DACT3-AS1

Summary

DACT3-AS1 (DACT3 antisense RNA 1, HGNC:44120) is a long non-coding RNA gene on chromosome 19q13.32.

At a glance

• Gene type: non-coding (lncRNA) — no protein product.
• Sense gene: antisense to DACT3 — the sense gene carries 119 ClinVar variants (the sense gene’s biology, not this transcript’s)
• GTEx eGene: eQTL in 19 tissues, sQTL in 1 (q < 0.05)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44120
Approved symbol	DACT3-AS1
Name	DACT3 antisense RNA 1
Location	19q13.32
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000245598
Ensembl biotype	lncRNA
Entrez	100506068
RNAcentral	URS000075C334 — lncRNA, 1320 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 lncRNA

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

ENST00000500689, ENST00000525008, ENST00000525352, ENST00000690000, ENST00000692220, ENST00000754480, ENST00000754481, ENST00000754482, ENST00000754483, ENST00000754484, ENST00000754485, ENST00000754486

RefSeq mRNA: 0

Canonical transcript exons

ENST00000500689 — 3 exons

Exon	Start	End
ENSE00001746672	46671141	46671341
ENSE00001974930	46669168	46669310
ENSE00001991771	46661478	46662437

Expression profiles

Bgee: expression breadth ubiquitous, 156 present calls, max score 83.43.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2689 / max 194.1457, expressed in 52 samples.

Highest expression (Bgee): male germ line stem cell (sensu Vertebrata) in testis, testis, cortical plate, coronary artery, popliteal artery.

Genetic regulation across tissues (GTEx eQTL / sQTL)

DACT3-AS1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 19 tissues and its splicing (sQTL) in 1 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

20 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Artery Tibial	eqtl	9.6e-18	-0.38	19:46669571:C:CATT
Artery Aorta	eqtl	1.3e-13	-0.31	19:46669216:C:T
Testis	eqtl	5.2e-10	-0.20	19:46661729:G:A
Brain Caudate basal ganglia	eqtl	1.3e-08	-0.57	19:46661729:G:A
Brain Putamen basal ganglia	eqtl	1.3e-06	-0.51	19:46669216:C:T
Brain Nucleus accumbens basal ganglia	eqtl	2.0e-06	-0.44	19:46673568:T:C
Brain Frontal Cortex BA9	eqtl	4.4e-06	-0.52	19:46669216:C:T
Brain Hypothalamus	eqtl	7.8e-05	-0.47	19:46669216:C:T
Testis	sqtl	2.0e-04	+0.24	19:46709336:A:G
Brain Cortex	eqtl	2.5e-04	-0.48	19:46751283:G:C
Brain Spinal cord cervical c-1	eqtl	2.5e-04	-0.66	19:46682662:G:C
Brain Anterior cingulate cortex BA24	eqtl	6.4e-04	-0.55	19:46690593:T:C
Lung	eqtl	3.1e-03	+0.16	19:46755585:C:T
Thyroid	eqtl	7.4e-03	+0.16	19:46737960:G:A
Heart Atrial Appendage	eqtl	9.2e-03	+0.29	19:46755585:C:T
Nerve Tibial	eqtl	1.2e-02	+0.24	19:46695675:A:C
Brain Amygdala	eqtl	1.2e-02	-0.48	19:46669216:C:T
Brain Hippocampus	eqtl	1.5e-02	-0.43	19:46658945:C:A
Skin Sun Exposed Lower leg	eqtl	2.9e-02	+0.49	19:45801059:A:G
Brain Substantia nigra	eqtl	3.0e-02	-0.44	19:46721350:C:T

FANTOM5 promoters

2 alternative TSS:

