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SPSB4 splA/ryanodine receptor domain and SOCS box containing 4 [ Homo sapiens (human) ]

Gene ID: 92369, updated on 11-Apr-2024

Summary

Official Symbol
SPSB4provided by HGNC
Official Full Name
splA/ryanodine receptor domain and SOCS box containing 4provided by HGNC
Primary source
HGNC:HGNC:30630
See related
Ensembl:ENSG00000175093 MIM:611660; AllianceGenome:HGNC:30630
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SSB4; SSB-4
Summary
Enables ubiquitin ligase-substrate adaptor activity. Involved in cellular protein metabolic process; positive regulation of protein polyubiquitination; and regulation of circadian rhythm. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

See SPSB4 in Genome Data Viewer
Location:
3q23
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (141051347..141148611)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (143798863..143896164)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (140770189..140867453)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L23a pseudogene 41 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:140661115-140661962 Neighboring gene solute carrier family 25 member 36 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14772 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:140789226-140789769 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:140789770-140790312 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:140792837-140793422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:140802197-140802706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:140805486-140806259 Neighboring gene NANOG hESC enhancer GRCh37_chr3:140821789-140822305 Neighboring gene NANOG hESC enhancer GRCh37_chr3:140923620-140924130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:140925635-140926136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14773 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:140978638-140979382 Neighboring gene 2-phosphoxylose phosphatase 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64847 Neighboring gene ribosomal protein L31 pseudogene 21 Neighboring gene uncharacterized LOC124909441 Neighboring gene PHF5A pseudogene 7

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

EBI GWAS Catalog

Description
Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE collaboration): a meta-analysis of genome-wide association studies.
EBI GWAS Catalog
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 
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

Preferred Names
SPRY domain-containing SOCS box protein 4
Names
SPRY domain-containing SOCS box protein SSB-4

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_080862.3NP_543138.1  SPRY domain-containing SOCS box protein 4

    See identical proteins and their annotated locations for NP_543138.1

    Status: VALIDATED

    Source sequence(s)
    AC022215, AC108727, AF403029, BC051354, BX376865, CN366621
    Consensus CDS
    CCDS3115.1
    UniProtKB/Swiss-Prot
    Q96A44
    Related
    ENSP00000311609.2, ENST00000310546.3
    Conserved Domains (2) summary
    cd12906
    Location:54227
    SPRY_SOCS1-2-4; SPRY domain in the suppressor of cytokine signaling 1, 2, 4 families (SOCS1, SOCS2, SOCS4)
    cl02533
    Location:232273
    SOCS; SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins ...

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

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    141051347..141148611
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007509.3XP_016862998.1  SPRY domain-containing SOCS box protein 4 isoform X1

RNA

  1. XR_924215.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    143798863..143896164
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348414.1XP_054204389.1  SPRY domain-containing SOCS box protein 4 isoform X1

RNA

  1. XR_008486852.1 RNA Sequence