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

Gene ID: 107815, updated on 11-Nov-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 and protein localization to chromosome. Located in XY body; chromatin; and nucleus. Orthologous to human SCML2 (Scm polycomb group protein like 2). [provided by Alliance of Genome Resources, Nov 2024]
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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See Scml2 in Genome Data Viewer
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 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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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
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 
located_in 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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