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

    Gene ID: 24148, updated on 3-Nov-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
    mouse all
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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 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. 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
    2. 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
    3. PRPF6 promotes androgen receptor/androgen receptor-variant 7 actions in castration-resistant prostate cancer cells. Liu W, et al. Int J Biol Sci, 2021. PMID 33390843, Free PMC Article
    4. 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
    5. 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

    See all (203) 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
    		not available

    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)

    Genotypes

    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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