LOCUS       NM_017922               3532 bp    mRNA    linear   PRI 05-APR-2024
DEFINITION  Homo sapiens pre-mRNA processing factor 39 (PRPF39), mRNA.
ACCESSION   NM_017922
VERSION     NM_017922.4
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 3532)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   2  (bases 1 to 3532)
  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   3  (bases 1 to 3532)
  AUTHORS   De Bortoli,F., Neumann,A., Kotte,A., Timmermann,B., Schuler,T.,
            Wahl,M.C., Loll,B. and Heyd,F.
  TITLE     Increased versatility despite reduced molecular complexity:
            evolution, structure and function of metazoan splicing factor
            PRPF39
  JOURNAL   Nucleic Acids Res 47 (11), 5867-5879 (2019)
   PUBMED   30949712
  REMARK    GeneRIF: organisms with higher splicing complexity have substituted
            the Prp39/Prp42 heterodimer with a PRPF39 homodimer
REFERENCE   4  (bases 1 to 3532)
  AUTHORS   Stark,A.L., Delaney,S.M., Wheeler,H.E., Im,H.K. and Dolan,M.E.
  TITLE     Functional consequences of PRPF39 on distant genes and cisplatin
            sensitivity
  JOURNAL   Hum Mol Genet 21 (19), 4348-4355 (2012)
   PUBMED   22773733
  REMARK    GeneRIF: Knockdown of PRPF39 expression resulted in a significant
            expression change of downstream gene.
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DC306976.1, BC125126.1, DB339898.1, BC051886.1 and AL121809.6.
            
            On May 17, 2019 this sequence version replaced NM_017922.3.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660807.84522.1,
                                           SRR1660807.253812.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000355765.11/ ENSP00000348010.6
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-80                DC306976.1         18-97
            81-2558             BC125126.1         1-2478
            2559-2849           DB339898.1         1-291               c
            2850-2851           BC051886.1         2125-2126
            2852-3532           AL121809.6         144042-144722       c
FEATURES             Location/Qualifiers
     source          1..3532
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="14"
                     /map="14q21.2"
     gene            1..3532
                     /gene="PRPF39"
                     /note="pre-mRNA processing factor 39"
                     /db_xref="GeneID:55015"
                     /db_xref="HGNC:HGNC:20314"
                     /db_xref="MIM:614907"
     exon            1..134
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            135..477
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     CDS             154..2163
                     /gene="PRPF39"
                     /note="PRP39 pre-mRNA processing factor 39 homolog; PRP39
                     homolog"
                     /codon_start=1
                     /product="pre-mRNA-processing factor 39"
                     /protein_id="NP_060392.3"
                     /db_xref="CCDS:CCDS9682.2"
                     /db_xref="GeneID:55015"
                     /db_xref="HGNC:HGNC:20314"
                     /db_xref="MIM:614907"
                     /translation="MQNSHMDEYRNSSNGSTGNSSEVVVEHPTDFSTEIMNVTEMEQS
                     PDDSPNVNASTEETEMASAVDLPVTLTETEANFPPEYEKFWKTVENNPQDFTGWVYLL
