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

Gene ID: 55015, updated on 5-Mar-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
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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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