Format

Send to:

Choose Destination

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

Gene ID: 58155, updated on 1-Jun-2020

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
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

Genomic context

See PTBP2 in Genome Data Viewer
Location:
1p21.3
Exon count:
16
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (96721605..96823739)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (97187161..97280605)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 270 Neighboring gene ribosomal protein L7 pseudogene 9 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
  • 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

NHGRI GWAS Catalog

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

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat 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

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ34897

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
cerebellum development IEA
Inferred from Electronic Annotation
more info
 
mRNA splice site selection IEA
Inferred from Electronic Annotation
more info
 
negative regulation of RNA splicing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of RNA splicing IDA
Inferred from Direct Assay
more info
PubMed 
regulation of RNA splicing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of neural precursor cell proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spinal cord development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
growth cone IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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/Swiss-Prot
    Q9UKA9
    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
    UniProtKB/Swiss-Prot
    Q9UKA9
    UniProtKB/TrEMBL
    B4DSU5
    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/Swiss-Prot
    Q9UKA9
    UniProtKB/TrEMBL
    B4DSS8
    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_001300988.1NP_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/Swiss-Prot
    Q9UKA9
    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/Swiss-Prot
    Q9UKA9
    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/Swiss-Prot
    Q9UKA9
    Conserved Domains (1) summary
    TIGR01649
    Location:5480
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  7. 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
    Q9UKA9
    Related
    ENSP00000412788.2, ENST00000426398.2
    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

    Description
    Transcript Variant: This variant (9) contains multiple differences at the 5' and 3' ends, compared to variant 1. This variant is represented as non-coding because translation of the longest in-frame ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD). This variant is similar to nPTB7.
    Source sequence(s)
    AI052528, AI968454, AK295384, BC016582, BP250235
  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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    96721605..96823739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541876.2XP_011540178.1  polypyrimidine tract-binding protein 2 isoform X3

    See identical proteins and their annotated locations for XP_011540178.1

    Conserved Domains (1) summary
    TIGR01649
    Location:65545
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  2. XM_011541875.2XP_011540177.1  polypyrimidine tract-binding protein 2 isoform X2

    See identical proteins and their annotated locations for XP_011540177.1

    Conserved Domains (1) summary
    TIGR01649
    Location:65539
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  3. XM_011541874.2XP_011540176.1  polypyrimidine tract-binding protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011540176.1

    Conserved Domains (1) summary
    TIGR01649
    Location:65544
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  4. XM_017001951.1XP_016857440.1  polypyrimidine tract-binding protein 2 isoform X4

    UniProtKB/TrEMBL
    B4DSS8
    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

RNA

  1. XR_946721.2 RNA Sequence

  2. XR_946720.2 RNA Sequence

  3. XR_946723.3 RNA Sequence

  4. XR_946722.2 RNA Sequence

  5. XR_001737346.2 RNA Sequence

  6. XR_001737347.2 RNA Sequence

Support Center