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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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