LOCUS       NM_004698               2414 bp    mRNA    linear   PRI 20-FEB-2025
DEFINITION  Homo sapiens pre-mRNA processing factor 3 (PRPF3), transcript
            variant 1, mRNA.
ACCESSION   NM_004698
VERSION     NM_004698.4
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 2414)
  AUTHORS   Khoroshkin,M., Buyan,A., Dodel,M., Navickas,A., Yu,J., Trejo,F.,
            Doty,A., Baratam,R., Zhou,S., Lee,S.B., Joshi,T., Garcia,K.,
            Choi,B., Miglani,S., Subramanyam,V., Modi,H., Carpenter,C.,
            Markett,D., Corces,M.R., Mardakheh,F.K., Kulakovskiy,I.V. and
            Goodarzi,H.
  TITLE     Systematic identification of post-transcriptional regulatory
            modules
  JOURNAL   Nat Commun 15 (1), 7872 (2024)
   PUBMED   39251607
  REMARK    Erratum:[Nat Commun. 2024 Oct 28;15(1):9277. doi:
            10.1038/s41467-024-52903-4.. PMID: 39468017]
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2414)
  AUTHORS   Cho,N.H., Cheveralls,K.C., Brunner,A.D., Kim,K., Michaelis,A.C.,
            Raghavan,P., Kobayashi,H., Savy,L., Li,J.Y., Canaj,H., Kim,J.Y.S.,
            Stewart,E.M., Gnann,C., McCarthy,F., Cabrera,J.P., Brunetti,R.M.,
            Chhun,B.B., Dingle,G., Hein,M.Y., Huang,B., Mehta,S.B.,
            Weissman,J.S., Gomez-Sjoberg,R., Itzhak,D.N., Royer,L.A., Mann,M.
            and Leonetti,M.D.
  TITLE     OpenCell: Endogenous tagging for the cartography of human cellular
            organization
  JOURNAL   Science 375 (6585), eabi6983 (2022)
   PUBMED   35271311
REFERENCE   3  (bases 1 to 2414)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   4  (bases 1 to 2414)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   5  (bases 1 to 2414)
  AUTHORS   Bertram,K., Agafonov,D.E., Dybkov,O., Haselbach,D., Leelaram,M.N.,
            Will,C.L., Urlaub,H., Kastner,B., Luhrmann,R. and Stark,H.
  TITLE     Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for
            Activation
  JOURNAL   Cell 170 (4), 701-713 (2017)
   PUBMED   28781166
REFERENCE   6  (bases 1 to 2414)
  AUTHORS   Heng,H.H., Wang,A. and Hu,J.
  TITLE     Mapping of the human HPRP3 and HPRP4 genes encoding
            U4/U6-associated splicing factors to chromosomes 1q21.1 and
            9q31-q33
  JOURNAL   Genomics 48 (2), 273-275 (1998)
   PUBMED   9521884
REFERENCE   7  (bases 1 to 2414)
  AUTHORS   Horowitz,D.S., Kobayashi,R. and Krainer,A.R.
  TITLE     A new cyclophilin and the human homologues of yeast Prp3 and Prp4
            form a complex associated with U4/U6 snRNPs
  JOURNAL   RNA 3 (12), 1374-1387 (1997)
   PUBMED   9404889
REFERENCE   8  (bases 1 to 2414)
  AUTHORS   Wang,A., Forman-Kay,J., Luo,Y., Luo,M., Chow,Y.H., Plumb,J.,
            Friesen,J.D., Tsui,L.C., Heng,H.H., Woolford,J.L. Jr. and Hu,J.
  TITLE     Identification and characterization of human genes encoding Hprp3p
            and Hprp4p, interacting components of the spliceosome
  JOURNAL   Hum Mol Genet 6 (12), 2117-2126 (1997)
   PUBMED   9328476
REFERENCE   9  (bases 1 to 2414)
  AUTHORS   Xu,S.Y., Schwartz,M., Rosenberg,T. and Gal,A.
  TITLE     A ninth locus (RP18) for autosomal dominant retinitis pigmentosa
            maps in the pericentromeric region of chromosome 1
  JOURNAL   Hum Mol Genet 5 (8), 1193-1197 (1996)
   PUBMED   8842740
REFERENCE   10 (bases 1 to 2414)
  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
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DC407158.1, AF016370.1,
            BQ002848.1 and AL611942.12.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_004698.3.
            
            Summary: The removal of introns from nuclear pre-mRNAs occurs on
            complexes called spliceosomes, which are made up of 4 small nuclear
            ribonucleoprotein (snRNP) particles and an undefined number of
            transiently associated splicing factors. This gene product is one
            of several proteins that associate with U4 and U6 snRNPs. Mutations
            in this gene are associated with retinitis pigmentosa-18. [provided
            by RefSeq, Jul 2008].
            
            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 :: SRR1803613.82973.1,
                                           SRR1803614.68246.1 [ECO:0000332]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000324862.7/ ENSP00000315379.6
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-495               DC407158.1         55-549
            496-2376            AF016370.1         460-2340
            2377-2409           BQ002848.1         18-50               c
            2410-2414           AL611942.12        36674-36678
FEATURES             Location/Qualifiers
     source          1..2414
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q21.2"
     gene            1..2414
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /note="pre-mRNA processing factor 3"
                     /db_xref="GeneID:9129"
                     /db_xref="HGNC:HGNC:17348"
                     /db_xref="MIM:607301"
     exon            1..60
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            61..253
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     CDS             109..2160
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /note="isoform 1 is encoded by transcript variant 1;
                     U4/U6-associated RNA splicing factor; U4/U6 small nuclear
                     ribonucleoprotein Prp3; pre-mRNA-splicing factor 3; U4/U6
                     snRNP 90 kDa protein; PRP3 pre-mRNA processing factor 3
                     homolog"
                     /codon_start=1
                     /product="U4/U6 small nuclear ribonucleoprotein Prp3
                     isoform 1"
                     /protein_id="NP_004689.1"
                     /db_xref="CCDS:CCDS951.1"
                     /db_xref="GeneID:9129"
                     /db_xref="HGNC:HGNC:17348"
                     /db_xref="MIM:607301"
                     /translation="MALSKRELDELKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDK
                     KKAADHLKPFLDDSTLRFVDKLFEAVEEGRSSRHSKSSSDRSRKRELKEVFGDDSEIS
                     KESSGVKKRRIPRFEEVEEEPEVIPGPPSESPGMLTKLQIKQMMEAATRQIEERKKQL
                     SFISPPTPQPKTPSSSQPERLPIGNTIQPSQAATFMNDAIEKARKAAELQARIQAQLA
                     LKPGLIGNANMVGLANLHAMGIAPPKVELKDQTKPTPLILDEQGRTVDATGKEIELTH
                     RMPTLKANIRAVKREQFKQQLKEKPSEDMESNTFFDPRVSIAPSQRQRRTFKFHDKGK
                     FEKIAQRLRTKAQLEKLQAEISQAARKTGIHTSTRLALIAPKKELKEGDIPEIEWWDS
                     YIIPNGFDLTEENPKREDYFGITNLVEHPAQLNPPVDNDTPVTLGVYLTKKEQKKLRR
                     QTRREAQKELQEKVRLGLMPPPEPKVRISNLMRVLGTEAVQDPTKVEAHVRAQMAKRQ
                     KAHEEANAARKLTAEQRKVKKIKKLKEDISQGVHISVYRVRNLSNPAKKFKIEANAGQ
                     LYLTGVVVLHKDVNVVVVEGGPKAQKKFKRLMLHRIKWDEQTSNTKGDDDEESDEEAV
                     KKTNKCVLVWEGTAKDRSFGEMKFKQCPTENMAREHFKKHGAEHYWDLALSESVLEST
                     D"
     exon            254..384
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            385..531
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            532..615
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            616..836
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            837..1143
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            1144..1310
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            1311..1390
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            1391..1534
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            1535..1634
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            1635..1748
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            1749..1867
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            1868..1951
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            1952..2013
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     exon            2014..2414
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2357..2362
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /note="hexamer: ATTAAA"
     polyA_site      2376
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
                     /note="major polyA site"
     polyA_site      2414
                     /gene="PRPF3"
                     /gene_synonym="HPRP3; HPRP3P; PRP3; Prp3p; RP18; SNRNP90"
ORIGIN      
        1 agaaggtttc cggttccggt gtaacgttcg ggctccgtct caggggctga agtttgtgag
       61 gtgtagtatt gagtcctgtt tgagctattg ttctcttttt cctgaaaaat ggcactgtca
      121 aagagggagc tggatgagct gaaaccatgg atagagaaga cagtgaagag ggtcctgggt
      181 ttctcagagc ctacggtggt cacagcagca ttgaactgtg tggggaaggg catggacaag
      241 aagaaggcag ccgatcatct gaaacctttt cttgatgatt ctactctccg atttgtggac
      301 aaactgtttg aggctgtgga ggaaggccga agctctaggc attccaagtc tagcagtgac
      361 aggagcagaa aacgagagct aaaggaggtg tttggtgatg actctgagat ctctaaagaa
      421 tcatcaggag taaagaagcg acgaataccc cgttttgagg aggtggaaga agagccagag
      481 gtgatccctg ggcctccatc agagagccct ggcatgctga ctaagctcca gatcaaacag
      541 atgatggagg cagcaacacg acaaatcgag gagaggaaaa aacagctgag cttcattagc
      601 ccccctacac ctcagccaaa gactccttct tcctcccaac cagaacgact tcctattggc
      661 aacactattc agccctccca ggctgccact ttcatgaatg atgccattga gaaggcaagg
      721 aaagcagctg aactgcaagc tcgaatccaa gcccagctgg cactgaagcc aggactcatc
      781 ggcaatgcca acatggtggg cctggctaat ctccatgcca tgggcattgc tcccccgaag
      841 gtggagttaa aagaccaaac gaaacctaca ccactgatcc tggatgagca agggcgcact
      901 gtagatgcaa caggcaagga gattgagctg acacaccgca tgcctactct gaaagccaat
      961 attcgtgctg tgaagaggga acaattcaag caacaactaa aggaaaagcc atcagaagac
     1021 atggaatcca ataccttttt tgacccccga gtctccattg ccccttccca gcgccagaga
     1081 cgcactttta aattccatga caagggcaaa tttgagaaga ttgctcagcg attacggaca
     1141 aaggctcaac tggagaagct acaggcagag atttcacaag cagctcgaaa aacaggcatc
     1201 catacttcga ctaggcttgc cctcattgct cctaagaagg agctaaagga aggagatatt
     1261 cctgaaattg agtggtggga ctcttacata atccccaatg gctttgatct tacagaggaa
     1321 aatcccaaga gagaagatta ttttggaatc acaaatcttg ttgaacatcc agcccagctc
     1381 aatcctccag ttgacaatga cacaccagtt actctgggag tatatcttac caagaaggaa
     1441 cagaaaaaac ttcggagaca aacaaggagg gaagcacaga aggaactaca agaaaaagtc
     1501 aggctgggcc tgatgcctcc tccagaaccc aaagtgagaa tttctaattt gatgcgagta
     1561 ttaggaacag aagctgttca agaccccacg aaggtagaag cccacgtcag agctcagatg
     1621 gcaaaaagac agaaagcgca tgaagaggcc aacgctgccc gaaaactcac agcagaacag
     1681 agaaaggtca agaaaattaa aaagcttaaa gaagacattt cacagggggt acacatatct
     1741 gtatatagag ttcgaaattt gagcaaccca gccaagaagt tcaagattga agccaatgct
     1801 gggcaactgt acctgacagg ggtggtggta ctgcacaagg atgtcaacgt ggtagtagtg
     1861 gaagggggcc ccaaggccca gaagaaattt aagcgtctta tgctgcatcg gataaagtgg
     1921 gatgaacaga catctaacac aaagggagat gatgatgagg agtctgatga ggaagctgtg
     1981 aagaaaacca acaaatgtgt actagtctgg gagggtacag ccaaagaccg gagctttgga
     2041 gagatgaagt ttaaacagtg tcctacagag aacatggctc gtgagcattt caaaaagcat
     2101 ggggctgaac actactggga ccttgcgctg agtgaatctg tgttagagtc cactgattga
     2161 gactactgca agcccttgcc tctcctccct tgcctttgtc tcttcagtcc tctcacttat
     2221 tctatttccc aaccccctcc cacttgtttg tgtgatctca gaactgtgcc aagcagacac
     2281 tgggacaaag ggagaatatc ttgctcccct cctgagtcag cctggtgttg ccctttattc
     2341 cccttatgtg catatgatta aagagttatt tttaaacttg gtgtgatatt tttcacacat
     2401 tcgtaagtat taga
//
