LINC-PINT

Summary

LINC-PINT (long intergenic non-protein coding RNA, p53 induced transcript, HGNC:26885) is a long non-coding RNA gene on chromosome 7q32.3. Enhances the binding of the PAF1 complex to target gene promoters and plays a role in negative regulation of transcription.

Involved in negative regulation of transcription by RNA polymerase II. Located in nucleus.

Source: NCBI Gene 378805 — RefSeq curated summary.

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:26885
Approved symbol	LINC-PINT
Name	long intergenic non-protein coding RNA, p53 induced transcript
Location	7q32.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	PINT, TISPL, FLJ43663, PINT87aa, LOC646329, LincRNA-Pint
Ensembl gene	ENSG00000231721
Ensembl biotype	lncRNA
OMIM	618212
Entrez	378805
RNAcentral	URS000075C16A — lncRNA, 3144 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 284 — 283 lncRNA, 1 retained_intron

ENST00000416999, ENST00000418546, ENST00000423414, ENST00000429901, ENST00000431189, ENST00000432045, ENST00000433079, ENST00000435523, ENST00000443623, ENST00000447307, ENST00000451786, ENST00000642156, ENST00000642483, ENST00000642602, ENST00000642963, ENST00000643135, ENST00000643373, ENST00000643452, ENST00000643779, ENST00000643855, ENST00000643866, ENST00000643874, ENST00000644188, ENST00000644432, ENST00000644804, ENST00000645248, ENST00000646429, ENST00000646587, ENST00000647102, ENST00000647288, ENST00000647388, ENST00000659385, ENST00000700935, ENST00000701119, ENST00000701173, ENST00000701177, ENST00000701297, ENST00000701381, ENST00000701464, ENST00000701481, ENST00000701550, ENST00000701594, ENST00000701656, ENST00000701757, ENST00000701783, ENST00000701790, ENST00000701954, ENST00000701979, ENST00000702156, ENST00000702162, ENST00000702406, ENST00000702426, ENST00000702467, ENST00000702498, ENST00000702534, ENST00000702568, ENST00000702589, ENST00000702681, ENST00000702729, ENST00000702813, ENST00000702824, ENST00000702839, ENST00000702859, ENST00000702866, ENST00000702906, ENST00000702917, ENST00000702983, ENST00000703012, ENST00000703250, ENST00000845165, ENST00000845166, ENST00000845167, ENST00000845168, ENST00000845169, ENST00000845170, ENST00000845171, ENST00000845172, ENST00000845173, ENST00000845174, ENST00000845175, ENST00000845176, ENST00000845177, ENST00000845178, ENST00000845179, ENST00000845180, ENST00000845181, ENST00000845182, ENST00000845183, ENST00000845184, ENST00000845185, ENST00000845186, ENST00000845187, ENST00000845188, ENST00000845189, ENST00000845190, ENST00000845191, ENST00000845192, ENST00000845193, ENST00000845194, ENST00000845195, ENST00000845196, ENST00000845197, ENST00000845198, ENST00000845199, ENST00000845200, ENST00000845201, ENST00000845202, ENST00000845203, ENST00000845204, ENST00000845205, ENST00000845206, ENST00000845207, ENST00000845208, ENST00000845209, ENST00000845210, ENST00000845211, ENST00000845212, ENST00000845213, ENST00000845214, ENST00000845215, ENST00000845216, ENST00000845217, ENST00000845218, ENST00000845219, ENST00000845220, ENST00000845221, ENST00000845222, ENST00000845223, ENST00000845224, ENST00000845225, ENST00000845226, ENST00000845227, ENST00000845228, ENST00000845229, ENST00000845230, ENST00000845231, ENST00000845232, ENST00000845233, ENST00000845234, ENST00000845235, ENST00000845236, ENST00000845237, ENST00000845238, ENST00000845239, ENST00000845240, ENST00000845241, ENST00000845242, ENST00000845243, ENST00000845244, ENST00000845245, ENST00000845246, ENST00000845247, ENST00000845248, ENST00000845249, ENST00000845250, ENST00000845251, ENST00000845252, ENST00000845253, ENST00000845254, ENST00000845255, ENST00000845256, ENST00000845257, ENST00000845258, ENST00000845259, ENST00000845260, ENST00000845261, ENST00000845262, ENST00000845263, ENST00000845264, ENST00000845265, ENST00000845266, ENST00000845267, ENST00000845268, ENST00000845269, ENST00000845270, ENST00000845271, ENST00000845272, ENST00000845273, ENST00000845274, ENST00000845275, ENST00000845276, ENST00000845277, ENST00000845278, ENST00000845279, ENST00000845280, ENST00000845281, ENST00000845282, ENST00000845283, ENST00000845284, ENST00000845285, ENST00000845286, ENST00000845287, ENST00000845288, ENST00000845289, ENST00000845290, ENST00000845291, ENST00000845292, ENST00000845293, ENST00000845294, ENST00000845295, ENST00000845296, ENST00000845297, ENST00000845298, ENST00000845299, ENST00000845300, ENST00000845301, ENST00000845302, ENST00000845303, ENST00000845304, ENST00000845305, ENST00000845306, ENST00000845307, ENST00000845308, ENST00000845309, ENST00000845310, ENST00000845311, ENST00000845312, ENST00000845313, ENST00000845314, ENST00000845315, ENST00000845316, ENST00000845317, ENST00000845318, ENST00000845319, ENST00000845320, ENST00000845321, ENST00000845322, ENST00000845323, ENST00000845324, ENST00000845325, ENST00000845326, ENST00000845327, ENST00000845328, ENST00000845329, ENST00000845330, ENST00000845331, ENST00000845332, ENST00000845333, ENST00000845334, ENST00000845335, ENST00000845336, ENST00000845337, ENST00000845338, ENST00000845339, ENST00000845340, ENST00000845341, ENST00000845342, ENST00000845343, ENST00000845344, ENST00000845345, ENST00000845346, ENST00000845347, ENST00000845348, ENST00000845349, ENST00000845350, ENST00000845351, ENST00000845352, ENST00000845353, ENST00000845354, ENST00000845355, ENST00000845356, ENST00000845357, ENST00000845358, ENST00000845359, ENST00000845360, ENST00000845361, ENST00000845362, ENST00000845363, ENST00000845364, ENST00000845365, ENST00000845366, ENST00000845367, ENST00000845368, ENST00000845369, ENST00000845370, ENST00000845371, ENST00000845372, ENST00000845373, ENST00000845374, ENST00000845375, ENST00000845376, ENST00000845377, ENST00000845378, ENST00000845379

