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    Sfmbt1 Scm-like with four mbt domains 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 58967, updated on 2-Nov-2024

    Summary

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    Symbol
    Sfmbt1provided by RGD
    Full Name
    Scm-like with four mbt domains 1provided by RGD
    Primary source
    RGD:61999
    See related
    EnsemblRapid:ENSRNOG00000016645 AllianceGenome:RGD:61999
    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
    Also known as
    Sfmbt
    Summary
    Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and negative regulation of muscle organ development. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Orthologous to human SFMBT1 (Scm like with four mbt domains 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 37.4), Adrenal (RPKM 36.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sfmbt1 in Genome Data Viewer
    Location:
    16p16
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 16 NC_086034.1 (5896686..6016311)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 16 NC_051351.1 (5889046..6009860)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 16 NC_005115.4 (6775648..6896155)

    Chromosome 16 - NC_086034.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134482446 Neighboring gene RFT1 homolog Neighboring gene small nucleolar RNA SNORA32 Neighboring gene farnesyl diphosphate synthase, pseudogene 1 Neighboring gene small nucleolar RNA SNORD113/SNORD114 family Neighboring gene uncharacterized LOC102555619 Neighboring gene STIM activating enhancer Neighboring gene uncharacterized LOC134482447

    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. Proteomic and functional analyses reveal the role of chromatin reader SFMBT1 in regulating epigenetic silencing and the myogenic gene program. Lin S, et al. J Biol Chem, 2013 Mar 1. PMID 23349461, Free PMC Article
    2. Human SFMBT is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3. Wu S, et al. FEBS Lett, 2007 Jul 10. PMID 17599839, Free PMC Article
    3. SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors. Zhang J, et al. Genes Dev, 2013 Apr 1. PMID 23592795, Free PMC Article
    4. Cloning of a novel murine gene Sfmbt, Scm-related gene containing four mbt domains, structurally belonging to the Polycomb group of genes. Usui H, et al. Gene, 2000 May 2. PMID 10806358
    5. A germline-specific class of small RNAs binds mammalian Piwi proteins. Girard A, et al. Nature, 2006 Jul 13. PMID 16751776

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC93349

    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
    		  
    enables histone binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables transcription corepressor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of muscle organ development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of muscle organ development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    scm-like with four MBT domains protein 1
    Names
    Scm-related gene containing four mbt domains

    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_031647.2 → NP_113835.2  scm-like with four MBT domains protein 1

      See identical proteins and their annotated locations for NP_113835.2

      Status: PROVISIONAL

      Source sequence(s)
      BC081770
      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A0A8I5ZVZ3, A6KG26
      Related
      ENSRNOP00000082833.1, ENSRNOT00000105144.2
      Conserved Domains (3) summary
      cd09581
      Location:779 → 863
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:23 → 120
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:499 → 614
      SLED; SLED domain

    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_086034.1 Reference GRCr8

      Range
      5896686..6016311
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006252658.4 → XP_006252720.1  scm-like with four MBT domains protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006252720.1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A0A8I5ZVZ3, A6KG26
      Conserved Domains (3) summary
      cd09581
      Location:779 → 863
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:23 → 120
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:499 → 614
      SLED; SLED domain

    2. XM_008771006.4 → XP_008769228.1  scm-like with four MBT domains protein 1 isoform X1

      See identical proteins and their annotated locations for XP_008769228.1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A0A8I5ZVZ3, A6KG26
      Conserved Domains (3) summary
      cd09581
      Location:779 → 863
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:23 → 120
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:499 → 614
      SLED; SLED domain

    3. XM_039094801.2 → XP_038950729.1  scm-like with four MBT domains protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A0A8I5ZVZ3, A6KG26
      Conserved Domains (3) summary
      cd09581
      Location:779 → 863
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:23 → 120
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:499 → 614
      SLED; SLED domain

    4. XM_063275676.1 → XP_063131746.1  scm-like with four MBT domains protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A6KG26
      Related
      ENSRNOP00000022865.4, ENSRNOT00000022865.7

    5. XM_063275677.1 → XP_063131747.1  scm-like with four MBT domains protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A6KG26

    6. XM_063275680.1 → XP_063131750.1  scm-like with four MBT domains protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A6KG26

    7. XM_039094800.2 → XP_038950728.1  scm-like with four MBT domains protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A0A8I5ZVZ3, A6KG26
      Conserved Domains (3) summary
      cd09581
      Location:779 → 863
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:23 → 120
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:499 → 614
      SLED; SLED domain

    8. XM_063275678.1 → XP_063131748.1  scm-like with four MBT domains protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A6KG26

    9. XM_063275675.1 → XP_063131745.1  scm-like with four MBT domains protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A6KG26

    10. XM_039094802.2 → XP_038950730.1  scm-like with four MBT domains protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A0A8I5ZVZ3, A6KG26
      Conserved Domains (3) summary
      cd09581
      Location:779 → 863
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:23 → 120
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:499 → 614
      SLED; SLED domain

    11. XM_063275681.1 → XP_063131751.1  scm-like with four MBT domains protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q66HN3, Q9JMD2
      UniProtKB/TrEMBL
      A6KG26
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9JMD2.2 GenPept UniProtKB/Swiss-Prot:Q9JMD2

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