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

Gene ID: 393951, updated on 27-Mar-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. 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, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 15
Exon count:
42
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 15 NC_007126.7 (28249160..28262634, 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
  • 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: Danio rerio Annotation Release 106 details...Open this link in a new tab

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..28262634 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005157646.4 → 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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