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    PRPF31 pre-mRNA processing factor 31 [ Homo sapiens (human) ]

    Gene ID: 26121, updated on 5-May-2024

    Summary

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    Official Symbol
    PRPF31provided by HGNC
    Official Full Name
    pre-mRNA processing factor 31provided by HGNC
    Primary source
    HGNC:HGNC:15446
    See related
    Ensembl:ENSG00000105618 MIM:606419; AllianceGenome:HGNC:15446
    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
    RP11; PRP31; SNRNP61; NY-BR-99
    Summary
    This gene encodes a component of the spliceosome complex and is one of several retinitis pigmentosa-causing genes. When the gene product is added to the spliceosome complex, activation occurs.[provided by RefSeq, Jan 2009]
    Expression
    Ubiquitous expression in spleen (RPKM 14.1), endometrium (RPKM 14.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    19q13.42
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54115754..54131713)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57194406..57210410)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (54619134..54635144)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene osteoclast associated Ig-like receptor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54605952-54606928 Neighboring gene NADH:ubiquinone oxidoreductase subunit A3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54617323-54618196 Neighboring gene TCF3 fusion partner Neighboring gene PRPF31 antisense RNA 1 Neighboring gene CCR4-NOT transcription complex subunit 3 Neighboring gene uncharacterized LOC102724273 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:54662792-54663461 Neighboring gene leukocyte receptor cluster member 1

    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. Comprehensive analysis of the PRPF31 gene in retinitis pigmentosa patients: Four novel Alu-mediated copy number variations at the PRPF31 locus. Chen Z, et al. Hum Mutat, 2022 Dec. PMID 36317469
    2. Disease progression of retinitis pigmentosa caused by PRPF31 variants in a Nordic population: a retrospective study with up to 36 years follow-up. Lisbjerg K, et al. Ophthalmic Genet, 2023 Apr. PMID 36164253
    3. Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells. Georgiou M, et al. Clin Transl Med, 2022 Mar. PMID 35297555, Free PMC Article
    4. Clinical Evidence for the Importance of the Wild-Type PRPF31 Allele in the Phenotypic Expression of RP11. Roshandel D, et al. Genes (Basel), 2021 Jun 14. PMID 34198599, Free PMC Article
    5. Heterozygous deletions of noncoding parts of the PRPF31 gene cause retinitis pigmentosa via reduced gene expression. Ruberto FP, et al. Mol Vis, 2021. PMID 33907366, Free PMC Article

    See all (238) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A Precision Therapy Approach for Retinitis Pigmentosa 11 Using Splice-Switching Antisense Oligonucleotides to Restore the Open Reading Frame of PRPF31.
      Title: A Precision Therapy Approach for Retinitis Pigmentosa 11 Using Splice-Switching Antisense Oligonucleotides to Restore the Open Reading Frame of PRPF31.
    2. 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.
    3. Long Noncoding RNA RP11-89K21.1 Interacts with miR-146a/b-5p to Promote Proliferation and Gefitinib Resistance Through Regulating RHPN2 and RhoA/ROCK Pathway in Lung Adenocarcinoma.
      Title: Long Noncoding RNA RP11-89K21.1 Interacts with miR-146a/b-5p to Promote Proliferation and Gefitinib Resistance Through Regulating RHPN2 and RhoA/ROCK Pathway in Lung Adenocarcinoma.
    4. Disease progression of retinitis pigmentosa caused by PRPF31 variants in a Nordic population: a retrospective study with up to 36 years follow-up.
      Title: Disease progression of retinitis pigmentosa caused by PRPF31 variants in a Nordic population: a retrospective study with up to 36 years follow-up.
    5. Comprehensive analysis of the PRPF31 gene in retinitis pigmentosa patients: Four novel Alu-mediated copy number variations at the PRPF31 locus.
      Title: Comprehensive analysis of the PRPF31 gene in retinitis pigmentosa patients: Four novel Alu-mediated copy number variations at the PRPF31 locus.
    6. PRPF31 interacts with PRPH2 confirmed by co-immunoprecipitation and co-localization.
      Title: PRPF31 interacts with PRPH2 confirmed by co-immunoprecipitation and co-localization.
    7. LncRNA RP11805J14.5 functions as a ceRNA to regulate CCND2 by sponging miR34b3p and miR1395p in lung adenocarcinoma.
      Title: LncRNA RP11‑805J14.5 functions as a ceRNA to regulate CCND2 by sponging miR‑34b‑3p and miR‑139‑5p in lung adenocarcinoma.
    8. Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells.
      Title: Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells.
    9. Determinants of Disease Penetrance in PRPF31-Associated Retinopathy.
      Title: Determinants of Disease Penetrance in PRPF31-Associated Retinopathy.
    10. Molecular genetics of inherited retinal degenerations in Icelandic patients.
      Title: Molecular genetics of inherited retinal degenerations in Icelandic patients.
    Submit: New GeneRIF Correction See all GeneRIFs (84)

