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

Summary

Symbol: Spsb2provided by RGD
Full Name: splA/ryanodine receptor domain and SOCS box containing 2provided by RGD
Primary source: RGD:1310854
See related: Ensembl: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 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, Apr 2022]
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: human mouse all
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Genomic context

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_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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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

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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)

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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)

NM_001009660.2 → NP_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, ENSRNOT00000020493.6

Conserved Domains (2) summary

cd03719
Location:223 → 264

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:46 → 217

SPRY_SOCS1-2-4; SPRY domain in the suppressor of cytokine signaling 1, 2, 4 families (SOCS1, SOCS2, SOCS4)
NM_001394356.1 → NP_001381285.1 SPRY domain-containing SOCS box protein 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

Q5M877

UniProtKB/TrEMBL

A6ILL1
NM_001394357.1 → NP_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

NC_086022.1 Reference GRCr8

Range

159298362..159301568

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8I5ZYR0
XM_063285904.1 → XP_063141974.1 SPRY domain-containing SOCS box protein 2 isoform X1

UniProtKB/TrEMBL

A0A8I5ZYR0
XM_063285906.1 → XP_063141976.1 SPRY domain-containing SOCS box protein 2 isoform X1

UniProtKB/TrEMBL

A0A8I5ZYR0