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    prpf8 pre-mRNA processing factor 8 [ Danio rerio (zebrafish) ]

    Gene ID: 393951, updated on 2-Nov-2024

    Summary

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    Official Symbol
    prpf8provided by ZNC
    Official Full Name
    pre-mRNA processing factor 8provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-577
    See related
    Ensembl:ENSDARG00000026180 AllianceGenome:ZFIN:ZDB-GENE-030131-577
    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:56504; id:ibd1257; im:7141966; tdsubc_2a9; wu:fb37c02; wu:fb73e06; ik:tdsubc_2a9; xx:tdsubc_2a9
    Summary
    Predicted to enable pre-mRNA intronic binding activity and snRNA binding activity. Acts upstream of or within spliceosomal tri-snRNP complex assembly. Predicted to be located in nucleus. Predicted to be part of U5 snRNP and catalytic step 2 spliceosome. Is expressed in brain and head. Human ortholog(s) of this gene implicated in retinitis pigmentosa and retinitis pigmentosa 13. Orthologous to human PRPF8 (pre-mRNA processing factor 8). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See prpf8 in Genome Data Viewer
    Location:
    chromosome: 15
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 15 NC_007126.7 (28249160..28262632, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 15 NC_007126.6 (28316284..28329756, complement)

    Chromosome 15 - NC_007126.7Genomic Context describing neighboring genes Neighboring gene scavenger receptor class F, member 1 Neighboring gene Rab interacting lysosomal protein Neighboring gene myosin Ic, paralog b Neighboring gene si:dkey-118k5.3

    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 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. Knocking Down Snrnp200 Initiates Demorphogenesis of Rod Photoreceptors in Zebrafish. Liu Y, et al. J Ophthalmol, 2015. PMID 26137319, Free PMC Article
    2. PRPF4 mutations cause autosomal dominant retinitis pigmentosa. Chen X, et al. Hum Mol Genet, 2014 Jun 1. PMID 24419317
    3. In vivo mutation of pre-mRNA processing factor 8 (Prpf8) affects transcript splicing, cell survival and myeloid differentiation. Keightley MC, et al. FEBS Lett, 2013 Jul 11. PMID 23714367, Free PMC Article
    4. Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy. Lee YR, et al. Nat Commun, 2020 Jul 23. PMID 32703943, Free PMC Article
    5. Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development. Tse WK, et al. BMC Genomics, 2009 Dec 30. PMID 20040115, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Within early haematopoiesis, myeloid differentiation is impaired, suggesting Prpf8 is required for haematopoietic development.
      Title: In vivo mutation of pre-mRNA processing factor 8 (Prpf8) affects transcript splicing, cell survival and myeloid differentiation.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC56504, MGC162871

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables U1 snRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables U2 snRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables U5 snRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables U5 snRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables U6 snRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables U6 snRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metallopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pre-mRNA intronic binding IBA
    Inferred from Biological aspect of Ancestor
    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
    		  
    acts_upstream_of_or_within mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spliceosomal tri-snRNP complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within spliceosomal tri-snRNP complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of U5 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    pre-mRNA-processing-splicing factor 8

    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_200976.2 → NP_957270.2  pre-mRNA-processing-splicing factor 8

      See identical proteins and their annotated locations for NP_957270.2

      Status: VALIDATED

      Source sequence(s)
      CR522882
      UniProtKB/TrEMBL
      A0A0R4J8E6, A0A8M2B4I2
      Related
      ENSDARP00000121091.2, ENSDART00000134601.3
      Conserved Domains (8) summary
      cd08056
      Location:2074 → 2324
      MPN_PRP8; Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8
      COG5178
      Location:34 → 2342
      PRP8; U5 snRNP spliceosome subunit [RNA processing and modification]
      cd13838
      Location:1773 → 2023
      RNase_H_like_Prp8_IV; Ribonuclease-like Prp8 domain IV core
      pfam08082
      Location:65 → 215
      PRO8NT; PRO8NT (NUC069), PrP8 N-terminal domain
      pfam08083
      Location:403 → 803
      PROCN; PROCN (NUC071) domain
      pfam10596
      Location:1449 → 1607
      U6-snRNA_bdg; U6-snRNA interacting domain of PrP8
      pfam10597
      Location:1217 → 1349
      U5_2-snRNA_bdg; U5-snRNA binding site 2 of PrP8
      pfam10598
      Location:993 → 1084
      RRM_4; RNA recognition motif of the spliceosomal PrP8

    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_007126.7 Reference GRCz11 Primary Assembly

      Range
      28249160..28262632 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005157646.5 → XP_005157703.1  pre-mRNA-processing-splicing factor 8 isoform X1

      See identical proteins and their annotated locations for XP_005157703.1

      UniProtKB/TrEMBL
      A0A0R4J8E6, A0A8M2B4I2
      Conserved Domains (8) summary
      cd08056
      Location:2074 → 2324
      MPN_PRP8; Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8
      COG5178
      Location:34 → 2342
      PRP8; U5 snRNP spliceosome subunit [RNA processing and modification]
      cd13838
      Location:1773 → 2023
      RNase_H_like_Prp8_IV; Ribonuclease-like Prp8 domain IV core
      pfam08082
      Location:65 → 215
      PRO8NT; PRO8NT (NUC069), PrP8 N-terminal domain
      pfam08083
      Location:403 → 803
      PROCN; PROCN (NUC071) domain
      pfam10596
      Location:1449 → 1607
      U6-snRNA_bdg; U6-snRNA interacting domain of PrP8
      pfam10597
      Location:1217 → 1349
      U5_2-snRNA_bdg; U5-snRNA binding site 2 of PrP8
      pfam10598
      Location:993 → 1084
      RRM_4; RNA recognition motif of the spliceosomal PrP8
    Nucleotide Protein Strain
    Heading Accession and Version

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