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

Gene ID: 58155, updated on 7-Apr-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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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. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. MALAT1 binds to SFPQ releasing PTBP2 from the SFPQ/PTBP2 complex, the increased SFPQ-detached PTBP2 promotes cell proliferation and migration in colorectal cancer.
    Title: Long non-coding RNA MALAT1 promotes tumour growth and metastasis in colorectal cancer through binding to SFPQ and releasing oncogene PTBP2 from SFPQ/PTBP2 complex.
Submit: New GeneRIF Correction See all GeneRIFs (17)

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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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

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