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    Prpf40a pre-mRNA processing factor 40A [ Mus musculus (house mouse) ]

    Gene ID: 56194, updated on 30-Apr-2024

    Summary

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    Official Symbol
    Prpf40aprovided by MGI
    Official Full Name
    pre-mRNA processing factor 40Aprovided by MGI
    Primary source
    MGI:MGI:1860512
    See related
    Ensembl:ENSMUSG00000061136 AllianceGenome:MGI:1860512
    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
    FBP11; Fnbp3; FBP-11; Fnbp11; 2810012K09Rik
    Summary
    Enables proline-rich region binding activity. Predicted to be involved in several processes, including mRNA splicing, via spliceosome; regulation of cell shape; and regulation of cytokinesis. Predicted to act upstream of or within RNA splicing and mRNA processing. Located in nuclear matrix. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; respiratory system; and sensory organ. Orthologous to human PRPF40A (pre-mRNA processing factor 40 homolog A). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 14.3), CNS E14 (RPKM 7.9) and 26 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    2 C1.1; 2 30.69 cM
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (53024714..53081450, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (53134702..53191438, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene predicted gene, 46741 Neighboring gene STARR-positive B cell enhancer ABC_E7814 Neighboring gene signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 Neighboring gene STARR-positive B cell enhancer ABC_E10102 Neighboring gene STARR-seq mESC enhancer starr_04490 Neighboring gene formin-like 2 Neighboring gene STARR-seq mESC enhancer starr_04498 Neighboring gene STARR-seq mESC enhancer starr_04499 Neighboring gene predicted gene, 52511 Neighboring gene STARR-positive B cell enhancer ABC_E1005 Neighboring gene STARR-positive B cell enhancer ABC_E7815 Neighboring gene STARR-positive B cell enhancer ABC_E7816 Neighboring gene ADP-ribosylation factor-like 6 interacting protein 6 Neighboring gene predicted gene, 25898

    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. Structural characterization of a new binding motif and a novel binding mode in group 2 WW domains. Ramirez-Espain X, et al. J Mol Biol, 2007 Nov 9. PMID 17915251
    2. FBP11 regulates nuclear localization of N-WASP and inhibits N-WASP-dependent microspike formation. Mizutani K, et al. Biochem Biophys Res Commun, 2004 Jan 16. PMID 14697212
    3. Interaction of the nuclear matrix protein NAKAP with HypA and huntingtin: implications for nuclear toxicity in Huntington's disease pathogenesis. Sayer JA, et al. Neuromolecular Med, 2005. PMID 16391387
    4. Formin binding proteins bear WWP/WW domains that bind proline-rich peptides and functionally resemble SH3 domains. Chan DC, et al. EMBO J, 1996 Mar 1. PMID 8605874, Free PMC Article
    5. FBP WW domains and the Abl SH3 domain bind to a specific class of proline-rich ligands. Bedford MT, et al. EMBO J, 1997 May 1. PMID 9171351, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FBP11 regulates localization of N-WASP, thus negatively regulating the function of N-WASP in the cytoplasm
      Title: FBP11 regulates nuclear localization of N-WASP and inhibits N-WASP-dependent microspike formation.
    2. Results suggest an essential role of WW/FF domain-containing factors such as FBP11 and CA150 in pre-mRNA splicing that likely occurs in concert with transcription in vivo.
      Title: The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 

    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

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables proline-rich region binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA cis splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cell shape ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cytokinesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of U1 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type prespliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear matrix ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pre-mRNA-processing factor 40 homolog A
    Names
    PRP40 pre-mRNA processing factor 40 homolog A
    formin binding protein 11
    formin-binding protein 3

    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_001371015.1 → NP_001357944.1  pre-mRNA-processing factor 40 homolog A isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL845170
      UniProtKB/TrEMBL
      A0A6Q6PUT5
      Conserved Domains (2) summary
      smart00441
      Location:759 → 813
      FF; Contains two conserved F residues
      COG5104
      Location:161 → 696
      PRP40; Splicing factor [RNA processing and modification]

