LOCUS       NM_001288996            5854 bp    mRNA    linear   PRI 06-APR-2024
DEFINITION  Homo sapiens lin-54 DREAM MuvB core complex component (LIN54),
            transcript variant 4, mRNA.
ACCESSION   NM_001288996 XM_005262751
VERSION     NM_001288996.2
KEYWORDS    RefSeq.
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 5854)
  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   2  (bases 1 to 5854)
  AUTHORS   Marceau,A.H., Felthousen,J.G., Goetsch,P.D., Iness,A.N., Lee,H.W.,
            Tripathi,S.M., Strome,S., Litovchick,L. and Rubin,S.M.
  TITLE     Structural basis for LIN54 recognition of CHR elements in cell
            cycle-regulated promoters
  JOURNAL   Nat Commun 7, 12301 (2016)
   PUBMED   27465258
  REMARK    GeneRIF: the DNA-binding properties of LIN54 and the structural
            basis for recognition of a cell cycle genes homology region
            sequence, are described.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 5854)
  AUTHORS   Matsuo,T., Kuramoto,H., Kumazaki,T., Mitsui,Y. and Takahashi,T.
  TITLE     LIN54 harboring a mutation in CHC domain is localized to the
            cytoplasm and inhibits cell cycle progression
  JOURNAL   Cell Cycle 11 (17), 3227-3236 (2012)
   PUBMED   22895175
  REMARK    GeneRIF: LIN54 harboring a mutation in CHC domain is localized to
            the cytoplasm and inhibits cell cycle progression.
REFERENCE   4  (bases 1 to 5854)
  AUTHORS   Litovchick,L., Florens,L.A., Swanson,S.K., Washburn,M.P. and
            DeCaprio,J.A.
  TITLE     DYRK1A protein kinase promotes quiescence and senescence through
            DREAM complex assembly
  JOURNAL   Genes Dev 25 (8), 801-813 (2011)
   PUBMED   21498570
REFERENCE   5  (bases 1 to 5854)
  AUTHORS   Schmit,F., Cremer,S. and Gaubatz,S.
  TITLE     LIN54 is an essential core subunit of the DREAM/LINC complex that
            binds to the cdc2 promoter in a sequence-specific manner
  JOURNAL   FEBS J 276 (19), 5703-5716 (2009)
   PUBMED   19725879
  REMARK    GeneRIF: the cysteine-rich CXC domain of LIN54 is a novel
            DNA-binding domain that binds to the cdc2 promoter in a
            sequence-specific manner
REFERENCE   6  (bases 1 to 5854)
  AUTHORS   Litovchick,L., Sadasivam,S., Florens,L., Zhu,X., Swanson,S.K.,
            Velmurugan,S., Chen,R., Washburn,M.P., Liu,X.S. and DeCaprio,J.A.
  TITLE     Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein
            complex represses human cell cycle-dependent genes in quiescence
  JOURNAL   Mol Cell 26 (4), 539-551 (2007)
   PUBMED   17531812
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DC335927.1, BC109278.2, BX640657.1, BX537919.1, AB111889.1,
            BX640966.1, AC021105.13, BX108765.1, AI208524.1 and CK819664.1.
            
            On May 31, 2019 this sequence version replaced NM_001288996.1.
            
            Summary: LIN54 is a component of the LIN, or DREAM, complex, an
            essential regulator of cell cycle genes (Schmit et al., 2009
            [PubMed 19725879]).[supplied by OMIM, Dec 2010].
