This gene encodes a member of the C-type lectin superfamily. The encoded protein is a secreted sulfated glycoprotein and functions as a growth factor for primitive hematopoietic progenitor cells. An alternative splice variant has been described but its biological nature has not been determined. [provided by RefSeq, Jul 2008] See more...

Aliases for CLEC11A Gene

Aliases for CLEC11A Gene

  • C-Type Lectin Domain Containing 11A 2 3 5
  • C-Type Lectin Domain Family 11 Member A 2 3 4
  • CLECSF3 2 3 4
  • LSLCL 2 3 4
  • P47 2 3 4
  • Stem Cell Growth Factor; Lymphocyte Secreted C-Type Lectin 2 3
  • C-Type Lectin Superfamily Member 3 3 4
  • Lymphocyte Secreted C-Type Lectin 3 4
  • Stem Cell Growth Factor 3 4
  • Osteolectin 3 4
  • SCGF 3 4
  • C-Type (Calcium Dependent, Carbohydrate-Recognition Domain) Lectin, Superfamily Member 3 3
  • Lymphocyte Secreted Long Form Of C-Type Lectin 3
  • C-Type Lectin Domain Family 11, Member A 2
  • CLEC11A 5

External Ids for CLEC11A Gene

Previous HGNC Symbols for CLEC11A Gene

  • SCGF

Previous GeneCards Identifiers for CLEC11A Gene

  • GC19P055919
  • GC19P051226
  • GC19P047561

Summaries for CLEC11A Gene

Entrez Gene Summary for CLEC11A Gene

  • This gene encodes a member of the C-type lectin superfamily. The encoded protein is a secreted sulfated glycoprotein and functions as a growth factor for primitive hematopoietic progenitor cells. An alternative splice variant has been described but its biological nature has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLEC11A Gene

CLEC11A (C-Type Lectin Domain Containing 11A) is a Protein Coding gene. Diseases associated with CLEC11A include Chronic Granulomatous Disease. Among its related pathways are ERK Signaling and Nanog in Mammalian ESC Pluripotency. Gene Ontology (GO) annotations related to this gene include carbohydrate binding and growth factor activity. An important paralog of this gene is CLEC3B.

UniProtKB/Swiss-Prot Summary for CLEC11A Gene

  • Promotes osteogenesis by stimulating the differentiation of mesenchymal progenitors into mature osteoblasts (PubMed:27976999). Important for repair and maintenance of adult bone (By similarity).

Gene Wiki entry for CLEC11A Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLEC11A Gene

Genomics for CLEC11A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLEC11A Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLEC11A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLEC11A

Top Transcription factor binding sites by QIAGEN in the CLEC11A gene promoter:
  • AP-1
  • AP-2gamma
  • c-Myc
  • Max1
  • NRSF form 1
  • NRSF form 2
  • Olf-1
  • STAT5A

Genomic Locations for CLEC11A Gene

Latest Assembly
chr19:50,723,364-50,725,718
(GRCh38/hg38)
Size:
2,355 bases
Orientation:
Plus strand

Previous Assembly
chr19:51,226,621-51,228,965
(GRCh37/hg19 by Entrez Gene)
Size:
2,345 bases
Orientation:
Plus strand

chr19:51,226,586-51,228,974
(GRCh37/hg19 by Ensembl)
Size:
2,389 bases
Orientation:
Plus strand

Genomic View for CLEC11A Gene

Genes around CLEC11A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLEC11A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLEC11A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLEC11A Gene

Proteins for CLEC11A Gene

  • Protein details for CLEC11A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y240-CLC11_HUMAN
    Recommended name:
    C-type lectin domain family 11 member A
    Protein Accession:
    Q9Y240
    Secondary Accessions:
    • B2RAD4

    Protein attributes for CLEC11A Gene

    Size:
    323 amino acids
    Molecular mass:
    35695 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CLEC11A Gene

Post-translational modifications for CLEC11A Gene

  • O-glycosylated. Probably sulfated on the O-glycans.
  • Glycosylation at Thr69
  • Ubiquitination at Lys49 and Lys186
  • Modification sites at PhosphoSitePlus

Other Protein References for CLEC11A Gene

Assay products for research

  • Boster Bio ELISA Kits for CLEC11A

No data available for DME Specific Peptides for CLEC11A Gene

Domains & Families for CLEC11A Gene

Gene Families for CLEC11A Gene

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

Protein Domains for CLEC11A Gene

Suggested Antigen Peptide Sequences for CLEC11A Gene

GenScript: Design optimal peptide antigens:
  • p47 (CLC11_HUMAN)
  • Stem cell growth factor (Q5U0B9_HUMAN)
genes like me logo Genes that share domains with CLEC11A: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CLEC11A Gene

Function for CLEC11A Gene

Molecular function for CLEC11A Gene

UniProtKB/Swiss-Prot Function:
Promotes osteogenesis by stimulating the differentiation of mesenchymal progenitors into mature osteoblasts (PubMed:27976999). Important for repair and maintenance of adult bone (By similarity).

