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    PTBP3 polypyrimidine tract binding protein 3 [ Homo sapiens (human) ]

    Gene ID: 9991, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PTBP3provided by HGNC
    Official Full Name
    polypyrimidine tract binding protein 3provided by HGNC
    Primary source
    HGNC:HGNC:10253
    See related
    Ensembl:ENSG00000119314 MIM:607527; AllianceGenome:HGNC:10253
    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
    ROD1
    Summary
    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]
    Expression
    Ubiquitous expression in appendix (RPKM 17.8), lymph node (RPKM 17.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PTBP3 in Genome Data Viewer
    Location:
    9q32
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (112217715..112379882, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (124388866..124504825, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (114979995..115095944, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene sushi domain containing 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:114906608-114907807 Neighboring gene RNA, U6 small nuclear 855, pseudogene Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:114928255-114928756 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:114928757-114929256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28820 Neighboring gene ribosomal protein L29 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28821 Neighboring gene RNA, 7SL, cytoplasmic 57, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 295 Neighboring gene RNA, 7SL, cytoplasmic 430, pseudogene Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 28 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:115086563-115087088 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20189 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:115095973-115096943 Neighboring gene HNF4 motif-containing MPRA enhancer 25 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28823 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:115141971-115142570 Neighboring gene ribosomal protein L32 pseudogene 22 Neighboring gene hydroxysteroid dehydrogenase like 2 Neighboring gene HSDL2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20193 Neighboring gene KIAA1958 Neighboring gene Sharpr-MPRA regulatory region 4745 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:115309395-115309946 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:115309947-115310499 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:115310500-115311051 Neighboring gene Sharpr-MPRA regulatory region 8480 Neighboring gene NANOG hESC enhancer GRCh37_chr9:115313867-115314374 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:115357836-115358025 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:115380828-115381410 Neighboring gene MPRA-validated peak7319 silencer

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. PTBP3 mediates TGF-β-induced EMT and metastasis of lung adenocarcinoma. Dong C, et al. Cell Cycle, 2022 Jul. PMID 35323096, Free PMC Article
    2. Regulator of differentiation 1 (ROD1) binds to the amphipathic C-terminal peptide of thrombospondin-4 and is involved in its mitogenic activity. Sadvakassova G, et al. J Cell Physiol, 2009 Sep. PMID 19441079
    3. Chromosome Conformation Capture Reveals Two Elements That Interact with the PTBP3 (ROD1) Transcription Start Site. Kubiak M, et al. Int J Mol Sci, 2019 Jan 9. PMID 30634466, Free PMC Article
    4. A new function of ROD1 in nonsense-mediated mRNA decay. Brazão TF, et al. FEBS Lett, 2012 Apr 24. PMID 22575643
    5. The RNA-binding protein ROD1/PTBP3 cotranscriptionally defines AID-loading sites to mediate antibody class switch in mammalian genomes. Chen J, et al. Cell Res, 2018 Oct. PMID 30143796, Free PMC Article

