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

Gene ID: 9991, updated on 16-Apr-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
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Genomic context

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Location:
9q32
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (112217715..112379882, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (124388866..124504825, complement)
105.20220307 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: 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

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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. PTBP3 contributes to colorectal cancer growth and metastasis via translational activation of HIF-1α. Hou P, et al. J Exp Clin Cancer Res, 2019 Jul 10. PMID 31291975, Free PMC Article
  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. 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
  5. Inhibition of polypyrimidine tract-binding protein 3 induces apoptosis and cell cycle arrest, and enhances the cytotoxicity of 5- fluorouracil in gastric cancer cells. Liang X, et al. Br J Cancer, 2017 Mar 28. PMID 28222070, Free PMC Article

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. MiR-297 inhibits tumour progression of liver cancer by targeting PTBP3.
    Title: MiR-297 inhibits tumour progression of liver cancer by targeting PTBP3.
  3. PTBP3 mediates TGF-beta-induced EMT and metastasis of lung adenocarcinoma.
    Title: PTBP3 mediates TGF-β-induced EMT and metastasis of lung adenocarcinoma.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. The Meg3-dependent association of PTBP3 with the promoters of p53 target genes suggests that Meg3 and PTBP3 restrain p53 activation. Our studies reveal a novel role of Meg3 and PTBP3 in regulating p53 signaling and endothelial function, which may serve as novel targets for therapies to restore endothelial homeostasis.
    Title: LncRNA Meg3 protects endothelial function by regulating the DNA damage response.
Submit: New GeneRIF Correction See all GeneRIFs (23)

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)

Genotypes

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_2023_10

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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