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

Gene ID: 368864, updated on 2-Nov-2024

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, Nov 2024]
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 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

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