VPS39-DT

Summary

VPS39-DT (VPS39 divergent transcript, HGNC:55378) is a long non-coding RNA gene on chromosome 15q15.1.

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:55378
Approved symbol	VPS39-DT
Name	VPS39 divergent transcript
Location	15q15.1
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000261002
Ensembl biotype	lncRNA
Entrez	105370795
RNAcentral	URS0002A46E93 — lncRNA, 835 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 lncRNA

ENST00000561800, ENST00000563846, ENST00000834857, ENST00000834858, ENST00000834859, ENST00000834860

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000561800 — 3 exons

Exon	Start	End
ENSE00002617549	42211169	42211333
ENSE00002625368	42208764	42208917
ENSE00004252726	42208411	42208684

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 97.02.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	97.02	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.28	gold quality
thymus	UBERON:0002370	77.40	silver quality
left testis	UBERON:0004533	73.99	gold quality
testis	UBERON:0000473	73.92	gold quality
sural nerve	UBERON:0015488	73.89	gold quality
right testis	UBERON:0004534	72.83	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	71.21	gold quality
colonic epithelium	UBERON:0000397	70.49	silver quality
bone marrow	UBERON:0002371	68.22	gold quality
bone marrow cell	CL:0002092	65.67	silver quality
skeletal muscle tissue	UBERON:0001134	64.49	silver quality
ganglionic eminence	UBERON:0004023	64.43	gold quality
endometrium	UBERON:0001295	63.90	gold quality
saliva-secreting gland	UBERON:0001044	60.83	gold quality
minor salivary gland	UBERON:0001830	60.81	gold quality
monocyte	CL:0000576	60.79	gold quality
right lung	UBERON:0002167	60.59	gold quality
rectum	UBERON:0001052	60.30	gold quality
duodenum	UBERON:0002114	59.67	gold quality
lymph node	UBERON:0000029	59.62	gold quality
skin of abdomen	UBERON:0001416	59.48	gold quality
adrenal tissue	UBERON:0018303	59.43	gold quality
vagina	UBERON:0000996	59.42	gold quality
zone of skin	UBERON:0000014	58.94	gold quality
ectocervix	UBERON:0012249	58.66	gold quality
skin of leg	UBERON:0001511	58.53	gold quality
upper lobe of left lung	UBERON:0008952	58.14	gold quality
urinary bladder	UBERON:0001255	58.12	gold quality
lung	UBERON:0002048	57.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.60

Regulation

Is transcription factor: no

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.