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PRPF6 pre-mRNA processing factor 6 [ Homo sapiens (human) ]

Gene ID: 24148, updated on 10-Dec-2024

Summary

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Official Symbol
PRPF6provided by HGNC
Official Full Name
pre-mRNA processing factor 6provided by HGNC
Primary source
HGNC:HGNC:15860
See related
Ensembl:ENSG00000101161 MIM:613979; AllianceGenome:HGNC:15860
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TOM; ANT1; Prp6; RP60; ANT-1; hPrp6; U5-102K; C20orf14; SNRNP102
Summary
The protein encoded by this gene appears to be involved in pre-mRNA splicing, possibly acting as a bridging factor between U5 and U4/U6 snRNPs in formation of the spliceosome. The encoded protein also can bind androgen receptor, providing a link between transcriptional activation and splicing. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 30.6), ovary (RPKM 27.5) and 25 other tissues See more
Orthologs
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Genomic context

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See PRPF6 in Genome Data Viewer
Location:
20q13.33
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63981132..64033100)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65800894..65853046)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62612485..62664453)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62587955-62588842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62588843-62589728 Neighboring gene UCKL1 antisense RNA 1 Neighboring gene zinc finger protein 512B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62599635-62600172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62600173-62600708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13196 Neighboring gene Sharpr-MPRA regulatory region 2003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62610429-62610944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13198 Neighboring gene sterile alpha motif domain containing 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62631004-62631506 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62636447-62636619 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:62642795-62643994 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:62648052-62649251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62667815-62668408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62668409-62669002 Neighboring gene chromosome 20 open reading frame 204 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62676871-62677791 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13204 Neighboring gene SOX18 promoter region Neighboring gene SRY-box transcription factor 18

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. The expression and bioinformatic analysis of a novel gene C20orf14 associated with lymphoma. Su L, et al. J Huazhong Univ Sci Technolog Med Sci, 2008 Feb. PMID 18278469
  2. A novel mammalian nuclear protein similar to Schizosaccharomyces pombe Prp1p/Zer1p and Saccharomyces cerevisiae Prp6p pre-mRNA splicing factors. Nishikimi A, et al. Biochim Biophys Acta, 1999 Nov 16. PMID 10561546
  3. Activation function-1 domain of androgen receptor contributes to the interaction between two distinct subnuclear compartments. Goto K, et al. J Steroid Biochem Mol Biol, 2003 Jun. PMID 12943705
  4. PRPF6 promotes metastasis and paclitaxel resistance of ovarian cancer via SNHG16/CEBPB/GATA3 axis. Wang H, et al. Oncol Res, 2021. PMID 37303939, Free PMC Article
  5. An integrative analysis of colon cancer identifies an essential function for PRPF6 in tumor growth. Adler AS, et al. Genes Dev, 2014 May 15. PMID 24788092, Free PMC Article

