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PTBP1 Gene

protein-coding   GIFtS: 61
GCID: GC19P000797

Polypyrimidine Tract Binding Protein 1

(Previous name: polypyrimidine tract binding protein (heterogeneous nuclear...)
(Previous symbol: PTB)
  See PTBP1-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Polypyrimidine Tract Binding Protein 11 2     PTB-12
PTB1 2 3 5     PTB-T2
Heterogeneous Nuclear Ribonucleoprotein I1 2 3     PTB22
Polypyrimidine Tract Binding Protein (Heterogeneous Nuclear
Ribonucleoprotein I)1 2
     PTB32
57 KDa RNA-Binding Protein PPTB-12 3     PTB42
HnRNP I2 3     Heterogeneous Nuclear Ribonucleoprotein Polypeptide I2
HNRNPI2 5     pPTB2
HNRNP-I2     Polypyrimidine Tract-Binding Protein 12
HNRPI2     RNA-Binding Protein2

External Ids:    HGNC: 95831   Entrez Gene: 57252   Ensembl: ENSG000000113047   OMIM: 6006935   UniProtKB: P265993   

Export aliases for PTBP1 gene to outside databases

Previous GC identifers: GC19P000856 GC19P000737 GC19P000748 GC19P000567


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PTBP1 Gene:
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)

GeneCards Summary for PTBP1 Gene:
PTBP1 (polypyrimidine tract binding protein 1) is a protein-coding gene. Diseases associated with PTBP1 include human t-cell leukemia virus type 2. GO annotations related to this gene include pre-mRNA binding and RNA binding. An important paralog of this gene is ENSG00000268083.

UniProtKB/Swiss-Prot: PTBP1_HUMAN, P26599
Function: Plays a role in pre-mRNA splicing and in the regulation of alternative splicing events. Activates exon
skipping of its own pre-mRNA during muscle cell differentiation. Binds to the polypyrimidine tract of introns.
May promote RNA looping when bound to two separate polypyrimidine tracts in the same pre-mRNA. May promote the
binding of U2 snRNP to pre-mRNA. Cooperates with RAVER1 to modulate switching between mutually exclusive exons
during maturation of the TPM1 pre-mRNA. Represses the splicing of MAPT/Tau exon 10

Gene Wiki entry for PTBP1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NT_011295.12  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PTBP1 gene promoter:
         AP-2alpha isoform 3   AP-2alpha isoform 2   AP-2alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPTBP1 promoter sequence
   Search Chromatin IP Primers for PTBP1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PTBP1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19p13.3   Ensembl cytogenetic band:  19p13.3   HGNC cytogenetic band: 19p13.3

PTBP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PTBP1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P000797:  view genomic region     (about GC identifiers)

Start:
797,075 bp from pter      End:
812,327 bp from pter
Size:
15,253 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PTBP1_HUMAN, P26599 (See protein sequence)
Recommended Name: Polypyrimidine tract-binding protein 1  
Size: 531 amino acids; 57221 Da
Subunit: Monomer. Part of a ternary complex containing KHSRP, PTBP1, PTBP2 and HNRPH1. Interacts with RAVER1 and
SFPQ
Selected PDB 3D structures from and Proteopedia for PTBP1 (see all 9):
1QM9 (3D)        1SJQ (3D)        1SJR (3D)        2AD9 (3D)        2ADB (3D)        2ADC (3D)    
Secondary accessions: Q9BUQ0
Alternative splicing: 3 isoforms:  P26599-1   P26599-2   P26599-3   

Explore the universe of human proteins at neXtProt for PTBP1: NX_P26599

Explore proteomics data for PTBP1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys134, Lys218, Lys259, Lys266, Lys410, Lys428, Lys482, Lys485, Lys528
  • Modification sites at PhosphoSitePlus

  • See PTBP1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_002810.1  NP_114367.1  NP_114368.1  

    ENSEMBL proteins: 
     ENSP00000349428   ENSP00000014112   ENSP00000468565   ENSP00000466250   ENSP00000408096  
     ENSP00000465652   ENSP00000465825   ENSP00000465451   ENSP00000342332  
    Reactome Protein details: P26599

    PTBP1 Human Recombinant Protein Products:

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    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for PTBP1

     
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    antibodies-online proteins for PTBP1 (9 products) 

     
    antibodies-online peptides for PTBP1

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    RBM: RNA binding motif (RRM) containing

    3 InterPro protein domains:
     IPR006536 HnRNP-L_PTB
     IPR012677 Nucleotide-bd_a/b_plait
     IPR000504 RRM_dom

    Graphical View of Domain Structure for InterPro Entry P26599

    ProtoNet protein and cluster: P26599

    1 Blocks protein domain: IPB000504 RNA-binding region RNP-1 (RNA recognition motif)

    UniProtKB/Swiss-Prot: PTBP1_HUMAN, P26599
    Similarity: Contains 4 RRM (RNA recognition motif) domains


    Find genes that share domains with PTBP1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PTBP1_HUMAN, P26599
    Function: Plays a role in pre-mRNA splicing and in the regulation of alternative splicing events. Activates exon
    skipping of its own pre-mRNA during muscle cell differentiation. Binds to the polypyrimidine tract of introns.
    May promote RNA looping when bound to two separate polypyrimidine tracts in the same pre-mRNA. May promote the
    binding of U2 snRNP to pre-mRNA. Cooperates with RAVER1 to modulate switching between mutually exclusive exons
    during maturation of the TPM1 pre-mRNA. Represses the splicing of MAPT/Tau exon 10

         Gene Ontology (GO): Selected molecular function terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding TAS1906036
    GO:0005515protein binding IPI10653975
    GO:0008187poly-pyrimidine tract binding TAS1906036
         
    Find genes that share ontologies with PTBP1           About GenesLikeMe


    Phenotypes:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Ptbp1):
     no phenotypic analysis 

    Find genes that share phenotypes with PTBP1           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for PTBP1

    miRNA
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    miRTarBase miRNAs that target PTBP1:
    hsa-mir-15b-5p (MIRT046541), hsa-mir-615-3p (MIRT039680), hsa-mir-17-3p (MIRT050776), hsa-mir-92a-3p (MIRT049413), hsa-mir-1 (MIRT001345), hsa-mir-92b-3p (MIRT040624), hsa-mir-378a-3p (MIRT043938), hsa-mir-124-3p (MIRT002647), hsa-mir-17-5p (MIRT050898), hsa-mir-30a-5p (MIRT049932)

    Block miRNA regulation of human, mouse, rat PTBP1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PTBP1 (see all 63):
    hsa-miR-193a-3p hsa-miR-429 hsa-miR-330-5p hsa-miR-106a hsa-miR-374a hsa-miR-138-2* hsa-miR-507 hsa-miR-548l
    SwitchGear 3'UTR luciferase reporter plasmidPTBP1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat PTBP1

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    Sino Biological Human cDNA Clone for PTBP1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PTBP1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PTBP1
    Addgene plasmids for PTBP1 

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PTBP1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PTBP1_HUMAN, P26599: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    peroxisome2
    extracellular1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005654nucleoplasm TAS--
    GO:0005730nucleolus TAS1641332
    GO:0070062extracellular vesicular exosome IDA--

    Find genes that share ontologies with PTBP1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for PTBP1 About    
    See pathways by source

    SuperPathContained pathways About
    1mRNA Splicing - Major Pathway
    mRNA Splicing - Major Pathway0.78
    mRNA Splicing0.78
    Processing of Capped Intron-Containing Pre-mRNA0.78
    mRNA processing0.44
    2Gene Expression
    Gene Expression0.40
    3Translational Control
    Translational Control


    Find genes that share SuperPaths with PTBP1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for PTBP1
        Translational Control

    1 BioSystems Pathway for PTBP1
        mRNA processing


    2 Reactome Pathways for PTBP1
        mRNA Splicing - Major Pathway
    Processing of Capped Intron-Containing Pre-mRNA


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PTBP1
    Interactions:

