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

Gene ID: 307106, updated on 3-Apr-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
Ensembl: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
    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
    Related
    ENSRNOP00000078227.1
    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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