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    Sfmbt2 Scm-like with four mbt domains 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 307106, updated on 10-Jul-2024

    Summary

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    Official Symbol
    Sfmbt2provided by RGD
    Official Full Name
    Scm-like with four mbt domains 2provided by RGD
    Primary source
    RGD:1305027
    See related
    EnsemblRapid:ENSRNOG00000029235 AllianceGenome:RGD:1305027
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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 gene expression and negative regulation of transcription, DNA-templated. Predicted to be located in aggresome; cytosol; and nuclear speck. Predicted to be active in nucleus. Orthologous to human SFMBT2 (Scm like with four mbt domains 2). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Testes (RPKM 16.2), Liver (RPKM 12.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sfmbt2 in Genome Data Viewer
    Location:
    17q12.3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (72844037..73038599, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (67934296..68128905, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (71719012..71904303, complement)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120097741 Neighboring gene uncharacterized LOC102552867 Neighboring gene ferritin heavy chain 1, pseudogene 3 Neighboring gene microRNA 466d Neighboring gene microRNA mir-466b-2 Neighboring gene microRNA 466c Neighboring gene microRNA mir-466b-1 Neighboring gene uncharacterized LOC134482735 Neighboring gene uncharacterized LOC120097910 Neighboring gene uncharacterized LOC134482737

    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
    • 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. Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene. Lehnert S, et al. BMC Genomics, 2011 May 23. PMID 21605348, Free PMC Article
    2. Regulation of DU145 prostate cancer cell growth by Scm-like with four mbt domains 2. Lee K, et al. J Biosci, 2013 Mar. PMID 23385818
    3. 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. a large miRNA gene cluster in intron 10 of the Sfmbt2 gene
      Title: Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene.
    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
    		  
    enables histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription corepressor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in aggresome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in aggresome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    scm-like with four MBT domains protein 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_001107364.2 → NP_001100834.2  scm-like with four MBT domains protein 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000017
      Related
      ENSRNOP00000078227.2, ENSRNOT00000117032.2
      Conserved Domains (3) summary
      cd09581
      Location:807 → 890
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:47 → 143
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:527 → 641
      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_086035.1 Reference GRCr8

      Range
      72844037..73038599 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006254210.5 → XP_006254272.1  scm-like with four MBT domains protein 2 isoform X1

      See identical proteins and their annotated locations for XP_006254272.1

      Conserved Domains (3) summary
      cd09581
      Location:807 → 890
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:47 → 143
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:527 → 641
      SLED; SLED domain

    2. XM_006254216.5 → XP_006254278.1  scm-like with four MBT domains protein 2 isoform X2

      UniProtKB/TrEMBL
      A0A8I5Y8B8
      Conserved Domains (4) summary
      cd09581
      Location:806 → 889
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00454
      Location:816 → 880
      SAM; Sterile alpha motif
      smart00561
      Location:47 → 143
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:526 → 640
      DUF3588; Protein of unknown function (DUF3588)

    3. XM_006254215.5 → XP_006254277.1  scm-like with four MBT domains protein 2 isoform X1

      See identical proteins and their annotated locations for XP_006254277.1

      Conserved Domains (3) summary
      cd09581
      Location:807 → 890
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:47 → 143
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:527 → 641
      SLED; SLED domain

    4. XM_006254213.5 → XP_006254275.1  scm-like with four MBT domains protein 2 isoform X1

      See identical proteins and their annotated locations for XP_006254275.1

      Conserved Domains (3) summary
      cd09581
      Location:807 → 890
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:47 → 143
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:527 → 641
      SLED; SLED domain

    5. XM_063276494.1 → XP_063132564.1  scm-like with four MBT domains protein 2 isoform X2

      UniProtKB/TrEMBL
      A0A8I5Y8B8

    6. XM_006254212.5 → XP_006254274.1  scm-like with four MBT domains protein 2 isoform X1

      See identical proteins and their annotated locations for XP_006254274.1

      Conserved Domains (3) summary
      cd09581
      Location:807 → 890
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:47 → 143
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:527 → 641
      SLED; SLED domain

    7. XM_063276493.1 → XP_063132563.1  scm-like with four MBT domains protein 2 isoform X2

      UniProtKB/TrEMBL
      A0A8I5Y8B8

    8. XM_039095776.1 → XP_038951704.1  scm-like with four MBT domains protein 2 isoform X3

      Conserved Domains (3) summary
      cd09581
      Location:556 → 639
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00561
      Location:132 → 224
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:276 → 390
      SLED; SLED domain
    Nucleotide Protein Strain
    Heading Accession and Version

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