    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 11
    MedGen: C1838601 OMIM: 600138 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
    		Compare labs

    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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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, pre-mRNA processing factor 31 homolog (PRPF31), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells 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

    Clone Names

    • DKFZp566J153

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables U4 snRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables U4atac snRNA 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 
    enables snRNP binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    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 
    acts_upstream_of_or_within mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    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 
    involved_in ribonucleoprotein complex localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    NOT involved_in snoRNA localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within spliceosomal tri-snRNP complex assembly IDA
    Inferred from Direct Assay
    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
    located_in Cajal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of MLL1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U2-type precatalytic spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U2-type spliceosomal complex IC
    Inferred by Curator
    more info
    		 PubMed 
    part_of U4 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U4 snRNP IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 U4atac snRNP IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U4atac snRNP TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    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 precatalytic spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal tri-snRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    U4/U6 small nuclear ribonucleoprotein Prp31
    Names
    PRP31 pre-mRNA processing factor 31 homolog
    U4/U6 snRNP 61 kDa protein
    hPrp31
    protein 61K
    serologically defined breast cancer antigen NY-BR-99

    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_009759.2 RefSeqGene

      Range
      5002..20961
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015629.4 → NP_056444.3  U4/U6 small nuclear ribonucleoprotein Prp31

      See identical proteins and their annotated locations for NP_056444.3

      Status: REVIEWED

      Source sequence(s)
      BC117389, CB854773
      Consensus CDS
      CCDS12879.1
      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439
      UniProtKB/TrEMBL
      E7EVX8
      Related
      ENSP00000324122.4, ENST00000321030.9
      Conserved Domains (2) summary
      pfam01798
      Location:100 → 330
      Nop; snoRNA binding domain, fibrillarin
      pfam09785
      Location:337 → 465
      Prp31_C; Prp31 C terminal domain

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      54115754..54131713
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006723137.5 → XP_006723200.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      See identical proteins and their annotated locations for XP_006723200.1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439
      UniProtKB/TrEMBL
      E7EVX8
      Conserved Domains (2) summary
      pfam01798
      Location:100 → 330
      Nop; snoRNA binding domain, fibrillarin
      pfam09785
      Location:337 → 465
      Prp31_C; Prp31 C terminal domain

    2. XM_047438587.1 → XP_047294543.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

      Related
      ENSP00000395894.1, ENST00000445811.5

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003571054.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      90247..106257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329672.1 → XP_054185647.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

    2. XM_054329673.1 → XP_054185648.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X3

    3. XM_054329674.1 → XP_054185649.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NW_003571055.2 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      90202..106257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330157.1 → XP_054186132.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    2. XM_054330156.1 → XP_054186131.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NW_003571056.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      90247..106257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330464.1 → XP_054186439.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

    2. XM_054330465.1 → XP_054186440.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NW_003571057.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      90202..106257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330718.1 → XP_054186693.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    2. XM_054330717.1 → XP_054186692.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NW_003571058.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      90247..106257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330948.1 → XP_054186923.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

    2. XM_054330949.1 → XP_054186924.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NW_003571059.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      90247..106257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331226.1 → XP_054187201.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

    2. XM_054331227.1 → XP_054187202.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NW_003571060.1 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      90202..106257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331502.1 → XP_054187477.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    2. XM_054331501.1 → XP_054187476.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

    Reference GRCh38.p14 ALT_REF_LOCI_8

    Genomic

    1. NW_003571061.2 Reference GRCh38.p14 ALT_REF_LOCI_8

      Range
      90247..106257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333537.1 → XP_054189512.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

    2. XM_054333538.1 → XP_054189513.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X4

    3. XM_054333539.1 → XP_054189514.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_9

    Genomic

    1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

      Range
      90247..106257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333639.1 → XP_054189614.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439

    2. XM_054333640.1 → XP_054189615.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      57194406..57210410
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320498.1 → XP_054176473.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X2

    2. XM_054320497.1 → XP_054176472.1  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1

      UniProtKB/Swiss-Prot
      E7ESA8, F1T0A4, F1T0A5, Q17RB4, Q8N7F9, Q8WWY3, Q9H271, Q9Y439
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WWY3.2 GenPept UniProtKB/Swiss-Prot:Q8WWY3

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