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    PTBP1 polypyrimidine tract binding protein 1 [ Homo sapiens (human) ]

    Gene ID: 5725, updated on 9-Dec-2024

    Summary

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    Official Symbol
    PTBP1provided by HGNC
    Official Full Name
    polypyrimidine tract binding protein 1provided by HGNC
    Primary source
    HGNC:HGNC:9583
    See related
    Ensembl:ENSG00000011304 MIM:600693; AllianceGenome:HGNC:9583
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PTB; PTB2; PTB3; PTB4; pPTB; HNRPI; PTB-1; PTB-T; HNRNPI; HNRNP-I
    Summary
    This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA-binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has four repeats of quasi-RNA recognition motif (RRM) domains that bind RNAs. This protein binds to the intronic polypyrimidine tracts that requires pre-mRNA splicing and acts via the protein degradation ubiquitin-proteasome pathway. It may also promote the binding of U2 snRNP to pre-mRNAs. This protein is localized in the nucleoplasm and it is also detected in the perinucleolar structure. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in placenta (RPKM 42.6), bone marrow (RPKM 39.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PTBP1 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (797452..812312)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (751931..766786)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (797452..812312)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928450 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:782349-782922 Neighboring gene long intergenic non-protein coding RNA 1836 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:787176-787746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:787747-788315 Neighboring gene CRISPRi-validated cis-regulatory element chr19.128 Neighboring gene CRISPRi-validated cis-regulatory element chr19.129 Neighboring gene hESC enhancers GRCh37_chr19:796571-797206 and GRCh37_chr19:797405-798290 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:798291-799174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:803235-803757 Neighboring gene microRNA 4745 Neighboring gene phospholipid phosphatase related 3 Neighboring gene microRNA 3187 Neighboring gene azurocidin 1

    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
    • 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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    Related articles in PubMed

    1. Conformation of polypyrimidine tract binding protein in solution. Petoukhov MV, et al. Structure, 2006 Jun. PMID 16765895
    2. Polypyrimidine tract-binding protein interacts with coxsackievirus B3 RNA and influences its translation. Verma B, et al. J Gen Virol, 2010 May. PMID 20071487
    3. Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Xue Y, et al. Mol Cell, 2009 Dec 25. PMID 20064465, Free PMC Article
    4. Hepatitis A virus (HAV) proteinase 3C inhibits HAV IRES-dependent translation and cleaves the polypyrimidine tract-binding protein. Kanda T, et al. J Viral Hepat, 2010 Sep. PMID 19889140
    5. The domains of polypyrimidine tract binding protein have distinct RNA structural preferences. Clerte C, et al. Biochemistry, 2009 Mar 17. PMID 19226116, Free PMC Article

    See all (467) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. M6A-modified lncRNA FAM83H-AS1 promotes colorectal cancer progression through PTBP1.
      Title: M6A-modified lncRNA FAM83H-AS1 promotes colorectal cancer progression through PTBP1.
    2. PTBP1-mediated repression of neuron-specific CDC42 splicing constitutes a genomic alteration-independent, developmentally conserved vulnerability in IDH-wildtype glioblastoma.
      Title: PTBP1-mediated repression of neuron-specific CDC42 splicing constitutes a genomic alteration-independent, developmentally conserved vulnerability in IDH-wildtype glioblastoma.
    3. Upregulated LncRNA-LINC00659 expression by H. pylori infection promoted the progression of gastritis to cancer by regulating PTBP1 expression.
      Title: Upregulated LncRNA-LINC00659 expression by H. pylori infection promoted the progression of gastritis to cancer by regulating PTBP1 expression.
    4. Splicing Factor PTBP1 Silencing Induces Apoptosis of Human Cervical Cancer Cells via PI3K/AKT Pathway and Autophagy.
      Title: Splicing Factor PTBP1 Silencing Induces Apoptosis of Human Cervical Cancer Cells via PI3K/AKT Pathway and Autophagy.
    5. Hsa_circ_0007590/PTBP1 complex reprograms glucose metabolism by reducing the stability of m[6]A-modified PTEN mRNA in pancreatic ductal adenocarcinoma.
      Title: Hsa_circ_0007590/PTBP1 complex reprograms glucose metabolism by reducing the stability of m(6)A-modified PTEN mRNA in pancreatic ductal adenocarcinoma.
    6. CircTOP1 targeted regulation of PTBP1 expression promotes the progression of coronary artery calcification.
      Title: CircTOP1 targeted regulation of PTBP1 expression promotes the progression of coronary artery calcification.
    7. LncRNA HCP5 Facilitates the Progression of Ovarian Cancer by Interacting with the PTBP1 Protein.
      Title: LncRNA HCP5 Facilitates the Progression of Ovarian Cancer by Interacting with the PTBP1 Protein.
    8. A novel link between melatonin and circ_0005753/PTBP1/TXNIP regulatory network in the modulation of osteogenic potential in mesenchymal stem cells.
      Title: A novel link between melatonin and circ_0005753/PTBP1/TXNIP regulatory network in the modulation of osteogenic potential in mesenchymal stem cells.
    9. Inhibition of IGF2BP1 attenuates the progression of endometriosis through PTBP1.
      Title: Inhibition of IGF2BP1 attenuates the progression of endometriosis through PTBP1.
    10. The leader RNA of SARS-CoV-2 sequesters polypyrimidine tract binding protein (PTBP1) and influences pre-mRNA splicing in infected cells.
      Title: The leader RNA of SARS-CoV-2 sequesters polypyrimidine tract binding protein (PTBP1) and influences pre-mRNA splicing in infected cells.
    Submit: New GeneRIF Correction See all GeneRIFs (165)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev hnRNP I binds to cis-acting repressive (CRS) sequences in HIV-1 RNA suggesting a role for this binding in influencing Rev function PubMed
    Tat tat Polypyrimidine tract binding protein 1 (PTBP1) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS PubMed
    tat Polypyrimidine tract-binding protein (PTB) stimulates the binding of RNA Polymerase II and TRP-185 to HIV-1 TAR RNA, suggesting an interaction between PTB and HIV-1 Tat PubMed
    retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human polypyrimidine tract binding protein 1 (PTBP1) at amino acid residues 164-165 by the HIV-1 protease PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • MGC8461, MGC10830