                     QYVEQENHLMAARKAFDRFFIHYPYCYGYWKKYADLEKRHDNIKPSDEVYRRGLQAIP
                     LSVDLWIHYINFLKETLDPGDPETNNTIRGTFEHAVLAAGTDFRSDRLWEMYINWENE
                     QGNLREVTAIYDRILGIPTQLYSHHFQRFKEHVQNNLPRDLLTGEQFIQLRRELASVN
                     GHSGDDGPPGDDLPSGIEDITDPAKLITEIENMRHRIIEIHQEMFNYNEHEVSKRWTF
                     EEGIKRPYFHVKPLEKAQLKNWKEYLEFEIENGTHERVVVLFERCVISCALYEEFWIK
                     YAKYMENHSIEGVRHVFSRACTIHLPKKPMVHMLWAAFEEQQGNINEARNILKTFEEC
                     VLGLAMVRLRRVSLERRHGNLEEAEHLLQDAIKNAKSNNESSFYAVKLARHLFKIQKN
                     LPKSRKVLLEAIERDKENTKLYLNLLEMEYSGDLKQNEENILNCFDKAVHGSLPIKMR
                     ITFSQRKVEFLEDFGSDVNKLLNAYDEHQTLLKEQDSLKRKAENGSEEPEEKKAHTED
                     TTSSSTQMIDGDLQANQAVYNYSAWYQYNYQNPWNYGQYYPPPPT"
     exon            478..603
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            604..722
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            723..890
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            891..1056
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            1057..1164
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            1165..1329
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            1330..1456
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            1457..1725
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            1726..1910
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            1911..1985
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            1986..2106
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     exon            2107..3532
                     /gene="PRPF39"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2826..2831
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PRPF39"
                     /note="hexamer: AATAAA"
     polyA_site      2851
                     /gene="PRPF39"
                     /note="major polyA site"
     regulatory      3308..3313
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PRPF39"
                     /note="hexamer: AACAAA"
     polyA_site      3331
                     /gene="PRPF39"
ORIGIN      
        1 gtgccctgga ccaggcggcc gtggcgcggg tggcggctgc tgtgctggct gtggggacgg
       61 aggcggtgaa gtgccatctt cggctaggtc gtcacaggct ccggctcatg gcatcaagtg
      121 gcatccatca taagatcgtt aactgaagac aatatgcaaa attctcacat ggatgaatac
      181 agaaattcta gtaatggcag cacaggcaac agttcagagg tagtggtaga acatcctact
      241 gatttcagta ctgagattat gaacgttaca gaaatggaac agtcacctga tgactctccc
      301 aatgtgaatg catctacaga agaaactgaa atggcaagtg ctgtggacct tccagtgacg
      361 ctgacagaaa cagaagcaaa tttccctcca gaatatgaaa aattttggaa aactgtagaa
      421 aataatcctc aggattttac aggctgggta tatttgcttc aatatgtaga acaggagaat
      481 cacttgatgg ctgccaggaa ggcatttgac agatttttca tacactatcc gtattgctat
      541 ggttactgga aaaagtatgc agaccttgaa aagcggcacg acaacattaa accatcagat
      601 gaggtttatc ggcgggggct tcaggcaata cctcttagtg ttgacctttg gatacattat
      661 ataaacttct taaaagaaac attggaccct ggtgatcctg agacaaacaa tacaataaga
      721 ggaacttttg agcatgctgt tctagctgca ggaacagatt tccgttctga cagactgtgg
      781 gaaatgtata taaactggga aaatgagcag ggaaacctga gagaagttac agctatatat
      841 gatcgtattc ttggtattcc aacacagctg tatagtcatc attttcagag atttaaagaa