    See all (88) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PTBP3 Mediates IL-18 Exon Skipping to Promote Immune Escape in Gallbladder Cancer.
      Title: PTBP3 Mediates IL-18 Exon Skipping to Promote Immune Escape in Gallbladder Cancer.
    2. YTHDC1 promotes the malignant progression of gastric cancer by promoting ROD1 translocation to the nucleus.
      Title: YTHDC1 promotes the malignant progression of gastric cancer by promoting ROD1 translocation to the nucleus.
    3. MiR-297 inhibits tumour progression of liver cancer by targeting PTBP3.
      Title: MiR-297 inhibits tumour progression of liver cancer by targeting PTBP3.
    4. PTBP3 mediates TGF-beta-induced EMT and metastasis of lung adenocarcinoma.
      Title: PTBP3 mediates TGF-β-induced EMT and metastasis of lung adenocarcinoma.
    5. PTBP3 modulates P53 expression and promotes colorectal cancer cell proliferation by maintaining UBE4A mRNA stability.
      Title: PTBP3 modulates P53 expression and promotes colorectal cancer cell proliferation by maintaining UBE4A mRNA stability.
    6. MiR-384 inhibits proliferation and migration of trophoblast cells via targeting PTBP3.
      Title: MiR-384 inhibits proliferation and migration of trophoblast cells via targeting PTBP3.
    7. PTBP3 promotes malignancy and hypoxia-induced chemoresistance in pancreatic cancer cells by ATG12 up-regulation.
      Title: PTBP3 promotes malignancy and hypoxia-induced chemoresistance in pancreatic cancer cells by ATG12 up-regulation.
    8. PTBP3 appears to be a novel oncogene of CRC through binding to the IRES region of HIF-1alpha mRNA, which regulates HIF-1alpha translation. PTBP3 can serve as a promising predictive biomarker for recurrence and prognosis in patients with CRC.
      Title: PTBP3 contributes to colorectal cancer growth and metastasis via translational activation of HIF-1α.
    9. findings provide experimental evidence that PTBP3 may function as a metastatic gene in gastric cancer by regulating CAV1 through alternative splicing.
      Title: PTBP3 contributes to the metastasis of gastric cancer by mediating CAV1 alternative splicing.
    10. ROD1 directly interacts with AID, which jointly bind bidirectionally transcribed RNAs to facilitate genome-wide AID targeting to Ig and non-Ig loci, suggesting that cooperative binding of the ROD1-AID complex on RNA provides the targeting specificity for AID.
      Title: The RNA-binding protein ROD1/PTBP3 cotranscriptionally defines AID-loading sites to mediate antibody class switch in mammalian genomes.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp781I1117

    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 RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in anatomical structure morphogenesis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in erythrocyte maturation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing 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 cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    polypyrimidine tract-binding protein 3
    Names
    ROD1 regulator of differentiation 1
    fission yeast differentiation regulator
    regulator of differentiation 1

    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_001163788.4 → NP_001157260.1  polypyrimidine tract-binding protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001157260.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 6. The resulting isoform (2) is shorter at the N-terminus and contains an alternate short internal segment compared to isoform 6.
      Source sequence(s)
      AK302558, AL158824, CN371677
      Consensus CDS
      CCDS55332.1
      UniProtKB/Swiss-Prot
      O95758
      Related
      ENSP00000363375.1, ENST00000374257.6
      Conserved Domains (1) summary
      TIGR01649
      Location:29 → 524
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    2. NM_001163790.2 → NP_001157262.1  polypyrimidine tract-binding protein 3 isoform 3

      See identical proteins and their annotated locations for NP_001157262.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 6. The resulting isoform (3) has a shorter and distinct N-terminus and contains an alternate short internal segment compared to isoform 6.
      Source sequence(s)
      AL158824, AL359073, BX097575, CN371677
      Consensus CDS
      CCDS55333.1
      UniProtKB/Swiss-Prot
      O95758
      Related
      ENSP00000334499.6, ENST00000334318.10
      Conserved Domains (1) summary
      TIGR01649
      Location:60 → 555
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    3. NM_001244896.2 → NP_001231825.1  polypyrimidine tract-binding protein 3 isoform 4

      See identical proteins and their annotated locations for NP_001231825.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence, uses an alternate in-frame splice junction at the 3' end of an exon, and lacks an alternate coding exon compared to variant 6. The resulting isoform (4) has a shorter and distinct N-terminus compared to isoform 6.
      Source sequence(s)
      AK001685, AL158824, BX097575, CN371677
      Consensus CDS
      CCDS59140.1
      UniProtKB/Swiss-Prot
      O95758
      Related
      ENSP00000340705.2, ENST00000343327.6
      Conserved Domains (1) summary
      TIGR01649
      Location:1 → 457
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    4. NM_001244897.2 → NP_001231826.1  polypyrimidine tract-binding protein 3 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence, uses an alternate in-frame splice junction at the 3' end of an exon, and uses an alternate splice junction at the 5' end of the last exon, that causes a frameshift, compared to variant 6. The resulting isoform (5) is shorter at the N-terminus, contains a short alternate internal segment, and has a shorter and distinct C-terminus compared to isoform 6.
      Source sequence(s)
      AL158824, BC039896, BX097575
      UniProtKB/Swiss-Prot
      O95758
      Conserved Domains (5) summary
      COG0724
      Location:329 → 471
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12693
      Location:151 → 246
      RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
      cd12779
      Location:26 → 115
      RRM1_ROD1; RNA recognition motif 1 in vertebrate regulator of differentiation 1 (Rod1)
      TIGR01661
      Location:38 → 398
      ELAV_HUD_SF; ELAV/HuD family splicing factor
      cl17169
      Location:331 → 423
      RRM_SF; RNA recognition motif (RRM) superfamily

