LINC00963

Summary

LINC00963 (long intergenic non-protein coding RNA 963, HGNC:48716) is a long non-coding RNA gene on chromosome 9q34.11.

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:48716
Approved symbol	LINC00963
Name	long intergenic non-protein coding RNA 963
Location	9q34.11
Locus type	RNA, long non-coding
Status	Approved
Aliases	MetaLnc9
Ensembl gene	ENSG00000204054
Ensembl biotype	lncRNA
Entrez	100506190
RNAcentral	URS000075C353 — lncRNA, 2123 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 82 — 80 lncRNA, 2 retained_intron

ENST00000412141, ENST00000419300, ENST00000423918, ENST00000427778, ENST00000444184, ENST00000453213, ENST00000454635, ENST00000454968, ENST00000607931, ENST00000608272, ENST00000608369, ENST00000608669, ENST00000622120, ENST00000622680, ENST00000622972, ENST00000623185, ENST00000624009, ENST00000624138, ENST00000624390, ENST00000625171, ENST00000652803, ENST00000653047, ENST00000653386, ENST00000653436, ENST00000653700, ENST00000654131, ENST00000654204, ENST00000654286, ENST00000654822, ENST00000655787, ENST00000655962, ENST00000656234, ENST00000656664, ENST00000657306, ENST00000657389, ENST00000658175, ENST00000658785, ENST00000658999, ENST00000659188, ENST00000659535, ENST00000659690, ENST00000660643, ENST00000661101, ENST00000662047, ENST00000662331, ENST00000663000, ENST00000663083, ENST00000663727, ENST00000664811, ENST00000665880, ENST00000665998, ENST00000666041, ENST00000666282, ENST00000666559, ENST00000667047, ENST00000667499, ENST00000668074, ENST00000668206, ENST00000668919, ENST00000669088, ENST00000669210, ENST00000669939, ENST00000671555, ENST00000671598, ENST00000671609, ENST00000843332, ENST00000843333, ENST00000843334, ENST00000843335, ENST00000843336, ENST00000843337, ENST00000843338, ENST00000843339, ENST00000843340, ENST00000843341, ENST00000843342, ENST00000843343, ENST00000843344, ENST00000843345, ENST00000843346, ENST00000843347, ENST00000843348

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000412141 — 5 exons

Exon	Start	End
ENSE00001649031	129504892	129505043
ENSE00001697014	129503323	129503672
ENSE00001722805	129513419	129513686
ENSE00001784287	129493416	129493595
ENSE00003854988	129491106	129491128

Expression profiles

Bgee: expression breadth ubiquitous, 201 present calls, max score 95.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.7910 / max 224.4358, expressed in 1792 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98922	8.6021	1690
98925	6.1668	1348
98924	2.8453	1276
98927	1.8393	1075
98933	1.8244	831
98930	1.0643	349
98923	0.6663	337
98921	0.2823	134
98926	0.1934	65
98920	0.1382	63

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
metanephros cortex	UBERON:0010533	95.60	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	95.20	gold quality
mucosa of stomach	UBERON:0001199	94.08	gold quality
right lobe of thyroid gland	UBERON:0001119	93.96	gold quality
sural nerve	UBERON:0015488	93.75	gold quality
left adrenal gland	UBERON:0001234	93.55	gold quality
body of pancreas	UBERON:0001150	93.52	gold quality
left adrenal gland cortex	UBERON:0035825	93.44	gold quality
right adrenal gland	UBERON:0001233	93.43	gold quality
right adrenal gland cortex	UBERON:0035827	93.24	gold quality
right lobe of liver	UBERON:0001114	93.15	gold quality
left uterine tube	UBERON:0001303	92.98	gold quality
right uterine tube	UBERON:0001302	92.97	gold quality
left lobe of thyroid gland	UBERON:0001120	92.92	gold quality
minor salivary gland	UBERON:0001830	92.46	gold quality
calcaneal tendon	UBERON:0003701	92.36	gold quality
monocyte	CL:0000576	91.93	gold quality
adenohypophysis	UBERON:0002196	91.85	gold quality
endocervix	UBERON:0000458	91.68	gold quality
thyroid gland	UBERON:0002046	91.64	gold quality
mononuclear cell	CL:0000842	91.55	gold quality
body of uterus	UBERON:0009853	91.51	gold quality
ascending aorta	UBERON:0001496	91.43	gold quality
thoracic aorta	UBERON:0001515	91.40	gold quality
adrenal gland	UBERON:0002369	91.34	gold quality
descending thoracic aorta	UBERON:0002345	91.33	gold quality
upper lobe of left lung	UBERON:0008952	91.20	gold quality
leukocyte	CL:0000738	91.15	gold quality
adrenal cortex	UBERON:0001235	90.88	gold quality
apex of heart	UBERON:0002098	90.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.85

