LOCUS       NM_006089               4162 bp    mRNA    linear   PRI 12-FEB-2025
DEFINITION  Homo sapiens Scm polycomb group protein like 2 (SCML2), transcript
            variant 1, mRNA.
ACCESSION   NM_006089
VERSION     NM_006089.3
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 4162)
  AUTHORS   Du,L., Wang,L., Yang,H., Duan,J., Lai,J., Wu,W., Fan,S. and Zhi,X.
  TITLE     Sex Comb on Midleg Like-2 Accelerates Hepatocellular Carcinoma Cell
            Proliferation and Metastasis by Activating Wnt/beta-Catenin/EMT
            Signaling
  JOURNAL   Yonsei Med J 62 (12), 1073-1082 (2021)
   PUBMED   34816637
  REMARK    GeneRIF: Sex Comb on Midleg Like-2 Accelerates Hepatocellular
            Carcinoma Cell Proliferation and Metastasis by Activating
            Wnt/beta-Catenin/EMT Signaling.
REFERENCE   2  (bases 1 to 4162)
  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 4162)
  AUTHORS   Lecona,E., Narendra,V. and Reinberg,D.
  TITLE     USP7 cooperates with SCML2 to regulate the activity of PRC1
  JOURNAL   Mol Cell Biol 35 (7), 1157-1168 (2015)
   PUBMED   25605328
  REMARK    GeneRIF: SCML2 directly interacts with USP7 and drives its
            localization. SCML2 connects USP7 to PRC1.4, allowing for the
            stabilization of BMI1, and USP7 is found on SCML2 and BMI1 target
            genes.
            Erratum:[Mol Cell Biol. 2017 Sep 12;37(19):e00631-15. doi:
            10.1128/MCB.00631-15.. PMID: 28900000]
REFERENCE   4  (bases 1 to 4162)
  AUTHORS   Bonasio,R., Lecona,E., Narendra,V., Voigt,P., Parisi,F., Kluger,Y.
            and Reinberg,D.
  TITLE     Interactions with RNA direct the Polycomb group protein SCML2 to
            chromatin where it represses target genes
  JOURNAL   Elife 3, e02637 (2014)
   PUBMED   24986859
  REMARK    GeneRIF: SCML2A, an SCML2 isoform tightly associated to chromatin,
            contributes to PRC1 localization and also directly enforces
            repression of certain Polycomb target genes.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 4162)
  AUTHORS   Bezsonova,I.
  TITLE     Solution NMR structure of the DNA-binding domain from Scml2 (sex
            comb on midleg-like 2)
  JOURNAL   J Biol Chem 289 (22), 15739-15749 (2014)
   PUBMED   24727478
  REMARK    GeneRIF: Because PRC1 complexes localize to the promoters of a
            specific subset of developmental genes in vivo, the SLED domain of
            Scml2 may provide an important link connecting the PRC1 complexes
            to their target genes.
REFERENCE   6  (bases 1 to 4162)
  AUTHORS   Lecona,E., Rojas,L.A., Bonasio,R., Johnston,A.,
            Fernandez-Capetillo,O. and Reinberg,D.
  TITLE     Polycomb protein SCML2 regulates the cell cycle by binding and
            modulating CDK/CYCLIN/p21 complexes
  JOURNAL   PLoS Biol 11 (12), e1001737 (2013)
   PUBMED   24358021
REFERENCE   7  (bases 1 to 4162)
  AUTHORS   Vandamme,J., Volkel,P., Rosnoblet,C., Le Faou,P. and Angrand,P.O.
  TITLE     Interaction proteomics analysis of polycomb proteins defines
            distinct PRC1 complexes in mammalian cells
  JOURNAL   Mol Cell Proteomics 10 (4), M110.002642 (2011)
   PUBMED   21282530
REFERENCE   8  (bases 1 to 4162)
  AUTHORS   Santiveri,C.M., Lechtenberg,B.C., Allen,M.D., Sathyamurthy,A.,
            Jaulent,A.M., Freund,S.M. and Bycroft,M.
  TITLE     The malignant brain tumor repeats of human SCML2 bind to peptides
            containing monomethylated lysine
  JOURNAL   J Mol Biol 382 (5), 1107-1112 (2008)
   PUBMED   18706910
  REMARK    GeneRIF: The malignant brain tumor repeats of SCML2 preferentially
            bind histone peptides monomethylated at lysine residues. The
            crystal structure of the complex reveals that the modified amino
            acid binds to an aromatic rich pocket.
REFERENCE   9  (bases 1 to 4162)
  AUTHORS   Sathyamurthy,A., Allen,M.D., Murzin,A.G. and Bycroft,M.
  TITLE     Crystal structure of the malignant brain tumor (MBT) repeats in Sex
            Comb on Midleg-like 2 (SCML2)
  JOURNAL   J Biol Chem 278 (47), 46968-46973 (2003)
   PUBMED   12952983
  REMARK    GeneRIF: 1.78-A crystal structure of the two MBT repeats of SCML2
            show significant structural similarities to the Tudor, PWWP, and
            chromo domains, suggesting probable evolutionary relationships and
            functional similarities between the MBT repeats and these domains.
REFERENCE   10 (bases 1 to 4162)
  AUTHORS   Montini,E., Buchner,G., Spalluto,C., Andolfi,G., Caruso,A., den
            Dunnen,J.T., Trump,D., Rocchi,M., Ballabio,A. and Franco,B.
  TITLE     Identification of SCML2, a second human gene homologous to the
            Drosophila sex comb on midleg (Scm): A new gene cluster on Xp22
  JOURNAL   Genomics 58 (1), 65-72 (1999)
   PUBMED   10331946
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC040497.1 and BC064617.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_006089.2.
            
            Summary: This gene encodes a member of the Polycomb group proteins.
            These proteins form the Polycomb repressive complexes which are
            involved in transcriptional repression. The encoded protein binds
            histone peptides that are monomethylated at lysine residues and may
            be involved in regulating homeotic gene expression during
            development. [provided by RefSeq, Jun 2010].
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the functional protein.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC040497.1, Y18004.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000251900.9/ ENSP00000251900.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-572               BC040497.1         41-612
            573-4162            BC064617.1         566-4155
FEATURES             Location/Qualifiers
     source          1..4162
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xp22.13"
     gene            1..4162
                     /gene="SCML2"
                     /note="Scm polycomb group protein like 2"
                     /db_xref="GeneID:10389"
                     /db_xref="HGNC:HGNC:10581"
                     /db_xref="MIM:300208"
     exon            1..97
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            98..143
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     CDS             122..2224
                     /gene="SCML2"
                     /note="sex comb on midleg like 2"
                     /codon_start=1
                     /product="sex comb on midleg-like protein 2"
                     /protein_id="NP_006080.1"
                     /db_xref="CCDS:CCDS14185.1"
                     /db_xref="GeneID:10389"
                     /db_xref="HGNC:HGNC:10581"
                     /db_xref="MIM:300208"
                     /translation="MGQTVNEDSMDVKKENQEKTPQSSTSSVQRDDFHWEEYLKETGS
                     ISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCIATVIGITGARLRLRLDGSDN
                     RNDFWRLVDSPDIQPVGTCEKEGDLLQPPLGYQMNTSSWPMFLLKTLNGSEMASATLF
                     KKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEVHITFDGWSGAFDYWCK
                     YDSRDIFPAGWCRLTGDVLQPPGTSVPIVKNIAKTESSPSEASQHSMQSPQKTTLILP
                     TQQVRRSSRIKPPGPTAVPKRSSSVKNITPRKKGPNSGKKEKPLPVICSTSAASLKSL
                     TRDRGMLYKDVASGPCKIVMSTVCVYVNKHGNFGPHLDPKRIQQLPDHFGPGPVNVVL
                     RRIVQACVDCALETKTVFGYLKPDNRGGEVITASFDGETHSIQLPPVNSASFALRFLE
                     NFCHSLQCDNLLSSQPFSSSRGHTHSSAEHDKNQSAKEDVTERQSTKRSPQQTVPYVV
                     PLSPKLPKTKEYASEGEPLFAGGSAIPKEENLSEDSKSSSLNSGNYLNPACRNPMYIH
                     TSVSQDFSRSVPGTTSSPLVGDISPKSSPHEVKFQMQRKSEAPSYIAVPDPSVLKQGF
                     SKDPSTWSVDEVIQFMKHTDPQISGPLADLFRQHEIDGKALFLLKSDVMMKYMGLKLG
                     PALKLCYYIEKLKEGKYS"
     exon            144..212
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            213..283
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            284..518
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            519..607
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            608..851
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            852..1069
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            1070..1190
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            1191..1394
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            1395..1577
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            1578..1691
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            1692..1943
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            1944..2095
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     exon            2096..4162
                     /gene="SCML2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4139..4144
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SCML2"
                     /note="hexamer: AATAAA"
     polyA_site      4162
                     /gene="SCML2"
                     /note="major polyA site"
ORIGIN      
        1 gcggcttctc aaacatggcg gcggcggtgt gaagctcggt gccggctcgc gcgatcggtg
       61 ggacagaatt tcgttgtttt caccgacgag actggaggaa acaacaccaa atagggatac
      121 catgggacaa acagtgaatg aagattccat ggatgtcaag aaggagaatc aagagaaaac
      181 tcctcagtca agtacatctt ctgtacaaag ggatgatttc cactgggagg agtatttgaa
      241 agagactggg tctataagtg ctccttcaga gtgcttccgt cagtctcaga ttccacctgt
      301 gaatgatttc aaagttggta tgaaattgga agcccgtgac cctcgcaatg ccacttcagt
      361 atgtattgct acggttattg gaattactgg ggccaggtta cggttacgac tggatggtag
      421 tgacaacaga aatgattttt ggaggcttgt cgattcccca gacatacaac ctgttgggac
      481 atgtgaaaag gaaggagact tacttcaacc tccactaggg taccagatga atacatcctc
      541 ctggccgatg ttcctcttaa agacactaaa tgggtctgaa atggcatctg ccacattatt
      601 taagaaggaa ccaccaaagc ccccactaaa taattttaaa gtggggatga aactggaagc
      661 tattgacaaa aagaacccgt atctcatctg tcctgcgacc attggagatg ttaaagggga
      721 tgaagttcat atcacatttg atggctggag tggagctttt gattactggt gcaagtatga
      781 ttctcgagat attttcccag ctgggtggtg tcgcctgaca ggagatgtat tacaaccccc
      841 aggaactagt gttcctattg taaagaatat agcaaaaaca gagtcttctc cttccgaagc
      901 aagccagcat tcaatgcagt ctccacagaa aactactcta atattaccaa cacagcaggt
      961 caggagatca agtcgaatta aaccacctgg acctactgca gtccccaaaa ggagcagttc
     1021 tgttaaaaat atcacaccaa ggaaaaaagg tccaaactca ggaaaaaagg aaaaaccttt
     1081 gcccgtgata tgttctacat ctgcagcttc tctaaaatcg ctgaccagag accgtggcat
     1141 gttatataaa gatgtcgctt ctgggccatg taaaatagtg atgtctacag tctgtgtcta
     1201 tgtaaacaaa catggaaact ttggccctca tctggatccc aagagaatcc agcagctgcc
