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

Gene ID: 5725, updated on 6-Jan-2019

Summary

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
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

Genomic context

See PTBP1 in Genome Data Viewer
Location:
19p13.3
Exon count:
16
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (797392..812327)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (797392..812327)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928450 Neighboring gene long intergenic non-protein coding RNA 1836 Neighboring gene microRNA 4745 Neighboring gene phospholipid phosphatase related 3 Neighboring gene microRNA 3187 Neighboring gene azurocidin 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 BioSystems

  • FGFR2 alternative splicing, organism-specific biosystem (from REACTOME)
    FGFR2 alternative splicing, organism-specific biosystemAlternative splicing of the FGFR2 nascent mRNA generates an epithelial specific isoform (FGFR2 IIIb) and a mesenchymal specific isoform (FGFR2 IIIc). The inclusion of exon 8 in FGFR2 IIIb or exon 9 ...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by FGFR, organism-specific biosystem (from REACTOME)
    Signaling by FGFR, organism-specific biosystemThe 22 members of the fibroblast growth factor (FGF) family of growth factors mediate their cellular responses by binding to and activating the different isoforms encoded by the four receptor tyrosin...
  • Signaling by FGFR2, organism-specific biosystem (from REACTOME)
    Signaling by FGFR2, organism-specific biosystemThe 22 members of the fibroblast growth factor (FGF) family of growth factors mediate their cellular responses by binding to and activating the different isoforms encoded by the four receptor tyrosin...
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mir-124 predicted interactions with cell cycle and differentiation, organism-specific biosystem (from WikiPathways)
    mir-124 predicted interactions with cell cycle and differentiation, organism-specific biosystemSchematic of predicted interactions of miR-124 with cell cycle and cell differentiation machinery. A genomewide miRNA mimic toxicity screen indicates common and selective vulnerabilities of epitheli...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Clone Names

  • MGC8461, MGC10830

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
poly-pyrimidine tract binding TAS
Traceable Author Statement
more info
PubMed 
pre-mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
membrane HDA PubMed 
nucleolus TAS
Traceable Author Statement
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

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)

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_002819.5NP_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
    Related
    ENSP00000349428.4, ENST00000356948.10
    Conserved Domains (1) summary
    TIGR01649
    Location:57557
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  2. NM_031990.3NP_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, X66975
    Consensus CDS
    CCDS45892.1
    UniProtKB/Swiss-Prot
    P26599
    Related
    ENSP00000408096.1, ENST00000394601.8
    Conserved Domains (1) summary
    TIGR01649
    Location:57550
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  3. NM_031991.3NP_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, X66975
    Consensus CDS
    CCDS32859.1
    UniProtKB/Swiss-Prot
    P26599
    Related
    ENSP00000014112.5, ENST00000349038.8
    Conserved Domains (1) summary
    TIGR01649
    Location:57531
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    797392..812327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005259597.2XP_005259654.1  polypyrimidine tract-binding protein 1 isoform X1

    See identical proteins and their annotated locations for XP_005259654.1

    Conserved Domains (5) summary
    cd12693
    Location:183278
    RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
    cd12695
    Location:366458
    RRM3_PTBP1; RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 1 (PTB)
    cd12777
    Location:61141
    RRM1_PTBP1; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein 1 (PTB)
    TIGR01649
    Location:59559
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    cl17169
    Location:479559
    RRM_SF; RNA recognition motif (RRM) superfamily
  2. XM_005259598.2XP_005259655.1  polypyrimidine tract-binding protein 1 isoform X2

    See identical proteins and their annotated locations for XP_005259655.1

    Conserved Domains (5) summary
    cd12693
    Location:183278
    RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
    cd12695
    Location:340432
    RRM3_PTBP1; RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 1 (PTB)
    cd12777
    Location:61141
    RRM1_PTBP1; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein 1 (PTB)
    TIGR01649
    Location:59533
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    cl17169
    Location:453533
    RRM_SF; RNA recognition motif (RRM) superfamily

RNA

  1. XR_244034.2 RNA Sequence

  2. XR_244035.2 RNA Sequence

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.
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