    2. NM_001371016.1 → NP_001357945.1  pre-mRNA-processing factor 40 homolog A isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL845170
      UniProtKB/TrEMBL
      A0A6Q6PUT5
      Conserved Domains (2) summary
      smart00441
      Location:737 → 791
      FF; Contains two conserved F residues
      COG5104
      Location:161 → 674
      PRP40; Splicing factor [RNA processing and modification]

    3. NM_001371017.1 → NP_001357946.1  pre-mRNA-processing factor 40 homolog A isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL845170
      UniProtKB/TrEMBL
      A0A6Q6PUT5
      Conserved Domains (2) summary
      smart00441
      Location:717 → 771
      FF; Contains two conserved F residues
      COG5104
      Location:119 → 654
      PRP40; Splicing factor [RNA processing and modification]

    4. NM_001371018.1 → NP_001357947.1  pre-mRNA-processing factor 40 homolog A isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL845170
      Consensus CDS
      CCDS89487.1
      UniProtKB/TrEMBL
      A0A1B0GRU8, A0A6Q6PUT5
      Related
      ENSMUSP00000147599.3, ENSMUST00000210789.3
      Conserved Domains (2) summary
      smart00441
      Location:713 → 767
      FF; Contains two conserved F residues
      COG5104
      Location:119 → 650
      PRP40; Splicing factor [RNA processing and modification]

    5. NM_001371019.1 → NP_001357948.1  pre-mRNA-processing factor 40 homolog A isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL845170
      UniProtKB/TrEMBL
      A0A6Q6PUT5
      Conserved Domains (2) summary
      smart00441
      Location:699 → 753
      FF; Contains two conserved F residues
      COG5104
      Location:119 → 636
      PRP40; Splicing factor [RNA processing and modification]

    6. NM_001371020.1 → NP_001357949.1  pre-mRNA-processing factor 40 homolog A isoform 7

      Status: VALIDATED

      Source sequence(s)
      AL845170
      UniProtKB/TrEMBL
      A0A6Q6PUT5
      Conserved Domains (2) summary
      smart00441
      Location:695 → 749
      FF; Contains two conserved F residues
      COG5104
      Location:119 → 632
      PRP40; Splicing factor [RNA processing and modification]

    7. NM_018785.3 → NP_061255.2  pre-mRNA-processing factor 40 homolog A isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL845170
      Consensus CDS
      CCDS16038.1
      UniProtKB/TrEMBL
      A0A6Q6PUT5
      Related
      ENSMUSP00000075655.8, ENSMUST00000076313.14
      Conserved Domains (2) summary
      smart00441
      Location:755 → 809
      FF; Contains two conserved F residues
      COG5104
      Location:161 → 692
      PRP40; Splicing factor [RNA processing and modification]

    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_000068.8 Reference GRCm39 C57BL/6J

      Range
      53024714..53081450 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011239140.4 → XP_011237442.1  pre-mRNA-processing factor 40 homolog A isoform X2

      UniProtKB/Swiss-Prot
      Q61049, Q8BQ76, Q8BRW4, Q8C2U1, Q9R1C7
      Conserved Domains (2) summary
      smart00441
      Location:645 → 699
      FF; Contains two conserved F residues
      COG5104
      Location:47 → 582
      PRP40; Splicing factor [RNA processing and modification]

    2. XM_030251893.2 → XP_030107753.1  pre-mRNA-processing factor 40 homolog A isoform X2

      UniProtKB/Swiss-Prot
      Q61049, Q8BQ76, Q8BRW4, Q8C2U1, Q9R1C7
      Conserved Domains (2) summary
      smart00441
      Location:645 → 699
      FF; Contains two conserved F residues
      COG5104
      Location:47 → 582
      PRP40; Splicing factor [RNA processing and modification]

    3. XM_006498193.3 → XP_006498256.2  pre-mRNA-processing factor 40 homolog A isoform X1

      UniProtKB/TrEMBL
      A0A6Q6PUT5
      Conserved Domains (2) summary
      smart00441
      Location:803 → 857
      FF; Contains two conserved F residues
      COG5104
      Location:223 → 740
      PRP40; Splicing factor [RNA processing and modification]
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9R1C7.1 GenPept UniProtKB/Swiss-Prot:Q9R1C7

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