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CLEC1B Gene

protein-coding GIFtS: 55
GCID: GC12M010502

C-Type Lectin Domain Family 1, Member B

See CLEC1B-related disease
at

MalaCards

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Aliases
C-Type Lectin Domain Family 1, Member B¹ ²		1810061I13Rik²
CLEC2² ³ ⁵		PRO1384²
CLEC-2² ³		QDED721²
C-Type Lectin-Like Receptor 2² ³		C-Type Lectin Domain Family 1 Member B²
CLEC2B² ⁵		C-Type Lectin-Like Receptor-2²

External Ids:	HGNC: 24356¹	Entrez Gene: 51266²	Ensembl: ENSG00000165682⁷	OMIM: 606783⁵	UniProtKB: Q9P126³

Export aliases for CLEC1B gene to outside databases

Previous GC identifers: GC12M010037 GC12M010145 GC12M009888 GC12M010147 GC12M010260

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CLEC1B Gene:

Natural killer (NK) cells express multiple calcium-dependent (C-type) lectin-like receptors, such as CD94 (KLRD1;

MIM 602894) and NKG2D (KLRC4; MIM 602893), that interact with major histocompatibility complex class I molecules

and either inhibit or activate cytotoxicity and cytokine secretion. CLEC2 is a C-type lectin-like receptor

expressed in myeloid cells and NK cells (Colonna et al., 2000 (PubMed 10671229)).(supplied by OMIM, Jan 2011)

GeneCards Summary for CLEC1B Gene:

CLEC1B (C-type lectin domain family 1, member B) is a protein-coding gene. Diseases associated with CLEC1B include thrombocytopenia due to platelet alloimmunization. GO annotations related to this gene include transmembrane signaling receptor activity and carbohydrate binding. An important paralog of this gene is OLR1.

UniProtKB/Swiss-Prot: CLC1B_HUMAN, Q9P126

Function: Acts as a receptor for the platelet-aggregating snake venom protein rhodocytin. Rhodocytin binding leads

to tyrosine phosphorylation and this promotes the binding of spleen tyrosine kinase (Syk) and initiation of

downstream tyrosine phosphorylation events and activation of PLC-gamma-2. Acts as an attachment factor for human

immunodeficiency virus type 1 (HIV-1) and facilitates its capture by platelets

Gene Wiki entry for CLEC1B Gene

(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:

NC_000012.11 NT_009714.18 NC_018923.2

Regulatory elements:

Regulatory transcription factor binding sites in the CLEC1B gene promoter:
TBP AML1a NRSF form 1 FOXD3 MyoD Pax-2 Pax-2a NRSF form 2 PPAR-gamma1 PPAR-gamma2
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: CLEC1B promoter sequence

Search Chromatin IP Primers for CLEC1B

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLEC1B

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

Entrez Gene cytogenetic band: 12p13.2 Ensembl cytogenetic band: 12p13.2 HGNC cytogenetic band: 12p13.31

CLEC1B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLEC1B gene location

GeneLoc information about chromosome 12 GeneLoc Exon Structure

GeneLoc location for GC12M010502: view genomic region (about GC identifiers)

Start:	10,138,241 bp from pter	End:	10,166,023 bp from pter
Size:	27,783 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CLC1B_HUMAN, Q9P126 (See protein sequence)

Recommended Name: C-type lectin domain family 1 member B

Size: 229 amino acids; 26596 Da

Subunit: Homodimer. Interacts (via cytoplasmic domain) with GNB2L1/RACK1; promotes CLEC1B ubiquitination and

proteasome-mediated degradation. Interacts (dimer) with SYK (via SH2 domains)

1 PDB 3D structure from and Proteopedia for CLEC1B:

2C6U (3D)

Secondary accessions: Q6UWX7 Q8NHR6

Alternative splicing: 2 isoforms: Q9P126-1 Q9P126-2

Explore the universe of human proteins at neXtProt for CLEC1B: NX_Q9P126

Explore proteomics data for CLEC1B at MOPED

Post-translational modifications:

