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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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