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    Prpf39 pre-mRNA processing factor 39 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 314171, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Prpf39provided by RGD
    Official Full Name
    pre-mRNA processing factor 39provided by RGD
    Primary source
    RGD:1308702
    See related
    EnsemblRapid:ENSRNOG00000004521 AllianceGenome:RGD:1308702
    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 contribute to pre-mRNA 5'-splice site binding activity. Predicted to be involved in mRNA 5'-splice site recognition. Predicted to be part of U1 snRNP; U2-type prespliceosome; and commitment complex. Orthologous to human PRPF39 (pre-mRNA processing factor 39). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 218.1), Spleen (RPKM 212.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Prpf39 in Genome Data Viewer
    Location:
    6q24
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (88825227..88851342)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (83088981..83113826)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (86785793..86810806)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene kelch-like family member 28 Neighboring gene TOG array regulator of axonemal microtubules 1 Neighboring gene small nucleolar RNA, C/D box 127 Neighboring gene FKBP prolyl isomerase 3 Neighboring gene FA complementation group M Neighboring gene MIS18 binding protein 1 Neighboring gene FAU ubiquitin like and ribosomal protein S30 fusion like 1

    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. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    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

    Function Evidence Code Pubs
    contributes_to pre-mRNA 5'-splice site binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA 5'-splice site recognition 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
    		  
    part_of commitment complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    pre-mRNA-processing factor 39
    Names
    PRP39 pre-mRNA processing factor 39 homolog

    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_001108026.2 → NP_001101496.2  pre-mRNA-processing factor 39

      Status: VALIDATED

      Source sequence(s)
      BQ782205, JAXUCZ010000006
      UniProtKB/TrEMBL
      D4A5S9
      Related
      ENSRNOP00000061487.1, ENSRNOT00000066702.6
      Conserved Domains (2) summary
      COG5107
      Location:67 → 537
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:452 → 480
      TPR; TPR repeat [structural motif]

    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_086024.1 Reference GRCr8

      Range
      88825227..88851342
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039112247.2 → XP_038968175.1  pre-mRNA-processing factor 39 isoform X2

      Conserved Domains (1) summary
      COG5107
      Location:67 → 263
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

    2. XM_063261917.1 → XP_063117987.1  pre-mRNA-processing factor 39 isoform X2

    3. XM_006240140.4 → XP_006240202.1  pre-mRNA-processing factor 39 isoform X1

      See identical proteins and their annotated locations for XP_006240202.1

      UniProtKB/TrEMBL
      A0A8I5YBM8
      Conserved Domains (2) summary
      COG5107
      Location:40 → 419
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:334 → 362
      TPR; TPR repeat [structural motif]

    4. XM_006240141.4 → XP_006240203.1  pre-mRNA-processing factor 39 isoform X1

      See identical proteins and their annotated locations for XP_006240203.1

      UniProtKB/TrEMBL
      A0A8I5YBM8
      Conserved Domains (2) summary
      COG5107
      Location:40 → 419
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:334 → 362
      TPR; TPR repeat [structural motif]

    5. XM_006240143.4 → XP_006240205.1  pre-mRNA-processing factor 39 isoform X1

      See identical proteins and their annotated locations for XP_006240205.1

      UniProtKB/TrEMBL
      A0A8I5YBM8
      Related
      ENSRNOP00000077104.1, ENSRNOT00000110268.2
      Conserved Domains (2) summary
      COG5107
      Location:40 → 419
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:334 → 362
      TPR; TPR repeat [structural motif]

    6. XM_006240144.4 → XP_006240206.1  pre-mRNA-processing factor 39 isoform X1

      See identical proteins and their annotated locations for XP_006240206.1

      UniProtKB/TrEMBL
      A0A8I5YBM8
      Conserved Domains (2) summary
      COG5107
      Location:40 → 419
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:334 → 362
      TPR; TPR repeat [structural motif]
    Nucleotide Protein Strain
    Heading Accession and Version

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