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000416999 — 3 exons

Exon	Start	End
ENSE00001594819	131042836	131042931
ENSE00001700457	131052425	131052550
ENSE00001736977	131049538	131049702

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 97.75.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 50.0074 / max 1400.1663, expressed in 1771 samples.

FANTOM5 promoters (27 alternative TSS)

Promoter ID	TPM avg	Samples expressed
86255	8.7282	956
86256	5.7896	1021
86253	5.0587	627
86177	5.0464	474
86258	4.0799	320
86259	3.5961	1030
86179	2.7370	420
86180	1.9674	288
86260	1.9641	871
86183	1.8142	583

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cardiac muscle of right atrium	UBERON:0003379	97.75	gold quality
calcaneal tendon	UBERON:0003701	97.14	gold quality
sural nerve	UBERON:0015488	97.09	gold quality
left ventricle myocardium	UBERON:0006566	97.03	gold quality
bone marrow cell	CL:0002092	96.71	gold quality
colonic epithelium	UBERON:0000397	95.92	gold quality
tibialis anterior	UBERON:0001385	95.32	silver quality
deltoid	UBERON:0001476	93.66	gold quality
cardiac atrium	UBERON:0002081	93.26	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.21	gold quality
corpus callosum	UBERON:0002336	93.08	gold quality
middle temporal gyrus	UBERON:0002771	93.07	gold quality
right atrium auricular region	UBERON:0006631	93.06	gold quality
gastrocnemius	UBERON:0001388	92.74	gold quality
substantia nigra	UBERON:0002038	92.40	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.40	gold quality
left ovary	UBERON:0002119	92.26	gold quality
left lobe of thyroid gland	UBERON:0001120	92.25	gold quality
epithelial cell of pancreas	CL:0000083	92.10	gold quality
thyroid gland	UBERON:0002046	92.10	gold quality
right lobe of thyroid gland	UBERON:0001119	92.03	gold quality
substantia nigra pars reticulata	UBERON:0001966	92.02	gold quality
spinal cord	UBERON:0002240	91.91	gold quality
muscle of leg	UBERON:0001383	91.88	gold quality
myocardium	UBERON:0002349	91.76	gold quality
midbrain	UBERON:0001891	91.59	gold quality
Ammon’s horn	UBERON:0001954	91.56	gold quality
amygdala	UBERON:0001876	91.47	gold quality
tibial nerve	UBERON:0001323	91.46	gold quality
substantia nigra pars compacta	UBERON:0001965	91.40	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	16.22
E-CURD-119	yes	10.23

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 35)

• Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2. (PMID:24070194)
• Our results provide additional insights into the opposing roles of the ESR1 and FLJ43663 genes in breast cancer onset and progression. (PMID:24127041)
• Long noncoding RNA (LIPCAR) is a novel biomarker of cardiac remodeling that predicts future death in patients with heart failure. (PMID:24663402)
• Long intergenic noncoding RNA locus is involved in melanoma progression. (PMID:26016895)
• TM4SF5-miR-4697-3P- CTD-2354A18.1 may play a key role in the pathogenesis of gastric cancer (PMID:26531872)
• Results provide evidence that lncRNA LOC646329 expression appears low in neocortical tissues but high in the radial glia subpopulation, regulating cell proliferation. (PMID:27081004)
• LINC-PINT acts as tumor suppressor lncRNA that inhibits the migration capacity of cancer cells by repressing an invasion gene signature in a PRC2-dependent manner. (PMID:29078818)
• An 87-amino-acid peptide encoded by the circular form of the long intergenic non-protein-coding RNA p53-induced transcript (LINC-PINT) suppresses glioblastoma cell proliferation in vitro and in vivo. This peptide directly interacts with polymerase associated factor complex (PAF1c) and inhibits the transcriptional elongation of multiple oncogenes. (PMID:30367041)
• LINC-PINT may participate in gastric cancer through the crosstalk with miR-21. (PMID:30569513)
• Study found that LncRNA LINC-PINT was inhibited, whereas miRNA-21 was promoted in tumor tissues of patients with osteosarcoma. LncRNA LINC-PINT and miRNA-21 were significantly and reversely correlated in both tumor cells and adjacent healthy tissues. LncRNA LINC-PINT overexpression led to downregulated miRNA-21 expression in cancer cells, whereas miRNA-21 overexpression did not significantly affect LINC-PINT expression. (PMID:31070482)
• LINC-PINT targeted miR-425-5p by three sites. miR-425-5p also targeted PTCH1 a protein of the Hedgehog pathway. Downregulation of LINC-PINT was associated with increased cancer stemness and chemoresistance to cisplatin. (PMID:31131448)
• Linc-PINT acted as a tumor suppressor by sponging miR-543 and miR-576-5p in esophageal cancer. (PMID:31464068)
• overexpression of Lincpint may inhibit the growth of gastric tumors via downregulation of HIF1alpha. (PMID:31524232)
• Long Non-coding RNA LINC-PINT and LINC00599 Polymorphisms are Associated With High-altitude Pulmonary Edema in Chinese. (PMID:31761491)
• LINC-PINT alleviates lung cancer progression via sponging miR-543 and inducing PTEN. (PMID:31981466)
• A lncRNA survey finds increases in neuroprotective LINC-PINT in Parkinson’s disease substantia nigra. (PMID:32080970)
• LncRNA LINC-PINT increases SOCS1 expression by sponging miR-155-5p to inhibit the activation of ERK signaling pathway in rheumatoid arthritis synovial fibroblasts induced by TNF-alpha. (PMID:32289665)
• Long non-coding RNA LINC-PINT can inhibit the proliferation and promote apoptosis of osteosarcoma cells through targeting miR-524-5p, which will provide a new target for the treatment of osteosarcoma. (PMID:32375449)
• Downregulation of lncRNA LINC-PINT Participates in the Recurrence of Esophageal Squamous Cell Carcinoma Possibly by Interacting miRNA-21. (PMID:32401035)
• Long non-coding RNA LINC-PINT attenuates paclitaxel resistance in triple-negative breast cancer cells via targeting the RNA-binding protein NONO. (PMID:32632453)
• LINC-PINT suppresses tumour cell proliferation, migration and invasion through targeting miR-374a-5p in ovarian cancer. (PMID:32638404)
• LncRNA Linc-PINT inhibits miR-523-3p to hamper retinoblastoma progression by upregulating Dickkopf-1 (DKK1). (PMID:32828314)
• Inhibition of Long Noncoding RNA Linc-Pint by Hepatitis C Virus in Infected Hepatocytes Enhances Lipogenesis. (PMID:33236406)
• Cellular senescence in hepatocellular carcinoma induced by a long non-coding RNA-encoded peptide PINT87aa by blocking FOXM1-mediated PHB2. (PMID:33754036)
• LINC-PINT impedes DNA repair and enhances radiotherapeutic response by targeting DNA-PKcs in nasopharyngeal cancer. (PMID:33963177)
• Association between LINC-PINT and LINC00599 gene polymorphism and the risk of steroid-induced osteonecrosis of the femoral head in the population of northern China. (PMID:34245766)
• LncRNA LINC-PINT Inhibits Malignant Behaviors of Laryngeal Squamous Cell Carcinoma Cells via Inhibiting ZEB1. (PMID:34257531)
• An NF-kappaB-responsive long noncoding RNA, PINT, regulates TNF-alpha gene transcription by scaffolding p65 and EZH2. (PMID:34405442)
• PINTology: A short history of the lncRNA LINC-PINT in different diseases. (PMID:35019222)
• Downregulation of long non-coding RNAs in patients with bipolar disorder. (PMID:35523833)
• TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma. (PMID:35694846)
• Effects of genetic polymorphisms of LINC-PINT gene on liver cancer susceptibility in the Chinese Han population. (PMID:37317835)
• Association of LINC-PINT polymorphisms with lumbar disc herniation risk among Chinese Han population: a case control study. (PMID:37553573)
• LINC-PINT suppresses breast cancer cell proliferation and migration via MEIS2/PPP3CC/NF-kappaB pathway by sponging miR-576-5p. (PMID:37660994)
• Identification of a novel RNA transcript TISPL upregulated by stressors that stimulate ATF4. (PMID:38615981)

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.