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 vari... See more...

Aliases for PTBP2 Gene

Aliases for PTBP2 Gene

  • Polypyrimidine Tract Binding Protein 2 2 3 5
  • PTBLP 2 3 4
  • NPTB 2 3 4
  • Polypyrimidine Tract-Binding Protein 2 3 4
  • Neurally-Enriched Homolog Of PTB 3 4
  • PTB-Like Protein 3 4
  • BrPTB 2 3
  • PTB 2 4
  • Neural Polypyrimidine Tract Binding Protein 3
  • Neural Polypyrimidine Tract-Binding Protein 4
  • PTBP2 5

External Ids for PTBP2 Gene

Previous GeneCards Identifiers for PTBP2 Gene

  • GC01P097483
  • GC01P096288
  • GC01P096472
  • GC01P096659
  • GC01P096899
  • GC01P096959
  • GC01P097187
  • GC01P095308

Summaries for PTBP2 Gene

Entrez Gene Summary for PTBP2 Gene

  • 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]

GeneCards Summary for PTBP2 Gene

PTBP2 (Polypyrimidine Tract Binding Protein 2) is a Protein Coding gene. Diseases associated with PTBP2 include Patellar Tendinitis and Cancer-Associated Retinopathy. Among its related pathways are TarBasePathway and mRNA Splicing - Major Pathway. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is PTBP1.

UniProtKB/Swiss-Prot Summary for PTBP2 Gene

  • RNA-binding protein which binds to intronic polypyrimidine tracts and mediates negative regulation of exons splicing. May antagonize in a tissue-specific manner the ability of NOVA1 to activate exon selection. In addition to its function in pre-mRNA splicing, plays also a role in the regulation of translation. Isoform 5 has a reduced affinity for RNA.

Gene Wiki entry for PTBP2 Gene

Additional gene information for PTBP2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PTBP2 Gene

Genomics for PTBP2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PTBP2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J096720 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 610.8 +1.0 1025 3.9 PRDM10 KDM1A ZNF692 POLR2A BACH1 LARP7 PRDM1 ZNF143 ZIC2 RBFOX2 PTBP2 NONHSAG002166.2
GH01J096461 Enhancer 0.7 Ensembl ENCODE 11.4 -257.5 -257531 3.3 SP1 CEBPB YY1 ZBTB33 JUND RAD21 HNF4A RXRA MAX NANOG PTBP2 piR-48049-004 lnc-DPYD-8
GH01J096714 Enhancer 0.8 Ensembl ENCODE dbSUPER 10.4 -5.9 -5904 1.8 USF1 NANOG SP1 USF2 POU5F1 PTBP2 RF00100-005
GH01J096415 Enhancer 0.8 Ensembl ENCODE 10.8 -305.0 -304973 1.9 RELA PKNOX1 RELB JUND CEBPB FOS BHLHE40 JUN ZNF217 GATA2 UBE2WP1 lnc-PTBP2-6 PTBP2 lnc-PTBP2-7
GH01J096472 Enhancer 0.6 Ensembl ENCODE 10.9 -247.9 -247852 3.3 POLR2A CREB1 FOS NANOG SP1 EGR1 PTBP2 piR-36393-027 LOC105378866
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTBP2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PTBP2

Top Transcription factor binding sites by QIAGEN in the PTBP2 gene promoter:
  • AML1a
  • AP-2alpha
  • Elk-1
  • FOXO1
  • FOXO1a
  • HSF2
  • Sox5
  • Sp1

Genomic Locations for PTBP2 Gene

Genomic Locations for PTBP2 Gene
chr1:96,721,605-96,823,739
(GRCh38/hg38)
Size:
102,135 bases
Orientation:
Plus strand
chr1:97,187,175-97,289,294
(GRCh37/hg19)
Size:
102,120 bases
Orientation:
Plus strand

Genomic View for PTBP2 Gene

Genes around PTBP2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTBP2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTBP2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTBP2 Gene

Proteins for PTBP2 Gene

  • Protein details for PTBP2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UKA9-PTBP2_HUMAN
    Recommended name:
    Polypyrimidine tract-binding protein 2
    Protein Accession:
    Q9UKA9
    Secondary Accessions:
    • Q8N0Z1
    • Q8N160
    • Q8NFB0
    • Q8NFB1
    • Q969N9
    • Q96Q76

    Protein attributes for PTBP2 Gene

    Size:
    531 amino acids
    Molecular mass:
    57491 Da
    Quaternary structure:
    • Monomer. Interacts with NOVA1; the interaction is direct. Interacts with NOVA2; the interaction is direct (By similarity). Identified in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. Part of a ternary complex containing KHSRP and HNRPH1.

