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Prpf40b pre-mRNA processing factor 40B [ Mus musculus (house mouse) ]

Gene ID: 54614, updated on 5-Mar-2024

Summary

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Official Symbol
Prpf40bprovided by MGI
Official Full Name
pre-mRNA processing factor 40Bprovided by MGI
Primary source
MGI:MGI:1925583
See related
Ensembl:ENSMUSG00000023007 AllianceGenome:MGI:1925583
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
Hypc; 2610317D23Rik
Summary
Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of U1 snRNP and U2-type prespliceosome. Orthologous to human PRPF40B (pre-mRNA processing factor 40 homolog B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E14 (RPKM 21.3), CNS E18 (RPKM 18.5) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
15 F1; 15 56.13 cM
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (99192957..99214899)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (99295076..99317018)

Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene potassium voltage-gated channel, subfamily H (eag-related), member 3 Neighboring gene RIKEN cDNA 1700120C14 gene Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:99082061-99082244 Neighboring gene STARR-positive B cell enhancer ABC_E1486 Neighboring gene STARR-positive B cell enhancer ABC_E7417 Neighboring gene microspherule protein 1 Neighboring gene predicted gene, 25999 Neighboring gene family with sequence similarity 186, member B Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:99163430-99163646 Neighboring gene formin-like 3 Neighboring gene STARR-seq mESC enhancer starr_39705 Neighboring gene STARR-positive B cell enhancer ABC_E9923 Neighboring gene STARR-positive B cell enhancer ABC_E3156 Neighboring gene predicted gene, 22951 Neighboring gene transmembrane BAX inhibitor motif containing 6

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. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
  2. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199
  3. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article
  4. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. Diez-Roux G, et al. PLoS Biol, 2011 Jan 18. PMID 21267068, Free PMC Article
  5. Antisense transcription in the mammalian transcriptome. Katayama S, et al. Science, 2005 Sep 2. PMID 16141073

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 

Pathways from PubChem

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General gene information

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Markers

Homology

Clone Names

  • MGC91243

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
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
  
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 nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
pre-mRNA-processing factor 40 homolog B
Names
PRP40 pre-mRNA processing factor 40 homolog A
PRP40 pre-mRNA processing factor 40 homolog B
huntingtin yeast partner C
huntingtin-interacting protein C
huntington yeast partner C

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_001348256.1 → NP_001335185.1  pre-mRNA-processing factor 40 homolog B isoform 1

    Status: VALIDATED

    Source sequence(s)
    AF135440, BC051961
    Consensus CDS
    CCDS88839.1
    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    UniProtKB/TrEMBL
    E9QP07
    Related
    ENSMUSP00000113282.3, ENSMUST00000118287.9
    Conserved Domains (2) summary
    smart00441
    Location:633 → 681
    FF; Contains two conserved F residues
    COG5104
    Location:89 → 581
    PRP40; Splicing factor [RNA processing and modification]

  2. NM_001370632.1 → NP_001357561.1  pre-mRNA-processing factor 40 homolog B isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) encodes the longest isoform (3).
    Source sequence(s)
    AC161198
    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:655 → 703
    FF; Contains two conserved F residues
    COG5104
    Location:111 → 603
    PRP40; Splicing factor [RNA processing and modification]

  3. NM_001370633.1 → NP_001357562.1  pre-mRNA-processing factor 40 homolog B isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC161198
    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:655 → 703
    FF; Contains two conserved F residues
    COG5104
    Location:111 → 603
    PRP40; Splicing factor [RNA processing and modification]

  4. NM_001370634.1 → NP_001357563.1  pre-mRNA-processing factor 40 homolog B isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC161198
    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:655 → 703
    FF; Contains two conserved F residues
    COG5104
    Location:111 → 603
    PRP40; Splicing factor [RNA processing and modification]

  5. NM_001370635.1 → NP_001357564.1  pre-mRNA-processing factor 40 homolog B isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC161198
    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Related
    ENSMUSP00000023745.7, ENSMUST00000023745.13
    Conserved Domains (2) summary
    smart00441
    Location:633 → 681
    FF; Contains two conserved F residues
    COG5104
    Location:89 → 581
    PRP40; Splicing factor [RNA processing and modification]

  6. NM_018786.3 → NP_061256.1  pre-mRNA-processing factor 40 homolog B isoform 2

    See identical proteins and their annotated locations for NP_061256.1

    Status: VALIDATED

    Source sequence(s)
    AF135440, AK140075, BC051961
    Consensus CDS
    CCDS27818.1
    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    UniProtKB/TrEMBL
    A0A0R4J1S2
    Related
    ENSMUSP00000115869.2, ENSMUST00000145482.8
    Conserved Domains (6) summary
    smart00441
    Location:633 → 681
    FF; Contains two conserved F residues
    COG5104
    Location:89 → 581
    PRP40; Splicing factor [RNA processing and modification]
    cd00201
    Location:137 → 166
    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 ...
    pfam00397
    Location:98 → 123
    WW; WW domain
    pfam01846
    Location:278 → 327
    FF; FF domain
    cl21455
    Location:400 → 458
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RNA

