CELF2-AS2

Summary

CELF2-AS2 (CELF2 antisense RNA 2, HGNC:44703) is a long non-coding RNA gene on chromosome 10p14.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• Sense gene: antisense to CELF2 — the sense gene carries 32 GWAS associations, 144 ClinVar variants (the sense gene’s biology, not this transcript’s)
• GTEx eGene: eQTL in 2 tissues, sQTL in 1 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44703
Approved symbol	CELF2-AS2
Name	CELF2 antisense RNA 2
Location	10p14
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000237986
Ensembl biotype	lncRNA
Entrez	439950
RNAcentral	URS000075A245 — lncRNA, 2277 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 15 lncRNA

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 3: 1, TSL 5: 3

ENST00000420634, ENST00000432370, ENST00000635166, ENST00000635624, ENST00000652917, ENST00000653050, ENST00000658499, ENST00000661681, ENST00000661890, ENST00000663606, ENST00000664601, ENST00000666482, ENST00000667228, ENST00000669017, ENST00000671624

RefSeq mRNA: 0

Canonical transcript exons

ENST00000420634 — 2 exons

Exon	Start	End
ENSE00001701516	11098072	11098160
ENSE00001740098	11097314	11097368

Expression profiles

Bgee: expression breadth broad, 100 present calls, max score 87.13.

Highest expression (Bgee): sural nerve, male germ line stem cell (sensu Vertebrata) in testis, corpus callosum, colonic epithelium, skeletal muscle tissue.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CELF2-AS2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 2 tissues and its splicing (sQTL) in 1 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

3 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Nerve Tibial	eqtl	1.3e-02	+0.30	10:12054965:G:T
Testis	sqtl	1.6e-02	-0.53	10:11096085:C:T
Testis	eqtl	3.6e-02	+0.09	10:10954633:T:G

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	87.13	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.81	gold quality
corpus callosum	UBERON:0002336	81.93	gold quality
colonic epithelium	UBERON:0000397	77.78	gold quality
skeletal muscle tissue	UBERON:0001134	72.56	gold quality
bone marrow cell	CL:0002092	70.74	silver quality
urinary bladder	UBERON:0001255	69.46	gold quality
calcaneal tendon	UBERON:0003701	67.65	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	65.81	gold quality
testis	UBERON:0000473	63.36	gold quality
tonsil	UBERON:0002372	62.50	silver quality
left testis	UBERON:0004533	62.33	gold quality
right testis	UBERON:0004534	61.41	gold quality
primary visual cortex	UBERON:0002436	60.70	gold quality
superior frontal gyrus	UBERON:0002661	60.35	gold quality
ganglionic eminence	UBERON:0004023	60.29	gold quality
uterine cervix	UBERON:0000002	60.22	silver quality
adrenal tissue	UBERON:0018303	60.19	gold quality
hindlimb stylopod muscle	UBERON:0004252	59.36	gold quality
adrenal gland	UBERON:0002369	58.92	gold quality
stomach	UBERON:0000945	56.83	gold quality
lung	UBERON:0002048	56.58	gold quality
monocyte	CL:0000576	55.71	gold quality
small intestine	UBERON:0002108	54.87	gold quality
thoracic mammary gland	UBERON:0005200	54.78	gold quality
liver	UBERON:0002107	54.62	silver quality
intestine	UBERON:0000160	53.60	gold quality
kidney	UBERON:0002113	52.68	gold quality
prefrontal cortex	UBERON:0000451	52.30	gold quality
left adrenal gland	UBERON:0001234	52.22	gold quality
muscle of leg	UBERON:0001383	52.08	gold quality
colon	UBERON:0001155	51.36	gold quality
islet of Langerhans	UBERON:0000006	51.01	gold quality
pancreas	UBERON:0001264	50.96	silver quality
myometrium	UBERON:0001296	50.70	gold quality
spleen	UBERON:0002106	50.48	gold quality
right adrenal gland cortex	UBERON:0035827	50.27	gold quality
blood	UBERON:0000178	50.16	gold quality
multicellular organism	UBERON:0000468	49.61	gold quality
caudate nucleus	UBERON:0001873	49.20	gold quality
ovary	UBERON:0000992	49.01	gold quality
gastrocnemius	UBERON:0001388	48.85	gold quality
cerebellum	UBERON:0002037	48.64	silver quality
frontal cortex	UBERON:0001870	48.58	gold quality
cerebellar cortex	UBERON:0002129	48.48	silver quality
adult mammalian kidney	UBERON:0000082	48.45	gold quality
brain	UBERON:0000955	48.07	gold quality
heart	UBERON:0000948	47.91	gold quality
cerebellar hemisphere	UBERON:0002245	47.91	silver quality
nucleus accumbens	UBERON:0001882	47.62	gold quality
right hemisphere of cerebellum	UBERON:0014890	47.55	silver quality
amygdala	UBERON:0001876	47.12	gold quality
thyroid gland	UBERON:0002046	46.91	gold quality
Ammon’s horn	UBERON:0001954	46.90	gold quality
putamen	UBERON:0001874	46.57	gold quality
prostate gland	UBERON:0002367	46.44	silver quality
esophagus	UBERON:0001043	46.42	gold quality
hypothalamus	UBERON:0001898	46.33	gold quality
smooth muscle tissue	UBERON:0001135	46.28	silver quality
left ovary	UBERON:0002119	46.28	gold quality
popliteal artery	UBERON:0002250	46.13	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	46.12	gold quality
right ovary	UBERON:0002118	46.11	gold quality
tibial artery	UBERON:0007610	46.08	gold quality
heart left ventricle	UBERON:0002084	45.71	gold quality
anterior cingulate cortex	UBERON:0009835	45.61	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	45.52	gold quality
upper lobe of left lung	UBERON:0008952	45.28	gold quality
body of uterus	UBERON:0009853	45.25	gold quality
body of pancreas	UBERON:0001150	45.23	silver quality
left coronary artery	UBERON:0001626	45.19	gold quality
Brodmann (1909) area 9	UBERON:0013540	44.99	gold quality
tibial nerve	UBERON:0001323	44.53	gold quality
esophagus mucosa	UBERON:0002469	44.49	gold quality
cortex of kidney	UBERON:0001225	44.48	silver quality
lower esophagus muscularis layer	UBERON:0035833	44.47	gold quality
small intestine Peyer’s patch	UBERON:0003454	44.33	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	44.25	gold quality
right atrium auricular region	UBERON:0006631	44.05	gold quality
subcutaneous adipose tissue	UBERON:0002190	43.93	gold quality
zone of skin	UBERON:0000014	43.86	silver quality
right frontal lobe	UBERON:0002810	43.73	gold quality
muscle layer of sigmoid colon	UBERON:0035805	43.60	gold quality
adipose tissue	UBERON:0001013	43.55	gold quality
transverse colon	UBERON:0001157	43.25	gold quality
skin of abdomen	UBERON:0001416	43.07	gold quality
omental fat pad	UBERON:0010414	43.07	gold quality
thoracic aorta	UBERON:0001515	42.89	gold quality
ascending aorta	UBERON:0001496	42.69	gold quality
skin of leg	UBERON:0001511	42.69	silver quality
body of stomach	UBERON:0001161	42.62	gold quality
substantia nigra	UBERON:0002038	42.17	gold quality
apex of heart	UBERON:0002098	42.13	silver quality
minor salivary gland	UBERON:0001830	41.83	gold quality
vagina	UBERON:0000996	41.76	gold quality
left lobe of thyroid gland	UBERON:0001120	40.36	gold quality
fundus of stomach	UBERON:0001160	39.10	silver quality
left uterine tube	UBERON:0001303	38.70	silver quality
pituitary gland	UBERON:0000007	38.58	silver quality
adenohypophysis	UBERON:0002196	38.01	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.25