    Three dimensional structures from OCA and Proteopedia for PTBP2 Gene

    Alternative splice isoforms for PTBP2 Gene

neXtProt entry for PTBP2 Gene

Post-translational modifications for PTBP2 Gene

  • Glycosylation at Asn31
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PTBP2_HUMAN (2061)

No data available for DME Specific Peptides for PTBP2 Gene

Domains & Families for PTBP2 Gene

Gene Families for PTBP2 Gene

Suggested Antigen Peptide Sequences for PTBP2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55578, highly similar to Polypyrimidine tract-binding protein 2 (B4DI28_HUMAN)
  • cDNA FLJ60858, highly similar to Polypyrimidine tract-binding protein 2 (B4DSI2_HUMAN)
  • cDNA FLJ55936, highly similar to Polypyrimidine tract-binding protein 2 (B4DSS8_HUMAN)
  • PTBP2 (O95652_HUMAN)
  • PTB-like protein (PTBP2_HUMAN)
genes like me logo Genes that share domains with PTBP2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PTBP2 Gene

Function for PTBP2 Gene

Molecular function for PTBP2 Gene

UniProtKB/Swiss-Prot Function:
RNA-binding protein which binds to intronic polypyrimidine tracts and mediates negative regulation of exons splicing. May antagonize in a tissue-specific manner the ability of NOVA1 to activate exon selection. In addition to its function in pre-mRNA splicing, plays also a role in the regulation of translation. Isoform 5 has a reduced affinity for RNA.

Phenotypes From GWAS Catalog for PTBP2 Gene

Gene Ontology (GO) - Molecular Function for PTBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA 22658674
GO:0003729 mRNA binding IBA 21873635
genes like me logo Genes that share ontologies with PTBP2: view
genes like me logo Genes that share phenotypes with PTBP2: view

Animal Models for PTBP2 Gene

MGI Knock Outs for PTBP2:

Animal Model Products

CRISPR Products

miRNA for PTBP2 Gene

miRTarBase miRNAs that target PTBP2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTBP2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PTBP2 Gene

Localization for PTBP2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTBP2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PTBP2 gene
Compartment Confidence
nucleus 4
cytosol 3
extracellular 2
cytoskeleton 2
plasma membrane 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PTBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005681 spliceosomal complex IEA --
GO:0030426 growth cone IEA --
GO:0043025 neuronal cell body IEA --
genes like me logo Genes that share ontologies with PTBP2: view

Pathways & Interactions for PTBP2 Gene

PathCards logo

SuperPathways for PTBP2 Gene

genes like me logo Genes that share pathways with PTBP2: view

Pathways by source for PTBP2 Gene

2 BioSystems pathways for PTBP2 Gene

SIGNOR curated interactions for PTBP2 Gene

Activates:
Inactivates:

Gene Ontology (GO) - Biological Process for PTBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006376 mRNA splice site selection IEA --
GO:0006397 mRNA processing IEA --
GO:0006417 regulation of translation IBA 21873635
GO:0008380 RNA splicing IEA --
GO:0021510 spinal cord development IEA --
genes like me logo Genes that share ontologies with PTBP2: view

Drugs & Compounds for PTBP2 Gene

No Compound Related Data Available

Transcripts for PTBP2 Gene

mRNA/cDNA for PTBP2 Gene

7 REFSEQ mRNAs :
23 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTBP2

Alternative Splicing Database (ASD) splice patterns (SP) for PTBP2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b · 13c
SP1: - -
SP2: - -
SP3: - - -
SP4: - -
SP5: - -
SP6:
SP7:

Relevant External Links for PTBP2 Gene

GeneLoc Exon Structure for
PTBP2

Expression for PTBP2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PTBP2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PTBP2 Gene

This gene is overexpressed in Testis (32.2), Fetal ovary (12.8), and Fetal Brain (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PTBP2 Gene



Protein tissue co-expression partners for PTBP2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PTBP2

SOURCE GeneReport for Unigene cluster for PTBP2 Gene:

Hs.743449

mRNA Expression by UniProt/SwissProt for PTBP2 Gene:

Q9UKA9-PTBP2_HUMAN
Tissue specificity: Mainly expressed in brain although also detected in other tissues like heart and skeletal muscle. Isoform 1 and isoform 2 are specifically expressed in neuronal tissues. Isoform 3 and isoform 4 are expressed in non-neuronal tissues. Isoform 5 and isoform 6 are truncated forms expressed in non-neuronal tissues.