Glycosylated¹

Phosphorylated on tyrosine residue in response to rhodocytin binding¹

Glycosylation² at Asn68, Asn120, Asn134

Modification sites at PhosphoSitePlus

See CLEC1B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts):

NP_001092901.1 NP_057593.3

ENSEMBL proteins:

ENSP00000381910 ENSP00000406338 ENSP00000298527 ENSP00000327169

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:

CLEC: C-type lectin domain containing

3 InterPro protein domains:

IPR016187 C-type_lectin_fold

IPR016186 C-type_lectin-like

IPR001304 C-type_lectin

Graphical View of Domain Structure for InterPro Entry Q9P126

ProtoNet protein and cluster: Q9P126

UniProtKB/Swiss-Prot: CLC1B_HUMAN, Q9P126

Similarity: Contains 1 C-type lectin domain

Find genes that share domains with CLEC1B About GenesLikeMe

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: CLC1B_HUMAN, Q9P126

Function: Acts as a receptor for the platelet-aggregating snake venom protein rhodocytin. Rhodocytin binding leads

to tyrosine phosphorylation and this promotes the binding of spleen tyrosine kinase (Syk) and initiation of

downstream tyrosine phosphorylation events and activation of PLC-gamma-2. Acts as an attachment factor for human

immunodeficiency virus type 1 (HIV-1) and facilitates its capture by platelets

Gene Ontology (GO): 3 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0004888	transmembrane signaling receptor activity	TAS	10671229
GO:0005515	protein binding	IPI	19785988
GO:0030246	carbohydrate binding	IEA	--

Find genes that share ontologies with CLEC1B About GenesLikeMe

Phenotypes:
9 MGI mutant phenotypes (inferred from 7 alleles) (MGI details for Clec1b):

cardiovascular system	digestive/alimentary	hematopoietic system	homeostasis/metabolism	immune system
integument	mortality/aging	nervous system	respiratory system

Find genes that share phenotypes with CLEC1B About GenesLikeMe

Animal Models:
MGI mouse knock-outs for CLEC1B: Clec1b^tm1.1Ksi Clec1b^tm1Lex Clec1b^tm1.2Arte Clec1b^tm1Mlkn

genOway: Develop your customized and physiologically relevant rodent model for CLEC1B

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In Situ Assay
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot

CLC1B_HUMAN, Q9P126: Membrane; Single-pass type II membrane protein (Probable)

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
plasma membrane	4
extracellular	2
cytosol	1
golgi apparatus	1
mitochondrion	1

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Gene Ontology (GO): 1 cellular component term: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005887	integral component of plasma membrane	IEA	--

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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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Custom Pathway & Disease-focused RT² Profiler PCR Arrays for CLEC1B
Interactions:

GeneGlobe Interaction Network for CLEC1B

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

2 Interacting proteins for CLEC1B (Q9P126^{2, 3} ENSP00000298527⁴) via UniProtKB, MINT, STRING, and/or I2D

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
NINL	Q9Y2I6²^,³, ENSP00000278886⁴	MINT-67394 I2D: score=5 STRING: ENSP00000278886
SYK	P43405³	I2D: score=1

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Gene Ontology (GO): 2 biological process terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006952	defense response	TAS	10671229
GO:0007166	cell surface receptor signaling pathway	TAS	10671229

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore

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Browse Tocris compounds for CLEC1B (CLC1B)

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for CLEC1B gene (2 alternative transcripts):

NM_001099431.1 NM_016509.3

Unigene Cluster for CLEC1B:

C-type lectin domain family 1, member B

Hs.409794 [show with all ESTs]

Unigene Representative Sequence: BX647321

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

ENST00000398937 ENST00000428126(uc009zhd.3) ENST00000298527(uc001qwu.3)

ENST00000348658

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Additional mRNA sequence:

AF124841.1 AY358599.1 BC029554.1 BX647321.1

2 DOTS entries:

DT.100744741 DT.441659

17 AceView cDNA sequences:

AI242915 BX102592 AF124841 NM_016509 BX647321 AI056227 BI463516 AY358599

BM971560 BC029554 AV655580 AI241548 H70491 H69644 R11441 H73462

H74038

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™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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CLEC1B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: CCTCGGAAAT

About this image

CLEC1B expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database
selected tissues (see all 7) fully expand


Blood (Cardiovascular System) fully expand to see all 2 entries
Megakaryocytes Hematopoietic Bone Marrow

Skeletal Muscle (Muscoskeletal System) fully expand to see all 2 entries
Myoblasts Mandibular Arch Muscles

Endothelium (Cardiovascular System)
Mature Endothelial Cells Blood Brain Barrier

Brain (Nervous System)
Mature Endothelial Cells Blood Brain Barrier

Yolk Sac (Extraembryonic Tissues)
Definitive Hematopoietic Stem Cells Definitive Yolk Sac

CLEC1B Protein expression data from MOPED¹, PaxDb² and MaxQB³:

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CLEC1B Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.409794

UniProtKB/Swiss-Prot: CLC1B_HUMAN, Q9P126

Tissue specificity: Expressed preferentially in the liver. Also expressed in immune cells of myeloid origin and on

the surface of platelets

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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)
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This gene was present in the common ancestor of chordates.

Orthologs for CLEC1B gene from Selected species (see all 8) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Clec1b^{1 , 5}	C-type lectin domain family 1, member b^{1, 5}	75.52(n)¹ 64.6(a)¹		6 (63.30 cM)⁵ 56760¹ NM_019985.3¹ NP_064369.1¹ 129397297⁵
lizard (Anolis carolinensis)	Reptilia	--	Uncharacterized protein	32(a)	1 → many	2(81818136-81823316)

ENSEMBL Gene Tree for CLEC1B (if available)
TreeFam Gene Tree for CLEC1B (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for CLEC1B gene

OLR1² CLEC9A² CLEC7A² CLEC12B² CLEC12A² CLEC1A²

11 SIMAP similar genes for CLEC1B using alignment to 2 protein entries: CLC1B_HUMAN (see all proteins):

KLRD1 KLRC1 KLRC2 OLR1 CLEC1A VCAN

CLEC10A CLEC2L CLEC7A CLEC12B NCAN

Find genes that share paralogs with CLEC1B About GenesLikeMe

1 Pseudogenes.org Pseudogene for CLEC1B
PGOHUM00000251014

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr 12 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs185754954^1,2		--	10145226(+)	`AAATAC/TGAGAA`	2	--	ds500¹		0	--	--	--	--
rs613871^1,2	C,F,O,A,H	--	10145341(-)	`AAGGCA/GGTGTA`	2	--	ds500¹		29		EA NA NS WA CSA	2540
rs146198541^1,2	C	--	10145389(+)	`TATTTC/TGCACA`	2	--	ds500¹		0	--	--	--	--
rs71450015^1,2	C	--	10145587(+)	`AAGAAG/AGGACT`	2	--	ds500¹		1		NA	2
rs188574713^1,2	C,F	--	10145739(+)	`TCTTTG/CCATTA`	2	--	ut3¹		1		EU	1323
rs199859311^1,2		--	10145761(+)	`CCACCC/TTGGTC`	4	K R	mis¹		0	--	--	--	--
rs202115320^1,2		--	10145767(+)	`TGGTCA/TTGCCA`	4	K M	mis¹		0	--	--	--	--
rs180901380^1,2	C	--	10145835(+)	`CCATTA/GTGAAA`	4	H	syn¹		0	--	--	--	--
rs12301036^1,2	C,F,H	--	10145937(+)	`CAATCA/CGTAAT`	2	--	int¹		4		NS EA	420
rs17734335^1,2	C,F	--	10145952(+)	`CTCTGC/TGTATA`	2	--	int¹		4		NA	260

