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    Scml2 Scm polycomb group protein like 2 [ Mus musculus (house mouse) ]

    Gene ID: 107815, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Scml2provided by MGI
    Official Full Name
    Scm polycomb group protein like 2provided by MGI
    Primary source
    MGI:MGI:1340042
    See related
    Ensembl:ENSMUSG00000000037 AllianceGenome:MGI:1340042
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    4932420G07Rik
    Summary
    Predicted to enable chromatin binding activity and histone binding activity. Acts upstream of or within apoptotic process; cellular protein localization; and histone H2A-K119 monoubiquitination. Located in XY body; chromatin; and nucleus. Orthologous to human SCML2 (Scm polycomb group protein like 2). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in testis adult (RPKM 3.3), limb E14.5 (RPKM 2.7) and 14 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    X F4; X 73.95 cM
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (159865521..160041214)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (161082525..161258218)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene nuclear encoded tRNA valine 3 (anticodon TAC) Neighboring gene STARR-seq mESC enhancer starr_48186 Neighboring gene retinoschisis (X-linked, juvenile) 1 (human) Neighboring gene cyclin dependent kinase like 5 Neighboring gene gap junction protein, alpha 6 Neighboring gene STARR-positive B cell enhancer mm9_chrX:157432549-157432849 Neighboring gene STARR-seq mESC enhancer starr_48187 Neighboring gene STARR-seq mESC enhancer starr_48188 Neighboring gene STARR-seq mESC enhancer starr_48189 Neighboring gene STARR-seq mESC enhancer starr_48190 Neighboring gene STARR-seq mESC enhancer starr_48191 Neighboring gene STARR-seq mESC enhancer starr_48192 Neighboring gene STARR-seq mESC enhancer starr_48193 Neighboring gene nuclear encoded tRNA leucine 1 (anticodon TAA) Neighboring gene vitamin K epoxide reductase complex, subunit 1-like 1 pseudogene 5 Neighboring gene STARR-seq mESC enhancer starr_48194 Neighboring gene BEN domain containing 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. A rapidly evolved domain, the SCML2 DNA-binding repeats, contributes to chromatin binding of mouse SCML2†. Maezawa S, et al. Biol Reprod, 2019 Feb 1. PMID 30137219, Free PMC Article
    2. SCML2 promotes heterochromatin organization in late spermatogenesis. Maezawa S, et al. J Cell Sci, 2018 Sep 3. PMID 30097555, Free PMC Article
    3. Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline. Maezawa S, et al. Proc Natl Acad Sci U S A, 2018 May 8. PMID 29686098, Free PMC Article
    4. Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis. Maezawa S, et al. Nucleic Acids Res, 2018 Jan 25. PMID 29126117, Free PMC Article
    5. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. Maezawa S, et al. Nat Struct Mol Biol, 2020 Oct. PMID 32895557, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin.
      Title: Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin.
    2. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition.
      Title: Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition.
    3. These results suggest that the rapid evolution of SCML2 is due to reproductive adaptation, which has promoted species-specific gene expression programs in spermatogenesis.
      Title: A rapidly evolved domain, the SCML2 DNA-binding repeats, contributes to chromatin binding of mouse SCML2†.
    4. SCML2 accumulates on pericentromeric heterochromatin (PCH) in male germ cells, where it suppresses PRC1-mediated monoubiquitylation of histone H2A at Lysine 119 (H2AK119ub) and promotes deposition of PRC2-mediated H3K27me3 during meiosis.
      Title: SCML2 promotes heterochromatin organization in late spermatogenesis.
    5. SCML2-dependent H3K27me3 in the male germline prepares the expression of developmental regulator and somatic genes in embryonic development.
      Title: Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline.
    6. RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 for gene activation on sex chromosomes.
      Title: RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes.
    7. Our results demonstrate that the SCML2/USP7 complex constitutes a novel molecular pathway in modulating the epigenetic state of sex chromosomes during male meiosis
      Title: Polycomb protein SCML2 associates with USP7 and counteracts histone H2A ubiquitination in the XY chromatin during male meiosis.
    8. Scml2 is specifically expressed in germ cells. SCML2 localizes to the XY body during male meiosis. SCML2 is associated with phosphorylated H2AX and USP7, a deubiquitinase. Loss of SCML2 in mice causes defective spermatogenesis, resulting in sharply reduced sperm production. In the absence of SCML2, USP7 fails to accumulate on the XY body, whereas H2A monoubiquitination is dramatically augmented in the XY chromatin.
      Title: Polycomb protein SCML2 associates with USP7 and counteracts histone H2A ubiquitination in the XY chromatin during male meiosis.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    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 MGI

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within apoptotic process 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
    		  
    acts_upstream_of_or_within protein localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within protein localization to chromosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of PcG protein complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in XY body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of chromatin 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 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    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.

    mRNA and Protein(s)

    1. NM_001290651.1 → NP_001277580.1  sex comb on midleg-like protein 2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK031490, AK040521, AL672233, BC056382, CK341235
      Consensus CDS
      CCDS72460.1
      UniProtKB/TrEMBL
      B1AVB5, E9Q796
      Related
      ENSMUSP00000019101.5, ENSMUST00000019101.11
      Conserved Domains (3) summary
      PRK12495
      Location:559 → 677
      PRK12495; hypothetical protein; Provisional
      smart00561
      Location:126 → 217
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:737 → 846
      DUF3588; Protein of unknown function (DUF3588)

    2. NM_001290652.1 → NP_001277581.1  sex comb on midleg-like protein 2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two alternate exons and uses an alternate splice site, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK031490, AK040521, AL672233, CK341235
      Consensus CDS
      CCDS81193.1
      UniProtKB/TrEMBL
      B1AVB4, Q8BYC8
      Related
      ENSMUSP00000074356.6, ENSMUST00000074802.12
      Conserved Domains (2) summary
      smart00561
      Location:126 → 217
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:677 → 786
      DUF3588; Protein of unknown function (DUF3588)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000086.8 Reference GRCm39 C57BL/6J

      Range
      159865521..160041214
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006528670.2 → XP_006528733.1  sex comb on midleg-like protein 2 isoform X1

      UniProtKB/TrEMBL
      B1AVB3
      Conserved Domains (4) summary
      PTZ00121
      Location:403 → 742
      PTZ00121; MAEBL; Provisional
      cd09578
      Location:1062 → 1132
      SAM_Scm; SAM domain of Scm proteins of Polycomb group
      smart00561
      Location:266 → 357
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:877 → 986
      SLED; SLED domain

    2. XM_006528672.2 → XP_006528735.1  sex comb on midleg-like protein 2 isoform X2

      UniProtKB/TrEMBL
      E9Q796
      Conserved Domains (3) summary
      PTZ00121
      Location:403 → 742
      PTZ00121; MAEBL; Provisional
      smart00561
      Location:266 → 357
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:877 → 986
      SLED; SLED domain

    3. XM_006528673.4 → XP_006528736.1  sex comb on midleg-like protein 2 isoform X3

      UniProtKB/TrEMBL
      B1AVB3
      Related
      ENSMUSP00000076593.5, ENSMUST00000077375.5
      Conserved Domains (4) summary
      PTZ00121
      Location:263 → 602
      PTZ00121; MAEBL; Provisional
      cd09578
      Location:922 → 992
      SAM_Scm; SAM domain of Scm proteins of Polycomb group
      smart00561
      Location:126 → 217
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:737 → 846
      SLED; SLED domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_133194.3: Suppressed sequence

      Description
      NM_133194.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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