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables poly-pyrimidine tract binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables pre-mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in IRES-dependent viral translational initiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in IRES-dependent viral translational initiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of RNA splicing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of muscle cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of calcineurin-NFAT signaling cascade IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of RNA splicing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in membrane HDA PubMed 
    located_in nucleolus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    polypyrimidine tract-binding protein 1
    Names
    57 kDa RNA-binding protein PPTB-1
    RNA-binding protein
    heterogeneous nuclear ribonucleoprotein I
    heterogeneous nuclear ribonucleoprotein polypeptide I
    hnRNP I
    polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)

    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.

    mRNA and Protein(s)

    1. NM_001411140.1 → NP_001398069.1  polypyrimidine tract-binding protein 1 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC006273
      Consensus CDS
      CCDS92475.1
      UniProtKB/TrEMBL
      A0A0U1RRM4, A0A7I2V621
      Related
      ENSP00000504829.1, ENST00000679114.1

    2. NM_002819.5 → NP_002810.1  polypyrimidine tract-binding protein 1 isoform a

      See identical proteins and their annotated locations for NP_002810.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC006273, BC002397, BQ068293
      Consensus CDS
      CCDS42456.1
      UniProtKB/Swiss-Prot
      P26599, Q9BUQ0
      UniProtKB/TrEMBL
      A0A0U1RRM4
      Related
      ENSP00000349428.4, ENST00000356948.11
      Conserved Domains (1) summary
      TIGR01649
      Location:57 → 557
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    3. NM_031990.4 → NP_114367.1  polypyrimidine tract-binding protein 1 isoform b

      See identical proteins and their annotated locations for NP_114367.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternative splice site resulting in it lacking 21 nt in the coding region compared to variant 1. Thus isoform b is 7 aa shorter than isoform a, but it maintains the same reading frame.
      Source sequence(s)
      AC006273, BC002397, BQ068293, X65371
      Consensus CDS
      CCDS45892.1
      UniProtKB/TrEMBL
      A0A0U1RRM4
      Related
      ENSP00000408096.1, ENST00000394601.8
      Conserved Domains (1) summary
      TIGR01649
      Location:57 → 550
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    4. NM_031991.4 → NP_114368.1  polypyrimidine tract-binding protein 1 isoform c

      See identical proteins and their annotated locations for NP_114368.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks 78 nt in the coding region compared to variant 1. Thus isoform c is 26 aa shorter than isoform a but it maintains the same reading frame.
      Source sequence(s)
      AC006273, BC002397, BQ068293, X60648
      Consensus CDS
      CCDS32859.1
      UniProtKB/TrEMBL
      A0A0U1RRM4
      Related
      ENSP00000014112.5, ENST00000349038.8
      Conserved Domains (1) summary
      TIGR01649
      Location:57 → 531
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      797452..812312
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005259598.3 → XP_005259655.1  polypyrimidine tract-binding protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005259655.1

      UniProtKB/TrEMBL
      A0A0U1RRM4
      Conserved Domains (5) summary
      cd12693
      Location:183 → 278
      RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
      cd12695
      Location:340 → 432
      RRM3_PTBP1; RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 1 (PTB)
      cd12777
      Location:61 → 141
      RRM1_PTBP1; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein 1 (PTB)
      TIGR01649
      Location:59 → 533
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
      cl17169
      Location:453 → 533
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. XM_047439114.1 → XP_047295070.1  polypyrimidine tract-binding protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PEX4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      751931..766786
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321515.1 → XP_054177490.1  polypyrimidine tract-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0U1RRM4

    2. XM_054321516.1 → XP_054177491.1  polypyrimidine tract-binding protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PEX4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_175847.2: Suppressed sequence

      Description
      NM_175847.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P26599.2 GenPept UniProtKB/Swiss-Prot:P26599

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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