LINC01397

Summary

LINC01397 (long intergenic non-protein coding RNA 1397, HGNC:50677) is a long non-coding RNA gene on chromosome 1p13.3.

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:50677
Approved symbol	LINC01397
Name	long intergenic non-protein coding RNA 1397
Location	1p13.3
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000258673
Ensembl biotype	lncRNA
Entrez	104355139
RNAcentral	URS00000ED31F — lncRNA, 579 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 26 lncRNA

ENST00000554808, ENST00000701866, ENST00000702583, ENST00000702814, ENST00000751945, ENST00000751946, ENST00000751947, ENST00000751948, ENST00000751949, ENST00000751950, ENST00000751951, ENST00000751952, ENST00000751953, ENST00000751954, ENST00000751955, ENST00000751956, ENST00000751957, ENST00000751958, ENST00000751959, ENST00000751960, ENST00000751961, ENST00000751962, ENST00000751963, ENST00000751964, ENST00000751965, ENST00000751966

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000554808 — 4 exons

Exon	Start	End
ENSE00002449386	110108845	110109028
ENSE00002486782	110082688	110082852
ENSE00002512217	110109299	110109413
ENSE00002528179	110109605	110109719

Expression profiles

Bgee: expression breadth ubiquitous, 102 present calls, max score 64.53.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2855 / max 58.1145, expressed in 60 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4509	0.2045	49
4507	0.0754	19
4508	0.0056	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bone marrow cell	CL:0002092	64.53	silver quality
sural nerve	UBERON:0015488	57.83	silver quality
mucosa of stomach	UBERON:0001199	57.42	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	57.35	gold quality
thoracic mammary gland	UBERON:0005200	57.08	gold quality
prefrontal cortex	UBERON:0000451	56.87	gold quality
lymph node	UBERON:0000029	55.83	gold quality
left uterine tube	UBERON:0001303	55.11	gold quality
gall bladder	UBERON:0002110	55.10	gold quality
adenohypophysis	UBERON:0002196	54.86	gold quality
monocyte	CL:0000576	54.29	gold quality
islet of Langerhans	UBERON:0000006	53.86	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	53.86	gold quality
pituitary gland	UBERON:0000007	53.40	gold quality
fallopian tube	UBERON:0003889	53.15	gold quality
myometrium	UBERON:0001296	52.52	gold quality
minor salivary gland	UBERON:0001830	52.09	gold quality
blood	UBERON:0000178	51.85	gold quality
smooth muscle tissue	UBERON:0001135	50.67	gold quality
tonsil	UBERON:0002372	50.39	gold quality
muscle of leg	UBERON:0001383	50.30	gold quality
cerebral cortex	UBERON:0000956	50.07	gold quality
skin of abdomen	UBERON:0001416	50.07	gold quality
gastrocnemius	UBERON:0001388	50.04	gold quality
right frontal lobe	UBERON:0002810	50.02	gold quality
right ovary	UBERON:0002118	49.82	gold quality
subcutaneous adipose tissue	UBERON:0002190	49.79	gold quality
putamen	UBERON:0001874	49.76	gold quality
adipose tissue	UBERON:0001013	49.70	gold quality
brain	UBERON:0000955	49.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.31

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.