See all (206) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Pathogenic Variants in USH1G/SANS Alter Protein Interaction with Pre-RNA Processing Factors PRPF6 and PRPF31 of the Spliceosome.
    Title: Pathogenic Variants in USH1G/SANS Alter Protein Interaction with Pre-RNA Processing Factors PRPF6 and PRPF31 of the Spliceosome.
  2. PRPF6 promotes metastasis and paclitaxel resistance of ovarian cancer via SNHG16/CEBPB/GATA3 axis.
    Title: PRPF6 promotes metastasis and paclitaxel resistance of ovarian cancer via SNHG16/CEBPB/GATA3 axis.
  3. PRPF6 promotes androgen receptor/androgen receptor-variant 7 actions in castration-resistant prostate cancer cells.
    Title: PRPF6 promotes androgen receptor/androgen receptor-variant 7 actions in castration-resistant prostate cancer cells.
  4. Splicing factor PRPF6 upregulates oncogenic androgen receptor signaling pathway in hepatocellular carcinoma.
    Title: Splicing factor PRPF6 upregulates oncogenic androgen receptor signaling pathway in hepatocellular carcinoma.
  5. an essential role for PRPF6 in cancer via splicing of distinct growth-related gene products.
    Title: An integrative analysis of colon cancer identifies an essential function for PRPF6 in tumor growth.
  6. Our results identify PRPF6 as the sixth gene involved in pre-mRNA splicing and dominant RP, corroborating the hypothesis that deficiencies in the spliceosome play an important role in the molecular pathology of this disease.
    Title: A missense mutation in PRPF6 causes impairment of pre-mRNA splicing and autosomal-dominant retinitis pigmentosa.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: New genetic associations detected in a host response study to hepatitis B vaccine.
  8. The authors provide evidence that PRP6 and PRP31 are directly phosphorylated by human PRP4 kinase (PRP4K) concomitant with their incorporation into B complexes.
    Title: Human PRP4 kinase is required for stable tri-snRNP association during spliceosomal B complex formation.
  9. C20orf14 may have a role in progression of lymphoma
    Title: The expression and bioinformatic analysis of a novel gene C20orf14 associated with lymphoma.
  10. The interaction of CD2BP2 with a tri-snRNP bridging protein (Prp6), coupled with CD2BP2's absence from the tri-snRNP, suggests it might function in tri-snRNP assembly
    Title: The human U5 snRNP 52K protein (CD2BP2) interacts with U5-102K (hPrp6), a U4/U6.U5 tri-snRNP bridging protein, but dissociates upon tri-snRNP formation.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Retinitis pigmentosa 60
MedGen: C3151434 OMIM: 613983 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
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EBI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of PRP6 pre-mRNA processing factor 6 homolog (S. cerevisiae, PRPF6) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, pre-mRNA processing factor 6 homolog (PRPF6), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with PRPF6 is increased by RRE PubMed

Go to the HIV-1, Human Interaction Database

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-macromolecule adaptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ribonucleoprotein complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within RNA localization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in RNA splicing NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in RNA splicing, via transesterification reactions NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spliceosomal complex assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in spliceosomal tri-snRNP complex assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spliceosomal tri-snRNP complex assembly IC
Inferred by Curator
more info
 PubMed 
involved_in spliceosomal tri-snRNP complex assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spliceosomal tri-snRNP complex assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4/U6 x U5 tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U4/U6 x U5 tri-snRNP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4/U6 x U5 tri-snRNP complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of U5 snRNP IDA
Inferred from Direct Assay
more info
 PubMed 
part_of catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane HDA PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of spliceosomal complex NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
pre-mRNA-processing factor 6
Names
PRP6 homolog
PRP6 pre-mRNA processing factor 6 homolog
U5 snRNP-associated 102 kDa protein
U5-102 kDa protein
androgen receptor N-terminal domain transactivating protein-1
p102 U5 small nuclear ribonucleoprotein particle-binding protein
putative mitochondrial outer membrane protein import receptor

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.

Genomic

  1. NG_029719.1 RefSeqGene

    Range
    5055..57023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_012469.4 → NP_036601.2  pre-mRNA-processing factor 6

    See identical proteins and their annotated locations for NP_036601.2

    Status: REVIEWED

    Source sequence(s)
    AF221842, BP366197
    Consensus CDS
    CCDS13550.1
    UniProtKB/Swiss-Prot
    B2RAR5, B3KMC6, O94906, O95109, Q5VXS5, Q9H3Z1, Q9H4T9, Q9H4U8, Q9NTE6
    Related
    ENSP00000266079.4, ENST00000266079.5
    Conserved Domains (3) summary
    TIGR02917
    Location:290 → 846
    PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
    sd00006
    Location:708 → 738
    TPR; TPR repeat [structural motif]
    pfam06424
    Location:13 → 169
    PRP1_N; PRP1 splicing factor, N-terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    63981132..64033100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006723769.4 → XP_006723832.1  pre-mRNA-processing factor 6 isoform X1

    Conserved Domains (3) summary
    sd00006
    Location:635 → 665
    TPR; TPR repeat [structural motif]
    pfam06424
    Location:13 → 169
    PRP1_N; PRP1 splicing factor, N-terminal
    cl26002
    Location:289 → 773
    TPR_11; TPR repeat

RNA

  1. XR_007067448.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65800894..65853046
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054323309.1 → XP_054179284.1  pre-mRNA-processing factor 6 isoform X1

RNA

  1. XR_008485248.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O94906.1 GenPept UniProtKB/Swiss-Prot:O94906

Gene LinkOut

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

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