XACT

Summary

XACT (X active specific transcript, HGNC:45056) is a long non-coding RNA gene on chromosome Xq23.

This gene produces a spliced long non-coding RNA that is thought to play a role in the control of X-chromosome inactivation (XCI). This transcript has been shown to specifically coat the active X chromosome in human pluripotent cells.

Source: NCBI Gene 105463123 — RefSeq curated summary.

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:45056
Approved symbol	XACT
Name	X active specific transcript
Location	Xq23
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000241743
Ensembl biotype	lncRNA
OMIM	300901
Entrez	105463123
RNAcentral	URS00008120E8 — lncRNA, 509 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 13 lncRNA

ENST00000468762, ENST00000649506, ENST00000674361, ENST00000765932, ENST00000765933, ENST00000765934, ENST00000765935, ENST00000765936, ENST00000765937, ENST00000765938, ENST00000765939, ENST00000765940, ENST00000811426

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000468762 — 5 exons

Exon	Start	End
ENSE00001873091	113616300	113616674
ENSE00001879311	113618058	113618153
ENSE00003675386	113938193	113938320
ENSE00003837620	113963553	113963599
ENSE00003840795	114059004	114059121

Expression profiles

Bgee: expression breadth broad, 34 present calls, max score 80.74.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.6242 / max 78.0103, expressed in 165 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200223	0.3008	67
200221	0.2053	80
200224	0.0794	44
200222	0.0387	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	80.74	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.89	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.09	gold quality
cardiac muscle of right atrium	UBERON:0003379	70.87	gold quality
left ventricle myocardium	UBERON:0006566	70.50	gold quality
nasal cavity epithelium	UBERON:0005384	67.61	gold quality
colonic epithelium	UBERON:0000397	66.76	silver quality
ileal mucosa	UBERON:0000331	66.22	silver quality
upper arm skin	UBERON:0004263	65.90	gold quality
testis	UBERON:0000473	63.76	gold quality
ganglionic eminence	UBERON:0004023	63.47	gold quality
cardiac atrium	UBERON:0002081	62.21	gold quality
upper lobe of lung	UBERON:0008948	61.00	silver quality
lower lobe of lung	UBERON:0008949	60.92	silver quality
vena cava	UBERON:0004087	59.22	silver quality
myocardium	UBERON:0002349	59.02	gold quality
mucosa of transverse colon	UBERON:0004991	58.41	gold quality
deltoid	UBERON:0001476	58.35	gold quality
mucosa of sigmoid colon	UBERON:0004993	57.55	silver quality
superficial temporal artery	UBERON:0001614	55.06	gold quality
islet of Langerhans	UBERON:0000006	54.79	gold quality
endothelial cell	CL:0000115	54.27	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
colonic mucosa	UBERON:0000317	53.40	gold quality
gastrocnemius	UBERON:0001388	52.13	silver quality
lateral globus pallidus	UBERON:0002476	52.09	gold quality
rectum	UBERON:0001052	51.72	gold quality
large intestine	UBERON:0000059	51.31	gold quality
intestine	UBERON:0000160	51.18	gold quality
transverse colon	UBERON:0001157	51.03	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.54

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• XACT is a novel lncRNA that coats the active X-chromosome specifically in human pluripotent cells highlighting the existence of human-specific mechanisms of X-chromosome regulation. (PMID:23948700)
• These findings therefore suggest a mechanism involving antagonistic activity of XIST and XACT in controlling X chromosome activity in early human embryos. (PMID:27989768)
• The endogenous retroviruses was hijacked by younger hominoid-specific endogenous retroviruses that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. (PMID:31827084)

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.