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    prpf39 PRP39 pre-mRNA processing factor 39 homolog (yeast) [ Danio rerio (zebrafish) ]

    Gene ID: 368864, updated on 4-Jan-2025

    Summary

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    Official Symbol
    prpf39provided by ZNC
    Official Full Name
    PRP39 pre-mRNA processing factor 39 homolog (yeast)provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030616-420
    See related
    Ensembl:ENSDARG00000100209 AllianceGenome:ZFIN:ZDB-GENE-030616-420
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fa10d07; wu:fa10d07; si:dz261o22.3
    Summary
    Predicted to contribute to pre-mRNA 5'-splice site binding activity. Predicted to be involved in mRNA 5'-splice site recognition. 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; U2-type prespliceosome; and commitment complex. Orthologous to human PRPF39 (pre-mRNA processing factor 39). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    human mouse all
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    Genomic context

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    See prpf39 in Genome Data Viewer
    Location:
    chromosome: 20
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 20 NC_007131.7 (54215014..54245372, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 20 NC_007131.6 (54478459..54508839)

    Chromosome 20 - NC_007131.7Genomic Context describing neighboring genes Neighboring gene ADP-ribosylation factor 6a Neighboring gene FAU ubiquitin like and ribosomal protein S30 fusion a Neighboring gene FKBP prolyl isomerase 3 Neighboring gene actin related protein 10

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression. Madera D, et al. Int J Mol Sci, 2023 Dec 19. PMID 38203224, Free PMC Article
    2. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
    3. 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
    4. 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 ZFIN

    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
    acts_upstream_of_or_within RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA 5'-splice site recognition IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    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
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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

    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_001004520.1 → NP_001004520.1  pre-mRNA-processing factor 39

      See identical proteins and their annotated locations for NP_001004520.1

      Status: PROVISIONAL

      Source sequence(s)
      AL591492
      UniProtKB/Swiss-Prot
      Q1JPZ7, Q801W4
      Related
      ENSDARP00000139799.1, ENSDART00000170482.2
      Conserved Domains (4) summary
      smart00386
      Location:442 → 474
      HAT; HAT (Half-A-TPR) repeats
      COG5107
      Location:148 → 495
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:495 → 524
      TPR; TPR repeat [structural motif]
      pfam13432
      Location:500 → 557
      TPR_16; Tetratricopeptide repeat

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007131.7 Reference GRCz11 Primary Assembly

      Range
      54215014..54245372 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q1JPZ7.2 GenPept UniProtKB/Swiss-Prot:Q1JPZ7

    Gene LinkOut

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

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