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    PRPF39 pre-mRNA processing factor 39 [ Homo sapiens (human) ]

    Gene ID: 55015, updated on 5-May-2024

    Summary

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    Official Symbol
    PRPF39provided by HGNC
    Official Full Name
    pre-mRNA processing factor 39provided by HGNC
    Primary source
    HGNC:HGNC:20314
    See related
    Ensembl:ENSG00000185246 MIM:614907; AllianceGenome:HGNC:20314
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to be involved in mRNA 5'-splice site recognition. Predicted to be part of U1 snRNP; U2-type prespliceosome; and commitment complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in skin (RPKM 15.3), prostate (RPKM 14.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PRPF39 in Genome Data Viewer
    Location:
    14q21.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (45084116..45116282)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (39276128..39308293)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (45553319..45585485)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancers GRCh37_chr14:45430821-45431335 and GRCh37_chr14:45431336-45431850 Neighboring gene TOG array regulator of axonemal microtubules 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8297 Neighboring gene Sharpr-MPRA regulatory region 2603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5694 Neighboring gene small nucleolar RNA SNORD58 Neighboring gene PRPF39 divergent transcript Neighboring gene small nucleolar RNA, C/D box 127 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr14:45602882-45603753 and GRCh37_chr14:45603754-45604624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8299 Neighboring gene FKBP prolyl isomerase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8301 Neighboring gene FA complementation group M Neighboring gene NANOG hESC enhancer GRCh37_chr14:45667610-45668129 Neighboring gene MIS18 binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:45720005-45720504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8303

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Functional consequences of PRPF39 on distant genes and cisplatin sensitivity. Stark AL, et al. Hum Mol Genet, 2012 Oct 1. PMID 22773733, Free PMC Article
    2. pSILAC method coupled with two complementary digestion approaches reveals PRPF39 as a new E7070-dependent DCAF15 substrate. Jia X, et al. J Proteomics, 2020 Jan 6. PMID 31626998
    3. Increased versatility despite reduced molecular complexity: evolution, structure and function of metazoan splicing factor PRPF39. De Bortoli F, et al. Nucleic Acids Res, 2019 Jun 20. PMID 30949712, Free PMC Article
    4. CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing. Li X, et al. Nat Commun, 2017 Oct 19. PMID 29051543, Free PMC Article
    5. FBXW7 Reduces the Cancer Stem Cell-Like Properties of Hepatocellular Carcinoma by Regulating the Ubiquitination and Degradation of ACTL6A. Wang X, et al. Stem Cells Int, 2022. PMID 36159747, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. organisms with higher splicing complexity have substituted the Prp39/Prp42 heterodimer with a PRPF39 homodimer
      Title: Increased versatility despite reduced molecular complexity: evolution, structure and function of metazoan splicing factor PRPF39.
    2. Knockdown of PRPF39 expression resulted in a significant expression change of downstream gene.
      Title: Functional consequences of PRPF39 on distant genes and cisplatin sensitivity.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11128, FLJ20666, FLJ45460, MGC149842, MGC149843

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to pre-mRNA 5'-splice site binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA 5'-splice site recognition IBA
    Inferred from Biological aspect of Ancestor
    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
    		  

    General protein information

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

    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_017922.4 → NP_060392.3  pre-mRNA-processing factor 39

      See identical proteins and their annotated locations for NP_060392.3

      Status: VALIDATED

      Source sequence(s)
      AL121809, BC051886, BC125126, DB339898, DC306976
      Consensus CDS
      CCDS9682.2
      UniProtKB/Swiss-Prot
      Q08AL1, Q08AL2, Q86UA1, Q9NUU5
      Related
      ENSP00000348010.6, ENST00000355765.11
      Conserved Domains (4) summary
      smart00386
      Location:367 → 399
      HAT; HAT (Half-A-TPR) repeats
      COG5107
      Location:50 → 455
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:455 → 483
      TPR; TPR repeat [structural motif]
      pfam13432
      Location:459 → 523
      TPR_16; Tetratricopeptide repeat

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      45084116..45116282
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      39276128..39308293
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_018333.1: Suppressed sequence

      Description
      NM_018333.1: This RefSeq was permanently suppressed because currently there is not sufficient data to support this transcript, and the CDS is partial.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86UA1.3 GenPept UniProtKB/Swiss-Prot:Q86UA1

    Gene LinkOut

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

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