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Aliases for PTBP3 Gene

Aliases for PTBP3 Gene

  • Polypyrimidine Tract Binding Protein 3 2 3 5
  • 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
  • Polypyrimidine Tract-Binding Protein 3 3
  • ROD1 Regulator Of Differentiation 1 3

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. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is MIR4745.

UniProtKB/Swiss-Prot 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).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PTBP3 Gene

Genomics for PTBP3 Gene

Regulatory Elements for PTBP3 Gene

Enhancers for PTBP3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09F112308 0.6 ENCODE 13 +25.0 24957 0.8 SOX5 ZNF316 RFX1 ATF3 HLF BCL6 SUSD1 PTBP3 RPL29P20 HSPE1P28
GH09F112310 0.5 ENCODE 13 +22.7 22682 0.3 ZSCAN29 ZNF600 PRDM1 PTBP3 RPL29P20 SUSD1 HSPE1P28
GH09F112376 1.1 ENCODE 5.3 -45.7 -45678 4.8 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 YY1 HSDL2 PRPF4 UGCG FKBP15 SUSD1 PTBP3 GC09M112376 RPL32P22
GH09F112312 0.4 Ensembl 13 +20.3 20267 1.2 HLF SUSD1 PTBP3 RPL29P20 HSPE1P28
GH09F111937 1.3 FANTOM5 Ensembl ENCODE 2.3 +395.3 395287 2.4 HDGF PKNOX1 BMI1 EBF1 RELA EGR1 POLR2A CBX5 EED ETV6 RNU6-710P RNU6-1013P GNG10 KIAA1958 C9orf84 PTBP3 SUSD1 DNAJC25 HSDL2 MIR4668
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PTBP3 on UCSC Golden Path with GeneCards custom track

Promoters for PTBP3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001311816 867 4001 PKNOX1 CREB3L1 ARID4B SIN3A YY1 ZNF143 ZNF207 SP3 SP5 MXD4

Genomic Location for PTBP3 Gene

Chromosome:
9
Start:
112,217,715 bp from pter
End:
112,333,667 bp from pter
Size:
115,953 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=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAA75466.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BI463123; Type=Frameshift; Positions=92; Evidence={ECO:0000305};

    Alternative splice isoforms for PTBP3 Gene

neXtProt entry for PTBP3 Gene

Post-translational modifications for PTBP3 Gene

  • Ubiquitination at Lys 106, Lys 400, Lys 418, Lys 472, and Lys 475
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PTBP3 Gene

Domains & Families for PTBP3 Gene

Gene Families for PTBP3 Gene

Protein Domains for PTBP3 Gene

Suggested Antigen Peptide Sequences for PTBP3 Gene

Graphical View of Domain Structure for InterPro Entry

O95758

UniProtKB/Swiss-Prot:

PTBP3_HUMAN :
  • Contains 4 RRM (RNA recognition motif) domains.
Domain:
  • Contains 4 RRM (RNA recognition motif) domains.
genes like me logo Genes that share domains with PTBP3: view

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).

Gene Ontology (GO) - Molecular Function for PTBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,TAS 10207106
GO:0044822 poly(A) RNA binding IDA 22658674
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

miRNA for PTBP3 Gene

miRTarBase miRNAs that target PTBP3

Flow Cytometry 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 2
plasma membrane 1
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for PTBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
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

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:0008380 RNA splicing IEA --
GO:0009653 anatomical structure morphogenesis TAS 10207106
GO:0016070 RNA metabolic process IEA --
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
  • Sodium
  • Sodium ion
7440-23-5
genes like me logo Genes that share compounds with PTBP3: view

Transcripts for PTBP3 Gene

Unigene Clusters for PTBP3 Gene

Polypyrimidine tract binding protein 3:
Representative Sequences:

Flow Cytometry 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
ECgene alternative splicing isoforms 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, PaxDb, MaxQB, and MOPED for PTBP3 Gene



Protein tissue co-expression partners for PTBP3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PTBP3 Gene:

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.
genes like me logo Genes that share expression patterns with PTBP3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery 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 34
  • 99.82 (n)
PTBP3 35
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PTBP3 35
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 95 (a)
OneToMany
-- 35
  • 82 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Ptbp3 34
  • 91.97 (n)
mouse
(Mus musculus)
Mammalia Ptbp3 34 16 35
  • 91.53 (n)
dog
(Canis familiaris)
Mammalia PTBP3 34 35
  • 91.51 (n)
oppossum
(Monodelphis domestica)
Mammalia PTBP3 35
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves ROD1 34
  • 76.24 (n)
PTBP3 35
  • 68 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PTBP3 35
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ptbp3 34
  • 77.26 (n)
Str.13021 34
zebrafish
(Danio rerio)
Actinopterygii ptbp3 34 35
  • 72.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta heph 35
  • 31 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ptb-1 35
  • 41 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 50 (a)
OneToMany
Species where no ortholog for PTBP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 PTBP3 Gene

ENSEMBL:
Gene Tree for PTBP3 (if available)
TreeFam:
Gene Tree for PTBP3 (if available)

Paralogs for PTBP3 Gene

Paralogs for PTBP3 Gene

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

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

Variants for PTBP3 Gene

Sequence variations from dbSNP and Humsavar for PTBP3 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs10114946 -- 112,289,487(+) CAACA(A/G)AAGTA intron-variant
rs10116045 -- 112,285,580(+) CAGAC(A/G)TTGTG intron-variant
rs10116098 -- 112,272,075(+) ttatt(A/T)tttat intron-variant
rs10116637 -- 112,233,962(+) GAGAG(A/C)GTAGT intron-variant
rs10117233 -- 112,327,584(+) AAATA(A/G)AACAA intron-variant

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

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

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)

Relevant External Links for PTBP3 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTBP3 Gene

Disorders for PTBP3 Gene

Relevant External Links for PTBP3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PTBP3

No disorders were found for PTBP3 Gene.

No data available for MalaCards , 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. (Mol. Cell. Biol. 1999) 2 3 4 22 64
  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 L.F. (J. Cell. Physiol. 2009) 3 4 64
  3. Expression of human nPTB is limited by extreme suboptimal codon content. (PMID: 18335065) Robinson F. … Smith C.W. (PLoS ONE 2008) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for PTBP3 Gene

Sources for PTBP3 Gene

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