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
CELF2-DT	ncRNA	101928322
CELF2-AS4	ncRNA	124902376
LINC00710	ncRNA	254312
CELF2-AS1	ncRNA	414196
USP6NL	protein-coding	9712
CELF2	protein-coding	10659

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 10 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

chr10p14, SUPT16H_TARGET_GENES, FAN_EMBRYONIC_CTX_EX_4_EXCITATORY_NEURON, ZHONG_PFC_C3_MICROGLIA, DESCARTES_FETAL_PANCREAS_MESOTHELIAL_CELLS, ZC3H11A_TARGET_GENES, ZNF697_TARGET_GENES, ZNF547_TARGET_GENES, ZNF34_TARGET_GENES, ZNF426_TARGET_GENES

ncRNA interactions

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

showing 24 of 25 interaction partners:

Partner	Partner type	Level	Source
WDR33	protein	RNA-Protein	High-throughput data
HNRNPA1	protein	RNA-Protein	GSE83923;High-throughput data combine LncPro prediction
ALKBH5	protein	RNA-Protein	High-throughput data
ZC3H7B	protein	RNA-Protein	High-throughput data combine LncPro prediction
RBM6	protein	RNA-Protein	High-throughput data combine LncPro prediction
hnRNPA2B1	protein	RNA-Protein	High-throughput data
FUS	protein	RNA-Protein	High-throughput data combine LncPro prediction
ELAVL2	protein	RNA-Protein	GSE53699
ELAV3	protein	RNA-Protein	GSE53699
CELF4	protein	RNA-Protein	GSE53699
MBNL2	protein	RNA-Protein	GSE68890
MOV10	protein	RNA-Protein	GSE70061
FBL	protein	RNA-Protein	GSE77027
RBFOX2	protein	RNA-Protein	GSE78507
FTO	protein	RNA-Protein	GSE79577
DBHS	protein	RNA-Protein	GSE90650
HDAC9	protein	RNA-Protein	GSE93744
SMARCA4	protein	RNA-Protein	GSE93744
AGO1	protein	RNA-Protein	High-throughput data
IGF2BP3	protein	RNA-Protein	High-throughput data
RBMX	protein	RNA-Protein	High-throughput data
IGF2BP1	protein	RNA-Protein	High-throughput data
AGO2	protein	RNA-Protein	High-throughput data
DHX36	protein	RNA-Protein	High-throughput data

Disease & clinical

ncRNA disease associations

Curated non-coding-RNA → disease associations (LncRNADisease, HMDD) — these are RNA-level associations for this gene, not the positional variant data omitted above.

1 ncRNA–disease associations:

Disease	Causal?	Validated by
Esophageal Squamous Cell Carcinoma	No	qRT-PCR, RNA-seq

Drugs & pharmacology

ncRNA–drug associations

Curated non-coding-RNA → drug associations (drug response / resistance / target).

1 ncRNA–drug associations:

Drug	Relation	Effect	Condition
Panobinostat	drug_target	down-regulated	“cell line (SK-NEP-1, G401)”