LOCUS       NM_005444               3820 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens CCR4-NOT transcription complex subunit 9 (CNOT9),
            transcript variant 2, mRNA.
ACCESSION   NM_005444
VERSION     NM_005444.3
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 3820)
  AUTHORS   von Wintzingerode,L., Ben-Zeev,B., Cesario,C., Chan,K.M.,
            Depienne,C., Elpeleg,O., Iascone,M., Kelley,W.V., Nassogne,M.C.,
            Niceta,M., Pezzani,L., Rahner,N., Revencu,N., Bekheirnia,M.R.,
            Santiago-Sim,T., Tartaglia,M., Thompson,M.L., Trivisano,M.,
            Hentschel,J., Sticht,H., Abou Jamra,R. and Oppermann,H.
  TITLE     De novo variants in CNOT9 cause a neurodevelopmental disorder with
            or without epilepsy
  JOURNAL   Genet Med 25 (7), 100859 (2023)
   PUBMED   37092538
  REMARK    GeneRIF: De novo variants in CNOT9 cause a neurodevelopmental
            disorder with or without epilepsy.
REFERENCE   2  (bases 1 to 3820)
  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   3  (bases 1 to 3820)
  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   4  (bases 1 to 3820)
  AUTHORS   Raisch,T., Chang,C.T., Levdansky,Y., Muthukumar,S., Raunser,S. and
            Valkov,E.
  TITLE     Reconstitution of recombinant human CCR4-NOT reveals molecular
            insights into regulated deadenylation
  JOURNAL   Nat Commun 10 (1), 3173 (2019)
   PUBMED   31320642
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3820)
  AUTHORS   Pavanello,L., Hall,B., Airhihen,B. and Winkler,G.S.
  TITLE     The central region of CNOT1 and CNOT9 stimulates deadenylation by
            the Ccr4-Not nuclease module
  JOURNAL   Biochem J 475 (21), 3437-3450 (2018)
   PUBMED   30309886
  REMARK    GeneRIF: Data suggest that the CCR4-NOT transcription complex
            subunit 1 (CNOT1)-CCR4-NOT transcription complex subunit 9 (CNOT9)
            components stimulate deadenylation by the nuclease module.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3820)
  AUTHORS   Lau,N.C., Kolkman,A., van Schaik,F.M., Mulder,K.W., Pijnappel,W.W.,
            Heck,A.J. and Timmers,H.T.
  TITLE     Human Ccr4-Not complexes contain variable deadenylase subunits
  JOURNAL   Biochem J 422 (3), 443-453 (2009)
   PUBMED   19558367
  REMARK    Publication Status: Online-Only
REFERENCE   7  (bases 1 to 3820)
  AUTHORS   Miyasaka,T., Morita,M., Ito,K., Suzuki,T., Fukuda,H., Takeda,S.,
            Inoue,J., Semba,K. and Yamamoto,T.
  TITLE     Interaction of antiproliferative protein Tob with the CCR4-NOT
            deadenylase complex
  JOURNAL   Cancer Sci 99 (4), 755-761 (2008)
   PUBMED   18377426
REFERENCE   8  (bases 1 to 3820)
  AUTHORS   Garapaty,S., Mahajan,M.A. and Samuels,H.H.
  TITLE     Components of the CCR4-NOT complex function as nuclear hormone
            receptor coactivators via association with the NRC-interacting
            Factor NIF-1
  JOURNAL   J Biol Chem 283 (11), 6806-6816 (2008)
   PUBMED   18180299
  REMARK    GeneRIF: CCR4 plays a role in the regulation of certain endogenous
            RARalpha target genes and RCD1 and CCR4 might mediate their
            function through their interaction with NIF-1
REFERENCE   9  (bases 1 to 3820)
  AUTHORS   Winkler,G.S., Mulder,K.W., Bardwell,V.J., Kalkhoven,E. and
            Timmers,H.T.
  TITLE     Human Ccr4-Not complex is a ligand-dependent repressor of nuclear
            receptor-mediated transcription
  JOURNAL   EMBO J 25 (13), 3089-3099 (2006)
   PUBMED   16778766
REFERENCE   10 (bases 1 to 3820)
  AUTHORS   Hiroi,N., Ito,T., Yamamoto,H., Ochiya,T., Jinno,S. and Okayama,H.
  TITLE     Mammalian Rcd1 is a novel transcriptional cofactor that mediates
            retinoic acid-induced cell differentiation
  JOURNAL   EMBO J 21 (19), 5235-5244 (2002)
   PUBMED   12356739
  REMARK    GeneRIF: mammalian protein is a novel transcriptional cofactor that
            mediates retinoic acid-induced cell differentiation
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DC299874.1, BC137455.1 and
            AC012510.8.
            
            On Jun 2, 2019 this sequence version replaced NM_005444.2.
            
            Summary: This gene encodes a member of the highly conserved RCD1
            protein family. The encoded protein is a transcriptional cofactor
            and a core protein of the CCR4-NOT complex. It may be involved in
            signal transduction as well as retinoic acid-regulated cell
            differentiation and development. Alternatively spliced transcript
            variants have been described for this gene. [provided by RefSeq,
            Oct 2012].
