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Aliases for SSC5D Gene

Aliases for SSC5D Gene

  • Scavenger Receptor Cysteine Rich Family Member With 5 Domains 2
  • Scavenger Receptor Cysteine Rich Family, 5 Domains 3 5
  • Scavenger Receptor Cysteine Rich Domain Containing (5 Domains) 2
  • Soluble Scavenger Protein With 5 SRCR Domains 4
  • Soluble Scavenger With 5 Domains 2
  • SSc5D 4

External Ids for SSC5D Gene

Previous GeneCards Identifiers for SSC5D Gene

  • GC19P060695
  • GC19P055999
  • GC19P052312

Summaries for SSC5D Gene

GeneCards Summary for SSC5D Gene

SSC5D (Scavenger Receptor Cysteine Rich Family Member With 5 Domains) is a Protein Coding gene. GO annotations related to this gene include scavenger receptor activity and laminin binding. An important paralog of this gene is SSC4D.

UniProtKB/Swiss-Prot for SSC5D Gene

  • Binds to extracellular matrix proteins. Binds to pathogen-associated molecular patterns (PAMPs) present on the cell walls of Gram-positive and Gram-negative bacteria and fungi, behaving as a pattern recognition receptor (PRR). Induces bacterial and fungal aggregation and subsequent inhibition of PAMP-induced cytokine release. Does not possess intrinsic bactericidal activity. May play a role in the innate defense and homeostasis of certain epithelial surfaces (By similarity).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SSC5D Gene

Genomics for SSC5D Gene

Regulatory Elements for SSC5D Gene

Promoters for SSC5D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SSC5D on UCSC Golden Path with GeneCards custom track

Genomic Location for SSC5D Gene

Chromosome:
19
Start:
55,488,404 bp from pter
End:
55,519,099 bp from pter
Size:
30,696 bases
Orientation:
Plus strand

Genomic View for SSC5D Gene

Genes around SSC5D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SSC5D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SSC5D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SSC5D Gene

Proteins for SSC5D Gene

  • Protein details for SSC5D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A1L4H1-SRCRL_HUMAN
    Recommended name:
    Soluble scavenger receptor cysteine-rich domain-containing protein SSC5D
    Protein Accession:
    A1L4H1
    Secondary Accessions:
    • B5MDQ5
    • C7S7T9
    • C7S7U0
    • K7EP70

    Protein attributes for SSC5D Gene

    Size:
    1573 amino acids
    Molecular mass:
    165743 Da
    Quaternary structure:
    • Interacts with LGALS1 and laminin.
    SequenceCaution:
    • Sequence=AAI30539.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI30541.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=ACJ02752.1; Type=Frameshift; Positions=934; Evidence={ECO:0000305};

    Alternative splice isoforms for SSC5D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SSC5D Gene

Proteomics data for SSC5D Gene at MOPED

Post-translational modifications for SSC5D Gene

  • Glycosylation at Asn 168, Asn 376, Asn 420, Asn 421, and Ser 694
  • Modification sites at PhosphoSitePlus

Other Protein References for SSC5D Gene

No data available for DME Specific Peptides for SSC5D Gene

Domains & Families for SSC5D Gene

Gene Families for SSC5D Gene

Protein Domains for SSC5D Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SSC5D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

A1L4H1

UniProtKB/Swiss-Prot:

SRCRL_HUMAN :
  • Contains 5 SRCR domains.
Domain:
  • Contains 5 SRCR domains.
genes like me logo Genes that share domains with SSC5D: view

Function for SSC5D Gene

Molecular function for SSC5D Gene

UniProtKB/Swiss-Prot Function:
Binds to extracellular matrix proteins. Binds to pathogen-associated molecular patterns (PAMPs) present on the cell walls of Gram-positive and Gram-negative bacteria and fungi, behaving as a pattern recognition receptor (PRR). Induces bacterial and fungal aggregation and subsequent inhibition of PAMP-induced cytokine release. Does not possess intrinsic bactericidal activity. May play a role in the innate defense and homeostasis of certain epithelial surfaces (By similarity).

Gene Ontology (GO) - Molecular Function for SSC5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005044 scavenger receptor activity IEA,ISS --
genes like me logo Genes that share ontologies with SSC5D: view

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SSC5D Gene

Localization for SSC5D Gene

Subcellular locations from UniProtKB/Swiss-Prot for SSC5D Gene

Secreted. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SSC5D Gene COMPARTMENTS Subcellular localization image for SSC5D gene
Compartment Confidence
extracellular 5
lysosome 1
plasma membrane 1
vacuole 1

Gene Ontology (GO) - Cellular Components for SSC5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with SSC5D: view

Pathways & Interactions for SSC5D Gene

SuperPathways for SSC5D Gene

No Data Available

Gene Ontology (GO) - Biological Process for SSC5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006898 receptor-mediated endocytosis IEA --
GO:0007275 multicellular organism development IEA --
GO:0050830 defense response to Gram-positive bacterium IEA --
GO:2000483 negative regulation of interleukin-8 secretion IEA,ISS --
genes like me logo Genes that share ontologies with SSC5D: view

No data available for Pathways by source and SIGNOR curated interactions for SSC5D Gene