    5. NM_001244898.1 → NP_001231827.1  polypyrimidine tract-binding protein 3 isoform 6

      See identical proteins and their annotated locations for NP_001231827.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) encodes the longest isoform (6).
      Source sequence(s)
      AL158824, BC044585, BX097575
      Consensus CDS
      CCDS59141.1
      UniProtKB/Swiss-Prot
      O95758
      Related
      ENSP00000414921.1, ENST00000458258.5
      Conserved Domains (1) summary
      TIGR01649
      Location:63 → 558
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    6. NM_001375918.1 → NP_001362847.1  polypyrimidine tract-binding protein 3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AB023967, AL158824, AL359073
      Conserved Domains (1) summary
      TIGR01649
      Location:26 → 521
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    7. NM_001375920.1 → NP_001362849.1  polypyrimidine tract-binding protein 3 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AL158824, AL359073
      Conserved Domains (1) summary
      TIGR01649
      Location:1 → 452
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    8. NM_005156.7 → NP_005147.3  polypyrimidine tract-binding protein 3 isoform 1

      See identical proteins and their annotated locations for NP_005147.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence compared to variant 6. The resulting isoform (1) has a shorter and distinct N-terminus compared to isoform 6.
      Source sequence(s)
      AL158824, AL359073, BX097575, CN371677
      Consensus CDS
      CCDS6784.1
      UniProtKB/Swiss-Prot
      B1ALY2, B1ALY3, B1ALY5, B1ALY6, B3KME7, O95758, Q68DB9, Q86YB3, Q86YH9
      Related
      ENSP00000363373.2, ENST00000374255.6
      Conserved Domains (1) summary
      TIGR01649
      Location:57 → 552
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      112217715..112379882 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424272.1 → XP_047280228.1  polypyrimidine tract-binding protein 3 isoform X7

    2. XM_047424274.1 → XP_047280230.1  polypyrimidine tract-binding protein 3 isoform X9

    3. XM_047424273.1 → XP_047280229.1  polypyrimidine tract-binding protein 3 isoform X8

    4. XM_047424271.1 → XP_047280227.1  polypyrimidine tract-binding protein 3 isoform X7

    5. XM_011519265.2 → XP_011517567.1  polypyrimidine tract-binding protein 3 isoform X3

      See identical proteins and their annotated locations for XP_011517567.1

      Conserved Domains (1) summary
      TIGR01649
      Location:66 → 561
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

    6. XM_047424268.1 → XP_047280224.1  polypyrimidine tract-binding protein 3 isoform X5

    7. XM_047424267.1 → XP_047280223.1  polypyrimidine tract-binding protein 3 isoform X4

    8. XM_047424266.1 → XP_047280222.1  polypyrimidine tract-binding protein 3 isoform X2

    9. XM_047424265.1 → XP_047280221.1  polypyrimidine tract-binding protein 3 isoform X1

    10. XM_047424270.1 → XP_047280226.1  polypyrimidine tract-binding protein 3 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      124388866..124504825 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054364418.1 → XP_054220393.1  polypyrimidine tract-binding protein 3 isoform X3

    2. XM_054364420.1 → XP_054220395.1  polypyrimidine tract-binding protein 3 isoform X5

    3. XM_054364419.1 → XP_054220394.1  polypyrimidine tract-binding protein 3 isoform X4

    4. XM_054364417.1 → XP_054220392.1  polypyrimidine tract-binding protein 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95758.2 GenPept UniProtKB/Swiss-Prot:O95758

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