      901 catgtacaga ataatttgcc tagagatctt ttaactggtg aacagtttat tcagttgcga
      961 agggaattag cttctgtaaa tggtcatagt ggtgatgatg gtcctcctgg tgatgatcta
     1021 ccatcgggaa ttgaagacat aaccgatcct gcaaagctaa ttacagaaat agaaaacatg
     1081 agacatagaa tcattgagat tcatcaagaa atgtttaatt ataatgagca tgaagttagt
     1141 aaaaggtgga catttgaaga aggtattaaa agaccttact ttcatgtgaa acctttggaa
     1201 aaggcacaac taaaaaactg gaaagaatac ttagaatttg aaattgaaaa tgggactcat
     1261 gaacgagttg tggttctctt tgaaagatgt gtcatatcat gtgccctcta tgaggagttt
     1321 tggattaagt atgccaagta catggaaaac catagcattg aaggagtgag gcatgtcttc
     1381 agcagagctt gtactataca tctcccaaag aaacccatgg tgcatatgct ttgggcagct
     1441 tttgaggaac agcagggtaa tattaatgaa gccaggaata tcttgaaaac atttgaagaa
     1501 tgtgttctag gattggcaat ggttcgttta cgaagagtaa gtttagaacg acggcatgga
     1561 aatctggaag aagctgaaca tttgcttcag gatgccatta agaatgccaa atcaaataat
     1621 gaatcttcat tttatgctgt caaactagcc cggcatcttt tcaaaataca gaaaaacctt
     1681 ccaaaatcaa gaaaggtgct tttggaagca atcgaaagag acaaagagaa cacaaagtta
     1741 tacctcaatt tacttgaaat ggaatatagt ggtgacctca aacaaaatga agaaaatatc
     1801 ctaaattgtt ttgacaaagc tgtacatggt tcattaccta ttaaaatgag aattacattt
     1861 tctcagagaa aagtggaatt tcttgaagat tttggttccg atgttaataa gcttctgaat
     1921 gcttatgatg aacatcaaac actcctgaaa gaacaggatt ctttaaaaag gaaagcagaa
     1981 aatggatcag aagaaccaga ggaaaagaaa gcacatacag aagatacaac ttcatcatct
     2041 acacagatga ttgatggtga tttacaggca aaccaagctg tatataatta tagtgcgtgg
     2101 tatcaataca attatcagaa tccttggaat tatggacaat attatcctcc ccctccaacc
     2161 tgatgggaaa aatgtaaatt tcaaatgcag tgtgtgaaaa gtatgaaatt attatttttt
     2221 ttaatgaggg atgtaaacag tataagcttg ttgtatttga taacctgtct tccttgtttc
     2281 tgtgtaacat gatttgttta gtaatagggg gaaaatgtca attagtagct taccacagat
     2341 actgtttcct accatttata aaatttactt tttattgaaa aactattttt tgatttttgc
     2401 attaagtggt ctagaattct tttgcaatgc atttgcaaca gaattttgta gccttaaggg
     2461 gtaggaagaa aaacctgact gcaaatcatg tcagtgtagt acaaaattct gaaaacacat
     2521 aagggctggt tatttacctc cttttttttt ttttttttta aagaaaaaag gacttttaac
     2581 ctttgctgac aaggttttgt ctgtttcagt tatacttgtg aattgtgatc taactgcaga
     2641 aaggatacat tattaaaata ctttgccttg gaatagatta taaatgagaa aatggaatgt
     2701 ttgcatccct ttaaaaatga aaatcatatc aaaagtatgt tgtttcagga gactttgtat
     2761 ttagaatatt catgtaaaac ttgtgaacaa gctttcattt tgatcaaact gatcttcatt
     2821 tttgtaataa aacggaagac tcatccagta attgtttatg aatttatttt ggggggatca
     2881 attagtaata ttaaccttat gttcaccttt attagtggct cattggtttt gaagtacacc
     2941 ttttctaaat tcaggtcttg atcttcctgc caagattttt ctgcttttag cattttgttt
     3001 cccctcaagc cttatgcttt tgccttctca ttatacaggc aatctgtcca gataatttta
     3061 ctgggagtta ctccctggtt tgatgaggtc cttagttcca attccctaat cagaacaata
     3121 atatattaac accaaacaaa tcacagtcag atcaagacag tggatcaatt tttattgagc
     3181 cacttaagtt tacaacatga ggtaaaagga aaaagttctc cttgaccagt attttacaca
     3241 gctgtaggaa agtattttag accagggatt cataagggat ttatctctca aaagctggga
     3301 ccaagtaaac aaattttatt aactccttga attttccagt tgactcttcc tttacaatag
     3361 taacaagttc taactagttg tgtaaatttc ttcaaggcca agttttatca ttgttgctaa
     3421 tatccttaga gctgaagcac tgctatttca atcaatatcc actaattcca cttcaaaagt
     3481 gagttttgca tttggtggaa ttctgttgaa gaagtcaagg tacatttgat aa
//
