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    Ptbp3 polypyrimidine tract binding protein 3 [ Mus musculus (house mouse) ]

    Gene ID: 230257, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Ptbp3provided by MGI
    Official Full Name
    polypyrimidine tract binding protein 3provided by MGI
    Primary source
    MGI:MGI:1923334
    See related
    Ensembl:ENSMUSG00000028382 AllianceGenome:MGI:1923334
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Rod1; 5830471K22Rik
    Summary
    Predicted to enable mRNA binding activity. Acts upstream of or within negative regulation of mRNA splicing, via spliceosome. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; liver; metanephros; sensory organ; and thymus primordium. Orthologous to human PTBP3 (polypyrimidine tract binding protein 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in placenta adult (RPKM 36.2), liver E14 (RPKM 17.5) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ptbp3 in Genome Data Viewer
    Location:
    4 B3; 4 32.57 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (59471868..59549288, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (59471868..59549378, complement)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_10371 Neighboring gene STARR-positive B cell enhancer mm9_chr4:59288450-59288750 Neighboring gene STARR-positive B cell enhancer mm9_chr4:59300165-59300466 Neighboring gene predicted gene, 35578 Neighboring gene STARR-positive B cell enhancer mm9_chr4:59344609-59344910 Neighboring gene STARR-positive B cell enhancer ABC_E9588 Neighboring gene STARR-positive B cell enhancer ABC_E9589 Neighboring gene sushi domain containing 1 Neighboring gene STARR-seq mESC enhancer starr_10373 Neighboring gene zinc finger, MYND domain containing 19 pseudogene Neighboring gene STARR-seq mESC enhancer starr_10375 Neighboring gene STARR-positive B cell enhancer ABC_E4630 Neighboring gene STARR-seq mESC enhancer starr_10376 Neighboring gene STARR-seq mESC enhancer starr_10379 Neighboring gene STARR-positive B cell enhancer ABC_E4631 Neighboring gene STARR-positive B cell enhancer ABC_E6183 Neighboring gene STARR-positive B cell enhancer ABC_E835 Neighboring gene STARR-seq mESC enhancer starr_10381 Neighboring gene RIKEN cDNA E130308A19 gene Neighboring gene hydroxysteroid dehydrogenase like 2 Neighboring gene predicted gene, 54283

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Generation of functionally distinct isoforms of PTBP3 by alternative splicing and translation initiation. Tan LY, et al. Nucleic Acids Res, 2015 Jun 23. PMID 25940628, Free PMC Article
    2. Essential requirement for polypyrimidine tract binding proteins 1 and 3 in the maturation and maintenance of mature B cells in mice. Monzón-Casanova E, et al. Eur J Immunol, 2021 Sep. PMID 34214192
    3. Polypyrimidine tract-binding proteins are essential for B cell development. Monzón-Casanova E, et al. Elife, 2020 Feb 21. PMID 32081131, Free PMC Article
    4. PTBP1 is required for embryonic development before gastrulation. Suckale J, et al. PLoS One, 2011 Feb 17. PMID 21423341, Free PMC Article
    5. Raver1, a dual compartment protein, is a ligand for PTB/hnRNPI and microfilament attachment proteins. Hüttelmaier S, et al. J Cell Biol, 2001 Nov 26. PMID 11724819, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Essential requirement for polypyrimidine tract binding proteins 1 and 3 in the maturation and maintenance of mature B cells in mice.
      Title: Essential requirement for polypyrimidine tract binding proteins 1 and 3 in the maturation and maintenance of mature B cells in mice.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Gene trapped (1) 
    • Targeted (1)  1 citation
    • Endonuclease-mediated (1) 

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC11742

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within erythrocyte maturation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within mRNA processing 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of RNA splicing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cell differentiation ISO
    Inferred from Sequence Orthology
    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
    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_001404433.1 → NP_001391362.1  polypyrimidine tract-binding protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL824704

    2. NM_001404434.1 → NP_001391363.1  polypyrimidine tract-binding protein 3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL824704
      UniProtKB/TrEMBL
      G3UXA6
      Related
      ENSMUSP00000133612.2, ENSMUST00000174586.8

    3. NM_001404435.1 → NP_001391364.1  polypyrimidine tract-binding protein 3 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL824704

    4. NM_001404436.1 → NP_001391365.1  polypyrimidine tract-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL824704
      UniProtKB/Swiss-Prot
      A2ANH0, A2ANH1, Q8BHD7, Q923C3

    5. NM_001404437.1 → NP_001391366.1  polypyrimidine tract-binding protein 3 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL824704
      Related
      ENSMUSP00000122840.3, ENSMUST00000148331.9

    6. NM_001404438.1 → NP_001391367.1  polypyrimidine tract-binding protein 3 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AL824704

    7. NM_001404439.1 → NP_001391368.1  polypyrimidine tract-binding protein 3 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AL824704

    8. NM_001404440.1 → NP_001391369.1  polypyrimidine tract-binding protein 3 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AL824704
      UniProtKB/TrEMBL
      G3UZ01
      Related
      ENSMUSP00000134290.2, ENSMUST00000173699.8

    9. NM_144904.3 → NP_659153.2  polypyrimidine tract-binding protein 3 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL824704
      Consensus CDS
      CCDS18220.2
      UniProtKB/TrEMBL
      G8JL74
      Related
      ENSMUSP00000099947.5, ENSMUST00000102883.11
      Conserved Domains (5) summary
      cd12693
      Location:178 → 273
      RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
      cd12703
      Location:471 → 551
      RRM4_ROD1; RNA recognition motif 4 in vertebrate regulator of differentiation 1 (Rod1)
      cd12779
      Location:53 → 142
      RRM1_ROD1; RNA recognition motif 1 in vertebrate regulator of differentiation 1 (Rod1)
      TIGR01649
      Location:56 → 551
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
      cl17169
      Location:358 → 450
      RRM_SF; RNA recognition motif (RRM) superfamily

    10. NM_178164.4 → NP_835458.1  polypyrimidine tract-binding protein 3 isoform 2

      See identical proteins and their annotated locations for NP_835458.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in its 5' end which results in the use of an in-frame downstream start codon and also uses an alternate splice site in its 5' coding region, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AL824704
      Consensus CDS
      CCDS18221.1
      UniProtKB/Swiss-Prot
      A2ANH0, A2ANH1, Q8BHD7, Q923C3
      Related
      ENSMUSP00000030076.6, ENSMUST00000030076.12
      Conserved Domains (5) summary
      cd12693
      Location:150 → 245
      RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
      cd12703
      Location:443 → 523
      RRM4_ROD1; RNA recognition motif 4 in vertebrate regulator of differentiation 1 (Rod1)
      cd12779
      Location:25 → 114
      RRM1_ROD1; RNA recognition motif 1 in vertebrate regulator of differentiation 1 (Rod1)
      TIGR01649
      Location:28 → 523
      hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
      cl17169
      Location:330 → 422
      RRM_SF; RNA recognition motif (RRM) superfamily

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      59471868..59549288 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BHD7.1 GenPept UniProtKB/Swiss-Prot:Q8BHD7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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