        GeneGlobe Interaction Network for PTBP1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for PTBP1 (P265991, 2, 3 ENSP000003494284) via UniProtKB, MINT, STRING, and/or I2D (see all 946)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PCBP1Q153651, 2, 3, ENSP000003055564EBI-350540,EBI-946095 MINT-2855482 MINT-2862164 MINT-7947479 I2D: score=3 STRING: ENSP00000305556
    FUSP356372, 3, ENSP000002541084MINT-7945693 MINT-7947479 I2D: score=2 STRING: ENSP00000254108
    PCBP2Q153662, 3, ENSP000003524384MINT-7945693 MINT-7947479 I2D: score=2 STRING: ENSP00000352438
    NSFP464592, 3MINT-7945693 MINT-7947479 I2D: score=1 
    RANBP2P497922, 3MINT-7945693 MINT-7947479 I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000380alternative mRNA splicing, via spliceosome IEA--
    GO:0000381regulation of alternative mRNA splicing, via spliceosome IDA16260624
    GO:0000398mRNA splicing, via spliceosome TAS--
    GO:0006397mRNA processing TAS1906036
    GO:0008380RNA splicing TAS--

    Find genes that share ontologies with PTBP1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PTBP1

    5 Novoseek inferred chemical compound relationships for PTBP1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    pyrimidine 62.2 26 17239394 (5), 9858533 (4), 8289396 (1), 11172810 (1) (see all 13)
    poly c 51 1 12527772 (1)
    oligonucleotide 15.9 2 16179478 (1), 14559795 (1)
    adenylate 10.8 1 9858533 (1)
    atp 0 1 9111366 (1)



    Find genes that share compounds with PTBP1           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PTBP1 gene (4 alternative transcripts): 
    NM_002819.4  NM_031990.3  NM_031991.3  NM_175847.2  

    Unigene Cluster for PTBP1:

    Polypyrimidine tract binding protein 1
    Hs.172550  [show with all ESTs]
    Unigene Representative Sequence: NM_002819
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 20):
    ENST00000356948(uc002lpp.2) ENST00000590887 ENST00000349038(uc002lpr.2)
    ENST00000586481 ENST00000586944 ENST00000585535 ENST00000394601(uc002lpq.2)
    ENST00000589575 ENST00000587191 ENST00000587094 ENST00000592113 ENST00000585956
    ENST00000587136 ENST00000592804 ENST00000589569 ENST00000589883 ENST00000589770
    ENST00000585932
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    hsa-miR-193a-3p hsa-miR-429 hsa-miR-330-5p hsa-miR-106a hsa-miR-374a hsa-miR-138-2* hsa-miR-507 hsa-miR-548l
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      QuantiFast Probe-based Assays in human, mouse, rat PTBP1

    Additional mRNA sequence: 

    BC002397.2 BC004383.1 BC013694.1 BC023219.1 BT006819.1 X60648.1 X62006.1 X65371.1 
    X65372.1 X66975.1 

    Selected DOTS entries (see all 59):

    DT.40213005  DT.408204  DT.100640038  DT.100687731  DT.91763165  DT.95264147  DT.91763170  DT.95084898 
    DT.100687740  DT.91763147  DT.99944030  DT.100863401  DT.100687725  DT.100059676  DT.100638120  DT.100687743 
    DT.100687728  DT.100687741  DT.95143790  DT.100687735  DT.100687737  DT.100770633  DT.75143311  DT.100687736 

    Selected AceView cDNA sequences (see all 1132):

    AI818502 AI304669 AW769447 AI199720 BF591038 CR625996 BC002397 CR594950 
    AA344214 BX349756 BM980575 BI909436 BU145177 BQ223693 CA950262 BC013694 
    BI826673 CR610714 BE883584 BE392478 CA773212 BE796993 BQ574619 BM789785 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PTBP1 (see all 21)    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c · 4d ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b · 8c · 8d ^ 9a · 9b · 9c · 9d ^ 10a · 10b ^ 11a · 11b ·
    SP1:                                                                                                                                -                           
    SP2:                                                                                                                                -                           
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                -                           
    SP5:                                                              -     -     -     -                                               -                           

    ExUns: 11c ^ 12a · 12b ^ 13 ^ 14a · 14b · 14c ^ 15a · 15b · 15c ^ 16
    SP1:                                                                  
    SP2:  -     -                                                         
    SP3:                                                                  
    SP4:  -     -                                                         
    SP5:                                                                  


