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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

SSC5D Gene

protein-coding GIFtS: 38
GCID: GC19P055999

scavenger receptor cysteine rich domain containing (5 domains)

Explore 1 disease affiliated with
SSC5D via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Scavenger Receptor Cysteine Rich Domain Containing (5 Domains)¹ ²		Soluble Scavenger Receptor Cysteine-Rich Domain-Containing Protein SSC5D²
Soluble Scavenger Protein With 5 SRCR Domains² ³		Soluble Scavenger With 5 Domains²
FLJ35258¹		SSc5D³
Scavenger Receptor Cysteine-Rich Glycoprotein²

External Ids:	HGNC: 26641¹	Entrez Gene: 284297²	Ensembl: ENSG00000179954⁷	UniProtKB: A1L4H1³

Export aliases for SSC5D gene to outside databases

Previous GC identifers: GC19P060695 GC19P052312

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: SRCRL_HUMAN, A1L4H1

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)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000019.9 NC_018930.1 NT_011109.16

Regulatory elements:

Search SABiosciences Regulatory transcription factor binding sites for SSC5D
Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids

Search SABiosciences Chromatin IP Primers for SSC5D

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SSC5D

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.42 Ensembl cytogenetic band: 19q13.42 HGNC cytogenetic band: 19q13.42

SSC5D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SSC5D gene location

GeneLoc information about chromosome 19 GeneLoc Exon Structure

GeneLoc location for GC19P055999: view genomic region (about GC identifiers)

Start:	55,999,864 bp from pter	End:	56,030,466 bp from pter
Size:	30,603 bases	Orientation:	plus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: SRCRL_HUMAN, A1L4H1 (See protein sequence)

Recommended Name: Soluble scavenger receptor cysteine-rich domain-containing protein SSC5D precursor

Size: 1573 amino acids; 165743 Da

Subunit: Interacts with LGALS1 and laminin (By similarity)

Subcellular location: Secreted (By similarity). Cytoplasm (By similarity)

Sequence caution: Sequence=AAI30539.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

Sequence=AAI30541.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

Secondary accessions: B5MDQ5 C7S7T9 C7S7U0

Alternative splicing: 2 isoforms: A1L4H1-1 A1L4H1-2

Explore the universe of human proteins at neXtProt for SSC5D: NX_A1L4H1

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_A1L4H1

SSC5D Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (2 alternative transcripts):

NP_001138422.1 NP_001182196.1

ENSEMBL proteins:

ENSP00000467252 ENSP00000374274 ENSP00000467434

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Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	IEA	--
GO:0005737	cytoplasm	IEA	--
GO:0016020	membrane	IEA	--

SSC5D for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

SSC5D for domains About GeneDecksing

2 InterPro domains/families:

IPR001190 Srcr_rcpt

IPR017448 Srcr_rcpt-rel

Graphical View of Domain Structure for InterPro Entry A1L4H1

ProtoNet protein and cluster: A1L4H1

UniProtKB/Swiss-Prot: SRCRL_HUMAN, A1L4H1

Similarity: Contains 5 SRCR domains

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: SRCRL_HUMAN, A1L4H1

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)

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Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005044	scavenger receptor activity	IEA	--

SSC5D for ontologies About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for SSC5D

Gene Ontology (GO): 2 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007275	multicellular organismal development	IEA	--
GO:0045087	innate immune response	IEA	--

SSC5D for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for SSC5D
Search CenterWatch for drugs/clinical trials and news about SSC5D / SRCRL

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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About This Section

REFSEQ mRNAs for SSC5D gene (3 alternative transcripts):

NM_182571.2 NM_001144950.1 NM_001195267.1

Unigene Cluster for SSC5D:

Scavenger receptor cysteine rich domain containing (5 domains)

Hs.554182 [show with all ESTs]

Unigene Representative Sequence: NM_001144950

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000588254 ENST00000587166 ENST00000389623(uc021vbw.1 uc002qlg.4)

ENST00000589020

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Additional cDNA sequence:

AF086519.1 AK092577.1 BC130538.1 BC130540.1 EU699476.1 EU699477.1

6 DOTS entries:

DT.307051 DT.91948756 DT.97788313 DT.97800079 DT.75182357 DT.91973954

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

SSC5D expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CCTGCACCAA

About this image

SSC5D expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

Stem Cell Differentiation: 4 LifeMap Cells

Name

Category

PureStem™ progenitor E68 (Embryonic Progenitor Cell)

PureStem™ mesenchymal progenitor 7SMOO32 (Embryonic Progenitor Cell)

Adipose, Bone, Cartilage

PureStem™ progenitor E69 (Embryonic Progenitor Cell)

PureStem™ progenitor SM22 (Embryonic Progenitor Cell)

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See SSC5D Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SSC5D

