LOCUS       NM_015629               1833 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens pre-mRNA processing factor 31 (PRPF31), mRNA.
ACCESSION   NM_015629
VERSION     NM_015629.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1833)
  AUTHORS   Grainok,J., Pitout,I.L., Chen,F.K., McLenachan,S., Heath
            Jeffery,R.C., Mitrpant,C. and Fletcher,S.
  TITLE     A Precision Therapy Approach for Retinitis Pigmentosa 11 Using
            Splice-Switching Antisense Oligonucleotides to Restore the Open
            Reading Frame of PRPF31
  JOURNAL   Int J Mol Sci 25 (6), 3391 (2024)
   PUBMED   38542364
  REMARK    GeneRIF: A Precision Therapy Approach for Retinitis Pigmentosa 11
            Using Splice-Switching Antisense Oligonucleotides to Restore the
            Open Reading Frame of PRPF31.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1833)
  AUTHORS   Fritze,J.S., Stiehler,F.F. and Wolfrum,U.
  TITLE     Pathogenic Variants in USH1G/SANS Alter Protein Interaction with
            Pre-RNA Processing Factors PRPF6 and PRPF31 of the Spliceosome
  JOURNAL   Int J Mol Sci 24 (24), 17608 (2023)
   PUBMED   38139438
  REMARK    GeneRIF: Pathogenic Variants in USH1G/SANS Alter Protein
            Interaction with Pre-RNA Processing Factors PRPF6 and PRPF31 of the
            Spliceosome.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1833)
  AUTHORS   Chen,Z., Chen,J., Gao,M., Liu,Y., Wu,Y., Wang,Y., Gong,Y., Yu,S.,
            Liu,W., Wan,X. and Sun,X.
  TITLE     Comprehensive analysis of the PRPF31 gene in retinitis pigmentosa
            patients: Four novel Alu-mediated copy number variations at the
            PRPF31 locus
  JOURNAL   Hum Mutat 43 (12), 2279-2294 (2022)
   PUBMED   36317469
  REMARK    GeneRIF: Comprehensive analysis of the PRPF31 gene in retinitis
            pigmentosa patients: Four novel Alu-mediated copy number variations
            at the PRPF31 locus.
REFERENCE   4  (bases 1 to 1833)
  AUTHORS   Liu,S., Li,P., Dybkov,O., Nottrott,S., Hartmuth,K., Luhrmann,R.,
            Carlomagno,T. and Wahl,M.C.
  TITLE     Binding of the human Prp31 Nop domain to a composite RNA-protein
            platform in U4 snRNP
  JOURNAL   Science 316 (5821), 115-120 (2007)
   PUBMED   17412961
  REMARK    GeneRIF: structural and biochemical analyses of hPrp31-15.5K-U4
            snRNA complexes show how the conserved Nop domain in hPrp31
            maintains high RNP binding selectivity despite relaxed RNA sequence
            requirements
REFERENCE   5  (bases 1 to 1833)
  AUTHORS   Sullivan,L.S., Bowne,S.J., Seaman,C.R., Blanton,S.H., Lewis,R.A.,
            Heckenlively,J.R., Birch,D.G., Hughbanks-Wheaton,D. and Daiger,S.P.
  TITLE     Genomic rearrangements of the PRPF31 gene account for 2.5% of
            autosomal dominant retinitis pigmentosa
  JOURNAL   Invest Ophthalmol Vis Sci 47 (10), 4579-4588 (2006)
   PUBMED   17003455
  REMARK    GeneRIF: MLPA (multiplex ligation-dependent probe amplification)
            was used to identify genomic rearrangements in PRPF31 in five
            families, suggesting a frequency of approximately 2.5%.
REFERENCE   6  (bases 1 to 1833)
  AUTHORS   Vithana,E.N., Abu-Safieh,L., Allen,M.J., Carey,A., Papaioannou,M.,
            Chakarova,C., Al-Maghtheh,M., Ebenezer,N.D., Willis,C., Moore,A.T.,
            Bird,A.C., Hunt,D.M. and Bhattacharya,S.S.