Drugs & Compounds for SSC5D Gene

No Compound Related Data Available

Transcripts for SSC5D Gene

mRNA/cDNA for SSC5D Gene

(5) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SSC5D Gene

Scavenger receptor cysteine rich domain containing (5 domains):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SSC5D Gene

No ASD Table

Relevant External Links for SSC5D Gene

GeneLoc Exon Structure for
SSC5D
ECgene alternative splicing isoforms for
SSC5D

Expression for SSC5D Gene

mRNA expression in normal human tissues for SSC5D Gene

Protein differential expression in normal tissues from HIPED for SSC5D Gene

This gene is overexpressed in Serum (47.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SSC5D Gene



SOURCE GeneReport for Unigene cluster for SSC5D Gene Hs.554182

mRNA Expression by UniProt/SwissProt for SSC5D Gene

A1L4H1-SRCRL_HUMAN
Tissue specificity: Highly expressed in monocytes/macrophages and T-lymphocytes. Highly expressed in placenta and spleen, and also detected at lower levels in colon, and more weakly in lung, heart and kidney.
genes like me logo Genes that share expression patterns with SSC5D: view

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for SSC5D Gene

Orthologs for SSC5D Gene

This gene was present in the common ancestor of animals.

Orthologs for SSC5D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SSC5D 36
  • 99 (a)
OneToOne
SSC5D 35
  • 99.28 (n)
  • 99.08 (a)
cow
(Bos Taurus)
Mammalia SSC5D 35
  • 77.1 (n)
  • 72.81 (a)
SSC5D 36
  • 76 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SSC5D 36
  • 76 (a)
OneToOne
SSC5D 35
  • 76.08 (n)
  • 72.4 (a)
mouse
(Mus musculus)
Mammalia Ssc5d 16
Ssc5d 36
  • 74 (a)
OneToOne
Ssc5d 35
  • 77.84 (n)
  • 75.75 (a)
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 31 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SSC5D 36
  • 71 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ssc5d 35
  • 78.5 (n)
  • 76.16 (a)
chicken
(Gallus gallus)
Aves SSC5D 36
  • 47 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 33 (a)
OneToMany
-- 36
  • 23 (a)
OneToMany
-- 36
  • 34 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii CABZ01100187.1 36
  • 11 (a)
ManyToMany
si:ch211-51a6.2 36
  • 31 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta lox 36
  • 18 (a)
ManyToMany
lox2 36
  • 13 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 14 (a)
OneToMany
Species with no ortholog for SSC5D:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SSC5D Gene

ENSEMBL:
Gene Tree for SSC5D (if available)
TreeFam:
Gene Tree for SSC5D (if available)

Paralogs for SSC5D Gene

Paralogs for SSC5D Gene

(8) SIMAP similar genes for SSC5D Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with SSC5D: view

Variants for SSC5D Gene

Sequence variations from dbSNP and Humsavar for SSC5D Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs594326 -- 55,512,320(-) TAACA(C/T)ATAAA intron-variant
rs594394 -- 55,512,257(-) GATAA(C/T)TCAGT intron-variant
rs889090 -- 55,493,534(-) CTAAG(C/T)TATGC intron-variant
rs500631 -- 55,510,235(+) ctcaa(C/G)tgatc intron-variant
rs543052 -- 55,514,027(+) TTATC(A/C)AGTGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SSC5D Gene

Variant ID Type Subtype PubMed ID
nsv912457 CNV Loss 21882294
nsv912463 CNV Loss 21882294
nsv912473 CNV Loss 21882294
nsv912478 CNV Loss 21882294
dgv4022n71 CNV Loss 21882294
dgv4023n71 CNV Loss 21882294
dgv4024n71 CNV Loss 21882294
nsv458833 CNV Loss 19166990
nsv912486 CNV Loss 21882294
dgv4025n71 CNV Loss 21882294
nsv2552 CNV Insertion 18451855
nsv912489 CNV Loss 21882294
esv1314346 CNV Insertion 17803354
nsv912493 CNV Loss 21882294
esv2673716 CNV Deletion 23128226
esv24327 CNV Loss 19812545
esv2116865 CNV Deletion 18987734
esv3217 CNV Deletion 18987735
nsv138517 CNV Loss 16902084
esv1093065 CNV Deletion 17803354
esv2718971 CNV Deletion 23290073
esv2718972 CNV Deletion 23290073
esv2718974 CNV Deletion 23290073
esv2678615 CNV Deletion 23128226
esv2718975 CNV Deletion 23290073
esv2718976 CNV Deletion 23290073

Variation tolerance for SSC5D Gene

Gene Damage Index Score: 18.68; 98.65% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SSC5D Gene

HapMap Linkage Disequilibrium report
SSC5D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SSC5D Gene

Disorders for SSC5D Gene

Relevant External Links for SSC5D

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SSC5D

No disorders were found for SSC5D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SSC5D Gene

Publications for SSC5D Gene

  1. Molecular cloning and analysis of SSc5D, a new member of the scavenger receptor cysteine-rich superfamily. (PMID: 19535143) Goncalves C.M. … Carmo A.M. (Mol. Immunol. 2009) 2 3 4 67
  2. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PMID: 16344560) Kimura K. … Sugano S. (Genome Res. 2006) 3
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3

Products for SSC5D Gene

Sources for SSC5D Gene

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