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    Scmh1 Scm polycomb group protein homolog 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362581, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Scmh1provided by RGD
    Official Full Name
    Scm polycomb group protein homolog 1provided by RGD
    Primary source
    RGD:1305788
    See related
    EnsemblRapid:ENSRNOG00000071308 AllianceGenome:RGD:1305788
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to act upstream of or within anterior/posterior pattern specification; chromatin remodeling; and spermatogenesis. Predicted to be located in chromocenter and male germ cell nucleus. Predicted to be active in nucleus. Orthologous to human SCMH1 (Scm polycomb group protein homolog 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Adrenal (RPKM 86.1), Heart (RPKM 82.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Scmh1 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (139276352..139401118)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (133991167..134115893)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (139379256..139466805)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134487083 Neighboring gene forkhead box O6 Neighboring gene CTP synthase 1 Neighboring gene schlafen-like 1 Neighboring gene large ribosomal subunit protein eL33-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Polycomb group proteins are essential for spinal cord development. Wang C, et al. Front Biosci (Landmark Ed), 2010 Jun 1. PMID 20515739
    2. Mammalian Polycomb Scmh1 mediates exclusion of Polycomb complexes from the XY body in the pachytene spermatocytes. Takada Y, et al. Development, 2007 Feb. PMID 17215307
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results suggest that the Polycomb proteins may be involved in spinal cord development.
      Title: Polycomb group proteins are essential for spinal cord development.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within anterior/posterior pattern specification ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromocenter ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in male germ cell nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 homolog 1

    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_001109669.1 → NP_001103139.1  polycomb protein SCMH1

      See identical proteins and their annotated locations for NP_001103139.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473968
      UniProtKB/TrEMBL
      A0A0G2K483, A2RRU0, D3ZRT7
      Related
      ENSRNOP00000111749.1, ENSRNOT00000144712.1
      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

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      139276352..139401118
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039110303.2 → XP_038966231.1  polycomb protein SCMH1 isoform X3

      UniProtKB/TrEMBL
      A0A0G2K483, A0A8I6A2M1
      Related
      ENSRNOP00000098562.1, ENSRNOT00000121004.2
      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

    2. XM_039110305.2 → XP_038966233.1  polycomb protein SCMH1 isoform X7

      Conserved Domains (3) summary
      smart00561
      Location:85 → 180
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:411 → 519
      SLED; SLED domain
      pfam17208
      Location:324 → 373
      RBR; RNA binding Region

    3. XM_039110302.2 → XP_038966230.1  polycomb protein SCMH1 isoform X2

      UniProtKB/TrEMBL
      A0A0G2K483
      Conserved Domains (4) summary
      cd09578
      Location:623 → 693
      SAM_Scm; SAM domain of Scm proteins of Polycomb group
      smart00561
      Location:85 → 180
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:411 → 519
      SLED; SLED domain
      pfam17208
      Location:324 → 373
      RBR; RNA binding Region

    4. XM_039110300.2 → XP_038966228.1  polycomb protein SCMH1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K483
      Conserved Domains (4) summary
      cd09578
      Location:645 → 715
      SAM_Scm; SAM domain of Scm proteins of Polycomb group
      smart00561
      Location:85 → 180
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:411 → 519
      SLED; SLED domain
      pfam17208
      Location:324 → 373
      RBR; RNA binding Region

    5. XM_063287983.1 → XP_063144053.1  polycomb protein SCMH1 isoform X5

    6. XM_063287984.1 → XP_063144054.1  polycomb protein SCMH1 isoform X6

      UniProtKB/TrEMBL
      A0A8J8XWQ9
      Related
      ENSRNOP00000112181.1, ENSRNOT00000170251.1

    7. XM_063287982.1 → XP_063144052.1  polycomb protein SCMH1 isoform X4

      UniProtKB/TrEMBL
      A2RRU0, D3ZRT7
      Related
      ENSRNOP00000098564.2, ENSRNOT00000121006.2
    Nucleotide Protein Strain
    Heading Accession and Version

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