SLIT2-IT1

Summary

SLIT2-IT1 (SLIT2 intronic transcript 1, HGNC:41383) is a long non-coding RNA gene on chromosome 4p15.31.

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:41383
Approved symbol	SLIT2-IT1
Name	SLIT2 intronic transcript 1
Location	4p15.31
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000248228
Ensembl biotype	lncRNA
Entrez	100505893
RNAcentral	URS000075E4A1 — lncRNA, 628 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 lncRNA

ENST00000515882, ENST00000728680, ENST00000728681, ENST00000728682

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000515882 — 4 exons

Exon	Start	End
ENSE00002031751	20393350	20393453
ENSE00002051917	20393566	20393659
ENSE00004055400	20392134	20392263
ENSE00004055401	20394529	20394882

Expression profiles

Bgee: expression breadth ubiquitous, 123 present calls, max score 89.97.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0192 / max 17.1412, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
47069	0.0122	3
47068	0.0070	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	89.97	gold quality
left testis	UBERON:0004533	89.53	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.41	gold quality
right testis	UBERON:0004534	87.84	gold quality
testis	UBERON:0000473	86.67	gold quality
adult organism	UBERON:0007023	72.29	gold quality
calcaneal tendon	UBERON:0003701	70.47	gold quality
colonic epithelium	UBERON:0000397	64.19	silver quality
tibialis anterior	UBERON:0001385	63.27	silver quality
ganglionic eminence	UBERON:0004023	62.62	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	62.52	gold quality
pancreatic ductal cell	CL:0002079	60.58	silver quality
tendon	UBERON:0000043	59.05	gold quality
ileal mucosa	UBERON:0000331	58.79	gold quality
adrenal tissue	UBERON:0018303	56.79	gold quality
sural nerve	UBERON:0015488	56.66	silver quality
deltoid	UBERON:0001476	55.29	silver quality
epithelial cell of pancreas	CL:0000083	54.72	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
upper leg skin	UBERON:0004262	52.99	gold quality
monocyte	CL:0000576	52.82	gold quality
gall bladder	UBERON:0002110	52.17	gold quality
muscle of leg	UBERON:0001383	52.16	gold quality
islet of Langerhans	UBERON:0000006	51.00	gold quality
myocardium	UBERON:0002349	50.25	gold quality
tonsil	UBERON:0002372	50.01	silver quality
rectum	UBERON:0001052	49.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.25

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• SLIT2 promoter hypermethylation-mediated SLIT2-IT1/miR-218 repression drives leukemogenesis and predicts adverse prognosis in myelodysplastic neoplasm. (PMID:35906386)

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.