LINC00649

Summary

LINC00649 (long intergenic non-protein coding RNA 649, HGNC:44305) is a long non-coding RNA gene on chromosome 21q22.11.

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:44305
Approved symbol	LINC00649
Name	long intergenic non-protein coding RNA 649
Location	21q22.11
Locus type	RNA, long non-coding
Status	Approved
Aliases	TCONS_00028768, lnc-ITSN1-2
Ensembl gene	ENSG00000237945
Ensembl biotype	lncRNA
Entrez	100506334
RNAcentral	URS0000A766F4 — lncRNA, 2657 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 71 — 71 lncRNA

ENST00000381181, ENST00000400353, ENST00000427447, ENST00000593977, ENST00000594370, ENST00000594752, ENST00000595747, ENST00000596365, ENST00000597626, ENST00000599421, ENST00000600155, ENST00000601471, ENST00000608431, ENST00000609132, ENST00000610236, ENST00000613667, ENST00000616030, ENST00000620580, ENST00000622171, ENST00000628906, ENST00000701334, ENST00000813276, ENST00000813277, ENST00000813278, ENST00000813279, ENST00000813280, ENST00000813281, ENST00000813282, ENST00000813283, ENST00000813284, ENST00000813285, ENST00000813286, ENST00000813287, ENST00000813288, ENST00000813289, ENST00000813290, ENST00000813291, ENST00000813292, ENST00000813293, ENST00000813294, ENST00000813295, ENST00000813296, ENST00000813297, ENST00000813298, ENST00000813299, ENST00000813300, ENST00000813301, ENST00000813302, ENST00000813303, ENST00000813304, ENST00000813305, ENST00000813306, ENST00000813307, ENST00000813308, ENST00000813309, ENST00000813310, ENST00000813311, ENST00000813312, ENST00000813313, ENST00000813314, ENST00000813315, ENST00000813316, ENST00000813317, ENST00000813318, ENST00000813319, ENST00000813320, ENST00000813321, ENST00000813322, ENST00000813323, ENST00000813324, ENST00000813325

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000381181 — 2 exons

Exon	Start	End
ENSE00001487739	33962065	33963958
ENSE00001487744	33948926	33949292

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 82.00.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2809 / max 70.2322, expressed in 290 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
188898	0.6479	196
188904	0.2866	73
188905	0.1823	60
188903	0.1196	57
209301	0.0446	23

Top tissues by expression

138 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	82.00	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.62	gold quality
granulocyte	CL:0000094	79.80	gold quality
lymph node	UBERON:0000029	79.80	gold quality
placenta	UBERON:0001987	79.65	gold quality
tonsil	UBERON:0002372	79.11	gold quality
bone marrow cell	CL:0002092	79.00	gold quality
blood	UBERON:0000178	78.48	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	76.03	gold quality
hindlimb stylopod muscle	UBERON:0004252	75.34	gold quality
colonic epithelium	UBERON:0000397	74.98	gold quality
skeletal muscle tissue	UBERON:0001134	74.80	gold quality
liver	UBERON:0002107	73.04	gold quality
corpus callosum	UBERON:0002336	73.00	gold quality
vermiform appendix	UBERON:0001154	72.82	gold quality
muscle tissue	UBERON:0002385	72.48	gold quality
sural nerve	UBERON:0015488	72.44	gold quality
muscle of leg	UBERON:0001383	71.67	gold quality
esophagus mucosa	UBERON:0002469	71.64	gold quality
gastrocnemius	UBERON:0001388	71.16	gold quality
right lobe of liver	UBERON:0001114	70.84	gold quality
prostate gland	UBERON:0002367	70.80	gold quality
leukocyte	CL:0000738	70.73	gold quality
skin of abdomen	UBERON:0001416	70.49	gold quality
thymus	UBERON:0002370	70.34	silver quality
lower esophagus mucosa	UBERON:0035834	70.29	gold quality
mucosa of transverse colon	UBERON:0004991	70.20	gold quality
spleen	UBERON:0002106	70.14	gold quality
zone of skin	UBERON:0000014	70.10	gold quality
duodenum	UBERON:0002114	69.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.45

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 8)

• Lnc-ITSN1-2, Derived From RNA Sequencing, Correlates With Increased Disease Risk, Activity and Promotes CD4(+) T Cell Activation, Proliferation and Th1/Th17 Cell Differentiation by Serving as a ceRNA for IL-23R via Sponging miR-125a in Inflammatory Bowel Disease. (PMID:32547537)
• LINC00649 underexpression is an adverse prognostic marker in acute myeloid leukemia. (PMID:32883226)
• LINC00649 Facilitates the Cellular Process of Bladder Cancer Cells via Signaling Axis miR-16-5p/JARID2. (PMID:33789312)
• Long non-coding RNA LINC00649 regulates YES-associated protein 1 (YAP1)/Hippo pathway to accelerate gastric cancer (GC) progression via sequestering miR-16-5p. (PMID:33975517)
• Long noncoding RNA LINC00649 functions as a microRNA4325p sponge to facilitate tumourigenesis in colorectal cancer by upregulating HDGF. (PMID:35088877)
• LncRNA LINC00649 promotes the growth and metastasis of triple-negative breast cancer by maintaining the stability of HIF-1alpha through the NF90/NF45 complex. (PMID:35188449)
• LncRNA LINC00649 recruits TAF15 and enhances MAPK6 expression to promote the development of lung squamous cell carcinoma via activating MAPK signaling pathway. (PMID:35228660)
• LncRNA LINC00649 aggravates the progression of cervical cancer through sponging miR-216a-3p. (PMID:36054700)

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.