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    SSC4D scavenger receptor cysteine rich family member with 4 domains [ Homo sapiens (human) ]

    Gene ID: 136853, updated on 2-May-2024

    Summary

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    Official Symbol
    SSC4Dprovided by HGNC
    Official Full Name
    scavenger receptor cysteine rich family member with 4 domainsprovided by HGNC
    Primary source
    HGNC:HGNC:14461
    See related
    Ensembl:ENSG00000146700 MIM:607639; AllianceGenome:HGNC:14461
    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
    SRCRB4D; S4D-SRCRB; SRCRB-S4D
    Summary
    The scavenger receptor cysteine-rich (SRCR) superfamily is an ancient and highly conserved group of cell surface and/or secreted proteins, some of which are involved in the development of the immune system and the regulation of both innate and adaptive immune responses. Group B SRCR domains usually contain 8 regularly spaced cysteines that give rise to a well-defined intradomain disulfide-bond pattern.[supplied by OMIM, Apr 2004]
    Expression
    Broad expression in kidney (RPKM 1.3), thyroid (RPKM 1.0) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    7q11.23
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (76389337..76409697, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (77676966..77697378, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (76018654..76039014, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75947431-75948427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:75957380-75957880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:75957881-75958381 Neighboring gene fibroblast proliferation associated lncRNA Neighboring gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma Neighboring gene ReSE screen-validated silencer GRCh37_chr7:75981845-75982083 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:75987439-75987629 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75987737-75988383 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:75993799-75994486 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr7:76008919-76009532 and GRCh37_chr7:76009533-76010146 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76018334-76019171 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76019172-76020008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18315 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18316 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:76035061-76035561 Neighboring gene Sharpr-MPRA regulatory region 7220 Neighboring gene zona pellucida glycoprotein 3 Neighboring gene Sharpr-MPRA regulatory region 8731 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:76073005-76073916 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:76073917-76074826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76085525-76086398 Neighboring gene deltex E3 ubiquitin ligase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76114631-76115532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76115533-76116434 Neighboring gene farnesyl diphosphate synthase pseudogene 2 Neighboring gene uncharacterized LOC124901675 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:76138251-76138456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76139334-76139906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:76139907-76140479 Neighboring gene uroplakin 3B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Physical Interactions With Bacteria and Protozoan Parasites Establish the Scavenger Receptor SSC4D as a Broad-Spectrum Pattern Recognition Receptor. Cardoso MS, et al. Front Immunol, 2021. PMID 35003072, Free PMC Article
    2. Cloning of S4D-SRCRB, a new soluble member of the group B scavenger receptor cysteine-rich family (SRCR-SF) mapping to human chromosome 7q11.23. Padilla O, et al. Immunogenetics, 2002 Dec. PMID 12466895
    3. The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. Warnatz HJ, et al. J Biol Chem, 2011 Jul 1. PMID 21555518, Free PMC Article
    4. PAK4 promotes kinase-independent stabilization of RhoU to modulate cell adhesion. Dart AE, et al. J Cell Biol, 2015 Nov 23. PMID 26598620, Free PMC Article
    5. Protein interactome reveals converging molecular pathways among autism disorders. Sakai Y, et al. Sci Transl Med, 2011 Jun 8. PMID 21653829, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Physical Interactions With Bacteria and Protozoan Parasites Establish the Scavenger Receptor SSC4D as a Broad-Spectrum Pattern Recognition Receptor.
      Title: Physical Interactions With Bacteria and Protozoan Parasites Establish the Scavenger Receptor SSC4D as a Broad-Spectrum Pattern Recognition Receptor.
    2. SRCRB4D is a target gene of the BACH1 transcription factor according to ChIP-seq analysis in HEK 293 cells.
      Title: The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    4. Cloning of S4D-SRCRB, a new soluble member of the group B scavenger receptor cysteine-rich family (SRCR-SF) mapping to human chromosome 7q11.23.
      Title: Cloning of S4D-SRCRB, a new soluble member of the group B scavenger receptor cysteine-rich family (SRCR-SF) mapping to human chromosome 7q11.23.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    scavenger receptor cysteine-rich domain-containing group B protein
    Names
    four scavenger receptor cysteine-rich domains-containing protein
    scavenger receptor cysteine rich domain containing, group B (4 domains)
    scavenger receptor cysteine rich family, 4 domains
    scavenger receptor cysteine-rich protein SRCRB-S4D

    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_080744.2 → NP_542782.1  scavenger receptor cysteine-rich domain-containing group B protein precursor

      See identical proteins and their annotated locations for NP_542782.1

      Status: VALIDATED

      Source sequence(s)
      AC005522, AJ312755
      Consensus CDS
      CCDS5585.1
      UniProtKB/Swiss-Prot
      Q2HIZ5, Q6ZMG3, Q8WTU2, Q96BF5
      Related
      ENSP00000275560.3, ENST00000275560.4
      Conserved Domains (2) summary
      smart00202
      Location:473 → 573
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:478 → 572
      SRCR; Scavenger receptor cysteine-rich domain

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      76389337..76409697 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017011750.2 → XP_016867239.1  scavenger receptor cysteine-rich domain-containing group B protein isoform X2

    2. XM_024446664.2 → XP_024302432.1  scavenger receptor cysteine-rich domain-containing group B protein isoform X1

      Conserved Domains (1) summary
      smart00202
      Location:502 → 602
      SR; Scavenger receptor Cys-rich

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      77676966..77697378 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357263.1 → XP_054213238.1  scavenger receptor cysteine-rich domain-containing group B protein isoform X2

    2. XM_054357262.1 → XP_054213237.1  scavenger receptor cysteine-rich domain-containing group B protein isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WTU2.1 GenPept UniProtKB/Swiss-Prot:Q8WTU2

    Gene LinkOut

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

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