    ECgene alternative splicing isoforms for PTBP1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PTBP1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CAGCTGGGGC
    PTBP1 Expression
    About this image


    PTBP1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 21) fully expand
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
    PTBP1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PTBP1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.172550
        Custom PCR Arrays for PTBP1
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for PTBP1 gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ptbp11 , 5 polypyrimidine tract binding protein 11, 5 86.43(n)1
    96.04(a)1
      10 (39.72 cM)5
    192051  NM_001077363.21  NP_001070831.11 
     798544275 
    chicken
    (Gallus gallus)
    Aves PTBP11 polypyrimidine tract binding protein 1 80.54(n)
    93.92(a)
      420098  NM_001030935.1  NP_001026106.1 
    lizard
    (Anolis carolinensis)
    Reptilia PTBP16
    polypyrimidine tract binding protein 1
    64(a)
    1 ↔ 1
    GL344833.1(4884-16591)
    African clawed frog
    (Xenopus laevis)
    Amphibia BC045068.12   -- 77.7(n)    BC045068.1 
    zebrafish
    (Danio rerio)
    Actinopterygii 570450162   -- 75.18(n)    57045016 
    fruit fly
    (Drosophila melanogaster)
    Insecta heph1 , 3 mRNA splicing RNA binding3
    hephaestus1
    52(a)3
    59.66(n)1
    60.8(a)1
      485711  NM_176599.21  NP_788776.21 
    worm
    (Caenorhabditis elegans)
    Secernentea ptb-11 , 3 polypyrimidine tract binding protein3
    ptb-11
    49(a)3
    55.28(n)1
    52.92(a)1
      1746471  NM_171035.41  NP_741041.11 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons PTB31 PTB3 48.17(n)
    41.08(a)
      840918  NM_001084204.1  NP_001077673.1 
    rice
    (Oryza sativa)
    Liliopsida Os01g08678001 Os01g0867800 49.92(n)
    41.04(a)
      4325048  NM_001051451.1  NP_001044916.1 


    ENSEMBL Gene Tree for PTBP1 (if available)
    TreeFam Gene Tree for PTBP1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PTBP1 gene
    ENSG000002680832  PTBP32  PTBP22  HNRNPL2  HNRNPLL2  
    4 SIMAP similar genes for PTBP1 using alignment to 7 protein entries:     PTBP1_HUMAN (see all proteins):
    PTBP2    PTBP3    MATR3    HNRNPL

    Find genes that share paralogs with PTBP1           About GenesLikeMe


    2 Pseudogenes.org Pseudogenes for PTBP1
    PGOHUM00000248204 PGOHUM00000249595


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PTBP1 (see all 453)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs3519731,2
    C,F,H--795457(+) GCACCG/AGACGC 3 -- us2k110Minor allele frequency- A:0.13NA WA CSA EA 370
    rs1471710731,2
    --795563(+) CTCGCC/GTGGAT 3 -- us2k10--------
    rs1395015761,2
    --795564(+) TCGCCG/TGGATT 3 -- us2k10--------
    rs1496871201,2
    --795604(+) CCTCCA/GTAGGT 3 -- us2k10--------
    rs1443561031,2
    --795652(+) AATCCC/TGCTAA 3 -- us2k10--------
    rs350138781,2
    C,F--795685(-) CGGCCC/TGGAGT 3 -- us2k13Minor allele frequency- T:0.04NA 96
    rs104260841,2
    C,F,H--795716(+) CCGCAG/ACCTCC 3 -- us2k19Minor allele frequency- A:0.03NS EA NA WA 754
    rs81133561,2
    C,A--795816(+) TCACAG/ACTCTG 3 -- us2k13Minor allele frequency- A:0.19WA NA 240
    rs1439042431,2
    C--795895(+) GGCCCA/GGGAGG 3 -- us2k10--------
    rs1167638411,2
    F--795964(+) GCCTCG/AAACTG 3 -- us2k11Minor allele frequency- A:0.14WA 118