Evidence on tissue expression from TISSUES for PTBP2 Gene

  • Nervous system(4.7)
  • Eye(4.4)
  • Lung(4.4)
  • Muscle(2.5)
  • Blood(2.3)
  • Skin(2.2)
  • Heart(2.2)
  • Kidney(2.1)
  • Intestine(2.1)
  • Lymph node(2)
  • Bone marrow(2)
  • Liver(2)
genes like me logo Genes that share expression patterns with PTBP2: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTBP2 Gene

Orthologs for PTBP2 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTBP2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PTBP2 30 31
  • 99.75 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PTBP2 31
  • 99 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PTBP2 31
  • 99 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia PTBP2 31
  • 99 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia PTBP2 30 31
  • 97.43 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ptbp2 30 17 31
  • 93.72 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ptbp2 30
  • 93.09 (n)
Chicken
(Gallus gallus)
Aves PTBP2 30 31
  • 88.64 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PTBP2 31
  • 97 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ptbp2 30
  • 81.73 (n)
Zebrafish
(Danio rerio)
Actinopterygii ptbp2a 31
  • 79 (a)
OneToMany
ptbp2b 30 31
  • 72.88 (n)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta heph 31 32
  • 31 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ptb-1 31 32
  • 40 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 49 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.964 30
Species where no ortholog for PTBP2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for PTBP2 Gene

ENSEMBL:
Gene Tree for PTBP2 (if available)
TreeFam:
Gene Tree for PTBP2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PTBP2: view image

Paralogs for PTBP2 Gene

Paralogs for PTBP2 Gene

(3) SIMAP similar genes for PTBP2 Gene using alignment to 4 proteins:

  • PTBP2_HUMAN
  • B4DI28_HUMAN
  • B4DSS8_HUMAN
  • O95652_HUMAN
genes like me logo Genes that share paralogs with PTBP2: view

Variants for PTBP2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PTBP2 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
713770 Benign: not provided 96,769,734(+) A/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
720990 Benign: not provided 96,785,115(+) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
786466 Benign: not provided 96,751,419(+) T/C INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for PTBP2 Gene

Structural Variations from Database of Genomic Variants (DGV) for PTBP2 Gene

Variant ID Type Subtype PubMed ID
esv2540979 CNV insertion 19546169
esv3348431 CNV insertion 20981092
nsv830681 CNV loss 17160897

Variation tolerance for PTBP2 Gene

Residual Variation Intolerance Score: 12.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.25; 5.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTBP2 Gene

Human Gene Mutation Database (HGMD)
PTBP2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTBP2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTBP2 Gene

Disorders for PTBP2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PTBP2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
patellar tendinitis
  • patellar tendonitis
cancer-associated retinopathy
  • car syndrome
pleural tuberculosis
  • pearly disease
familial febrile seizures
  • familial febrile convulsions
- elite association - COSMIC cancer census association via MalaCards
Search PTBP2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PTBP2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with PTBP2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PTBP2 Gene

Publications for PTBP2 Gene

  1. Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein. (PMID: 11003644) Markovtsov V … Black DL (Molecular and cellular biology 2000) 2 3 4 23
  2. Alternative splicing of brain-specific PTB defines a tissue-specific isoform pattern that predicts distinct functional roles. (PMID: 12213192) Rahman L … Zajac-Kaye M (Genomics 2002) 3 4 23
  3. Molecular cloning and characterization of human PTB-like protein: a possible retinal autoantigen of cancer-associated retinopathy. (PMID: 11694331) Tateiwa H … Yoshimura N (Journal of neuroimmunology 2001) 3 4 23
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  5. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. (PMID: 19571811) International Schizophrenia Consortium … Sklar P (Nature 2009) 3 41

Products for PTBP2 Gene

Sources for PTBP2 Gene