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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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