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    Prpf38b PRP38 pre-mRNA processing factor 38 (yeast) domain containing B [ Mus musculus (house mouse) ]

    Gene ID: 66921, updated on 12-May-2024

    Summary

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    Official Symbol
    Prpf38bprovided by MGI
    Official Full Name
    PRP38 pre-mRNA processing factor 38 (yeast) domain containing Bprovided by MGI
    Primary source
    MGI:MGI:1914171
    See related
    Ensembl:ENSMUSG00000027881 AllianceGenome:MGI:1914171
    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
    1110021E09Rik
    Summary
    Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of precatalytic spliceosome. Is expressed in several structures, including central nervous system; gut; male reproductive gland or organ; thymus; and urinary system. Orthologous to human PRPF38B (pre-mRNA processing factor 38B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 27.0), thymus adult (RPKM 25.1) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Prpf38b in Genome Data Viewer
    Location:
    3 F3; 3 47.92 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (108810121..108819055, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (108902805..108911729, complement)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene syntaxin binding protein 3 Neighboring gene STARR-positive B cell enhancer mm9_chr3:108642483-108642783 Neighboring gene STARR-positive B cell enhancer mm9_chr3:108643371-108643672 Neighboring gene fibronectin type III domain containing 7 Neighboring gene STARR-positive B cell enhancer ABC_E3460 Neighboring gene STARR-positive B cell enhancer ABC_E4576 Neighboring gene HEN1 methyltransferase homolog 1 (Arabidopsis) Neighboring gene EEIG family member 2 Neighboring gene predicted gene 43221

    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. Conserved expression of ultra-conserved noncoding RNA in mammalian nervous system. Zhou J, et al. Biochim Biophys Acta Gene Regul Mech, 2017 Dec. PMID 29055695
    2. Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies. Murtaza N, et al. Cell Rep, 2022 Nov 22. PMID 36417873
    3. The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Koscielny G, et al. Nucleic Acids Res, 2014 Jan. PMID 24194600, Free PMC Article
    4. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Ko MS, et al. Development, 2000 Apr. PMID 10725249
    5. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199

    See all (16) 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) 
    • Targeted (2) 

    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 MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of precatalytic spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    pre-mRNA-splicing factor 38B

    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_001356292.1 → NP_001343221.1  pre-mRNA-splicing factor 38B isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL671894
      Conserved Domains (1) summary
      TIGR01642
      Location:213 → 321
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    2. NM_025845.3 → NP_080121.1  pre-mRNA-splicing factor 38B isoform 1

      See identical proteins and their annotated locations for NP_080121.1

      Status: VALIDATED

      Source sequence(s)
      AL671894
      Consensus CDS
      CCDS17770.1
      UniProtKB/Swiss-Prot
      Q80SY5, Q9CTD9, Q9CU48, Q9CUI6
      Related
      ENSMUSP00000029480.9, ENSMUST00000029480.9
      Conserved Domains (1) summary
      pfam03371
      Location:48 → 228
      PRP38; PRP38 family

    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_000069.7 Reference GRCm39 C57BL/6J

      Range
      108810121..108819055 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036163233.1 → XP_036019126.1  pre-mRNA-splicing factor 38B isoform X3

      Conserved Domains (1) summary
      TIGR01642
      Location:226 → 334
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    2. XM_036163234.1 → XP_036019127.1  pre-mRNA-splicing factor 38B isoform X4

      Conserved Domains (1) summary
      TIGR01642
      Location:213 → 321
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    3. XM_030252761.1 → XP_030108621.1  pre-mRNA-splicing factor 38B isoform X4

      Conserved Domains (1) summary
      TIGR01642
      Location:213 → 321
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    4. XM_006501914.3 → XP_006501977.1  pre-mRNA-splicing factor 38B isoform X1

      Conserved Domains (2) summary
      TIGR01642
      Location:299 → 407
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
      pfam03371
      Location:15 → 116
      PRP38; PRP38 family

    5. XM_006501915.3 → XP_006501978.1  pre-mRNA-splicing factor 38B isoform X2

      Conserved Domains (2) summary
      TIGR01642
      Location:265 → 373
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
      pfam03371
      Location:1 → 82
      PRP38; PRP38 family

    6. XM_036163235.1 → XP_036019128.1  pre-mRNA-splicing factor 38B isoform X4

      Conserved Domains (1) summary
      TIGR01642
      Location:213 → 321
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q80SY5.1 GenPept UniProtKB/Swiss-Prot:Q80SY5

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