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Aliases for SSC5D Gene

Aliases for SSC5D Gene

  • Scavenger Receptor Cysteine Rich Family, 5 Domains 2 3
  • 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, 5 Domains) is a Protein Coding gene. GO annotations related to this gene include scavenger receptor activity. An important paralog of this gene is LOXL1.

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

Genomic Location for SSC5D Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SSC5D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SSC5D Gene

No data available for Regulatory Elements 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 Asn168, Asn376, Asn420, Thr693, Ser694, Thr696, Thr697, Thr699, and Thr701
  • Modification sites at PhosphoSitePlus

Other Protein References for SSC5D Gene

No data available for DME Specific Peptides for SSC5D Gene

Domains 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 :
  • A1L4H1
Domain:
  • Contains 5 SRCR domains.
genes like me logo Genes that share domains with SSC5D: view

No data available for Gene Families 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).

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 --
GO:0050840 extracellular matrix binding ISS --
genes like me logo Genes that share ontologies with SSC5D: view

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , miRNA , Transcription Factor Targeting 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 2
lysosome 1
nucleus 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SSC5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space ISS --
GO:0005622 intracellular ISS --
GO:0005737 cytoplasm IEA --
GO:0016020 membrane IEA --
GO:0031012 extracellular matrix ISS --
genes like me logo Genes that share ontologies with SSC5D: view

Pathways 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 ISS --
GO:0006952 defense response --
GO:0007275 multicellular organismal development IEA --
GO:0042494 detection of bacterial lipoprotein ISS --
GO:0045087 innate immune response IEA --
genes like me logo Genes that share ontologies with SSC5D: view

No data available for Pathways by source for SSC5D Gene

Transcripts for SSC5D Gene

mRNA/cDNA for SSC5D Gene

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

Integrated Proteomics: protein expression 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 expressions with SSC5D: view

No data available for mRNA differential expression in normal tissues 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 35
  • 99.28 (n)
  • 99.08 (a)
SSC5D 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SSC5D 35
  • 77.1 (n)
  • 72.81 (a)
SSC5D 36
  • 76 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SSC5D 35
  • 76.08 (n)
  • 72.4 (a)
SSC5D 36
  • 76 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ssc5d 35
  • 77.84 (n)
  • 75.75 (a)
Ssc5d 16
Ssc5d 36
  • 74 (a)
OneToOne
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

Selected 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 MAF
rs10217 -- 55,519,061(-) TGGGG(G/T)TTTTT utr-variant-3-prime
rs476765 -- 55,511,392(+) TTTTG(C/G)GTTTG intron-variant
rs477933 -- 55,511,567(+) TGTAC(C/T)CATGA intron-variant
rs481503 -- 55,511,920(+) ttgtt(C/T)gggtg intron-variant
rs484144 -- 55,512,178(+) ctggg(C/T)ggcag 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

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

No disorders were found for SSC5D Gene.

No data available for UniProtKB/Swiss-Prot 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
  2. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3
  3. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J. … Lucas S.M. (Nature 2004) 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 4
  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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