    HapMap Linkage Disequilibrium report for PTBP1 (797075 - 812327 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PTBP1 (see all 29):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv470101CNV Loss18288195
    dgv3557n71CNV Loss21882294
    dgv3550n71CNV Loss21882294
    dgv3547n71CNV Loss21882294
    nsv910292CNV Loss21882294
    dgv3556n71CNV Loss21882294
    dgv3548n71CNV Loss21882294
    dgv3555n71CNV Loss21882294
    dgv3552n71CNV Loss21882294
    dgv3554n71CNV Loss21882294

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 600693    OMIM disorders: --

    1 disease for PTBP1:    
    About MalaCards
    human t-cell leukemia virus type 2

    1 disease from the University of Copenhagen DISEASES database for PTBP1:
    Tuberculosis

    Find genes that share disorders with PTBP1           About GenesLikeMe

    10 Novoseek inferred disease relationships for PTBP1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    foot-and-mouth disease 49.4 3 16314455 (1), 10364367 (1), 17445855 (1)
    hepatitis c 42.2 12 10938288 (2), 15669107 (2), 16051805 (1), 7666538 (1) (see all 7)
    leukemia t-cell 28.3 2 11172810 (1), 7474099 (1)
    glioblastoma multiforme 13.4 2 10728679 (2)
    astrocytoma 4.16 2 14769134 (1), 10728679 (1)
    virus infection 1.93 4 16314455 (1), 10364367 (1), 17445855 (1)
    glioblastoma 0.529 1 14769134 (1)
    tumors 0 20 17310993 (6), 14769134 (4), 18499661 (2), 10728679 (2) (see all 6)
    cancer 0 11 18499661 (4), 20010808 (1)
    immunodeficiency 0 2 11172810 (1)

    Genetic Association Database (GAD): PTBP1
    Human Genome Epidemiology (HuGE) Navigator: PTBP1 (1 document)

    Export disorders for PTBP1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PTBP1 gene, integrated from 10 sources (see all 240):
    (articles sorted by number of sources associating them with PTBP1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization and molecular cloning of polypyrimidine tract- binding protein: a component of a complex necessary for pre-mRNA splicing. (PubMed id 1906036)1, 2, 3 Patton J.G.... Nadal-Ginard B. (Genes Dev. 1991)
    2. hnRNP I, the polypyrimidine tract-binding protein: distinct nuclear localization and association with hnRNAs. (PubMed id 1641332)1, 2, 9 Ghetti A.... Dreyfuss G. (Nucleic Acids Res. 1992)
    3. Organization of the human gene encoding heterogeneous nuclear ribonucleoprotein type I (hnRNP I) and characterization of hnRNP I related pseudogene. (PubMed id 11024286)1, 3, 9 Romanelli M.G....Morandi C. (Gene 2000)
    4. Structure and RNA interactions of the N-terminal RRM domains of PTB. (PubMed id 15341728)1, 2, 9 Simpson P.J.... Matthews S. (Structure 2004)
    5. Structure of PTB bound to RNA: specific binding and implications for splicing regulation. (PubMed id 16179478)1, 2, 9 Oberstrass F.C....Allain F.H. (Science 2005)
    6. Structure of the two most C-terminal RNA recognition motifs of PTB using segmental isotope labeling. (PubMed id 16362043)1, 2, 9 Vitali F.... Allain F.H. (EMBO J. 2006)
    7. Structure of tandem RNA recognition motifs from polypyrimidine tract binding protein reveals novel features of the RRM fold. (PubMed id 10856256)1, 2, 9 Conte M.R....Curry S. (EMBO J. 2000)
    8. RBM4 down-regulates PTB and antagonizes its activity in muscle cell- specific alternative splicing. (PubMed id 21518792)1, 2 Lin J.C. and Tarn W.Y. (J. Cell Biol. 2011)
    9. Exon selection in alpha-tropomyosin mRNA is regulated by the antagonistic action of RBM4 and PTB. (PubMed id 16260624)1, 2 Lin J.C. and Tarn W.Y. (Mol. Cell. Biol. 2005)
    10. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (Nature 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 5725 HGNC: 9583 AceView: PTBP1 Ensembl:ENSG00000011304 euGenes: HUgn5725
    ECgene: PTBP1 H-InvDB: PTBP1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for PTBP1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for PTBP1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PTBP1 gene:
    Search GeneIP for patents involving PTBP1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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