SPSB2 splA/ryanodine receptor domain and SOCS box containing 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPSB2provided by HGNC
Official Full Name: splA/ryanodine receptor domain and SOCS box containing 2provided by HGNC
Primary source: HGNC:HGNC:29522
See related: Ensembl:ENSG00000111671 MIM:611658; AllianceGenome:HGNC:29522
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SSB2; GRCC9
Summary: This gene encodes a member of a subfamily of proteins containing a central SPRY (repeats in splA and RyR) domain and a C-terminal suppressor of cytokine signaling (SOCS) box. This protein plays a role in cell signaling. This gene is present in a gene-rich cluster on chromosome 12p13 in the vicinity of the CD4 antigen and triosephosphate isomerase genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
Expression: Broad expression in brain (RPKM 50.3), appendix (RPKM 44.2) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.31

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (6870935..6873303, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (6880233..6882601, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (6980099..6982467, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Structural basis for the regulation of inducible nitric oxide synthase by the SPRY domain-containing SOCS box protein SPSB2, an E3 ubiquitin ligase.
Title: Structural basis for the regulation of inducible nitric oxide synthase by the SPRY domain-containing SOCS box protein SPSB2, an E3 ubiquitin ligase.
Results demonstrated that cellular factor SPSB2 interacts with and decreases viral protein NS5A to inhibit HCV replication. SPSBP2 interacts with the HCV protein NS5A via its SPRY domain and inhibits HCV replication by ubiquitination and degradation of NS5A.
Title: SPSB2 inhibits hepatitis C virus replication by targeting NS5A for ubiquitination and degradation.
C-terminal His6 tag of the recombinant protein binds to a shallow pocket adjacent to the iNOS-binding site on a crystallographically related SPSB2 molecule
Title: Crystal structure of the SPRY domain of human SPSB2 in the apo state.
crystal structure of SPSB2 in complex with cyclic peptide inhibitor cR8, at a resolution of 1.34 A
Title: Crystal structure of SPSB2 in complex with a rational designed RGD-containing cyclic peptide inhibitor of SPSB2-iNOS interaction.
Shows that this gene is associated with the regulation of cell proliferation in canine mammary cancer cell lines.
Title: Transcriptomic profile of two canine mammary cancer cell lines with different proliferative and anti-apoptotic potential.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-M10036 (e-PCR)
- UniSTS:31504

D1S3365 (e-PCR)
- UniSTS:66707

G32324 (e-PCR)
- UniSTS:116917

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin-like ligase-substrate adaptor activity	IPI Inferred from Physical Interaction more info	PubMed

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	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of SCF ubiquitin ligase complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement 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 SSB-2; gene-rich cluster protein C9

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.

Genomic

NG_013308.1 RefSeqGene

Range

5055..7423

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001146316.2 → NP_001139788.1 SPRY domain-containing SOCS box protein 2

See identical proteins and their annotated locations for NP_001139788.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 4 encode the same protein.

Source sequence(s)

BC071933, U47924

Consensus CDS

CCDS8567.1

UniProtKB/Swiss-Prot

B7Z4W1, D3DUT0, Q99619

Related

ENSP00000430872.1, ENST00000523102.5

Conserved Domains (2) summary

cd03719
Location:222 → 263

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_001319670.2 → NP_001306599.1 SPRY domain-containing SOCS box protein 2

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate segment in the 5' UTR compared to variant 1. Variants 1, 2, and 4 encode the same protein.

Source sequence(s)

U47924

Consensus CDS

CCDS8567.1

UniProtKB/Swiss-Prot

B7Z4W1, D3DUT0, Q99619

Conserved Domains (2) summary

cd03719
Location:222 → 263

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_032641.4 → NP_116030.1 SPRY domain-containing SOCS box protein 2

See identical proteins and their annotated locations for NP_116030.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) is the reference variant. Variants 1, 2, and 4 encode the same protein.

Source sequence(s)

BC002983, DT220163

Consensus CDS

CCDS8567.1

UniProtKB/Swiss-Prot

B7Z4W1, D3DUT0, Q99619

Related

ENSP00000428338.1, ENST00000524270.6

Conserved Domains (2) summary

cd03719
Location:222 → 263

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)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

6870935..6873303 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

6880233..6882601 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001146317.1: Suppressed sequence

Description

NM_001146317.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein, and the transcript appears to retain intronic sequence.