Promoter ID	TPM avg	Samples expressed
176598	0.2504	47
176599	0.0185	4

Top tissues by expression

showing 100 of 243 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.43	gold quality
right testis	UBERON:0004534	76.79	gold quality
left testis	UBERON:0004533	75.95	gold quality
cortical plate	UBERON:0005343	73.47	gold quality
right coronary artery	UBERON:0001625	73.32	gold quality
testis	UBERON:0000473	73.14	gold quality
popliteal artery	UBERON:0002250	73.06	gold quality
tibial artery	UBERON:0007610	73.04	gold quality
descending thoracic aorta	UBERON:0002345	72.88	gold quality
aorta	UBERON:0000947	72.55	gold quality
thoracic aorta	UBERON:0001515	72.31	gold quality
ascending aorta	UBERON:0001496	72.17	gold quality
sperm	CL:0000019	70.22	silver quality
sural nerve	UBERON:0015488	69.87	gold quality
left coronary artery	UBERON:0001626	68.33	gold quality
ganglionic eminence	UBERON:0004023	67.53	gold quality
coronary artery	UBERON:0001621	67.20	gold quality
stromal cell of endometrium	CL:0002255	66.84	gold quality
anterior cingulate cortex	UBERON:0009835	64.56	gold quality
apex of heart	UBERON:0002098	64.51	gold quality
body of uterus	UBERON:0009853	64.44	gold quality
prefrontal cortex	UBERON:0000451	64.43	gold quality
smooth muscle tissue	UBERON:0001135	64.25	gold quality
granulocyte	CL:0000094	64.08	gold quality
ventricular zone	UBERON:0003053	63.22	gold quality
muscle layer of sigmoid colon	UBERON:0035805	62.78	gold quality
nucleus accumbens	UBERON:0001882	62.77	gold quality
right frontal lobe	UBERON:0002810	62.65	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	62.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	62.33	gold quality
leukocyte	CL:0000738	62.31	gold quality
mucosa of stomach	UBERON:0001199	62.20	gold quality
monocyte	CL:0000576	62.12	gold quality
amygdala	UBERON:0001876	61.29	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	61.27	gold quality
putamen	UBERON:0001874	61.16	gold quality
spleen	UBERON:0002106	61.03	gold quality
lower esophagus muscularis layer	UBERON:0035833	60.72	gold quality
spinal cord	UBERON:0002240	60.70	gold quality
lower esophagus	UBERON:0013473	60.69	gold quality
right atrium auricular region	UBERON:0006631	60.67	gold quality
neocortex	UBERON:0001950	60.28	gold quality
cardiac atrium	UBERON:0002081	60.15	gold quality
hypothalamus	UBERON:0001898	60.11	gold quality
caudate nucleus	UBERON:0001873	59.98	gold quality
ectocervix	UBERON:0012249	59.98	gold quality
lymph node	UBERON:0000029	59.77	gold quality
gall bladder	UBERON:0002110	59.55	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	59.51	gold quality
endothelial cell	CL:0000115	59.41	gold quality
frontal cortex	UBERON:0001870	59.38	gold quality
calcaneal tendon	UBERON:0003701	59.29	gold quality
left uterine tube	UBERON:0001303	58.97	gold quality
blood	UBERON:0000178	58.84	gold quality
substantia nigra	UBERON:0002038	58.81	gold quality
esophagus	UBERON:0001043	58.46	gold quality
vermiform appendix	UBERON:0001154	58.29	gold quality
mucosa of transverse colon	UBERON:0004991	58.21	gold quality
hindlimb stylopod muscle	UBERON:0004252	58.14	gold quality
small intestine Peyer’s patch	UBERON:0003454	57.47	gold quality
heart	UBERON:0000948	57.41	gold quality
cerebral cortex	UBERON:0000956	57.41	gold quality
body of stomach	UBERON:0001161	57.36	gold quality
forebrain	UBERON:0001890	57.24	gold quality
cerebellar vermis	UBERON:0004720	57.21	gold quality
myometrium	UBERON:0001296	57.20	gold quality
transverse colon	UBERON:0001157	56.76	gold quality
upper lobe of left lung	UBERON:0008952	56.74	gold quality
colon	UBERON:0001155	56.66	gold quality
midbrain	UBERON:0001891	56.55	gold quality
stomach	UBERON:0000945	56.53	gold quality
esophagus mucosa	UBERON:0002469	56.47	gold quality
brain	UBERON:0000955	56.42	gold quality
rectum	UBERON:0001052	56.42	gold quality
vagina	UBERON:0000996	56.26	gold quality
small intestine	UBERON:0002108	56.25	gold quality
intestine	UBERON:0000160	56.15	gold quality
large intestine	UBERON:0000059	56.08	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	55.98	gold quality
anatomical system	UBERON:0000467	55.89	gold quality
prostate gland	UBERON:0002367	55.88	gold quality
material anatomical entity	UBERON:0000465	55.58	gold quality
multicellular organism	UBERON:0000468	55.57	gold quality
right lobe of liver	UBERON:0001114	55.52	gold quality
uterus	UBERON:0000995	55.49	gold quality
lower esophagus mucosa	UBERON:0035834	55.31	gold quality
upper lobe of lung	UBERON:0008948	55.11	gold quality
uterine cervix	UBERON:0000002	55.10	gold quality
right adrenal gland cortex	UBERON:0035827	55.07	gold quality
caecum	UBERON:0001153	55.05	gold quality
Ammon’s horn	UBERON:0001954	54.73	gold quality
heart left ventricle	UBERON:0002084	54.63	gold quality
endocervix	UBERON:0000458	54.62	gold quality
adult mammalian kidney	UBERON:0000082	54.60	gold quality
left ovary	UBERON:0002119	54.30	gold quality
fundus of stomach	UBERON:0001160	54.12	gold quality
cardiac ventricle	UBERON:0002082	54.12	gold quality
omental fat pad	UBERON:0010414	53.95	gold quality
peritoneum	UBERON:0002358	53.91	gold quality
right ovary	UBERON:0002118	53.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.59

