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    prpf31 PRP31 pre-mRNA processing factor 31 homolog (yeast) [ Danio rerio (zebrafish) ]

    Gene ID: 393476, updated on 9-Dec-2024

    Summary

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    Official Symbol
    prpf31provided by ZNC
    Official Full Name
    PRP31 pre-mRNA processing factor 31 homolog (yeast)provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-1561
    See related
    Ensembl:ENSDARG00000095904 AllianceGenome:ZFIN:ZDB-GENE-040426-1561
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:66177
    Summary
    Predicted to enable U4atac snRNA binding activity. Acts upstream of or within mRNA splicing, via spliceosome; regulation of alternative mRNA splicing, via spliceosome; and retina development in camera-type eye. Predicted to be located in nucleus. Predicted to be part of nucleus. Is expressed in brain; head; retina; and retinal neural layer. Used to study retinitis pigmentosa. Human ortholog(s) of this gene implicated in retinitis pigmentosa 11. Orthologous to human PRPF31 (pre-mRNA processing factor 31). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See prpf31 in Genome Data Viewer
    Location:
    chromosome: 16
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 16 NC_007127.7 (32082334..32090673)
    105 previous assembly GRCz10 (GCF_000002035.5) 16 NC_007127.6 (32128345..32136643)

    Chromosome 16 - NC_007127.7Genomic Context describing neighboring genes Neighboring gene leukocyte receptor cluster (LRC) member 1 Neighboring gene lemur tyrosine kinase 3 Neighboring gene uncharacterized LOC137487923 Neighboring gene CCR4-NOT transcription complex, subunit 3a

    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. Mutant Prpf31 causes pre-mRNA splicing defects and rod photoreceptor cell degeneration in a zebrafish model for Retinitis pigmentosa. Yin J, et al. Mol Neurodegener, 2011 Jul 30. PMID 21801444, Free PMC Article
    2. Dysregulation of Spliceosomes Complex Induces Retinitis Pigmentosa-Like Characteristics in sf3b4-Depleted Zebrafish. Ulhaq ZS, et al. Am J Pathol, 2023 Sep. PMID 37263342
    3. Knocking Down Snrnp200 Initiates Demorphogenesis of Rod Photoreceptors in Zebrafish. Liu Y, et al. J Ophthalmol, 2015. PMID 26137319, Free PMC Article
    4. PRPF4 mutations cause autosomal dominant retinitis pigmentosa. Chen X, et al. Hum Mol Genet, 2014 Jun 1. PMID 24419317
    5. Anxiety-related behavior and associated brain transcriptome and epigenome alterations in adult female zebrafish exposed to atrazine during embryogenesis. Horzmann KA, et al. Chemosphere, 2022 Dec. PMID 36126741

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The splicing factor Prpf31 is required for hematopoietic stem and progenitor cell expansion during zebrafish embryogenesis.
      Title: The splicing factor Prpf31 is required for hematopoietic stem and progenitor cell expansion during zebrafish embryogenesis.
    2. Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing.
      Title: Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Clone Names

    • MGC66177

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables U4atac snRNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within regulation of alternative mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within retina development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within spliceosomal tri-snRNP complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Cajal body IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of MLL1 complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of U2-type precatalytic spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of U4 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U4/U6 x U5 tri-snRNP complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of U4/U6 x U5 tri-snRNP complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of U4atac snRNP ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of precatalytic spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of spliceosomal tri-snRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    U4/U6 small nuclear ribonucleoprotein Prp31
    Names
    pre-mRNA-processing factor 31

    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_200504.2 → NP_956798.1  U4/U6 small nuclear ribonucleoprotein Prp31

      See identical proteins and their annotated locations for NP_956798.1

      Status: VALIDATED

      Source sequence(s)
      CR854927
      UniProtKB/Swiss-Prot
      Q7SXM7
      UniProtKB/TrEMBL
      B2GS36
      Related
      ENSDARP00000120708.1, ENSDART00000137029.2
      Conserved Domains (3) summary
      smart00931
      Location:104 → 155
      NOSIC; NOSIC (NUC001) domain
      pfam01798
      Location:110 → 340
      Nop; snoRNA binding domain, fibrillarin
      pfam09785
      Location:348 → 476
      Prp31_C; Prp31 C terminal domain

    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_007127.7 Reference GRCz11 Primary Assembly

      Range
      32082334..32090673
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7SXM7.1 GenPept UniProtKB/Swiss-Prot:Q7SXM7

    Gene LinkOut

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