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Aliases for SSC5D Gene

Aliases for SSC5D Gene

  • Scavenger Receptor Cysteine Rich Family Member With 5 Domains 2 3 5
  • Scavenger Receptor Cysteine Rich Domain Containing (5 Domains) 2 3
  • Soluble Scavenger Protein With 5 SRCR Domains 3 4
  • Soluble Scavenger With 5 Domains 2 3
  • Soluble Scavenger Receptor Cysteine-Rich Domain-Containing Protein SSC5D 3
  • Scavenger Receptor Cysteine Rich Family, 5 Domains 3
  • Scavenger Receptor Cysteine-Rich Glycoprotein 3
  • S5D-SRCRB 3
  • 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. Diseases associated with SSC5D include Mental Retardation, X-Linked, Snyder-Robinson Type. GO annotations related to this gene include scavenger receptor activity and laminin binding. An important paralog of this gene is DMBT1.

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).

Additional gene information for SSC5D Gene

No data available for Entrez Gene Summary , CIViC 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

Enhancers for SSC5D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H055519 1.6 FANTOM5 Ensembl ENCODE 51.1 +31.8 31806 0 HDGF ATF1 ZNF493 ZNF133 YBX1 GLI4 ZNF416 FOS ZNF548 ATF7 U2AF2 ZNF471 FIZ1 ZNF582 ZNF581 ZNF580 SSC5D ENSG00000267523 NAT14 ZNF667
GH19H055215 1.5 ENCODE dbSUPER 49 -271.7 -271700 2 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 ZNF548 SP3 NFYC LENG8-AS1 U2AF2 LENG8 ENSG00000235681 ENSG00000267523 SSC5D ZNF580 ZNF628 ENSG00000267096 BRSK1
GH19H055471 2 FANTOM5 Ensembl ENCODE dbSUPER 21.3 -13.2 -13246 6 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 U2AF2 ZNF628 ENSG00000267523 SSC5D ENSG00000267096 ZNF581 NAT14 ZNF583 HSPBP1 ISOC2
GH19H055483 1 ENCODE 41.7 -1.6 -1644 6 ATF1 ARID4B SIN3A GLI4 ETS1 GLIS2 ELK1 FOS KLF7 ZNF548 SSC5D U2AF2 ENSG00000267523 NAT14
GH19H055503 1.3 Ensembl ENCODE 24 +15.6 15565 1 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 CBX5 ZNF416 ZNF143 ZNF548 U2AF2 FIZ1 ZNF667 ZNF582-AS1 NAT14 ZNF667-AS1 ZNF542P ZNF582 ZNF583 ENSG00000267523
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers 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

Post-translational modifications for SSC5D Gene

  • Glycosylation at Asn168, posLast=376376, posLast=420420, posLast=421421, and Ser694
  • 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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

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

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

No data available for UniProtKB/Swiss-Prot for SSC5D Gene

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).

Phenotypes From GWAS Catalog for SSC5D Gene

Gene Ontology (GO) - Molecular Function for SSC5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001968 fibronectin binding ISS --
GO:0005044 scavenger receptor activity ISS --
GO:0005515 protein binding IPI 25416956
GO:0043236 laminin binding ISS,IEA --
GO:0050840 extracellular matrix binding IEA,ISS --
genes like me logo Genes that share ontologies with SSC5D: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SSC5D
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SSC5D gene
Compartment Confidence
extracellular 5
plasma membrane 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SSC5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IEA,ISS --
GO:0005622 intracellular IEA,ISS --
GO:0005737 cytoplasm IEA --
GO:0016020 membrane 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:0002376 immune system process IEA --
GO:0006898 receptor-mediated endocytosis IEA --
GO:0006952 defense response IEA --
GO:0007275 multicellular organism development IEA --
GO:0042494 detection of bacterial lipoprotein 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

(3) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(5) 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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SSC5D
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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



NURSA nuclear receptor signaling pathways regulating expression of SSC5D Gene:

SSC5D

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.

Evidence on tissue expression from TISSUES for SSC5D Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with SSC5D: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.28 (n)
rat
(Rattus norvegicus)
Mammalia Ssc5d 33
  • 78.5 (n)
mouse
(Mus musculus)
Mammalia Ssc5d 33 16 34
  • 77.84 (n)
cow
(Bos Taurus)
Mammalia SSC5D 33 34
  • 77.1 (n)
dog
(Canis familiaris)
Mammalia SSC5D 33 34
  • 76.08 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SSC5D 34
  • 71 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 31 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SSC5D 34
  • 47 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 34 (a)
OneToMany
-- 34
  • 33 (a)
OneToMany
-- 34
  • 23 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii si:ch211-51a6.2 34
  • 31 (a)
ManyToMany
CABZ01100187.1 34
  • 11 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta lox 34
  • 18 (a)
ManyToMany
lox2 34
  • 13 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 14 (a)
OneToMany
Species where no ortholog for SSC5D was found in the sources mined by GeneCards:
  • 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
rs1000094188 -- 55,489,377(+) ATGGC(C/T)CCCAT reference, missense
rs1000318490 -- 55,488,449(+) CAAAG(C/T)GTCCA upstream-variant-2KB
rs1000372843 -- 55,499,479(+) GACCT(G/T)TCAGA intron-variant
rs1000470245 -- 55,492,883(+) ATAGC(A/G)GGGCA intron-variant
rs1000558073 -- 55,508,282(+) CCGGA(A/G)GTTTA intron-variant

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

Variant ID Type Subtype PubMed ID
esv1093065 CNV deletion 17803354
esv1314346 CNV insertion 17803354
esv2116865 CNV deletion 18987734
esv24327 CNV loss 19812545
esv2673716 CNV deletion 23128226
esv2678615 CNV deletion 23128226
esv2718971 CNV deletion 23290073
esv2718972 CNV deletion 23290073
esv2718974 CNV deletion 23290073
esv2718975 CNV deletion 23290073
esv2718976 CNV deletion 23290073
esv3217 CNV loss 18987735
esv3442619 CNV duplication 20981092
esv3556651 CNV deletion 23714750
esv3575009 CNV gain 25503493
esv3644841 CNV loss 21293372
esv9001 CNV gain 19470904
nsv1071553 CNV deletion 25765185
nsv1135856 CNV deletion 24896259
nsv138517 CNV deletion 16902084
nsv2552 CNV insertion 18451855
nsv458833 CNV loss 19166990
nsv580343 CNV loss 21841781
nsv953624 CNV deletion 24416366

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

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SSC5D

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

Disorders for SSC5D Gene

MalaCards: The human disease database

(1) MalaCards diseases for SSC5D Gene - From: DISEASES

Disorder Aliases PubMed IDs
mental retardation, x-linked, snyder-robinson type
  • syndromic x-linked intellectual disability snyder type
- elite association - COSMIC cancer census association via MalaCards
Search SSC5D in MalaCards View complete list of genes associated with diseases

Relevant External Links for SSC5D

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SSC5D
genes like me logo Genes that share disorders with SSC5D: view

No data available for 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) Gonçalves CM … Carmo AM (Molecular immunology 2009) 2 3 4 60
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  3. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 60
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PMID: 16344560) Kimura K … Sugano S (Genome research 2006) 3 60
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 60

Products for SSC5D Gene

Sources for SSC5D Gene

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