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    PTBP2 polypyrimidine tract binding protein 2 [ Homo sapiens (human) ]

    Gene ID: 58155, updated on 13-May-2024

    Summary

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    Official Symbol
    PTBP2provided by HGNC
    Official Full Name
    polypyrimidine tract binding protein 2provided by HGNC
    Primary source
    HGNC:HGNC:17662
    See related
    Ensembl:ENSG00000117569 MIM:608449; AllianceGenome:HGNC:17662
    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
    nPTB; PTBLP; brPTB
    Summary
    The protein encoded by this gene binds to intronic polypyrimidine clusters in pre-mRNA molecules and is implicated in controlling the assembly of other splicing-regulatory proteins. This protein is very similar to the polypyrimidine tract binding protein (PTB) but most of its isoforms are expressed primarily in the brain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
    Expression
    Broad expression in testis (RPKM 15.6), brain (RPKM 9.8) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PTBP2 in Genome Data Viewer
    Location:
    1p21.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (96721784..96823739)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (96569913..96671844)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (97187340..97289295)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 13515 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:97180360-97181288 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:97181289-97182216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1108 Neighboring gene RN7SK pseudogene 270 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:97227285-97227992 Neighboring gene ribosomal protein L7 pseudogene 9 Neighboring gene NANOG hESC enhancer GRCh37_chr1:97580130-97580999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1355 Neighboring gene VISTA enhancer hs671 Neighboring gene DPYD antisense RNA 1 Neighboring gene dihydropyrimidine dehydrogenase Neighboring gene uncharacterized LOC105378867

    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. Mapping PTBP2 binding in human brain identifies SYNGAP1 as a target for therapeutic splice switching. Dawicki-McKenna JM, et al. Nat Commun, 2023 May 6. PMID 37149717, Free PMC Article
    2. PTBP2 exon 10 inclusion is associated with the progression of CML and it is BCR-ABL1 dependent. Nandagopalan SR, et al. Int J Biochem Cell Biol, 2019 Apr. PMID 30726713
    3. Solution and crystal structures of a C-terminal fragment of the neuronal isoform of the polypyrimidine tract binding protein (nPTB). Joshi A, et al. PeerJ, 2014. PMID 24688880, Free PMC Article
    4. New insights into functional roles of the polypyrimidine tract-binding protein. Romanelli MG, et al. Int J Mol Sci, 2013 Nov 20. PMID 24264039, Free PMC Article
    5. Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2. Keppetipola N, et al. Crit Rev Biochem Mol Biol, 2012 Jul-Aug. PMID 22655688, Free PMC Article

    See all (70) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. KIS counteracts PTBP2 and regulates alternative exon usage in neurons.
      Title: KIS counteracts PTBP2 and regulates alternative exon usage in neurons.
    2. Mapping PTBP2 binding in human brain identifies SYNGAP1 as a target for therapeutic splice switching.
      Title: Mapping PTBP2 binding in human brain identifies SYNGAP1 as a target for therapeutic splice switching.
    3. Associations between Gene-Gene Interaction and Overweight/Obesity of 12-Month-Old Chinese Infants.
      Title: Associations between Gene-Gene Interaction and Overweight/Obesity of 12-Month-Old Chinese Infants.
    4. LncRNA nuclear-enriched abundant transcript 1 shuttled by prostate cancer cells-secreted exosomes initiates osteoblastic phenotypes in the bone metastatic microenvironment via miR-205-5p/runt-related transcription factor 2/splicing factor proline- and glutamine-rich/polypyrimidine tract-binding protein 2 axis.
      Title: LncRNA nuclear-enriched abundant transcript 1 shuttled by prostate cancer cells-secreted exosomes initiates osteoblastic phenotypes in the bone metastatic microenvironment via miR-205-5p/runt-related transcription factor 2/splicing factor proline- and glutamine-rich/polypyrimidine tract-binding protein 2 axis.
    5. SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity.
      Title: SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity.
    6. PTBP2 exon 10 inclusion is associated with the progression of CML and it is BCR-ABL1 dependent
      Title: PTBP2 exon 10 inclusion is associated with the progression of CML and it is BCR-ABL1 dependent.
    7. It has been established that PTBP1 and PTBP2 are members of a family of cryptic exon repressors.
      Title: PTBP1 and PTBP2 Repress Nonconserved Cryptic Exons.
    8. PTBP1 and PTBP2 impaired autoregulation of SRSF3 in oral squamous cell carcinoma cancer cells.
      Title: PTBP1 and PTBP2 impaired autoregulation of SRSF3 in cancer cells.
    9. Data show that polypyrimidine tract-binding proteins nPTB and ROD1 interact with mitochondrial tRNA(Thr) in the cytoplasm outside of mitochondria.
      Title: Human polypyrimidine tract-binding protein interacts with mitochondrial tRNA(Thr) in the cytosol.
    10. In T98G glioma cells, the level of sumoylated PTBP2 was reduced compared to that of normal brain cells. Overall, this study shows that PTBP2 is posttranslationally modified by SUMO1.
      Title: Characterization of a novel posttranslational modification in polypyrimidine tract-binding proteins by SUMO1.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    EBI GWAS Catalog
    Common polygenic variation contributes to risk of schizophrenia and bipolar disorder.
    EBI GWAS Catalog
    Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.
    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

