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

    Gene ID: 58155, updated on 19-Sep-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PTBP2 in Genome Data Viewer
    Location:
    1p21.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (96721784..96823739)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (96569913..96671844)
    RS_2024_09 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    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

    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)

    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_001300985.2NP_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:57537
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    2. NM_001300986.2NP_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:65540
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    3. NM_001300987.2NP_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:189284
      RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
      cd12696
      Location:341447
      RRM3_PTBP2; RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      cd12702
      Location:468548
      RRM4_PTBP2; RNA recognition motif 4 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      cd12778
      Location:69150
      RRM1_PTBP2; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      TIGR01649
      Location:68548
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    4. NM_001300988.2NP_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:57536
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    5. NM_001300989.2NP_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:57532
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    6. NM_001300990.2NP_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:5480
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    7. NM_001410833.1NP_001397762.1  polypyrimidine tract-binding protein 2 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AL357150
      Consensus CDS
      CCDS91006.1
      UniProtKB/TrEMBL
      A0A6Q8PFE6, B4DSU5
      Related
      ENSP00000501779.1, ENST00000675735.1
    8. NM_021190.4NP_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:57531
      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_2024_08

    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_011541876.3XP_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:65545
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    2. XM_011541874.3XP_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:65544
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    3. XM_047426538.1XP_047282494.1  polypyrimidine tract-binding protein 2 isoform X4

      UniProtKB/TrEMBL
      A0A6Q8PH43
      Related
      ENSP00000502522.1, ENST00000674579.1
    4. XM_047426539.1XP_047282495.1  polypyrimidine tract-binding protein 2 isoform X5

      UniProtKB/TrEMBL
      B4DI28
      Related
      ENSP00000501834.1, ENST00000476419.5
    5. XM_047426537.1XP_047282493.1  polypyrimidine tract-binding protein 2 isoform X3

      UniProtKB/TrEMBL
      A0A6Q8PFC0
    6. XM_017001951.2XP_016857440.1  polypyrimidine tract-binding protein 2 isoform X6

      UniProtKB/TrEMBL
      B4DSS8, B4DSU5
      Conserved Domains (5) summary
      cd12693
      Location:189284
      RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
      cd12696
      Location:341447
      RRM3_PTBP2; RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      cd12702
      Location:468548
      RRM4_PTBP2; RNA recognition motif 4 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      cd12778
      Location:69150
      RRM1_PTBP2; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)
      TIGR01649
      Location:68548
      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_054337982.1XP_054193957.1  polypyrimidine tract-binding protein 2 isoform X1

      UniProtKB/TrEMBL
      B4DSU5
    2. XM_054337983.1XP_054193958.1  polypyrimidine tract-binding protein 2 isoform X2

      UniProtKB/TrEMBL
      B4DSU5
    3. XM_054337985.1XP_054193960.1  polypyrimidine tract-binding protein 2 isoform X4

      UniProtKB/TrEMBL
      A0A6Q8PH43
    4. XM_054337986.1XP_054193961.1  polypyrimidine tract-binding protein 2 isoform X5

      UniProtKB/TrEMBL
      B4DI28
    5. XM_054337984.1XP_054193959.1  polypyrimidine tract-binding protein 2 isoform X3

      UniProtKB/TrEMBL
      A0A6Q8PFC0
    6. XM_054337987.1XP_054193962.1  polypyrimidine tract-binding protein 2 isoform X6

      UniProtKB/TrEMBL
      B4DSS8, B4DSU5