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    Prpf40a pre-mRNA processing factor 40 homolog A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 295607, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Prpf40aprovided by RGD
    Official Full Name
    pre-mRNA processing factor 40 homolog Aprovided by RGD
    Primary source
    RGD:1311401
    See related
    EnsemblRapid:ENSRNOG00000004864 AllianceGenome:RGD:1311401
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Fnbp3
    Summary
    Predicted to enable RNA binding activity and 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 be located in nuclear matrix and nuclear speck. Predicted to be part of U1 snRNP and U2-type prespliceosome. Orthologous to human PRPF40A (pre-mRNA processing factor 40 homolog A). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 266.3), Spleen (RPKM 229.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Prpf40a in Genome Data Viewer
    Location:
    3q12
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (58036779..58098996, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (37625585..37689859, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (38680583..38741570, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene formin-like 2 Neighboring gene uncharacterized LOC134486095 Neighboring gene uncharacterized LOC134486096 Neighboring gene ADP ribosylation factor like GTPase 6 interacting protein 6 Neighboring gene NADH:ubiquinone oxidoreductase subunit B1, pseudogene 2 Neighboring gene U6 spliceosomal RNA

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    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. 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
    3. Huntingtin: an iron-regulated protein essential for normal nuclear and perinuclear organelles. Hilditch-Maguire P, et al. Hum Mol Genet, 2000 Nov 22. PMID 11092755
    4. Identification and characterization of a set of conserved and new regulators of cytoskeletal organization, cell morphology and migration. Bai SW, et al. BMC Biol, 2011 Aug 11. PMID 21834987, Free PMC Article
    5. The sclerostin-bone protein interactome. Devarajan-Ketha H, et al. Biochem Biophys Res Commun, 2012 Jan 13. PMID 22206666, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 RGD

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables proline-rich region binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    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
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    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 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_001106480.1 → NP_001099950.1  pre-mRNA-processing factor 40 homolog A

      See identical proteins and their annotated locations for NP_001099950.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473983
      UniProtKB/TrEMBL
      A0A8I5ZVY5, A6JF33
      Related
      ENSRNOP00000107993.1, ENSRNOT00000128758.1
      Conserved Domains (4) summary
      smart00441
      Location:740 → 794
      FF; Contains two conserved F residues
      COG5104
      Location:146 → 677
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:146 → 173
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam01846
      Location:391 → 440
      FF; FF domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      58036779..58098996 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039104476.2 → XP_038960404.1  pre-mRNA-processing factor 40 homolog A isoform X6

      UniProtKB/TrEMBL
      A0A8I5ZVY5

    2. XM_008761712.4 → XP_008759934.1  pre-mRNA-processing factor 40 homolog A isoform X5

      UniProtKB/TrEMBL
      A0A8I5ZVY5
      Conserved Domains (3) summary
      smart00441
      Location:761 → 815
      FF; Contains two conserved F residues
      cd00201
      Location:181 → 208
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam01846
      Location:408 → 457
      FF; FF domain

    3. XM_008761711.4 → XP_008759933.1  pre-mRNA-processing factor 40 homolog A isoform X3

      UniProtKB/TrEMBL
      A0A8I5ZVI3, A0A8I5ZVY5
      Conserved Domains (3) summary
      smart00441
      Location:779 → 833
      FF; Contains two conserved F residues
      cd00201
      Location:181 → 208
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam01846
      Location:426 → 475
      FF; FF domain

    4. XM_039104475.2 → XP_038960403.1  pre-mRNA-processing factor 40 homolog A isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZVY5

    5. XM_008761710.4 → XP_008759932.1  pre-mRNA-processing factor 40 homolog A isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZVY5
      Related
      ENSRNOP00000083490.2, ENSRNOT00000095713.2
      Conserved Domains (3) summary
      smart00441
      Location:803 → 857
      FF; Contains two conserved F residues
      cd00201
      Location:223 → 250
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam01846
      Location:450 → 499
      FF; FF domain

    6. XM_008761709.4 → XP_008759931.1  pre-mRNA-processing factor 40 homolog A isoform X8

      UniProtKB/TrEMBL
      A0A8I5ZVY5
      Conserved Domains (3) summary
      smart00441
      Location:821 → 875
      FF; Contains two conserved F residues
      cd00201
      Location:223 → 250
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam01846
      Location:468 → 517
      FF; FF domain

    7. XM_063283248.1 → XP_063139318.1  pre-mRNA-processing factor 40 homolog A isoform X7

    8. XM_006234164.5 → XP_006234226.1  pre-mRNA-processing factor 40 homolog A isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZVY5
      Conserved Domains (4) summary
      smart00441
      Location:775 → 829
      FF; Contains two conserved F residues
      COG5104
      Location:181 → 712
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:181 → 208
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam01846
      Location:426 → 475
      FF; FF domain

    9. XM_008761713.4 → XP_008759935.1  pre-mRNA-processing factor 40 homolog A isoform X9

      UniProtKB/TrEMBL
      A0A8I5ZVY5
      Related
      ENSRNOP00000083163.2, ENSRNOT00000104801.2
      Conserved Domains (4) summary
      smart00441
      Location:661 → 715
      FF; Contains two conserved F residues
      COG5104
      Location:63 → 598
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:63 → 90
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam01846
      Location:308 → 357
      FF; FF domain

    10. XM_063283249.1 → XP_063139319.1  pre-mRNA-processing factor 40 homolog A isoform X10

    Nucleotide Protein Strain
    Heading Accession and Version

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