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

    Gene ID: 54614, updated on 27-Nov-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 be located in nuclear speck. 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, Nov 2024]
    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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    See Prpf40b in Genome Data Viewer
    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. Genetic determinants of micronucleus formation in vivo. Adams DJ, et al. Nature, 2024 Mar. PMID 38355793, Free PMC Article
    5. 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

    See all (14) 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
    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
    		  
    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 speck 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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