The protein encoded by this gene binds RNA and is a regulator of cell differentiation. The encoded protein preferentially binds to poly(G) and poly(U) sequences in vitro. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011] See more...

Aliases for PTBP3 Gene

Aliases for PTBP3 Gene

  • Polypyrimidine Tract Binding Protein 3 2 3 5
  • Polypyrimidine Tract-Binding Protein 3 3 4
  • Regulator Of Differentiation 1 3 4
  • ROD1 3 4
  • ROD1 Regulator Of Differentiation 1 (S. Pombe) 2
  • Regulator Of Differentiation (In S. Pombe) 1 2
  • Fission Yeast Differentiation Regulator 3
  • ROD1 Regulator Of Differentiation 1 3
  • DKFZp781I1117 2
  • PTBP3 5
  • Rod1 4

External Ids for PTBP3 Gene

Previous HGNC Symbols for PTBP3 Gene

  • ROD1

Previous GeneCards Identifiers for PTBP3 Gene

  • GC09M114981

Summaries for PTBP3 Gene

Entrez Gene Summary for PTBP3 Gene

  • The protein encoded by this gene binds RNA and is a regulator of cell differentiation. The encoded protein preferentially binds to poly(G) and poly(U) sequences in vitro. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

GeneCards Summary for PTBP3 Gene

PTBP3 (Polypyrimidine Tract Binding Protein 3) is a Protein Coding gene. Diseases associated with PTBP3 include Prune Belly Syndrome and Frontometaphyseal Dysplasia. 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 PTBP3 Gene

  • RNA-binding protein that mediates pre-mRNA alternative splicing regulation. Plays a role in the regulation of cell proliferation, differentiation and migration. Positive regulator of EPO-dependent erythropoiesis. Participates in cell differentiation regulation by repressing tissue-specific exons. Promotes FAS exon 6 skipping. Binds RNA, preferentially to both poly(G) and poly(U).

Additional gene information for PTBP3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PTBP3 Gene

Genomics for PTBP3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PTBP3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTBP3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PTBP3

Genomic Locations for PTBP3 Gene

Genomic Locations for PTBP3 Gene
chr9:112,217,715-112,333,669
(GRCh38/hg38)
Size:
115,955 bases
Orientation:
Minus strand
chr9:114,980,715-115,095,947
(GRCh37/hg19)
Size:
115,233 bases
Orientation:
Minus strand

Genomic View for PTBP3 Gene

Genes around PTBP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTBP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTBP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTBP3 Gene

Proteins for PTBP3 Gene

  • Protein details for PTBP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95758-PTBP3_HUMAN
    Recommended name:
    Polypyrimidine tract-binding protein 3
    Protein Accession:
    O95758
    Secondary Accessions:
    • B1ALY2
    • B1ALY3
    • B1ALY5
    • B1ALY6
    • B3KME7
    • Q68DB9
    • Q86YB3
    • Q86YH9

    Protein attributes for PTBP3 Gene

    Size:
    552 amino acids
    Molecular mass:
    59690 Da
    Quaternary structure:
    • Interacts with THBS4 (via the acidic amphipathic C-terminus).
    SequenceCaution:
    • Sequence=AAH39896.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAA75466.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BI463123; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for PTBP3 Gene

neXtProt entry for PTBP3 Gene

Post-translational modifications for PTBP3 Gene

  • Ubiquitination at Lys137, Lys431, Lys449, Lys503, and Lys506
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PTBP3 Gene

Domains & Families for PTBP3 Gene

Gene Families for PTBP3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for PTBP3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ51619, highly similar to Regulator of differentiation 1 (B1ALY5_HUMAN)
  • Regulator of differentiation 1 (ROD1_HUMAN)
genes like me logo Genes that share domains with PTBP3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PTBP3 Gene

Function for PTBP3 Gene

Molecular function for PTBP3 Gene

UniProtKB/Swiss-Prot Function:
RNA-binding protein that mediates pre-mRNA alternative splicing regulation. Plays a role in the regulation of cell proliferation, differentiation and migration. Positive regulator of EPO-dependent erythropoiesis. Participates in cell differentiation regulation by repressing tissue-specific exons. Promotes FAS exon 6 skipping. Binds RNA, preferentially to both poly(G) and poly(U).

Phenotypes From GWAS Catalog for PTBP3 Gene

Gene Ontology (GO) - Molecular Function for PTBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding TAS,HDA 22658674
GO:0003729 mRNA binding IBA 21873635
genes like me logo Genes that share ontologies with PTBP3: view
genes like me logo Genes that share phenotypes with PTBP3: view

Animal Model Products

CRISPR Products

miRNA for PTBP3 Gene

miRTarBase miRNAs that target PTBP3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTBP3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PTBP3 Gene

Localization for PTBP3 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 PTBP3 gene
Compartment Confidence
nucleus 4
cytoskeleton 3
plasma membrane 2
cytosol 2
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PTBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with PTBP3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PTBP3 Gene

Pathways & Interactions for PTBP3 Gene

PathCards logo

SuperPathways for PTBP3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PTBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006397 mRNA processing IEA --
GO:0006417 regulation of translation IBA 21873635
GO:0008380 RNA splicing IEA --
GO:0009653 anatomical structure morphogenesis TAS 10207106
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with PTBP3: view

