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Scmh1 sex comb on midleg homolog 1 [ Mus musculus (house mouse) ]

Gene ID: 29871, updated on 11-Nov-2024

Summary

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Official Symbol
Scmh1provided by MGI
Official Full Name
sex comb on midleg homolog 1provided by MGI
Primary source
MGI:MGI:1352762
See related
Ensembl:ENSMUSG00000000085 AllianceGenome:MGI:1352762
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
Scml1; Scml3
Summary
Predicted to enable chromatin binding activity and histone binding activity. Acts upstream of or within anterior/posterior pattern specification; chromatin remodeling; and spermatogenesis. Located in chromocenter and male germ cell nucleus. Is expressed in several structures, including branchial arch; genitourinary system; gut; limb; and nervous system. Orthologous to human SCMH1 (Scm polycomb group protein homolog 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis adult (RPKM 9.0), bladder adult (RPKM 6.2) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Scmh1 in Genome Data Viewer
Location:
4 D2.1; 4 56.52 cM
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (120262347..120387397)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (120405150..120530200)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 36499 Neighboring gene predicted gene, 36574 Neighboring gene VISTA enhancer mm145 Neighboring gene STARR-seq mESC enhancer starr_11247 Neighboring gene STARR-seq mESC enhancer starr_11248 Neighboring gene STARR-seq mESC enhancer starr_11249 Neighboring gene schlafen like 1 Neighboring gene cytidine 5'-triphosphate synthase 1

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. CircRNA SCMH1 regulates the miR-200a-3p/ZEB1 signaling axis to promote diabetes-induced retinal epithelial-mesenchymal transition.
    Title: CircRNA SCMH1 regulates the miR-200a-3p/ZEB1 signaling axis to promote diabetes-induced retinal epithelial-mesenchymal transition.
  2. Loss of Scmh1 caused derepression of Hoxb4 and Hoxa9, direct targets of Polycomb-group complex 1-mediated transcriptional silencing in hematopoietic cells.
    Title: Scmh1 has E3 ubiquitin ligase activity for geminin and histone H2A and regulates geminin stability directly or indirectly via transcriptional repression of Hoxa9 and Hoxb4.
  3. Scmh1 is involved in regulating the sequential changes in chromatin modifications at the XY chromatin domain of the pachytene spermatocytes.
    Title: Mammalian Polycomb Scmh1 mediates exclusion of Polycomb complexes from the XY body in the pachytene spermatocytes.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Targeted (5)  1 citation

Pathways from PubChem

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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 anterior/posterior pattern specification IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in heterochromatin formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
acts_upstream_of_or_within spermatogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within spermatogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in chromocenter IDA
Inferred from Direct Assay
more info
 PubMed 
located_in male germ cell nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
polycomb protein SCMH1
Names
sex comb on midleg 1
sex comb on midleg-like 1
sex comb on midleg-like 3

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_001159630.2 → NP_001153102.1  polycomb protein SCMH1 isoform 2

    See identical proteins and their annotated locations for NP_001153102.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate segment in the 3' coding region, compared to variant 1. The resulting isoform (2) has a longer and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL611924, AL626767
    Consensus CDS
    CCDS51292.1
    UniProtKB/Swiss-Prot
    B1AS51, Q8K214, Q9JME0
    Related
    ENSMUSP00000101908.2, ENSMUST00000106301.8
    Conserved Domains (4) summary
    cd09578
    Location:591 → 661
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:594 → 661
    SAM; Sterile alpha motif
    smart00561
    Location:31 → 126
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:357 → 465
    DUF3588; Protein of unknown function (DUF3588)

  2. NM_001379184.1 → NP_001366113.1  polycomb protein SCMH1 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL611924, AL626767
    Conserved Domains (4) summary
    cd09578
    Location:599 → 669
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00561
    Location:39 → 134
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:365 → 473
    SLED; SLED domain
    pfam17208
    Location:278 → 327
    RBR; RNA binding Region

  3. NM_001379185.1 → NP_001366114.1  polycomb protein SCMH1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL611924, AL626767
    Consensus CDS
    CCDS18589.1
    Conserved Domains (4) summary
    cd09578
    Location:591 → 661
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00561
    Location:31 → 126
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:357 → 465
    SLED; SLED domain
    pfam17208
    Location:270 → 319
    RBR; RNA binding Region

  4. NM_001379186.1 → NP_001366115.1  polycomb protein SCMH1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL611924, AL626767
    Conserved Domains (4) summary
    cd09578
    Location:567 → 637
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00561
    Location:7 → 102
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:333 → 441
    SLED; SLED domain
    pfam17208
    Location:246 → 295
    RBR; RNA binding Region

  5. NM_001404090.1 → NP_001391019.1  polycomb protein SCMH1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL611924, AL626767
    UniProtKB/Swiss-Prot
    B1AS51, Q8K214, Q9JME0

  6. NM_001404102.1 → NP_001391031.1  polycomb protein SCMH1 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AL611924, AL626767

  7. NM_001404103.1 → NP_001391032.1  polycomb protein SCMH1 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AL611924, AL626767

  8. NM_013883.3 → NP_038911.1  polycomb protein SCMH1 isoform 1

    See identical proteins and their annotated locations for NP_038911.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform (1). Variants 1 and 3 encode the same isoform (1).
    Source sequence(s)
    AL611924, AL626767
    Consensus CDS
    CCDS18589.1
    UniProtKB/Swiss-Prot
    Q8K214
    Related
    ENSMUSP00000000087.7, ENSMUST00000000087.13
    Conserved Domains (4) summary
    cd09578
    Location:591 → 661
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00561
    Location:31 → 126
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:357 → 465
    SLED; SLED domain
    pfam17208
    Location:270 → 319
    RBR; RNA binding Region

RNA

  1. NR_175812.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL611924, AL626767

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_000070.7 Reference GRCm39 C57BL/6J

    Range
    120262347..120387397
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006503149.3 → XP_006503212.1  polycomb protein SCMH1 isoform X3

    Conserved Domains (4) summary
    smart00561
    Location:39 → 134
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:365 → 473
    SLED; SLED domain
    pfam17208
    Location:278 → 327
    RBR; RNA binding Region
    cl15755
    Location:599 → 636
    SAM_superfamily; SAM (Sterile alpha motif )

  2. XM_017320253.2 → XP_017175742.1  polycomb protein SCMH1 isoform X1

    UniProtKB/Swiss-Prot
    Q8K214
    Related
    ENSMUSP00000101905.4, ENSMUST00000106298.10
    Conserved Domains (4) summary
    cd09578
    Location:591 → 661
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00561
    Location:31 → 126
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:357 → 465
    SLED; SLED domain
    pfam17208
    Location:270 → 319
    RBR; RNA binding Region

RNA

  1. XR_004941919.1 RNA Sequence

  2. XR_003954960.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8K214.1 GenPept UniProtKB/Swiss-Prot:Q8K214

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