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

Gene ID: 56194, updated on 8-Feb-2024

Summary

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
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Genomic context

See Prpf40a in Genome Data Viewer
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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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_001371015.1NP_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:759813
    FF; Contains two conserved F residues
    COG5104
    Location:161696
    PRP40; Splicing factor [RNA processing and modification]
  2. NM_001371016.1NP_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:737791
    FF; Contains two conserved F residues
    COG5104
    Location:161674
    PRP40; Splicing factor [RNA processing and modification]
  3. NM_001371017.1NP_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:717771
    FF; Contains two conserved F residues
    COG5104
    Location:119654
    PRP40; Splicing factor [RNA processing and modification]
  4. NM_001371018.1NP_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:713767
    FF; Contains two conserved F residues
    COG5104
    Location:119650
    PRP40; Splicing factor [RNA processing and modification]
  5. NM_001371019.1NP_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:699753
    FF; Contains two conserved F residues
    COG5104
    Location:119636
    PRP40; Splicing factor [RNA processing and modification]
  6. NM_001371020.1NP_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:695749
    FF; Contains two conserved F residues
    COG5104
    Location:119632
    PRP40; Splicing factor [RNA processing and modification]
  7. NM_018785.3NP_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:755809
    FF; Contains two conserved F residues
    COG5104
    Location:161692
    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_011239140.4XP_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:645699
    FF; Contains two conserved F residues
    COG5104
    Location:47582
    PRP40; Splicing factor [RNA processing and modification]
  2. XM_030251893.2XP_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:645699
    FF; Contains two conserved F residues
    COG5104
    Location:47582
    PRP40; Splicing factor [RNA processing and modification]
  3. XM_006498193.3XP_006498256.2  pre-mRNA-processing factor 40 homolog A isoform X1

    UniProtKB/TrEMBL
    A0A6Q6PUT5
    Conserved Domains (2) summary
    smart00441
    Location:803857
    FF; Contains two conserved F residues
    COG5104
    Location:223740
    PRP40; Splicing factor [RNA processing and modification]