No data available for Pathways by source and SIGNOR curated interactions for PTBP3 Gene

Drugs & Compounds for PTBP3 Gene

(1) Additional Compounds for PTBP3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Na(+)
  • Na+
  • SODIUM ion
7440-23-5
genes like me logo Genes that share compounds with PTBP3: view

Transcripts for PTBP3 Gene

mRNA/cDNA for PTBP3 Gene

8 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
8 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 PTBP3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PTBP3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b · 8c ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^
SP1: - - - - - -
SP2: - - - - -
SP3: - - - - - - -
SP4: - - - - - -
SP5: - - -
SP6: - -
SP7: - - - - - - - - -
SP8:
SP9:

ExUns: 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for PTBP3 Gene

GeneLoc Exon Structure for
PTBP3

Expression for PTBP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PTBP3 Gene

mRNA differential expression in normal tissues according to GTEx for PTBP3 Gene

This gene is overexpressed in Whole Blood (x4.5).

Protein differential expression in normal tissues from HIPED for PTBP3 Gene

This gene is overexpressed in CD8 Tcells (9.6), Lymph node (7.4), and Monocytes (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PTBP3 Gene



Protein tissue co-expression partners for PTBP3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PTBP3

SOURCE GeneReport for Unigene cluster for PTBP3 Gene:

Hs.269988

mRNA Expression by UniProt/SwissProt for PTBP3 Gene:

O95758-PTBP3_HUMAN
Tissue specificity: Expressed in several hematopoietic cell lines examined.

Evidence on tissue expression from TISSUES for PTBP3 Gene

  • Intestine(3.1)
  • Lung(2.6)
  • Skin(2.6)
  • Kidney(2.4)
  • Nervous system(2.4)
  • Eye(2.4)
  • Spleen(2.3)
  • Heart(2.3)
  • Muscle(2.2)
  • Lymph node(2.1)
  • Pancreas(2.1)
genes like me logo Genes that share expression patterns with PTBP3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTBP3 Gene

Orthologs for PTBP3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTBP3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ROD1 30
  • 99.82 (n)
PTBP3 31
  • 98 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia PTBP3 31
  • 95 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 95 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Ptbp3 30
  • 91.97 (n)
Mouse
(Mus musculus)
Mammalia Ptbp3 30 17 31
  • 91.53 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PTBP3 30 31
  • 91.51 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PTBP3 31
  • 87 (a)
OneToOne
Chicken
(Gallus gallus)
Aves ROD1 30
  • 76.24 (n)
PTBP3 31
  • 68 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PTBP3 31
  • 87 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ptbp3 30
  • 77.26 (n)
Str.13021 30
Zebrafish
(Danio rerio)
Actinopterygii ptbp3 30 31
  • 72.67 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta heph 31
  • 31 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ptb-1 31
  • 41 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 50 (a)
OneToMany
Species where no ortholog for PTBP3 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 Vase (Ciona intestinalis)
  • 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 PTBP3 Gene

ENSEMBL:
Gene Tree for PTBP3 (if available)
TreeFam:
Gene Tree for PTBP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PTBP3: view image

Paralogs for PTBP3 Gene

Paralogs for PTBP3 Gene

(2) SIMAP similar genes for PTBP3 Gene using alignment to 2 proteins:

  • PTBP3_HUMAN
  • B1ALY4_HUMAN
genes like me logo Genes that share paralogs with PTBP3: view

Variants for PTBP3 Gene

Additional dbSNP identifiers (rs#s) for PTBP3 Gene

Structural Variations from Database of Genomic Variants (DGV) for PTBP3 Gene

Variant ID Type Subtype PubMed ID
esv2279381 CNV deletion 18987734
esv2461102 CNV deletion 19546169
esv2662225 CNV deletion 23128226
esv2672483 CNV deletion 23128226
esv2738946 CNV deletion 23290073
esv3621510 CNV loss 21293372
esv3621511 CNV gain 21293372
esv3621512 CNV loss 21293372
nsv1035315 CNV gain 25217958
nsv1053706 CNV loss 25217958
nsv1124464 CNV deletion 24896259
nsv1129305 CNV insertion 24896259
nsv466487 CNV loss 19166990
nsv511430 CNV loss 21212237
nsv518422 CNV gain 19592680
nsv615196 CNV loss 21841781
nsv825045 CNV loss 20364138
nsv950926 CNV duplication 24416366

Variation tolerance for PTBP3 Gene

Residual Variation Intolerance Score: 28.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.42; 27.95% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTBP3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTBP3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PTBP3 Gene

Disorders for PTBP3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PTBP3 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search PTBP3 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with PTBP3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PTBP3 Gene

Publications for PTBP3 Gene

  1. Isolation of a mammalian homologue of a fission yeast differentiation regulator. (PMID: 10207106) Yamamoto H … Okayama H (Molecular and cellular biology 1999) 2 3 4 23
  2. Regulator of differentiation 1 (ROD1) binds to the amphipathic C-terminal peptide of thrombospondin-4 and is involved in its mitogenic activity. (PMID: 19441079) Sadvakassova G … Congote LF (Journal of cellular physiology 2009) 3 4
  3. Expression of human nPTB is limited by extreme suboptimal codon content. (PMID: 18335065) Robinson F … Smith CW (PloS one 2008) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for PTBP3 Gene

Sources for PTBP3 Gene