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    Sobp sine oculis binding protein [ Mus musculus (house mouse) ]

    Gene ID: 109205, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Sobpprovided by MGI
    Official Full Name
    sine oculis binding proteinprovided by MGI
    Primary source
    MGI:MGI:1924427
    See related
    Ensembl:ENSMUSG00000038248 AllianceGenome:MGI:1924427
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    jc; JXC1; 2900009C16Rik; 5330439J01Rik
    Summary
    Enables SUMO polymer binding activity. Involved in cochlea development. Acts upstream of or within inner ear morphogenesis; locomotory behavior; and sensory perception of sound. Located in nucleus. Is expressed in cerebellum Purkinje cell layer and forebrain. Orthologous to human SOBP (sine oculis binding protein homolog). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in frontal lobe adult (RPKM 6.6), CNS E18 (RPKM 6.5) and 18 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Sobp in Genome Data Viewer
    Location:
    10 B2; 10 22.89 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (42878484..43059144, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (43002488..43183139, complement)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr10:42582153-42582336 Neighboring gene predicted gene, 34006 Neighboring gene Scm polycomb group protein like 4 Neighboring gene STARR-seq mESC enhancer starr_26496 Neighboring gene STARR-positive B cell enhancer ABC_E6835 Neighboring gene STARR-seq mESC enhancer starr_26499 Neighboring gene STARR-positive B cell enhancer mm9_chr10:42709746-42710047 Neighboring gene predicted gene, 51402 Neighboring gene predicted gene 5079 Neighboring gene STARR-seq mESC enhancer starr_26500 Neighboring gene predicted gene, 47815 Neighboring gene RIKEN cDNA 9030612E09 gene Neighboring gene STARR-seq mESC enhancer starr_26502 Neighboring gene STARR-seq mESC enhancer starr_26503 Neighboring gene prenyl (solanesyl) diphosphate synthase, subunit 2 Neighboring gene predicted gene, 40631 Neighboring gene ribosomal protein S19, pseudogene 11

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. SOBP is mutated in syndromic and nonsyndromic intellectual disability and is highly expressed in the brain limbic system. Birk E, et al. Am J Hum Genet, 2010 Nov 12. PMID 21035105, Free PMC Article
    2. Jxc1/Sobp, encoding a nuclear zinc finger protein, is critical for cochlear growth, cell fate, and patterning of the organ of corti. Chen Z, et al. J Neurosci, 2008 Jun 25. PMID 18579736, Free PMC Article
    3. Molecular basis of human Usher syndrome: deciphering the meshes of the Usher protein network provides insights into the pathomechanisms of the Usher disease. Reiners J, et al. Exp Eye Res, 2006 Jul. PMID 16545802
    4. Poly-small ubiquitin-like modifier (PolySUMO)-binding proteins identified through a string search. Sun H, et al. J Biol Chem, 2012 Dec 7. PMID 23086935, Free PMC Article
    5. Cochlear developmental defect and background-dependent hearing thresholds in the Jackson circler (jc) mutant mouse. Calderon A, et al. Hear Res, 2006 Nov. PMID 16962269

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. In situ RNA expression studies in postnatal mouse brain showed strong expression in the limbic system at the time interval of active synaptogenesis.
      Title: SOBP is mutated in syndromic and nonsyndromic intellectual disability and is highly expressed in the brain limbic system.
    2. These data support a role for Jxc1 in controlling a critical step in cochlear growth, cell fate, and patterning of the organ of Corti.
      Title: Jxc1/Sobp, encoding a nuclear zinc finger protein, is critical for cochlear growth, cell fate, and patterning of the organ of corti.
    Submit: New GeneRIF Correction

    Phenotypes

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    Associated conditions

    Description Tests
    Jackson circler
    GeneReviews: Not available

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Spontaneous (2)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC67344

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables SUMO polymer binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in animal organ development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cochlea development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cognition IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cognition ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in inner ear morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within inner ear morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within locomotory behavior IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sine oculis-binding protein homolog
    Names
    jackson circler protein 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_175407.3 → NP_780616.4  sine oculis-binding protein homolog

      See identical proteins and their annotated locations for NP_780616.4

      Status: VALIDATED

      Source sequence(s)
      AC112265, BC059851, BY712464
      Consensus CDS
      CCDS35890.1
      UniProtKB/Swiss-Prot
      Q0P5V2
      Related
      ENSMUSP00000040072.8, ENSMUST00000040275.9
      Conserved Domains (2) summary
      TIGR04213
      Location:59 → 114
      PGF_pre_PGF; PGF-pre-PGF domain
      pfam15279
      Location:224 → 524
      SOBP; Sine oculis-binding protein

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      42878484..43059144 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030244821.2 → XP_030100681.1  sine oculis-binding protein homolog isoform X2

      Conserved Domains (1) summary
      pfam15279
      Location:1 → 278
      SOBP; Sine oculis-binding protein

    2. XM_030244820.2 → XP_030100680.1  sine oculis-binding protein homolog isoform X2

      Conserved Domains (1) summary
      pfam15279
      Location:1 → 278
      SOBP; Sine oculis-binding protein

    3. XM_017313763.3 → XP_017169252.1  sine oculis-binding protein homolog isoform X1

      Conserved Domains (1) summary
      pfam15279
      Location:192 → 492
      SOBP; Sine oculis-binding protein
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q0P5V2.1 GenPept UniProtKB/Swiss-Prot:Q0P5V2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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