            
            Transcript Variant: This variant (4) lacks two consecutive
            alternate exons in the 5' coding region, compared to variant 1. It
            encodes isoform c, which lacks an internal in-frame segment and is
            shorter, compared to isoform a.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660807.32168.1,
                                           SRR1660805.175391.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-114               DC335927.1         12-125
            115-2552            BC109278.2         1-2438
            2553-3306           BX640657.1         1894-2647
            3307-4118           BX537919.1         2814-3625
            4119-4909           AB111889.1         3716-4506
            4910-5098           BX640966.1         5181-5369
            5099-5099           AC021105.13        124608-124608
            5100-5492           BX108765.1         14-406              c
            5493-5812           AI208524.1         13-332
            5813-5854           CK819664.1         12-53               c
FEATURES             Location/Qualifiers
     source          1..5854
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="4"
                     /map="4q21.22"
     gene            1..5854
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /note="lin-54 DREAM MuvB core complex component"
                     /db_xref="GeneID:132660"
                     /db_xref="HGNC:HGNC:25397"
                     /db_xref="MIM:613367"
     exon            1..340
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     exon            341..1056
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     CDS             373..2355
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /note="isoform c is encoded by transcript variant 4;
                     protein lin-54 homolog; CXC domain-containing protein 1"
                     /codon_start=1
                     /product="protein lin-54 homolog isoform c"
                     /protein_id="NP_001275925.1"
                     /db_xref="CCDS:CCDS75157.1"
                     /db_xref="GeneID:132660"
                     /db_xref="HGNC:HGNC:25397"
                     /db_xref="MIM:613367"
                     /translation="MEVVPAEVNSLLPEEIMDTGITLVDDDSIEAVIVSSPIPMETEL
                     EEIVNINSTGDSTATPISTEPITVYSNHTNQVAVNTTITKADSNTTVKPAFPSGLQKL
                     GAQTPVTISANQIILNKVSQTSDLKLGNQTLKPDGQKLILTTLGKSGSPIVLALPHSQ
                     LPQAQKVTTQAQSGDAKLPPQQIKVVTIGGRPEVKPVIGVSALTPGSQLINTTTQPSV
                     LQTQQLKTVQAVKSTVQTITVGGVSTSQFKTIIPLATAPNVQQIQVPGSKFHYVRLVT
                     ATSASSSTQPVSQNPSTNTQPLQQAKPVVVNTTPVRMSVPIVSAQAVKQVVPKPINPT
                     SQIVTTSQPQQRLIMPATPLPQIQPNLTNLPPGTVLAPAPGTGNVGYAVLPAQYVTQL
                     QQSSYVSIASNSTFTGTSGIQTQARLPFNGIIPSESASRPRKPCNCTKSLCLKLYCDC
                     FANGEFCNNCNCTNCYNNLEHENERQKAIKACLDRNPEAFKPKIGKGKEGESDRRHSK
                     GCNCKRSGCLKNYCECYEAKIMCSSICKCIGCKNFEESPERKTLMHLADAAEVRVQQQ
                     TAAKTKLSSQISDLLTRPTPALNSGGGKLPFTFVTKEVAEATCNCLLAQAEQADKKGK
                     SKAAAERMILEEFGRCLMSVINSAGKAKSDPCAMNC"
     exon            1057..1273
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     exon            1274..1347
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     exon            1348..1545
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     exon            1546..1637
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     exon            1638..1709
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     exon            1710..1812
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     exon            1813..1950
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     exon            1951..2153
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     exon            2154..5854
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4714..4719
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /note="hexamer: AATAAA"
     polyA_site      4742
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /note="major polyA site"
     regulatory      5468..5473
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /note="hexamer: AATAAA"
     polyA_site      5492
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
     regulatory      5828..5833
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
                     /note="hexamer: ATTAAA"
     polyA_site      5854
                     /gene="LIN54"
                     /gene_synonym="CXCDC1; JC8.6; MIP120; TCX1"
ORIGIN      
        1 actggtggtg gcggcggcgg cggcggcccg ggctccggct gtcggggaag ctgctgagct
       61 gtgatggtga tgacgaggtg aaaatggcgg atctttcgaa atacaatccc ggcccctgac
      121 ataccagagg cggcggcgac ggcgacgtcg ccaccccggc tcccttctcg gtccccgggt
      181 accctggagc gctccagttt ggacaaactg ggaaaggaag ctgctggcca gagctatcgt
      241 gcacgggcaa aacaagcccc gccggggctc gggattgccc aggaccttct ggagccccta
      301 cctcggagcc cgagggagga gaaagcggca gccgctggag tgcctgatca actttctagc
      361 gggagaacga tcatggaggt ggtgccagct gaggtgaata gtttgcttcc agaggaaata
      421 atggacactg gtataacttt agtggatgat gatagtattg aggctgttat tgtttcatcc
      481 ccaattccca tggagacaga actggaagaa attgtcaaca taaattctac tggtgactct
      541 acagccacgc ccatttccac ggaaccaatc acagtgtaca gtaaccacac taaccaagtt
      601 gcagtgaata ccacaattac taaagcagat tctaatacca cagtgaaacc agcttttcca
      661 agtggccttc aaaaacttgg tgctcagact cctgtgacta tatcagccaa tcagattatt
      721 ttaaacaaag tatcacagac atctgatctt aaacttggca atcagaccct taaaccagat
      781 ggacagaagt taattttaac aactttgggc aagtctggtt caccaattgt tttagcacta
      841 ccccatagcc aactacccca ggctcagaaa gttacaactc aggcccagtc aggagatgct
      901 aagttaccac cgcagcaaat taaagtagtt accattggag ggaggccaga ggtgaaacct
      961 gtcattggtg tctcagcatt gaccccagga agtcaactga ttaatactac aactcagccc
     1021 tctgtgttac agacccaaca gttaaaaaca gtacaggcag tgaaatcaac tgtgcagacc
     1081 atcactgttg gaggagtgag cacatcacag tttaagacaa ttattcctct ggcaactgct
     1141 cccaatgtcc agcagattca agtgcctgga agcaagtttc attatgtccg acttgttact
     1201 gccacatcag ccagtagctc aacccagcca gttagtcaga atcccagtac aaacactcag
     1261 cctcttcagc aagcaaagcc agtggttgtt aatacaaccc cagtgcggat gtcagttcca
     1321 attgtctcag ctcaggctgt caaacaagtt gttccaaaac caatcaatcc aacttcacaa
     1381 atagtaacta ctagccagcc acagcaacgg cttatcatgc ctgccacacc actgccacag
     1441 atccagccca acctcactaa cctgccacca ggcactgtcc tggcaccagc tccgggaaca
     1501 gggaatgtgg gttatgcagt gcttccagct cagtatgtta ctcagctaca gcagtcttca
     1561 tatgtatcaa tagcaagcaa ctctaccttt actggaacat ctggtatcca gacccaggca
     1621 cggcttccat tcaatggcat aatcccatca gagtcggcca gtcggccccg aaagccctgt
     1681 aattgtacaa aatcactgtg tttgaaattg tattgtgatt gctttgcaaa tggtgaattt
     1741 tgcaacaact gcaattgtac taattgttac aacaatttgg aacatgaaaa tgaaaggcaa
     1801 aaagcaataa aggcatgcct tgacagaaat ccagaagcct ttaagcctaa gatagggaaa
     1861 ggaaaggagg gagaatctga tcgacgtcat agcaaagggt gtaattgcaa acgatcagga
     1921 tgtcttaaaa actactgtga atgctatgag gcaaaaataa tgtgttcctc aatatgcaaa
     1981 tgtattggct gtaagaattt tgaagaaagc ccggaaagga agacattgat gcatttggca
     2041 gatgcagctg aagtaagggt acagcaacaa acagcagcca agacgaagtt atcctctcaa
     2101 atttcagact tgcttactag gccaacacca gctttaaata gtggaggcgg aaaattgcca
     2161 tttacatttg taactaagga agtagctgaa gccacatgta attgcctcct tgcccaggca
     2221 gagcaggcag acaagaaggg aaaatcaaag gcagcagcgg aacggatgat acttgaggaa
     2281 ttcggacgat gtttgatgag tgtcatcaac tctgcaggaa aggcaaaaag tgacccttgt
     2341 gccatgaatt gctaactctt gcacaaaaga ctgataaatg gaactgtaca gaaaatttaa
     2401 ggtgcaggga cacttgattt tctggaagaa aaacaattac tgtattttaa ttcagtcctt
     2461 gttttaaaag acctgaaatt ataatactga aggagaagaa attttaaatg aggaaattag
     2521 tacattttaa atcttagtta aatctgctta tgccccttct aaattgaatt tttctttatt
     2581 atatagattt tttaatttgc ttgggtttct taagaattag atgttctctt tctgatacct
     2641 ttgacaaaaa atgtttataa attcatataa tttataatgt atggtgttgt atgactttgt
