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    Spsb2 splA/ryanodine receptor domain and SOCS box containing 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 297592, updated on 27-Nov-2024

    Summary

    Symbol
    Spsb2provided by RGD
    Full Name
    splA/ryanodine receptor domain and SOCS box containing 2provided by RGD
    Primary source
    RGD:1310854
    See related
    EnsemblRapid:ENSRNOG00000015125 AllianceGenome:RGD:1310854
    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
    Grcc9
    Summary
    Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process and protein ubiquitination. Predicted to be located in cytosol. Predicted to be part of SCF ubiquitin ligase complex. Orthologous to human SPSB2 (splA/ryanodine receptor domain and SOCS box containing 2). [provided by Alliance of Genome Resources, Nov 2024]
    Annotation information
    Note: LOC100911548 (GeneID: 100911548) appears to be a duplicate placement of Spsb2 (GeneID: 297592) on Rnor_6.0 (Annot. Release 105) that is absent from Rn_Celera and is not supported by syntenic regions in mouse and human. BLAST analysis of the underlying component AABR07066868.1 against the rat genome shows 88% coverage and 99% identity with NC_005103.4, at the location where Spsb2 is annotated. Annotation of Spsb2 (GeneID: 297592) at this location on Rnor_6.0 is supported by annotation on Rn_Celera and synteny with mouse and human. This apparent duplication could be explained by misassembly of several underlying components on Rnor_6.0. LOC100911548 is bracketed by two genes, Gpr116 and Gpr110, which serve as a useful frame of reference, on the rat reference assembly. The region between these two genes also includes several other genes with names beginning with "LOC". However, on the Celera assembly as well as at the syntenic region in the mouse genome, these "LOC" genes are not annotated between Gpr116 and Gpr110. This suggests that the underlying components for these "LOC" genes could be misassembled in Rnor_6.0, including AABR07066868.1, AABR07066869.1, and AABR07066870.1. [14 Apr 2021]
    Expression
    Biased expression in Muscle (RPKM 308.5), Heart (RPKM 90.2) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Spsb2 in Genome Data Viewer
    Location:
    4q42
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (159298362..159301568)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (157613404..157615293)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (157325980..157328380)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120102384 Neighboring gene enolase 2 Neighboring gene leucine rich repeat containing 23 Neighboring gene uncharacterized LOC134486638 Neighboring gene triosephosphate isomerase 1 Neighboring gene ubiquitin specific peptidase 5 Neighboring gene cell division cycle associated 3 Neighboring gene G protein subunit beta 3

    Genomic regions, transcripts, and products

    Expression

    • 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

    General gene information

    Markers

    Clone Names

    • MGC108858

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ubiquitin-like ligase-substrate adaptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ubiquitin-like ligase-substrate adaptor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables ubiquitin-like ligase-substrate adaptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in intracellular signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein ubiquitination ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in ubiquitin-dependent protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    part_of SCF ubiquitin ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    SPRY domain-containing SOCS box protein 2
    Names
    SPRY domain-containing SOCS box protein 2-like
    SPRY domain-containing SOCS box protein SSB-2
    SSB-2
    gene rich cluster, C9 gene protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001009660.2NP_001009660.1  SPRY domain-containing SOCS box protein 2

      See identical proteins and their annotated locations for NP_001009660.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/Swiss-Prot
      Q5M877
      UniProtKB/TrEMBL
      A6ILL1
      Related
      ENSRNOP00000020493.4, ENSRNOT00000020493.7
      Conserved Domains (2) summary
      cd03719
      Location:223264
      SOCS_SSB2; SOCS (suppressors of cytokine signaling) box of SSB2 (SPRY domain-containing SOCS box proteins)-like proteins. SSB proteins contain a central SPRY domain and a C-terminal SOCS. SSB2 has been shown to bind to MET, the receptor protein-tyrosine kinase for ...
      cd12906
      Location:46217
      SPRY_SOCS1-2-4; SPRY domain in the suppressor of cytokine signaling 1, 2, 4 families (SOCS1, SOCS2, SOCS4)
    2. NM_001394356.1NP_001381285.1  SPRY domain-containing SOCS box protein 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/Swiss-Prot
      Q5M877
      UniProtKB/TrEMBL
      A6ILL1
    3. NM_001394357.1NP_001381286.1  SPRY domain-containing SOCS box protein 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/Swiss-Prot
      Q5M877
      UniProtKB/TrEMBL
      A6ILL1

    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_086022.1 Reference GRCr8

      Range
      159298362..159301568
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063285905.1XP_063141975.1  SPRY domain-containing SOCS box protein 2 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYR0
    2. XM_063285904.1XP_063141974.1  SPRY domain-containing SOCS box protein 2 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYR0
      Related
      ENSRNOP00000100710.1, ENSRNOT00000136731.1
    3. XM_063285906.1XP_063141976.1  SPRY domain-containing SOCS box protein 2 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYR0