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    SCML2 Scm polycomb group protein like 2 [ Homo sapiens (human) ]

    Gene ID: 10389, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SCML2provided by HGNC
    Official Full Name
    Scm polycomb group protein like 2provided by HGNC
    Primary source
    HGNC:HGNC:10581
    See related
    Ensembl:ENSG00000102098 MIM:300208; AllianceGenome:HGNC:10581
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    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]
    Expression
    Broad expression in testis (RPKM 5.8), adrenal (RPKM 1.8) and 19 other tissues See more
    Orthologs
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    Genomic context

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    See SCML2 in Genome Data Viewer
    Location:
    Xp22.13
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (18239313..18355118, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (17821927..17937732, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (18257433..18372808, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18244195-18244696 Neighboring gene BEN domain containing 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:18247834-18248500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18296901-18297401 Neighboring gene uncharacterized LOC124905253 Neighboring gene thymosin beta 10 pseudogene 2 Neighboring gene Sharpr-MPRA regulatory region 2020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18460197-18460698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18460699-18461198 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:18487190-18487391 Neighboring gene cyclin dependent kinase like 5 Neighboring gene gap junction protein alpha 6, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Sex Comb on Midleg Like-2 Accelerates Hepatocellular Carcinoma Cell Proliferation and Metastasis by Activating Wnt/β-Catenin/EMT Signaling. Du L, et al. Yonsei Med J, 2021 Dec. PMID 34816637, Free PMC Article
    2. Crystal structure of the malignant brain tumor (MBT) repeats in Sex Comb on Midleg-like 2 (SCML2). Sathyamurthy A, et al. J Biol Chem, 2003 Nov 21. PMID 12952983
    3. Interactions with RNA direct the Polycomb group protein SCML2 to chromatin where it represses target genes. Bonasio R, et al. Elife, 2014 Jul 1. PMID 24986859, Free PMC Article
    4. The malignant brain tumor repeats of human SCML2 bind to peptides containing monomethylated lysine. Santiveri CM, et al. J Mol Biol, 2008 Oct 24. PMID 18706910
    5. Solution NMR structure of the DNA-binding domain from Scml2 (sex comb on midleg-like 2). Bezsonova I. J Biol Chem, 2014 May 30. PMID 24727478, Free PMC Article

    See all (56) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Sex Comb on Midleg Like-2 Accelerates Hepatocellular Carcinoma Cell Proliferation and Metastasis by Activating Wnt/beta-Catenin/EMT Signaling.
      Title: Sex Comb on Midleg Like-2 Accelerates Hepatocellular Carcinoma Cell Proliferation and Metastasis by Activating Wnt/β-Catenin/EMT Signaling.
    2. SCML2A, an SCML2 isoform tightly associated to chromatin, contributes to PRC1 localization and also directly enforces repression of certain Polycomb target genes.
      Title: Interactions with RNA direct the Polycomb group protein SCML2 to chromatin where it represses target genes.
    3. 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.
      Title: USP7 cooperates with SCML2 to regulate the activity of PRC1.
    4. 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.
      Title: Solution NMR structure of the DNA-binding domain from Scml2 (sex comb on midleg-like 2).
    5. 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.
      Title: The malignant brain tumor repeats of human SCML2 bind to peptides containing monomethylated lysine.
    6. 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.
      Title: Crystal structure of the malignant brain tumor (MBT) repeats in Sex Comb on Midleg-like 2 (SCML2).
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in anatomical structure morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of PcG protein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sex comb on midleg-like protein 2
    Names
    sex comb on midleg like 2

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_021431.2 RefSeqGene

      Range
      5037..120412
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_006089.3 → NP_006080.1  sex comb on midleg-like protein 2

      See identical proteins and their annotated locations for NP_006080.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.
      Source sequence(s)
      BC040497, BC064617
      Consensus CDS
      CCDS14185.1
      UniProtKB/Swiss-Prot
      Q5JXE6, Q86U98, Q8IWD0, Q8NDP2, Q9UGC5, Q9UQR0
      UniProtKB/TrEMBL
      B4DZR9, E7ERN2
      Related
      ENSP00000251900.4, ENST00000251900.9
      Conserved Domains (4) summary
      cd09578
      Location:625 → 696
      SAM_Scm; SAM domain of Scm proteins of Polycomb group
      smart00454
      Location:628 → 696
      SAM; Sterile alpha motif
      smart00561
      Location:142 → 240
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:356 → 465
      DUF3588; Protein of unknown function (DUF3588)

    RNA

    1. NR_033717.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal segment, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC040497, BC051913

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      18239313..18355118 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017029219.2 → XP_016884708.1  sex comb on midleg-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5JXE6, Q86U98, Q8IWD0, Q8NDP2, Q9UGC5, Q9UQR0
      UniProtKB/TrEMBL
      B4DZR9, E7ERN2
      Conserved Domains (4) summary
      cd09578
      Location:625 → 696
      SAM_Scm; SAM domain of Scm proteins of Polycomb group
      smart00454
      Location:628 → 696
      SAM; Sterile alpha motif
      smart00561
      Location:142 → 240
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:356 → 465
      DUF3588; Protein of unknown function (DUF3588)

    2. XM_006724458.1 → XP_006724521.1  sex comb on midleg-like protein 2 isoform X2

      UniProtKB/TrEMBL
      B4DZR9, E7ERN2
      Conserved Domains (2) summary
      smart00561
      Location:142 → 240
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:356 → 465
      DUF3588; Protein of unknown function (DUF3588)

    3. XM_017029220.3 → XP_016884709.1  sex comb on midleg-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5JXE6, Q86U98, Q8IWD0, Q8NDP2, Q9UGC5, Q9UQR0
      UniProtKB/TrEMBL
      B4DZR9, E7ERN2
      Conserved Domains (4) summary
      cd09578
      Location:625 → 696
      SAM_Scm; SAM domain of Scm proteins of Polycomb group
      smart00454
      Location:628 → 696
      SAM; Sterile alpha motif
      smart00561
      Location:142 → 240
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:356 → 465
      DUF3588; Protein of unknown function (DUF3588)

    4. XM_017029222.2 → XP_016884711.1  sex comb on midleg-like protein 2 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      17821927..17937732 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326365.1 → XP_054182340.1  sex comb on midleg-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5JXE6, Q86U98, Q8IWD0, Q8NDP2, Q9UGC5, Q9UQR0
      UniProtKB/TrEMBL
      B4DZR9, E7ERN2

    2. XM_054326367.1 → XP_054182342.1  sex comb on midleg-like protein 2 isoform X2

      UniProtKB/TrEMBL
      B4DZR9, E7ERN2

    3. XM_054326366.1 → XP_054182341.1  sex comb on midleg-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5JXE6, Q86U98, Q8IWD0, Q8NDP2, Q9UGC5, Q9UQR0
      UniProtKB/TrEMBL
      B4DZR9, E7ERN2

    4. XM_054326368.1 → XP_054182343.1  sex comb on midleg-like protein 2 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UQR0.1 GenPept UniProtKB/Swiss-Prot:Q9UQR0

    Gene LinkOut

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