            
            Transcript Variant: This variant (2) lacks an alternate in-frame
            exon in the coding region compared to variant 1. It encodes isoform
            2 which is shorter compared to isoform 1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: SRR1803612.121076.1,
                                           SRR7346977.1204565.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000273064.11/ ENSP00000273064.6
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-19                DC299874.1         261-279
            20-1071             BC137455.1         1-1052
            1072-3820           AC012510.8         41449-44197
FEATURES             Location/Qualifiers
     source          1..3820
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q35"
     gene            1..3820
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /note="CCR4-NOT transcription complex subunit 9"
                     /db_xref="GeneID:9125"
                     /db_xref="HGNC:HGNC:10445"
                     /db_xref="MIM:612054"
     exon            1..140
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /inference="alignment:Splign:2.1.0"
     CDS             117..1016
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     protein involved in sexual development; cancer/testis
                     antigen 129; cell differentiation protein RCD1 homolog;
                     RCD1 required for cell differentiation1 homolog; cell
                     differentiation protein RQCD1 homolog"
                     /codon_start=1
                     /product="CCR4-NOT transcription complex subunit 9 isoform
                     2"
                     /protein_id="NP_005435.1"
                     /db_xref="CCDS:CCDS33379.1"
                     /db_xref="GeneID:9125"
                     /db_xref="HGNC:HGNC:10445"
                     /db_xref="MIM:612054"
                     /translation="MHSLATAAPVPTTLAQVDREKIYQWINELSSPETRENALLELSK
                     KRESVPDLAPMLWHSFGTIAALLQEIVNIYPSINPPTLTAHQSNRVCNALALLQCVAS
                     HPETRSAFLAAHIPLFLYPFLHTVSKTRPFEYLRLTSLGVIGALVKTDEQEVINFLLT
                     TEIIPLCLRIMESGSELSKTVATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVL
                     QLSKEPSARLLKHVVRCYLRLSDNPRAREALRQCLPDQLKDTTFAQVLKDDTTTKRWL
                     AQLVKNLQEGQVTDPRGIPLPPQ"
     exon            141..320
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /inference="alignment:Splign:2.1.0"
     exon            321..436
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /inference="alignment:Splign:2.1.0"
     exon            437..546
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /inference="alignment:Splign:2.1.0"
     exon            547..656
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /inference="alignment:Splign:2.1.0"
     exon            657..755
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /inference="alignment:Splign:2.1.0"
     exon            756..847
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /inference="alignment:Splign:2.1.0"
     exon            848..3820
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1849..1854
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /note="hexamer: ATTAAA"
     polyA_site      1877
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /note="major polyA site"
     regulatory      3141..3146
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /note="hexamer: AATAAA"
     polyA_site      3172
                     /gene="CNOT9"
                     /gene_synonym="CAF40; CT129; RCD-1; RCD1; RQCD1"
                     /note="major polyA site"
ORIGIN      
        1 gagccggagt cggatggcgg ctacggcggc tcattgtttt ccgctgcagg ggtgctgaag
       61 gggggacgcg ggtcggacgc gtccggctgt ggaagagagc ggcggccgct cacaacatgc
      121 acagcctggc gacggctgcg cctgtgccta ctacactggc acaagtggat agagaaaaga
      181 tctatcagtg gatcaatgag ctgtccagtc ctgagactag ggaaaatgct ttgctggagc
      241 taagtaagaa gcgagaatct gttcctgacc ttgcacccat gctgtggcat tcatttggta
      301 ctattgcagc acttttacag gaaattgtaa atatttatcc atctatcaac ccacccacct
      361 tgacagcaca ccagtctaac agagtttgca atgctctggc attactgcaa tgtgtagcat
      421 cacatccaga aaccaggtca gcgtttctcg cagcacacat cccacttttt ttgtacccct