SOURCE GeneReport for Unigene cluster: Hs.554182

UniProtKB/Swiss-Prot: SRCRL_HUMAN, A1L4H1

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

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for SSC5D gene from 4/15 species (see all 15) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	CD6⁶ PIT 54⁶ (see all 3)	PIT 54 protein (see all 3)	25(a) 24(a) (see all 3)	1 ↔ 1 possible ortholog (see all 3)	5(18063742-18086404) E64(113564-157729)
lizard (Anolis carolinensis)	Reptilia	-- CD163L1⁶ (see all 5)	--	44(a) 34(a) (see all 5)	possible ortholog possible ortholog (see all 5)	GL344260.1(27460-41460) AAWZ02039160(472-3900)
zebrafish (Danio rerio)	Actinopterygii	BX324164.1⁶ CU693475.1⁶ (see all 3)	--	43(a) 26(a) (see all 3)	1 ↔ 1 possible ortholog (see all 3)	4(5354165-5372986) 5(3490902-3502617)
fruit fly (Drosophila melanogaster)	Insecta	lox⁶	lysyl oxidase-like	10(a)	possible ortholog	3R(27284102-27285591)

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

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for SSC5D gene

LOXL2² CD6² CD163L1² LOXL4² LOXL3² CD163² PRSS12² CD5L²

LOX² SRCRB4D² LOC619207² LOXL1²

3 SIMAP similar genes for SSC5D using alignment to 4 protein entries: SRCRL_HUMAN (see all proteins):

LGALS3BP LOXL3 CD5L

SSC5D for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 19 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs55799523^1,2	C,F,	--	55999545(+)	`CTGCGA/CCCCCC`	2	--	us2k¹		3		NA WA	6
rs4405662^1,2	C,F,A,H,	--	55999993(+)	`GATCCG/ATTCTC`	2	--	int¹		22		NS EA NA WA CSA	2347
rs201489699^1,2		--	56000016(+)	`GGGGG-/CCTA GGCCC`	2	--	int¹		0	--	--	--	--
rs115930876^1,2	F,	--	56000025(+)	`GGCCCC/TCACCT`	2	--	int¹		1		WA	118
rs181707137^1,2		--	56000028(+)	`CCCCAC/TCTCTG`	2	--	int¹		0	--	--	--	--
rs186839720^1,2		--	56000124(+)	`TCCCTA/GCTCAA`	2	--	int¹		0	--	--	--	--
rs77020325^1,2	F,	--	56000157(+)	`CAGAAG/ACCCAA`	2	--	int¹		1		NA	120
rs116264118^1,2	F,	--	56000178(+)	`CCCTGC/TCCGCC`	2	--	int¹		1		WA	118
rs144869187^1,2		--	56000244(+)	`ATGTGG/TGTGTG`	2	--	int¹		0	--	--	--	--
rs57080356^1,2	C	--	56000430(+)	`CCCCC-/CCAGGCC`	2	--	int¹		1		NA	2

HapMap Linkage Disequilibrium report for SSC5D (55999864 - 56030466 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 6 variations for SSC5D
1 CNV: 67618
5 Indels: 26347 45800 42004 60280 12039

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SSC5D

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

SSC5D for disorders About GeneDecksing

1 disease for SSC5D: About MalaCards

dental caries

Export disorders for SSC5D gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for SSC5D gene integrated from 9 sources:
(articles sorted by number of sources associating them with SSC5D)

Utopia: connect your pdf to the dynamic
world of online information

Molecular cloning and analysis of SSc5D, a new member of the scavenger receptor cysteine-rich superfamily. (PubMed id 19535143)^{1, 2, 3} Goncalves C.M.... Carmo A.M. (2009)
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)¹ Kimura K.... Sugano S. (2006)
The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)² Grimwood J.... Lucas S.M. (2004)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)² Gerhard D.S....Malek J. (2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)¹ Ota T.... Sugano S. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 284297	HGNC: 26641	Ensembl:ENSG00000179954	euGenes: HUgn284297	ECgene: SSC5D
H-InvDB: SSC5D

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Intellectual Property for SSC5D gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for SSC5D gene:
Search GeneIP for patents involving SSC5D

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section


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	OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SSC5D		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SSC5D
	Browse OriGene GFP tagged cDNA clones in CMV expression vector		Browse OriGene MicroRNA Expression Plasmids
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	Browse OriGene full length recombinant human proteins expressed in human HEK293 cells		OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
	OriGene Custom Antibody Services for SSC5D		OriGene Custom Protein Services for SSC5D
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	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat SSC5D
	QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SSC5D
	QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SSC5D
	QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SSC5D
	QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SSC5D
	QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SSC5D

	GenScript Custom Purified and Recombinant Proteins Services for SSC5D		GenScript cDNA clones with any tag delivered in your preferred vector for SSC5D
	GenScript Custom Assay Services for SSC5D		GenScript Custom Superior Antibodies Services for SSC5D
	GenScript Custom overexpressing Cell Line Services for SSC5D		CloneReady with Over 120,000 Genes
	Gene Synthesis: Any Gene in Any Vector		Vector-based siRNA and miRNA, Ready for Transfection
	Gene Mutant Library, Variants up to 10^11		Plasmid Preparation
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SSC5D

GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes Disease genes SSC5D gene at Home site.

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SSC5D Gene

scavenger receptor cysteine rich domain containing (5 domains)

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SSC5D Gene

scavenger receptor cysteine rich domain containing (5 domains)

Aliasesfor SSC5D gene

Summariesfor SSC5D gene

Genomic Viewsfor SSC5D gene

Proteinsfor SSC5D gene

Protein Domains /Familiesfor SSC5D gene

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