     1261 tgaccacttc ggcccgggcc cggtgaatgt ggtgcttcgc cggattgtgc aggcctgtgt
     1321 ggattgtgcc cttgaaacta aaactgtttt tggatacctg aagccagata atcgtggagg
     1381 agaagtgata actgcctcct ttgatgggga aactcattcc atccagctcc ctccagtgaa
     1441 cagtgcatca tttgctcttc gctttcttga gaacttctgc cacagtctgc agtgtgataa
     1501 ccttttgagt agccagcctt ttagttcttc caggggtcat actcacagct ctgcagagca
     1561 tgataaaaat cagtcagcaa aagaagatgt aacagaaagg caaagcacca aacgatctcc
     1621 tcagcaaact gtaccatatg ttgttcctct ctctcctaag ctccccaaaa caaaggagta
     1681 tgcgtctgaa ggagaaccat tgtttgctgg gggaagtgcc attcccaaag aggagaatct
     1741 ttcagaagat tctaagagct catcactaaa ttcaggaaat tatttgaatc ctgcctgtag
     1801 aaatcctatg tatattcata cttcagtctc ccaggatttt tctcgaagtg tgccaggcac
     1861 cacaagttca ccactagttg gggacatatc ccccaagagc agtccccatg aagttaaatt
     1921 ccaaatgcag aggaaaagtg aagctccaag ttatatagct gtacctgatc ccagtgtcct
     1981 gaaacaaggc ttctctaagg acccttcaac ctggtctgtg gatgaagtga tacagtttat
     2041 gaaacataca gatcctcaga tatcaggccc cctcgccgac ctcttcaggc aacatgaaat
     2101 tgatgggaag gctctgttcc tactcaagag tgatgtgatg atgaagtata tggggctgaa
     2161 gctggggcca gcattaaagc tgtgttacta cattgaaaag cttaaagaag gaaaatacag
     2221 ttaaaaaaat gtgtaagttt agattggaca taattctcag gtgtactgtt aacattttaa
     2281 tttaaaagta tttctcttag cagtttttgt tttgtagaca gttcccataa aaatatttta
     2341 tcagaattgc agaactgtag taacagttca gtcaactttg tttttttcct ggagtcacca
     2401 accagctttg ggagacacag ccgccactcc cccagtctac ttctttaaaa agcatttaac
     2461 aggttagtat tggcatattc aaattggcag ttctttatgt ctttttaaat tttcattgta
     2521 cagtttacaa atatacttaa tgtagttaac agagaaaaac ctttgatttt ggttaacctt
     2581 tatatctaga accaaaacag ctaaatccca aaggggaaaa tatcagggat tgacaacttc
     2641 tataattaaa tccatgagaa tttttcctca ctagagaatt taaaggtgca cctgtagata
     2701 tcatcttttc tcagatattt tgtgtgatac tctgtggtgt tctgttcatg ttctatcagt
     2761 atatctagaa agggaatagc catataaatt attttccttt tattatttct ctgtatgttg
     2821 tatttgatca tatttaaagg aaaaaagcaa gcttataagc tttcatgaag tgttcttacc
     2881 agtttttgat aaatttttta aattatagga tagaattgtc attttatgca ggagatattt
     2941 atactacgag ggttgtttgg atggagtcag attaaatttt ttcagtgaaa ttcctattat
     3001 tttaaaactt tccatatttt cactacgctt ggacatttaa ctaggcattc ttttcttaca
     3061 tctctatatg aagatacctg tgtccaaaat ttttgaagat atatattgta tgtgtttatt
     3121 cttcatatgg tactttacca tatttatata ttgttttata cctgtaggtt tacacacaag
     3181 taaatctttt ttttcttgaa tttaatctgg cactttgcac tgccacagag gtgacgatga
     3241 actatgtata tagttagatg ttttgatttc gtaaaaaata tatgtccatc gtttgctatc
     3301 accagtacct ctcagcttac tcttcagggg atatgaaaca atctgtagat tggtttccat
     3361 acagggaagt tctctgtcct atgcaatgtt tctaattaat ttgcttagtt ctgagccatt
     3421 tattctgcta cactttgaaa gatatattag ttctgactta ttgtttgggg ctttatttta
     3481 tttttatttt tttgagatgg agtttcactc ttgttgccca ggctggagtg caatagctcg
     3541 atctcggctc actgcaacct cgcctccctg gttcaagcaa ttctcctgcc tcagcgatta
     3601 caggaatgca ccaccacgcc cagctaattt tgtagagatg gggtttctcc atgttggtca
     3661 ggctggtctc aaactcctga cctcaggtga tccgcccacc tcggccttgc aaaatgctgg
     3721 gattacaggc atgagccacc atgcccagcc atgtttgggg ctttatttta taagttagaa
     3781 ctttgaagag gaaatggtgc tatatgttta ttgttattac tttgtgtaac tttgatgtaa
     3841 tgtttataag ctatgagaat cagttataaa agtattagcc atttgttgta aatgccaata
     3901 aaatattcac caggggcaag aatgtacatt ttctttttag aaaaccaaat gtactttaga
     3961 catgaatgca actatttaaa gaatagcttc atttatgtta ttccttacat gtcataagat
     4021 tcttacttaa acttggtctt ctttcaagtt gtttgtatga agatgctgta cccacttgaa
     4081 cagtcctcag gtgtttacat aaatactatg ttttacagtt ttcatatttt aaaatattaa
     4141 taaagttaat cgcaacgatt ca
//