  TITLE     A human homolog of yeast pre-mRNA splicing gene, PRP31, underlies
            autosomal dominant retinitis pigmentosa on chromosome 19q13.4
            (RP11)
  JOURNAL   Mol Cell 8 (2), 375-381 (2001)
   PUBMED   11545739
REFERENCE   7  (bases 1 to 1833)
  AUTHORS   Al-Maghtheh,M., Vithana,E., Tarttelin,E., Jay,M., Evans,K.,
            Moore,T., Bhattacharya,S. and Inglehearn,C.F.
  TITLE     Evidence for a major retinitis pigmentosa locus on 19q13.4 (RP11)
            and association with a unique bimodal expressivity phenotype
  JOURNAL   Am J Hum Genet 59 (4), 864-871 (1996)
   PUBMED   8808602
REFERENCE   8  (bases 1 to 1833)
  AUTHORS   al-Maghtheh,M., Inglehearn,C.F., Keen,T.J., Evans,K., Moore,A.T.,
            Jay,M., Bird,A.C. and Bhattacharya,S.S.
  TITLE     Identification of a sixth locus for autosomal dominant retinitis
            pigmentosa on chromosome 19
  JOURNAL   Hum Mol Genet 3 (2), 351-354 (1994)
   PUBMED   8004108
REFERENCE   9  (bases 1 to 1833)
  AUTHORS   Fahim,A.T., Daiger,S.P. and Weleber,R.G.
  TITLE     Nonsyndromic Retinitis Pigmentosa Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301590
REFERENCE   10 (bases 1 to 1833)
  AUTHORS   Tarizzo,M.L.
  TITLE     The World Health Organization and the prevention of blindness
  JOURNAL   Trans Sect Ophthalmol Am Acad Ophthalmol Otolaryngol 79 (3 Pt 2),
            OP453-OP456 (1975)
   PUBMED   1154573
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC117389.1 and CB854773.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_015629.3.
            
            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].
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AB593025.1, SRR3476690.463790.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000321030.9/ ENSP00000324122.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1579              BC117389.1         269-1847
            1580-1833           CB854773.1         25-278              c
FEATURES             Location/Qualifiers
     source          1..1833
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="19"
                     /map="19q13.42"
     gene            1..1833
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /note="pre-mRNA processing factor 31"
                     /db_xref="GeneID:26121"
                     /db_xref="HGNC:HGNC:15446"
                     /db_xref="MIM:606419"
     exon            1..44
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            45..229
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     CDS             53..1552
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /note="hPrp31; protein 61K; PRP31 pre-mRNA processing
                     factor 31 homolog; U4/U6 snRNP 61 kDa protein;
                     serologically defined breast cancer antigen NY-BR-99"
                     /codon_start=1
                     /product="U4/U6 small nuclear ribonucleoprotein Prp31"
                     /protein_id="NP_056444.3"
                     /db_xref="CCDS:CCDS12879.1"
                     /db_xref="GeneID:26121"
                     /db_xref="HGNC:HGNC:15446"
                     /db_xref="MIM:606419"
                     /translation="MSLADELLADLEEAAEEEEGGSYGEEEEEPAIEDVQEETQLDLS
                     GDSVKTIAKLWDSKMFAEIMMKIEEYISKQAKASEVMGPVEAAPEYRVIVDANNLTVE
                     IENELNIIHKFIRDKYSKRFPELESLVPNALDYIRTVKELGNSLDKCKNNENLQQILT
                     NATIMVVSVTASTTQGQQLSEEELERLEEACDMALELNASKHRIYEYVESRMSFIAPN
                     LSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQRKTLSGFSSTSVLPHTGYIYH
                     SDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTEGKVGYELKDEIERKFDKWQEP
                     PPVKQVKPLPAPLDGQRKKRGGRRYRKMKERLGLTEIRKQANRMSFGEIEEDAYQEDL
                     GFSLGHLGKSGSGRVRQTQVNEATKARISKTLQRTLQKQSVVYGGKSTIRDRSSGTAS
                     SVAFTPLQGLEIVNPQAAEKKVAEANQKYFSSMAEFLKVKGEKSGLMST"
     exon            230..290
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            291..374
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            375..472
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            473..579
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            580..749
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            750..907
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            908..997
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            998..1125
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            1126..1198
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            1199..1327
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            1328..1426
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     exon            1427..1833
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1813..1818
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /note="hexamer: ATTAAA"
     polyA_site      1833
                     /gene="PRPF31"
                     /gene_synonym="NY-BR-99; PRP31; RP11; SNRNP61"
                     /note="major polyA site"
ORIGIN      
        1 ggtgagcgac taacgctaga aacagtggtg cgcggagagg agaggcctcg ggatgtctct
       61 ggcagatgag ctcttagctg atctcgaaga ggcagcagaa gaggaggaag gaggaagcta
      121 tggggaggaa gaagaggagc cagcgatcga ggatgtgcag gaggagacac agctggatct
      181 ttccggggat tcagtcaaga ccatcgccaa gctatgggat agtaagatgt ttgctgagat
      241 tatgatgaag attgaggagt atatcagcaa gcaagccaaa gcttcagaag tgatgggacc
      301 agtggaggcc gcgcctgaat accgcgtcat cgtggatgcc aacaacctga ccgtggagat
      361 cgaaaacgag ctgaacatca tccataagtt catccgggat aagtactcaa agagattccc
      421 tgaactggag tccttggtcc ccaatgcact ggattacatc cgcacggtca aggagctggg
      481 caacagcctg gacaagtgca agaacaatga gaacctgcag cagatcctca ccaatgccac
      541 catcatggtc gtcagcgtca ccgcctccac cacccagggg cagcagctgt cggaggagga
      601 gctggagcgg ctggaggagg cctgcgacat ggcgctggag ctgaacgcct ccaagcaccg
      661 catctacgag tatgtggagt cccggatgtc cttcatcgca cccaacctgt ccatcattat
      721 cggggcatcc acggccgcca agatcatggg tgtggccggc ggcctgacca acctctccaa
      781 gatgcccgcc tgcaacatca tgctgctcgg ggcccagcgc aagacgctgt cgggcttctc
      841 gtctacctca gtgctgcccc acaccggcta catctaccac agtgacatcg tgcagtccct
      901 gccaccggat ctgcggcgga aagcggcccg gctggtggcc gccaagtgca cactggcagc
      961 ccgtgtggac agtttccacg agagcacaga agggaaggtg ggctacgaac tgaaggatga
     1021 gatcgagcgc aaattcgaca agtggcagga gccgccgcct gtgaagcagg tgaagccgct
     1081 gcctgcgccc ctggatggac agcggaagaa gcgaggcggc cgcaggtacc gcaagatgaa
     1141 ggagcggctg gggctgacgg agatccggaa gcaggccaac cgtatgagct tcggagagat
     1201 cgaggaggac gcctaccagg aggacctggg attcagcctg ggccacctgg gcaagtcggg
     1261 cagtgggcgt gtgcggcaga cacaggtaaa cgaggccacc aaggccagga tctccaagac
     1321 gctgcagcgg accctgcaga agcagagcgt cgtatatggc gggaagtcca ccatccgcga
     1381 ccgctcctcg ggcacggcct ccagcgtggc cttcacccca ctccagggcc tggagattgt
     1441 gaacccacag gcggcagaga agaaggtggc tgaggccaac cagaagtatt tctccagcat
     1501 ggctgagttc ctcaaggtca agggcgagaa gagtggcctt atgtccacct gaatgactgc
     1561 gtgtgtccaa ggtggcttcc cactgaaggg acacagaggt ccagtccttc tgaagggcta
     1621 ggatcgggtt ctggcaggga gaacctgccc tgccactggc cccattgctg ggactgccca
     1681 gggaggaggc cttggaagag tccggcctgg cctcccccag gaccgagatc accgcccagt
     1741 atgggctaga gcaggtcttc atcatgcctt gtctttttta actgagaaag gagatttttt
     1801 gaaaagagta caattaaaag gacattgtca aga
//