HapMap Linkage Disequilibrium report for CLEC1B (10138241 - 10166023 bp)

Structural Variations
Database of Genomic Variants (DGV) 5 variations for CLEC1B: About this table

Variant ID	Type	Subtype	PubMed ID
nsv898755	CNV	Loss	21882294
nsv604	CNV	Loss	18451855
nsv898756	CNV	Loss	21882294
nsv525593	CNV	Loss	19592680
esv9698	OTHER	Inversion	19470904

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing CLEC1B

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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.)
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OMIM gene information: 606783 OMIM disorders: --

1 disease for CLEC1B:
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thrombocytopenia due to platelet alloimmunization

1 inferred disease relationship from the University of Copenhagen DISEASES database for CLEC1B:

Thrombocytopenia due to platelet alloimmunization

Find genes that share disorders with CLEC1B About GenesLikeMe

Genetic Association Database (GAD): CLEC1B
Human Genome Epidemiology (HuGE) Navigator: CLEC1B (2 documents)

Export disorders for CLEC1B 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)
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PubMed articles for CLEC1B gene, integrated from 10 sources (see all 38):
(articles sorted by number of sources associating them with CLEC1B)

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

Molecular characterization of two novel C-type lectin-like receptors, one of which is selectively expressed in human dendritic cells. (PubMed id 10671229)^{1, 2, 3, 9} Colonna M.... Angman L. (Eur. J. Immunol. 2000)
DC-SIGN and CLEC-2 mediate human immunodeficiency virus type 1 capture by platelets. (PubMed id 16940507)^{1, 2, 9} Chaipan C.... Poehlmann S. (J. Virol. 2006)
A novel cluster of lectin-like receptor genes expressed in monocytic, dendritic and endothelial cells maps close to the NK receptor genes in the human NK gene complex. (PubMed id 11745369)^{1, 3, 9} Sobanov Y.... Hofer E. (Eur. J. Immunol. 2001)
CLEC-2 activates Syk through dimerization. (PubMed id 20154219)^{1, 2} Hughes C.E.... Watson S.P. (Blood 2010)
Genome-wide searching of rare genetic variants in WTCCC data. (PubMed id 20549515)^{1, 4} Feng T. and Zhu X. (Hum. Genet. 2010)
The platelet receptor CLEC-2 is active as a dimer. (PubMed id 19824697)^{1, 2} Watson A.A.... O'Callaghan C.A. (Biochemistry 2009)
RACK1 associates with CLEC-2 and promotes its ubiquitin-proteasome degradation. (PubMed id 19785988)^{1, 2} Ruan Y.... Gu J. (Biochem. Biophys. Res. Commun. 2009)
The crystal structure and mutational binding analysis of the extracellular domain of the platelet-activating receptor CLEC-2. (PubMed id 17132623)^{1, 2} Watson A.A....O'Callaghan C.A. (J. Biol. Chem. 2007)
A novel Syk-dependent mechanism of platelet activation by the C-type lectin receptor CLEC-2. (PubMed id 16174766)^{1, 2} Suzuki-Inoue K.... Watson S.P. (Blood 2006)
The finished DNA sequence of human chromosome 12. (PubMed id 16541075)^{1, 2} Scherer S.E.... Gibbs R.A. (Nature 2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 51266	HGNC: 24356	AceView: CLEC2	Ensembl:ENSG00000165682	euGenes: HUgn51266
ECgene: CLEC1B	H-InvDB: CLEC1B

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for CLEC1B	Pharmacogenomics, SNPs, Pathways
Functional Glycomics Gateway - Glycan Binding	http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_240

Intellectual Property for CLEC1B gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for CLEC1B gene:
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CLEC1B Gene

C-Type Lectin Domain Family 1, Member B

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CLEC1B Gene

C-Type Lectin Domain Family 1, Member B

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