    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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    Markers

    Homology

    Clone Names

    • FLJ34897

    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
    		  
    Process Evidence Code Pubs
    involved_in mRNA splice site recognition IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of RNA splicing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of RNA splicing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of neural precursor cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    polypyrimidine tract-binding protein 2
    Names
    PTB-like protein
    neural polypyrimidine tract binding protein
    neurally-enriched homolog of PTB

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001300985.2 → NP_001287914.1  polypyrimidine tract-binding protein 2 isoform 1

      See identical proteins and their annotated locations for NP_001287914.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as nPTB3 and PTBLP-L') encodes isoform 1.
      Source sequence(s)
      AF530580, AI052528, AI968454, AL357150, AL357952, BC016582
      Consensus CDS
      CCDS72828.1
      UniProtKB/TrEMBL
      B4DSU5
      Related
      ENSP00000359216.1, ENST00000370197.5
      Conserved Domains (1) summary
      TIGR01649
      Location:57 → 537
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    2. NM_001300986.2 → NP_001287915.1  polypyrimidine tract-binding protein 2 isoform 2

      See identical proteins and their annotated locations for NP_001287915.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses alternate in-frame splice sites in the 5' and 3' coding regions, compared to variant 1. The encoded isoform (2) is longer than isoform 1.
      Source sequence(s)
      AI052528, AI968454, AK299922, AL357150, AL357952, BC016582
      Consensus CDS
      CCDS91005.1
      UniProtKB/TrEMBL
      A0A7I2RVZ4, B4DSU5
      Related
      ENSP00000412788.3, ENST00000426398.3
      Conserved Domains (1) summary
      TIGR01649
      Location:65 → 540
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    3. NM_001300987.2 → NP_001287916.1  polypyrimidine tract-binding protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001287916.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon in the 5' region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is longer than isoform 1.
      Source sequence(s)
      AI052528, AI968454, AK299897, AL357150, AL357952, BC016582
      UniProtKB/TrEMBL
      B4DSS8, B4DSU5
      Conserved Domains (5) summary
      cd12693
      Location:189 → 284
      RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
      cd12696
      Location:341 → 447
      RRM3_PTBP2; RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      cd12702
      Location:468 → 548
      RRM4_PTBP2; RNA recognition motif 4 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      cd12778
      Location:69 → 150
      RRM1_PTBP2; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      TIGR01649
      Location:68 → 548
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    4. NM_001300988.2 → NP_001287917.1  polypyrimidine tract-binding protein 2 isoform 4

      See identical proteins and their annotated locations for NP_001287917.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4, also known as nPTB4) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AF530581, AI052528, AI968454, AL357150, BC016582
      Consensus CDS
      CCDS72829.1
      UniProtKB/TrEMBL
      B4DSU5
      Related
      ENSP00000359217.1, ENST00000370198.5
      Conserved Domains (1) summary
      TIGR01649
      Location:57 → 536
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    5. NM_001300989.2 → NP_001287918.1  polypyrimidine tract-binding protein 2 isoform 5

      See identical proteins and their annotated locations for NP_001287918.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5, also known as nPTB2 or PTBLP-L) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
      Source sequence(s)
      AI052528, AI968454, AL357150, AL357952, BC016582
      Consensus CDS
      CCDS72830.1
      UniProtKB/TrEMBL
      B4DSU5
      Related
      ENSP00000477024.1, ENST00000609116.5
      Conserved Domains (1) summary
      TIGR01649
      Location:57 → 532
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    6. NM_001300990.2 → NP_001287919.1  polypyrimidine tract-binding protein 2 isoform 7