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 18)

• Study shows that lncRNA Linc00963 is found to be involved in the progression from Androgen-Dependent to Androgen-Independent of prostate cancer. (PMID:24691949)
• Data show that LINC00963 (MetaLnc9) interacted with the glycolytic kinase PGK1 and prevented its ubiquitination in non-small cell lung cancer (NSCLC) cells, leading to activation of the oncogenic AKT/mTOR signaling pathway. (PMID:28923857)
• Our data revealed that LINC00963 was upregulated in hepatocellular carcinoma, which significantly extended the G0/G1 phase and promoted the proliferative ability of HCC cells. (PMID:29630107)
• LINC00963 knockdown dramatically suppressed melanoma cell proliferation, migration and invasion (PMID:30180950)
• LINC00963 predicts poor prognosis and promotes esophageal cancer cells invasion via targeting miR-214-5p/RAB14 axis. (PMID:31957829)
• Long noncoding RNA LINC00963 promotes breast cancer progression by functioning as a molecular sponge for microRNA-625 and thereby upregulating HMGA1. (PMID:32052688)
• Long noncoding RNA LINC00963 induces NOP2 expression by sponging tumor suppressor miR-542-3p to promote metastasis in prostate cancer. (PMID:32554858)
• LncRNA LINC00963 promotes proliferation and migration through the miR-124-3p/FZD4 pathway in colorectal cancer. (PMID:32744689)
• lncRNA LINC00963 downregulation regulates colorectal cancer tumorigenesis and progression via the miR10b/FGF13 axis. (PMID:33495804)
• The potential roles of lncRNAs DUXAP8, LINC00963, and FOXD2-AS1 in luminal breast cancer based on expression analysis and bioinformatic approaches. (PMID:34043149)
• LncRNA LINC00963 promotes osteogenic differentiation of hBMSCs and alleviates osteoporosis progression by targeting miRNA-760/ETS1 axis. (PMID:34184952)
• LncRNA LINC00963 promotes colorectal cancer cell proliferation and metastasis by regulating miR1281 and TRIM65. (PMID:34498706)
• LINC00963/miR-4458 regulates the effect of oxaliplatin in gastric cancer by mediating autophagic flux through targeting of ATG16L1. (PMID:34697403)
• The Long Noncoding RNA LINC00963 Inhibits Corneal Fibrosis Scar Formation by Targeting miR-143-3p. (PMID:35262384)
• MetaLnc9-Antisense RNA Contributes to Lung Cancer Metastasis via Modulating RNA-RNA Duplex with MetaLnc9. (PMID:35333617)
• Decrease in LINC00963 attenuates the progression of pulmonary arterial hypertension via microRNA-328-3p/profilin 1 axis. (PMID:35349725)
• LINC00963 promotes the malignancy and metastasis of lung adenocarcinoma by stabilizing Zeb1 and exosomes-induced M2 macrophage polarization. (PMID:36604626)
• Novel splice variants of LINC00963 suppress colorectal cancer cell proliferation via miR-10a/miR-143/miR-217/miR-512-mediated regulation of PI3K/AKT and Wnt/beta-catenin signaling pathways. (PMID:36804476)

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.