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Hypoxia-induced LncRNA DACT3-AS1 upregulates PKM2 to promote metastasis in hepatocellular carcinoma through the HDAC2/FOXA3 pathway. (PMID:35764883)

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
DACT3	protein-coding	147906
PRKD2	protein-coding	25865
STRN4	protein-coding	29888
FKRP	protein-coding	79147
MIR320E	ncRNA	100422913
GNG8	protein-coding	94235
PTGIR	protein-coding	5739
CALM3	protein-coding	808
SLC1A5	protein-coding	6510
PNMA8B	protein-coding	57469

Protein

Non-coding RNA — no protein product.

Function

Gene-set membership (MSigDB)

This non-coding RNA is a member of 20 curated MSigDB gene sets — regulatory-target and signature collections that include it (it has no protein-based pathway / GO / interaction data).

CEBPZ_TARGET_GENES, HAND1_TARGET_GENES, HOXC6_TARGET_GENES, MEF2D_TARGET_GENES, RBM34_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF436_TARGET_GENES, ZNF513_TARGET_GENES, ZNF618_TARGET_GENES, ZNF768_TARGET_GENES, DESCARTES_MAIN_FETAL_MESANGIAL_CELLS, MZF1_TARGET_GENES, CUX1_TARGET_GENES, HDGF_TARGET_GENES, MEF2C_TARGET_GENES, MYOCD_TARGET_GENES, ZSCAN4_TARGET_GENES, BARX2_TARGET_GENES, HARALAMBIEVA_PBMC_M_M_R_II_AGE_11_22YO_VACCINATED_VS_UNVACCINATED_7YR_UP, chr19q13

ncRNA interactions

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

showing 45 of 49 interaction partners:

Partner	Partner type	Level	Source
ADAR	protein	RNA-Protein	High-throughput data
WDR33	protein	RNA-Protein	High-throughput data
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
hsa-mir-181a/181b/18	miRNA	RNA-RNA	miRanda with Ago CLIP data
hsa-mir-181b-3p	miRNA	RNA-RNA	miRanda with Ago CLIP data
hsa-mir-181d	miRNA	RNA-RNA	miRanda with Ago CLIP data
ILF3	protein	RNA-Protein	ENCODE
PRPF8	protein	RNA-Protein	ENCODE
ZC11A	protein	RNA-Protein	ENCODE
CPSF6	protein	RNA-Protein	ENCODE
DDX55	protein	RNA-Protein	ENCODE
FMR1	protein	RNA-Protein	ENCODE
FXR2	protein	RNA-Protein	ENCODE
LIN28B	protein	RNA-Protein	ENCODE
RBM15	protein	RNA-Protein	ENCODE
RPS3	protein	RNA-Protein	ENCODE
T2FA	protein	RNA-Protein	ENCODE
UCHL5	protein	RNA-Protein	ENCODE
XRCC6	protein	RNA-Protein	ENCODE
YBOX3	protein	RNA-Protein	ENCODE
RBM39	protein	RNA-Protein	GSE101631
ELAVL2	protein	RNA-Protein	GSE53699
ELAV3	protein	RNA-Protein	GSE53699
CELF4	protein	RNA-Protein	GSE53699
LAR4B	protein	RNA-Protein	GSE69169
MOV10	protein	RNA-Protein	GSE70061
FBL	protein	RNA-Protein	GSE77027
IGF2BP3	protein	RNA-Protein	GSE78507
HNRNPA1	protein	RNA-Protein	GSE83923
DBHS	protein	RNA-Protein	GSE90650
PSF	protein	RNA-Protein	GSE90650
SSB	protein	RNA-Protein	GSE95683
EWSR1	protein	RNA-Protein	GSE98836
ADAM32	mRNA	RNA-RNA	RISE database
SCAF8	protein	RNA-Protein	High-throughput data
ZC3HAV1	protein	RNA-Protein	High-throughput data
ZMAT3	protein	RNA-Protein	High-throughput data
SRSF2	protein	RNA-Protein	High-throughput data
CPSF1	protein	RNA-Protein	High-throughput data
SOX2	protein	RNA-Protein	High-throughput data
CPSF7	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.