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    Sim1 SIM bHLH transcription factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309888, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Sim1provided by RGD
    Official Full Name
    SIM bHLH transcription factor 1provided by RGD
    Primary source
    RGD:1309949
    See related
    Ensembl:ENSRNOG00000037600 AllianceGenome:RGD:1309949
    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 DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated and ureteric bud development. Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in obesity. Orthologous to human SIM1 (SIM bHLH transcription factor 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Restricted expression toward (RPKM 80.6) See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    20q13
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (55409814..55489450)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (53827601..53907219)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (55590810..55674002)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene sperm motility kinase like, pseudogene 8 Neighboring gene uncharacterized LOC134483837 Neighboring gene activating signal cointegrator 1 complex subunit 3 Neighboring gene cytochrome c, somatic-like Neighboring gene lysophospholipase 1, pseudogene 2

    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. Profound obesity associated with a balanced translocation that disrupts the SIM1 gene. Holder JL Jr, et al. Hum Mol Genet, 2000 Jan 1. PMID 10587584
    2. Two new members of the murine Sim gene family are transcriptional repressors and show different expression patterns during mouse embryogenesis. Ema M, et al. Mol Cell Biol, 1996 Oct. PMID 8927054, Free PMC Article
    3. NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors. Wu D, et al. Elife, 2016 Oct 26. PMID 27782878, Free PMC Article
    4. Spatial gene expression in the T-stage mouse metanephros. Caruana G, et al. Gene Expr Patterns, 2006 Oct. PMID 16545622
    5. Differential activities of murine single minded 1 (SIM1) and SIM2 on a hypoxic response element. Cross-talk between basic helix-loop-helix/per-Arnt-Sim homology transcription factors. Woods SL, et al. J Biol Chem, 2002 Mar 22. PMID 11782478

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Clone Names

    • MGC189161

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ureteric bud development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    single-minded homolog 1
    Names
    single-minded 1
    single-minded family bHLH transcription factor 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_001107641.1 → NP_001101111.1  single-minded homolog 1

      See identical proteins and their annotated locations for NP_001101111.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474025
      UniProtKB/TrEMBL
      A6K6T3, D3ZMU8
      Related
      ENSRNOP00000053843.2, ENSRNOT00000057010.3
      Conserved Domains (5) summary
      cd00083
      Location:2 → 52
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:229 → 328
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      pfam00989
      Location:79 → 141
      PAS; PAS fold
      pfam06621
      Location:360 → 668
      SIM_C; Single-minded protein C-terminus
      pfam08447
      Location:243 → 329
      PAS_3; PAS fold

    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_086038.1 Reference GRCr8

      Range
      55409814..55489450
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006256604.4 → XP_006256666.1  single-minded homolog 1 isoform X1

      See identical proteins and their annotated locations for XP_006256666.1

      UniProtKB/TrEMBL
      A6K6T3, D3ZMU8
      Conserved Domains (5) summary
      cd00083
      Location:2 → 52
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      cd00130
      Location:229 → 328
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      pfam00989
      Location:79 → 141
      PAS; PAS fold
      pfam06621
      Location:360 → 668
      SIM_C; Single-minded protein C-terminus
      pfam08447
      Location:243 → 329
      PAS_3; PAS fold
    Nucleotide Protein Strain
    Heading Accession and Version

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