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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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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

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