      481 ttttgcacac tgtcagcaaa acacgtccct ttgagtatct ccggctcacc agccttggag
      541 ttattggggc cctggtgaaa acagatgaac aagaagtaat caacttttta ttaacaacag
      601 aaattatccc tttatgtttg cgaattatgg aatctggaag tgaactttct aaaacagttg
      661 ccacattcat cctccagaag atcttgttag atgacactgg tttggcttat atatgtcaga
      721 cgtatgagcg tttctcccat gttgccatga tcttgggtaa gatggtcctg cagctatcca
      781 aagagccttc tgcccgtctg ctgaagcatg tagtgagatg ttaccttcga ctttcagata
      841 accccagggc acgtgaagca ctcagacagt gcctccctga ccagctgaaa gacacaacct
      901 tcgcccaggt gctaaaagat gacaccacca cgaaacgctg gcttgcacaa ctggtgaaga
      961 acctgcaaga gggccaggtc accgatcccc ggggtatccc cctgccccct cagtgatcct
     1021 tccctgttcc ctcccactac tcccccaagt tggggaaagg agggggaacc tacgagaaaa
     1081 acagctcagg ttttatcacc gactgggaat agacaacctc aatgctgaac cgcactggag
     1141 aaaaggggca aggtacccct gctgaggtgt atgggctgcc atctcaggct gtcttgagga
     1201 cctgggctcc ctctgctact cccaggaaat gggctcctga cacagcagtc tgccaccaca
     1261 gccccaggag ggtgtcaaca ccagcaaatg ctgtatttgc agcatgtcca agatgaccct
     1321 tctcccctac ctctacctag ccactggcag ggaggggaga cagtggtgat agcagcagca
     1381 ctctaggcat ggtgaacgcc tgggaccaag ccatgtggcg ttttttattt tgcctttctg
     1441 gaagactcaa gatatgtctc ttcattctct ctcagtattt gtttactttg gtttttttgt
     1501 ttttaatctc agagagaggt gtgtttagtg ggcacaagct gtaatattca gcaaaacttt
     1561 gtcgactggc actgtttaca agtctgttag ctgcataagc tcaataaaaa gttggtctgg
     1621 gcattacatc ccctctggca ggccaatagc tgcatcaagc tgttgggaga aatgggaggg
     1681 caggggaaag atgtaaagcc aaagtacagc aggaacccac cacctgtttc ccttccttct
     1741 cccattctac tcccagtccg gaatgccacg aggaccttaa ccttgtttct ggctttagct
     1801 gctagttttc ccaaatctca gtgctttccc tttttgaact tcccttctat taaacttaaa
     1861 acagatgtct taattaatca ggctgtcttg gaagggtatt gtattgggag acaaggggcg
     1921 gtggtggacc tcaccttcaa tccaagtttt caaagatatt ttctcaataa ctctaaaagg
     1981 gaggtgcttg ggattaaggt gacagtccac ttgatccttt tctttgtttt agtgtgaatt
     2041 tcagcagctc catctgtctt catgattgta cttgagcagt attagctgta tgagttaatt
     2101 ttattcagat tgaagatgga gggctgggtt ctgctcactc agtctttttt tttttttttt
     2161 tttttttttt ttgaccattc tcttttagtc tatgggaatt acagggttgc cgctaaaata
     2221 ttcacttgtt catatcgtgt cagagatttc ctcttctctg gagcttaggt ggctcttcac
     2281 aatccatagg cttgaatctg caacctagtg taaactgcct tgctttcccc ggttctttcc
     2341 cctgctagca cctgctttct catccctatc tccagtcaaa gatgggattg cttaatccaa
     2401 ctctggagag ggaccaagtc ttttctgccc acatctcaca caattgaggt gtctgaacaa
     2461 gcttggggag ggtctataag gggtaggctc aaaaaaaaaa aaacccattt gcagaggcag
     2521 ttttgccaac acaagggctc tttcaagccg actttcacaa agagagccgg acttgttagt
     2581 tggcttctgt ctctttagag ccaagaaaat agtaattaag tggcctagat ataggaaggg
     2641 cagaataagc acttactccc cctgccttcc aagatgaaga ggagaagcag gccaaccctc
     2701 aataattgca agcctgaaga gaagtgatct tagagaaagc agagaacaga atggactgga
     2761 tagacatctt gactctattc agcccgtagt ctgtgatctg gagagtccag ttaaggtaac
     2821 ccagattttt gacaaccgcc ttcctgctga gccaaagttt tctcattacc cctccactgg
     2881 ggaagcagct gaggcccagg gccttgctcc ctgggaaatt ctcttctctc catctttcgg
     2941 tgcattggcc atgttactgt gccaaagtgt cttaattctt gtcccatcta ttctcagctg
     3001 gccttggaac ccacatagga gttggtgggg gagggatgga atgggtatta ttcattgtag
     3061 ttgatcctgg tgtgtgtatt atataaagag acccctcccc ttattttgtg ttttccatcc
     3121 ctctccctta acaggattga aataaaacat gcttctgttt ttgtaaaaat aatttttcct
     3181 ttacactgga gattttattc tatcagtata tgggtaacta ggcactttgg tcaggtgatc
     3241 cttgtcatgc ctgcttctcc cctctgtcta cctacacaac acacacacac acacacacac
     3301 agccctgcta agatggcagt agtggttctt ttgtgaacat gttttttggg gagactccat
     3361 ctgaggtaca aaagctgttt gggaggctgg gagggggatg atgcccctta cctgataaaa
     3421 gtatgtttta ctgggacaga acttcactcc tggccatatt ggccagaact tagtgccagt
     3481 gtagggagag acttccatag tgacaaggta atgcttgaaa catcttacga actttgatgt
     3541 tcatttcctc aagttcaagg cttggagcac atctccagga ttgtttccat gcctggctgt
     3601 cagtgggaca cagctgccct atgcttccac gttctttttt caagagcctt agagggcctg
     3661 tggcctgttt cactggtgga acaggagcag cattggtagc cttcagagca tgccttgctt
     3721 actaactaca tattattcct ctgctcattg ttcctgctgc ttaaaggcta ggaaaagggg
     3781 gatatacaaa gttgttgctt tcaaaaactc agagaaaaaa
//