     2701 taatagaaaa gccaaagcag cagtggttag cacccattct ttgggacttg atctagaata
     2761 tctgcagaca gaatgttaca taaacaaatt cttatgaaac acattcaaat gacattttgt
     2821 atttagaaaa ggactatctt ttaaagaaaa agcagccttt tagggccgat tctggaataa
     2881 tatcctgttg tcactttggg aatgtcagaa ggggaaacaa tccccaggca cactaaaaat
     2941 tttttaaagt tatttaaaaa aacatataaa atattaaagg acagtaaatc tcagaggatg
     3001 ggcaatgtgt ttctataata aggaaaggct aacagatgct ctgggctgtc tccattttct
     3061 ttcaaagagg tggtatgtat ttgaagtaat aaattgtcaa agtgattact gggtactatt
     3121 aaaatgatag gtggatataa atggaagtaa acattatgta gtgataatat agaacctcac
     3181 atagtaatca agtataaaat ttggcatggg tggagaaaca aagaataggg aagctgcaaa
     3241 agatgaattt agagaagttt tcatctatac aatcaattat ttttacagac tttttttttt
     3301 ttttttttga gacggagtct cgctgtgtag cccaggctgg agtgcaatgg tgagatctca
     3361 gctcactgca acgcctctgc ctcccaggtt caagcgattc tcctgcctca gcctcccgtg
     3421 tagctgggac tacaggtgca tgccaccatg cccggctcat tttttgtatt tttagtagag
     3481 acggggtttc accgtgttag ccaggatggt ctcgatctcc tgacctcgtg attcgcccgc
     3541 ctcggcctcc caaagtgctg ggattacagg cataagccgc cgtgccaggc cctttttata
     3601 gacttttgaa ctaagaggtt tcaaaccaaa tcgcaactct tacttgattt acagaaatgg
     3661 gcctcctaac aaaattttca aaattgtggt gggatttctt tttataaggg aagtttaata
     3721 tggcattatt ttcagccagt gatttggaag gtctgttttc ctataattac taaaataacc
     3781 taaatcattt tcagtattca aaaactctat gaatttaaga gcctgttgtg acaggactct
     3841 tgattttatg acaagaaaaa accatgttgg aattcaggca ttttgttagg taccttaatc
     3901 atcagtaatt agtatatgat tatttcattt cctacaagga ctctatagtt gtatgtatta
     3961 agtgtgtata tatgttcata tgaacatgca agatataggc aatagaaatt aagtaatcca
     4021 aaagaggatt ccgttattca ctaaagtatc ttccttttaa atttggattt ataaaatcat
     4081 agtgcagtaa ctttaaatgt agatagttca aacattctta gcacctcaat ctagtatgtt
     4141 taattaaaat ttgtataaat gtaaattagt gtaagagggt aaaataataa tcaagttatt
     4201 tttcaaaaga ttgcaataag tttttggtct aaacttaaac tttgttcatt ttgtacatac
     4261 tctgtgttaa ttctaattgc acctttgtga tgtgtattta tatacagtgt gcagaaaatg
     4321 ttcgtgaaat tttgattaca attgtagatt atgtatgatg gcattgctta cgaatgtttt
     4381 gcttgtaaaa aaatttcaag gtgcaatcaa atgctactag tttttctgat tttcaaaaat
     4441 ctatctatct aaaatattaa gccttttcct tcctgtgtag tacttactaa ataacttttt
     4501 gtattcaggc atttgcatca aattgctgaa caagatgaat agccacatta attcaatgat
     4561 tttaaaagac tatttgggga gggttgggta tataattttt tagctctatt tacatcccaa
     4621 agtagaaaga ttaaatttat atttactaga gctattcaaa gaatacactt ttctatattg
     4681 taaaaacagg acagcaaagt aaatcataca gaaaataaac atttatacta ttctgtaaaa
     4741 aaggttttgc attttttctt tagtataata acaccacttt attaaccatt taatatgcaa
     4801 aaaacctttt aaattatctg aagtaaattt gacattactt ctgaaaacac acaactaaaa
     4861 aattctatca ttttgctcag ttattactaa cataaattgc tttgaaatga gaatatgtct
     4921 tctctttttt tccccactgt ttcttttaag agcagaaact cagccgggca tggtggctca
     4981 cgcctgtaat tccagcactt tgggaggtca aggcgggtga atcacttgag tccaggagtt
     5041 ctagaccagc ccaggctaca tggtgaaacc ctgtctctac taaaaatata aaaaaattca
     5101 ctgcgtgtgg tggcgcacac ctgcagtcct cgctactttg aaggcctgag cctgcagagg
     5161 ttgaggctgt agtgagtcaa aattacacca ctgcactcca gcctggcaat cagagtgaga
     5221 ccttgtctca aaaacaaaaa tacctagaaa atcaatctac tctgtctttt aatgtgaaat
     5281 gttcttatga tagctatctt tcttagtttc ctttttttct gaagcactaa acacaacctg
     5341 taggtcttat ctctggggtc tgggaaacag aaccttaatg ttacaggtac aaaagcaaac
     5401 agagtgatta gttccccatt ttctggtagt gaacaactga cattttttca atcttatgta
     5461 aaatgtgaat aaaaataatt ttagaaaagt tatctatttt tattgttctg taacacaaat
     5521 agttaagaaa atgaatactt gttatgtaaa tgaagcttca cagcaggacc tccggccata
     5581 actttgatca tgttgtatct cttaagcatt ttatatagga attctggtgt ggctacccaa
     5641 agcagaaggg aaggcaatca actaaaaatc cctttctatt ggagttattt tcatcatgta
     5701 aattacttca ggcttttctt gttagggctt cttgaatgca cattttgtca ttatctgtat
     5761 accaaaggtg agcttttttt tttaatccat gtgattttat gagttgaaag ctataaggtt
     5821 ttttttaatt aaaaatttcc ttctaaatgg caaa
//
