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

Gene ID: 109205, updated on 8-May-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, Apr 2022]
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 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

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