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    Sobp sine oculis binding protein homolog [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309860, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Sobpprovided by RGD
    Official Full Name
    sine oculis binding protein homologprovided by RGD
    Primary source
    RGD:1560479
    See related
    EnsemblRapid:ENSRNOG00000000316 AllianceGenome:RGD:1560479
    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
    Also known as
    jcx1; Sobpl; RGD1560479
    Summary
    Predicted to enable SUMO polymer binding activity. Predicted to be involved in cochlea development; cognition; and inner ear morphogenesis. Predicted to act upstream of or within locomotory behavior and sensory perception of sound. Predicted to be active in nucleus. Orthologous to human SOBP (sine oculis binding protein homolog). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Muscle (RPKM 53.6), Brain (RPKM 43.3) and 6 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sobp in Genome Data Viewer
    Location:
    20q13
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (48064445..48243607, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (46482265..46661452, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (47731713..47910466, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene Scm polycomb group protein like 4 Neighboring gene uncharacterized LOC134483826 Neighboring gene RIKEN cDNA 9030612E09 gene like Neighboring gene uncharacterized LOC134483827 Neighboring gene decaprenyl diphosphate synthase subunit 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. 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. 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
    4. 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
    5. 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

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables SUMO polymer binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within locomotory behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    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
    sine oculis-binding protein homolog
    Names
    jackson circler protein 1
    sine oculis-binding protein homolog-like

    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_001104640.2 → NP_001098110.1  sine oculis-binding protein homolog

      See identical proteins and their annotated locations for NP_001098110.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/Swiss-Prot
      A7XYI6
      Related
      ENSRNOP00000000348.5, ENSRNOT00000000348.8
      Conserved Domains (1) summary
      pfam15279
      Location:224 → 524
      SOBP; Sine oculis-binding protein

    2. NM_001412110.1 → NP_001399039.1  sine oculis-binding protein homolog

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/Swiss-Prot
      A7XYI6

    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
      48064445..48243607 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063279176.1 → XP_063135246.1  sine oculis-binding protein homolog isoform X2

      UniProtKB/TrEMBL
      A0A8I6A3P2
      Related
      ENSRNOP00000087149.1, ENSRNOT00000116176.2

    2. XM_063279175.1 → XP_063135245.1  sine oculis-binding protein homolog isoform X1

      UniProtKB/Swiss-Prot
      A7XYI6

    3. XM_063279178.1 → XP_063135248.1  sine oculis-binding protein homolog isoform X3

    4. XM_063279177.1 → XP_063135247.1  sine oculis-binding protein homolog isoform X3

    5. XM_039098771.2 → XP_038954699.1  sine oculis-binding protein homolog isoform X3

      Conserved Domains (1) summary
      pfam15279
      Location:1 → 278
      SOBP; Sine oculis-binding protein
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A7XYI6.1 GenPept UniProtKB/Swiss-Prot:A7XYI6

    Gene LinkOut

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

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