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    Prpf38b pre-mRNA processing factor 38B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 499691, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Prpf38bprovided by RGD
    Official Full Name
    pre-mRNA processing factor 38Bprovided by RGD
    Primary source
    RGD:1562940
    See related
    EnsemblRapid:ENSRNOG00000020438 AllianceGenome:RGD:1562940
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be part of precatalytic spliceosome. Orthologous to human PRPF38B (pre-mRNA processing factor 38B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 248.5), Spleen (RPKM 183.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Prpf38b in Genome Data Viewer
    Location:
    2q34
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (199241312..199250342, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (196553224..196562271, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (211706245..211715271, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134485674 Neighboring gene fibronectin type III domain containing 7 Neighboring gene microRNA 6314 Neighboring gene HEN methyltransferase 1 Neighboring gene EEIG family member 2

    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
    • 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. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    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
    Names
    PRP38 pre-mRNA processing factor 38 domain containing B

    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_001024305.2 → NP_001019476.1  pre-mRNA-splicing factor 38B

      See identical proteins and their annotated locations for NP_001019476.1

      Status: VALIDATED

      Source sequence(s)
      BC079264, BF283777, CB720005, DY314904
      UniProtKB/Swiss-Prot
      Q6AXY7
      UniProtKB/TrEMBL
      A6HV34
      Related
      ENSRNOP00000027738.4, ENSRNOT00000027738.7
      Conserved Domains (2) summary
      pfam03371
      Location:47 → 227
      PRP38; PRP38 family
      pfam08648
      Location:443 → 542
      DUF1777; Protein of unknown function (DUF1777)

    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_086020.1 Reference GRCr8

      Range
      199241312..199250342 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006233172.4 → XP_006233234.1  pre-mRNA-splicing factor 38B isoform X1

      See identical proteins and their annotated locations for XP_006233234.1

      Conserved Domains (1) summary
      pfam03371
      Location:18 → 152
      PRP38; PRP38 family

    2. XM_039102942.2 → XP_038958870.1  pre-mRNA-splicing factor 38B isoform X2

      Conserved Domains (1) summary
      pfam03371
      Location:15 → 116
      PRP38; PRP38 family

    3. XM_039102941.2 → XP_038958869.1  pre-mRNA-splicing factor 38B isoform X2

      Conserved Domains (1) summary
      pfam03371
      Location:15 → 116
      PRP38; PRP38 family

    4. XM_063282405.1 → XP_063138475.1  pre-mRNA-splicing factor 38B isoform X3

    RNA

    1. XR_005500347.2 RNA Sequence

    2. XR_010063654.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6AXY7.1 GenPept UniProtKB/Swiss-Prot:Q6AXY7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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