      See identical proteins and their annotated locations for NP_001287919.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an alternate exon in the 5' region, initiates translation at a downstream in-frame start codon, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (7) is shorter than isoform 1.
      Source sequence(s)
      AF176085, AI052528, AI968454, AK092216, AL357150, AL357952, BC016582
      UniProtKB/TrEMBL
      A0A6Q8PFC0
      Conserved Domains (1) summary
      TIGR01649
      Location:5 → 480
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    7. NM_001410833.1 → NP_001397762.1  polypyrimidine tract-binding protein 2 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AL357150
      Consensus CDS
      CCDS91006.1
      UniProtKB/TrEMBL
      A0A6Q8PFE6
      Related
      ENSP00000501779.1, ENST00000675735.1

    8. NM_021190.4 → NP_067013.1  polypyrimidine tract-binding protein 2 isoform 6

      See identical proteins and their annotated locations for NP_067013.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6, also known as nPTB1) uses two alternate in-frame splice sites in the 3' coding region, compared to variant 1. The encoded isoform (6) is shorter than isoform 1.
      Source sequence(s)
      AF176085, AI052528, AI968454, BC016582, DB473562
      Consensus CDS
      CCDS754.1
      UniProtKB/Swiss-Prot
      Q8N0Z1, Q8N160, Q8NFB0, Q8NFB1, Q969N9, Q96Q76, Q9UKA9
      UniProtKB/TrEMBL
      B4DSU5
      Related
      ENSP00000502818.1, ENST00000674951.1
      Conserved Domains (1) summary
      TIGR01649
      Location:57 → 531
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    RNA

    1. NR_125356.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AI052528, AI968454, AK295384, BC016582, BP250235
      Related
      ENST00000675401.1

    2. NR_125357.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) uses an alternate internal splice site and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD). This variant is similar to nPTB5 and PTBLP-S.
      Source sequence(s)
      AB051233, AI052528, AI968454, AL357150, AL357952, BC016582

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      96721784..96823739
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541876.3 → XP_011540178.1  polypyrimidine tract-binding protein 2 isoform X1

      See identical proteins and their annotated locations for XP_011540178.1

      UniProtKB/TrEMBL
      B4DSU5
      Conserved Domains (1) summary
      TIGR01649
      Location:65 → 545
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    2. XM_011541874.3 → XP_011540176.1  polypyrimidine tract-binding protein 2 isoform X2

      See identical proteins and their annotated locations for XP_011540176.1

      UniProtKB/TrEMBL
      B4DSU5
      Conserved Domains (1) summary
      TIGR01649
      Location:65 → 544
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    3. XM_047426538.1 → XP_047282494.1  polypyrimidine tract-binding protein 2 isoform X4

      Related
      ENSP00000502522.1, ENST00000674579.1

    4. XM_047426539.1 → XP_047282495.1  polypyrimidine tract-binding protein 2 isoform X5

      Related
      ENSP00000501834.1, ENST00000476419.5

    5. XM_047426537.1 → XP_047282493.1  polypyrimidine tract-binding protein 2 isoform X3

    6. XM_017001951.2 → XP_016857440.1  polypyrimidine tract-binding protein 2 isoform X6

      UniProtKB/TrEMBL
      B4DSS8, B4DSU5
      Conserved Domains (5) summary
      cd12693
      Location:189 → 284
      RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
      cd12696
      Location:341 → 447
      RRM3_PTBP2; RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      cd12702
      Location:468 → 548
      RRM4_PTBP2; RNA recognition motif 4 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      cd12778
      Location:69 → 150
      RRM1_PTBP2; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      TIGR01649
      Location:68 → 548
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      96569913..96671844
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337982.1 → XP_054193957.1  polypyrimidine tract-binding protein 2 isoform X1

    2. XM_054337983.1 → XP_054193958.1  polypyrimidine tract-binding protein 2 isoform X2

    3. XM_054337985.1 → XP_054193960.1  polypyrimidine tract-binding protein 2 isoform X4

    4. XM_054337986.1 → XP_054193961.1  polypyrimidine tract-binding protein 2 isoform X5

    5. XM_054337984.1 → XP_054193959.1  polypyrimidine tract-binding protein 2 isoform X3

    6. XM_054337987.1 → XP_054193962.1  polypyrimidine tract-binding protein 2 isoform X6

      UniProtKB/TrEMBL
      B4DSS8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UKA9.1 GenPept UniProtKB/Swiss-Prot:Q9UKA9

    Gene LinkOut

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