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LINC-PINT long intergenic non-protein coding RNA, p53 induced transcript [ Homo sapiens (human) ]

Gene ID: 378805, updated on 2-Nov-2024

Summary

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Official Symbol
LINC-PINTprovided by HGNC
Official Full Name
long intergenic non-protein coding RNA, p53 induced transcriptprovided by HGNC
Primary source
HGNC:HGNC:26885
See related
Ensembl:ENSG00000231721 MIM:618212; AllianceGenome:HGNC:26885
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PINT; TISPL; PINT87aa; MKLN1-AS1; LincRNA-Pint
Summary
Involved in negative regulation of transcription by RNA polymerase II. Located in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in bone marrow (RPKM 3.9), brain (RPKM 3.1) and 24 other tissues See more
Orthologs
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Genomic context

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See LINC-PINT in Genome Data Viewer
Location:
7q32.3
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (130877562..131109925, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (132195054..132427432, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (130562321..130794684, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130571236-130572435 Neighboring gene Sharpr-MPRA regulatory region 2521 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:130588151-130589350 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancers GRCh37_chr7:130595421-130595954 and GRCh37_chr7:130595955-130596488 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:130597482-130598681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18651 Neighboring gene microRNA 29b-1 Neighboring gene microRNA 29a Neighboring gene long intergenic non-protein coding RNA 513 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:130635654-130635822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26659 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130644756-130645955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26664 Neighboring gene Sharpr-MPRA regulatory region 13565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26667 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130729465 Neighboring gene Sharpr-MPRA regulatory region 6658 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130743720 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130743868 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 7:130744026 and 7:130744055 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130746088 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130750088 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130751320 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130751957 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130754812 Neighboring gene RNA, U6 small nuclear 1010, pseudogene Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130757740 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130758576 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130763709 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:130775512-130776367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:130792685-130793536 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18658 Neighboring gene MKLN1 intron CAGE-defined mid-level expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26669 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130848608-130849807 Neighboring gene muskelin 1 Neighboring gene MPRA-validated peak6722 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:130872973-130874172 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:130875573-130876331 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130880490 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:130888388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26673 Neighboring gene MPRA-validated peak6724 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26675 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:130929013-130929606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:130930791-130931382 Neighboring gene ribosomal protein L27 pseudogene 11 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:131012400-131012976 Neighboring gene MKLN1 antisense RNA

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of a novel RNA transcript TISPL upregulated by stressors that stimulate ATF4.
    Title: Identification of a novel RNA transcript TISPL upregulated by stressors that stimulate ATF4.
  2. LINC-PINT suppresses breast cancer cell proliferation and migration via MEIS2/PPP3CC/NF-kappaB pathway by sponging miR-576-5p.
    Title: LINC-PINT suppresses breast cancer cell proliferation and migration via MEIS2/PPP3CC/NF-κB pathway by sponging miR-576-5p.
  3. Association of LINC-PINT polymorphisms with lumbar disc herniation risk among Chinese Han population: a case control study.
    Title: Association of LINC-PINT polymorphisms with lumbar disc herniation risk among Chinese Han population: a case control study.
  4. Effects of genetic polymorphisms of LINC-PINT gene on liver cancer susceptibility in the Chinese Han population.
    Title: Effects of genetic polymorphisms of LINC-PINT gene on liver cancer susceptibility in the Chinese Han population.
  5. TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma.
    Title: TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma.
  6. PINTology: A short history of the lncRNA LINC-PINT in different diseases.
    Title: PINTology: A short history of the lncRNA LINC-PINT in different diseases.
  7. Downregulation of long non-coding RNAs in patients with bipolar disorder.
    Title: Downregulation of long non-coding RNAs in patients with bipolar disorder.
  8. 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.
    Title: 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.
  9. Inhibition of Long Noncoding RNA Linc-Pint by Hepatitis C Virus in Infected Hepatocytes Enhances Lipogenesis.
    Title: Inhibition of Long Noncoding RNA Linc-Pint by Hepatitis C Virus in Infected Hepatocytes Enhances Lipogenesis.
  10. LncRNA LINC-PINT Inhibits Malignant Behaviors of Laryngeal Squamous Cell Carcinoma Cells via Inhibiting ZEB1.
    Title: LncRNA LINC-PINT Inhibits Malignant Behaviors of Laryngeal Squamous Cell Carcinoma Cells via Inhibiting ZEB1.
Submit: New GeneRIF Correction See all GeneRIFs (36)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies breast cancer risk variant at 10q21.2: results from the Asia Breast Cancer Consortium.
EBI GWAS Catalog
Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
EBI GWAS Catalog
Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Markers

Homology

Other Names

  • MKLN1 antisense RNA 1 (head to head)
  • p53 induced noncoding transcript
  • transcript induced by stressors from LINC-PINT locus

Clone Names

  • FLJ38230, FLJ43663, hCG_2038586

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

RNA

  1. NR_015431.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) is the reference variant.
    Source sequence(s)
    AA281849, AC013434, AK125651, AL569506, AL713664, BC130416, BX451434, CA412672, DB472406, R67739
    Related
    ENST00000702156.2

  2. NR_024153.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' and 3' exon structure and lacks an alternate internal exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AL569506, BC039420, CA412672, R67739
    Related
    ENST00000433079.5

  3. NR_034120.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9) uses an alternate promoter and represents an alternate exon structure, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC016831, AK095549

  4. NR_109850.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate internal exon, resulting in a longer transcript, compared to variant 1.
    Source sequence(s)
    AA281849, AC058791, AK125651, AL569506, AL713664, BC130416, BX451434, CA412672, DB472406, R67739
    Related
    ENST00000451786.6

  5. NR_109851.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate internal exon, resulting in a longer transcript, compared to variant 1.
    Source sequence(s)
    AA281849, AK125651, AL569506, AL713664, BC130416, BI833488, BX451434, CA412672, DB472406, R67739

  6. NR_109852.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate internal exon, resulting in a longer transcript, compared to variant 1.
    Source sequence(s)
    AA281849, AK125651, AL569506, AL713664, BC130416, BI914823, BX451434, CA412672, DB472406, R67739

  7. NR_109853.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 3' exon structure, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AL569506, BC130416, BG706681, CA412672, DB472406, R67739

  8. NR_109854.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs in the 3' exon structure, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AL569506, AV727262, BC047367, BC130416, CA412672, DB472406, R67739

  9. NR_109855.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) lacks an alternate internal exon and differs in the 3' exon structure, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    BC130416, DA321983, DB472406

  10. NR_110472.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (10) uses an alternate promoter and represents an alternate exon structure, resulting in a shorter transcript, compared to variant 1. It uses an alternate splice site in the 3' terminal exon, compared to variant 9.
    Source sequence(s)
    AC016831

  11. NR_110473.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (11) uses an alternate promoter and represents an alternate exon structure, resulting in a shorter transcript, compared to variant 1. It uses an alternate 3' terminal exon, compared to variant 9.
    Source sequence(s)
    AC016831, AK095549, GU321462

  12. NR_170175.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC013434, AC016831, AC058791

  13. NR_170176.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC013434, AC016831, AC058791

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    130877562..131109925 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    132195054..132427432 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001085379.1: Suppressed sequence

    Description
    NM_001085379.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version

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