	gold quality
pharyngeal mucosa	UBERON:0000355	65.36	gold quality
lateral globus pallidus	UBERON:0002476	65.35	gold quality
pons	UBERON:0000988	65.34	gold quality
substantia nigra pars compacta	UBERON:0001965	65.34	gold quality
trigeminal ganglion	UBERON:0001675	65.22	gold quality
lateral nuclear group of thalamus	UBERON:0002736	65.19	gold quality
superior vestibular nucleus	UBERON:0007227	65.15	gold quality
synovial joint	UBERON:0002217	65.12	gold quality
pylorus	UBERON:0001166	64.80	gold quality
lymph node	UBERON:0000029	64.73	gold quality
layer of synovial tissue	UBERON:0007616	64.59	gold quality
renal medulla	UBERON:0000362	64.57	gold quality
penis	UBERON:0000989	64.55	gold quality
gingival epithelium	UBERON:0001949	64.48	gold quality
thymus	UBERON:0002370	64.12	gold quality
nasal cavity epithelium	UBERON:0005384	64.01	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	63.94	gold quality
jejunum	UBERON:0002115	63.35	gold quality
Brodmann (1909) area 23	UBERON:0013554	63.03	gold quality
superficial temporal artery	UBERON:0001614	62.46	gold quality
biceps brachii	UBERON:0001507	62.28	gold quality
urethra	UBERON:0000057	61.97	gold quality
adult organism	UBERON:0007023	61.91	silver quality
corpus callosum	UBERON:0002336	61.37	gold quality
deltoid	UBERON:0001476	61.33	gold quality
tonsil	UBERON:0002372	61.30	gold quality
gingiva	UBERON:0001828	61.27	gold quality
blood	UBERON:0000178	61.18	gold quality
jejunal mucosa	UBERON:0000399	61.17	gold quality
middle temporal gyrus	UBERON:0002771	61.15	gold quality
tibia	UBERON:0000979	60.41	gold quality
cartilage tissue	UBERON:0002418	60.07	gold quality
parietal pleura	UBERON:0002400	59.91	gold quality
mammary duct	UBERON:0001765	59.26	gold quality
visceral pleura	UBERON:0002401	59.02	gold quality
heart right ventricle	UBERON:0002080	58.84	gold quality
cortex of kidney	UBERON:0001225	58.73	silver quality
uterine cervix	UBERON:0000002	58.31	silver quality
amniotic fluid	UBERON:0000173	57.89	gold quality
trabecular bone tissue	UBERON:0002483	57.76	gold quality
skeletal muscle tissue	UBERON:0001134	57.65	gold quality
primary visual cortex	UBERON:0002436	57.61	silver quality
anatomical system	UBERON:0000467	56.92	gold quality
fundus of stomach	UBERON:0001160	56.86	silver quality
endometrium	UBERON:0001295	56.24	gold quality
material anatomical entity	UBERON:0000465	56.22	gold quality
multicellular organism	UBERON:0000468	56.13	gold quality
bronchus	UBERON:0002185	56.03	gold quality
midbrain	UBERON:0001891	55.72	gold quality
bronchial epithelial cell	CL:0002328	55.62	gold quality
oral cavity	UBERON:0000167	55.53	gold quality
monocyte	CL:0000576	55.26	gold quality
germinal epithelium of ovary	UBERON:0001304	55.21	gold quality
prefrontal cortex	UBERON:0000451	55.18	silver quality
palpebral conjunctiva	UBERON:0001812	54.95	gold quality
parietal lobe	UBERON:0001872	54.58	gold quality
caecum	UBERON:0001153	54.56	gold quality
superior frontal gyrus	UBERON:0002661	54.31	gold quality
mammalian vulva	UBERON:0000997	54.09	gold quality
metanephros	UBERON:0000081	53.90	gold quality
esophagus squamous epithelium	UBERON:0006920	53.54	gold quality
Brodmann (1909) area 46	UBERON:0006483	53.51	gold quality
corpus epididymis	UBERON:0004359	53.41	gold quality
thyroid gland	UBERON:0002046	52.85	gold quality
caput epididymis	UBERON:0004358	52.80	gold quality
nasal cavity mucosa	UBERON:0001826	52.79	gold quality
mucosa of sigmoid colon	UBERON:0004993	52.55	gold quality
brain	UBERON:0000955	52.48	silver quality
postcentral gyrus	UBERON:0002581	52.26	gold quality
entorhinal cortex	UBERON:0002728	52.19	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.26

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
CSMD2	protein-coding	114784
HMGB4	protein-coding	127540
C1orf94	protein-coding	84970
ZSCAN20	protein-coding	7579

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 3 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

chr1p35, IRF5_TARGET_GENES, GSE25088_CTRL_VS_IL4_AND_ROSIGLITAZONE_STIM_MACROPHAGE_DN

ncRNA interactions

Experimentally supported non-coding-RNA interaction partners (NPInter).

4 interaction partners:

Partner	Partner type	Level	Source
YJEFN3	mRNA	RNA-RNA	RISE database
IGF2BP3	protein	RNA-Protein	High-throughput data
IGF2BP1	protein	RNA-Protein	High-throughput data
DHX36	protein	RNA-Protein	High-throughput data

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No curated drug or pharmacology associations for this gene.