  1. NR_163483.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC161198

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_000081.7 Reference GRCm39 C57BL/6J

    Range
    99192957..99214899
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030248664.1 → XP_030104524.1  pre-mRNA-processing factor 40 homolog B isoform X5

    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:655 → 703
    FF; Contains two conserved F residues
    COG5104
    Location:111 → 603
    PRP40; Splicing factor [RNA processing and modification]

  2. XM_006521188.3 → XP_006521251.1  pre-mRNA-processing factor 40 homolog B isoform X15

    UniProtKB/TrEMBL
    D3Z4N6
    Conserved Domains (2) summary
    smart00441
    Location:628 → 676
    FF; Contains two conserved F residues
    COG5104
    Location:84 → 576
    PRP40; Splicing factor [RNA processing and modification]

  3. XM_006521182.2 → XP_006521245.1  pre-mRNA-processing factor 40 homolog B isoform X6

    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  4. XM_006521183.3 → XP_006521246.1  pre-mRNA-processing factor 40 homolog B isoform X7

    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  5. XM_006521185.2 → XP_006521248.1  pre-mRNA-processing factor 40 homolog B isoform X13

    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  6. XM_006521184.3 → XP_006521247.1  pre-mRNA-processing factor 40 homolog B isoform X9

    UniProtKB/TrEMBL
    E9QMI6
    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  7. XM_006521190.4 → XP_006521253.1  pre-mRNA-processing factor 40 homolog B isoform X17

    UniProtKB/TrEMBL
    E9QMI6
    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  8. XM_036159523.1 → XP_036015416.1  pre-mRNA-processing factor 40 homolog B isoform X8

    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  9. XM_036159524.1 → XP_036015417.1  pre-mRNA-processing factor 40 homolog B isoform X10

    UniProtKB/TrEMBL
    E9QMI6
    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  10. XM_017316707.2 → XP_017172196.1  pre-mRNA-processing factor 40 homolog B isoform X14

    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:633 → 681
    FF; Contains two conserved F residues
    COG5104
    Location:89 → 581
    PRP40; Splicing factor [RNA processing and modification]

  11. XM_011245697.3 → XP_011243999.1  pre-mRNA-processing factor 40 homolog B isoform X1

    See identical proteins and their annotated locations for XP_011243999.1

    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  12. XM_030248665.2 → XP_030104525.1  pre-mRNA-processing factor 40 homolog B isoform X11

    UniProtKB/TrEMBL
    E9QMI6
    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  13. XM_006521178.4 → XP_006521241.1  pre-mRNA-processing factor 40 homolog B isoform X2

    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  14. XM_030248666.2 → XP_030104526.1  pre-mRNA-processing factor 40 homolog B isoform X12

    UniProtKB/TrEMBL
    E9QMI6
    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  15. XM_006521179.5 → XP_006521242.1  pre-mRNA-processing factor 40 homolog B isoform X3

    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  16. XM_006521180.5 → XP_006521243.1  pre-mRNA-processing factor 40 homolog B isoform X4

    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  17. XM_006521186.4 → XP_006521249.1  pre-mRNA-processing factor 40 homolog B isoform X14

    See identical proteins and their annotated locations for XP_006521249.1

    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:633 → 681
    FF; Contains two conserved F residues
    COG5104
    Location:89 → 581
    PRP40; Splicing factor [RNA processing and modification]

  18. XM_006521189.4 → XP_006521252.1  pre-mRNA-processing factor 40 homolog B isoform X16

    UniProtKB/TrEMBL
    D3Z4N6
    Conserved Domains (2) summary
    smart00441
    Location:627 → 675
    FF; Contains two conserved F residues
    COG5104
    Location:83 → 575
    PRP40; Splicing factor [RNA processing and modification]

  19. XM_011245698.3 → XP_011244000.1  pre-mRNA-processing factor 40 homolog B isoform X1

    See identical proteins and their annotated locations for XP_011244000.1

    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:662 → 710
    FF; Contains two conserved F residues
    COG5104
    Location:118 → 610
    PRP40; Splicing factor [RNA processing and modification]

  20. XM_030248667.1 → XP_030104527.1  pre-mRNA-processing factor 40 homolog B isoform X14

    UniProtKB/Swiss-Prot
    Q5XKB4, Q80W14, Q9CS39, Q9WVC9
    Conserved Domains (2) summary
    smart00441
    Location:633 → 681
    FF; Contains two conserved F residues
    COG5104
    Location:89 → 581
    PRP40; Splicing factor [RNA processing and modification]

RNA

  1. XR_004938858.1 RNA Sequence

  2. XR_004938857.1 RNA Sequence

  3. XR_004938856.1 RNA Sequence

    Related
    ENSMUST00000138036.8

  4. XR_875304.1 RNA Sequence

  5. XR_003951411.1 RNA Sequence

  6. XR_003951410.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80W14.2 GenPept UniProtKB/Swiss-Prot:Q80W14

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