LINC00544

Summary

LINC00544 (long intergenic non-protein coding RNA 544, HGNC:43679) is a long non-coding RNA gene on chromosome 13q12.3.

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:43679
Approved symbol	LINC00544
Name	long intergenic non-protein coding RNA 544
Location	13q12.3
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000122043
Ensembl biotype	lncRNA
Entrez	440131
RNAcentral	URS000075CDCD — lncRNA, 709 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 17 lncRNA

ENST00000400540, ENST00000481738, ENST00000656266, ENST00000658535, ENST00000662443, ENST00000692335, ENST00000777689, ENST00000777690, ENST00000777691, ENST00000777692, ENST00000777693, ENST00000777694, ENST00000777695, ENST00000777696, ENST00000777697, ENST00000777698, ENST00000777699

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000400540 — 6 exons

Exon	Start	End
ENSE00000827436	29950317	29950488
ENSE00001485711	29937202	29937281
ENSE00001543394	29936516	29936701
ENSE00001543395	29935905	29936224
ENSE00003521124	29947603	29947771
ENSE00003595600	29937906	29938009

Expression profiles

Bgee: expression breadth broad, 90 present calls, max score 92.31.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0847 / max 8.7996, expressed in 45 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134607	0.0847	45

Top tissues by expression

187 total, 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	92.31	gold quality
secondary oocyte	CL:0000655	67.05	gold quality
buccal mucosa cell	CL:0002336	65.81	gold quality
myocardium	UBERON:0002349	63.11	gold quality
sperm	CL:0000019	62.24	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	60.74	gold quality
leukocyte	CL:0000738	57.86	gold quality
cerebellar vermis	UBERON:0004720	57.80	gold quality
lymph node	UBERON:0000029	57.76	gold quality
esophagus squamous epithelium	UBERON:0006920	55.64	gold quality
monocyte	CL:0000576	55.60	gold quality
blood	UBERON:0000178	55.45	gold quality
corpus callosum	UBERON:0002336	55.19	gold quality
decidua	UBERON:0002450	54.71	gold quality
mammary duct	UBERON:0001765	54.61	gold quality
granulocyte	CL:0000094	54.41	gold quality
oocyte	CL:0000023	53.69	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	53.43	gold quality
vena cava	UBERON:0004087	53.38	gold quality
saphenous vein	UBERON:0007318	52.83	gold quality
ventral tegmental area	UBERON:0002691	52.66	gold quality
mammalian vulva	UBERON:0000997	52.62	gold quality
inferior vagus X ganglion	UBERON:0005363	52.55	gold quality
islet of Langerhans	UBERON:0000006	52.51	gold quality
trigeminal ganglion	UBERON:0001675	52.23	gold quality
left testis	UBERON:0004533	52.23	gold quality
body of tongue	UBERON:0011876	52.19	gold quality
nipple	UBERON:0002030	52.18	gold quality
pharyngeal mucosa	UBERON:0000355	52.10	gold quality
dorsal root ganglion	UBERON:0000044	51.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.89

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Study found a novel lncRNA00544, which was highly expressed in the metastatic axillary nodes compared with corresponding luminal breast cancer (BC) tissues. Results were confirmed in luminal BC cell lines and paired breast cancer samples compared with corresponding controls. Survival curves of breast cancer patients indicated that disease-free survival was significantly poor in patients with high lncRNA00544 expression. (PMID:28959047)

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.