Phenotypes From GWAS Catalog for CLEC11A Gene

Gene Ontology (GO) - Molecular Function for CLEC11A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
GO:0008083 growth factor activity IBA,IDA 11920266
GO:0030246 carbohydrate binding IEA,NAS 9705843
genes like me logo Genes that share ontologies with CLEC11A: view
genes like me logo Genes that share phenotypes with CLEC11A: view

Animal Models for research

  • Taconic Biosciences Mouse Models for CLEC11A

miRNA for CLEC11A Gene

miRTarBase miRNAs that target CLEC11A

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLEC11A

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLEC11A Gene

Localization for CLEC11A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLEC11A Gene

Cytoplasm. Secreted.

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 CLEC11A gene
Compartment Confidence
extracellular 5
plasma membrane 2
cytoskeleton 2
mitochondrion 2
cytosol 2
nucleus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CLEC11A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA,IDA 9442024
GO:0005615 extracellular space IBA 21873635
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with CLEC11A: view

Pathways & Interactions for CLEC11A Gene

PathCards logo

SuperPathways for CLEC11A Gene

SuperPathway Contained pathways
1 Apoptotic Pathways in Synovial Fibroblasts
.85
.85
.84
.84
.74
.72
.66
.65
.64
.62
.61
.60
.57
.57
2 GPCR Pathway
.73
.73
.62
.59
.58
.58
.55
3 ERK Signaling
.61
.61
.58
.51
.49
4 Nanog in Mammalian ESC Pluripotency
.61
.61
.59
.48
5 CREB Pathway
.68
.68
.63
.50
genes like me logo Genes that share pathways with CLEC11A: view

Pathways by source for CLEC11A Gene

54 Qiagen pathways for CLEC11A Gene
  • 14-3-3 Induced Intracellular Signaling
  • Actin-Based Motility by Rho Family GTPases
  • Activation of cAMP-Dependent PKA
  • Activation of PKA through GPCR
  • Activation of PKC through GPCR

Gene Ontology (GO) - Biological Process for CLEC11A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001503 ossification IBA 21873635
GO:0007165 signal transduction IEA --
GO:0008284 positive regulation of cell proliferation IDA 11920266
genes like me logo Genes that share ontologies with CLEC11A: view

No data available for SIGNOR curated interactions for CLEC11A Gene

Drugs & Compounds for CLEC11A Gene

(2) Drugs for CLEC11A Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for CLEC11A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLEC11A: view

Transcripts for CLEC11A Gene

mRNA/cDNA for CLEC11A Gene

1 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLEC11A

Alternative Splicing Database (ASD) splice patterns (SP) for CLEC11A Gene

No ASD Table

Relevant External Links for CLEC11A Gene

GeneLoc Exon Structure for
CLEC11A

Expression for CLEC11A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLEC11A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLEC11A Gene

This gene is overexpressed in Serum (25.0), Breast (15.4), Bone marrow mesenchymal stem cell (12.7), and Pancreas (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLEC11A Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLEC11A

SOURCE GeneReport for Unigene cluster for CLEC11A Gene:

Hs.512680

mRNA Expression by UniProt/SwissProt for CLEC11A Gene:

Q9Y240-CLC11_HUMAN
Tissue specificity: Expressed in skeletal tissues including bone marrow, chondrocytes, primary ossification center-associated cells, the perichondrium and periosteum. Lower levels of expression were detected in spleen, thymus, appendix and fetal liver.

Evidence on tissue expression from TISSUES for CLEC11A Gene

  • Heart(4.3)
  • Bone(3.3)
  • Bone marrow(2.6)
  • Blood(2)
genes like me logo Genes that share expression patterns with CLEC11A: view

Primer products for research

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 CLEC11A Gene

Orthologs for CLEC11A Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLEC11A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CLEC11A 30 31
  • 99.28 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CLEC11A 30 31
  • 88.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CLEC11A 30 31
  • 86.27 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Clec11a 30 17 31
  • 82.77 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Clec11a 30
  • 81.42 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia CLEC11A 31
  • 72 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CLEC11A 31
  • 60 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CLEC11A 31
  • 44 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii CU929133.1 31
  • 37 (a)
OneToOne
Species where no ortholog for CLEC11A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Chicken (Gallus gallus)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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 Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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 CLEC11A Gene

ENSEMBL:
Gene Tree for CLEC11A (if available)
TreeFam:
Gene Tree for CLEC11A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLEC11A: view image

Paralogs for CLEC11A Gene

Paralogs for CLEC11A Gene

(1) SIMAP similar genes for CLEC11A Gene using alignment to 4 proteins:

  • CLC11_HUMAN
  • M0R081_HUMAN
  • Q5U0B9_HUMAN
  • V9H0X6_HUMAN
genes like me logo Genes that share paralogs with CLEC11A: view

Variants for CLEC11A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLEC11A Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
785833 Likely Benign: not provided 50,725,314(+) C/CGCCCA
NM_002975.3(CLEC11A):c.822_826CCAGC[3] (p.Ala278fs)
FRAMESHIFT
rs2303688 - p.Pro104Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CLEC11A Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CLEC11A Gene

Variant ID Type Subtype PubMed ID
nsv1140251 OTHER inversion 24896259
nsv579951 CNV gain 21841781
nsv828583 CNV loss 20364138

Variation tolerance for CLEC11A Gene

Residual Variation Intolerance Score: 74.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.95; 36.19% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLEC11A Gene

Human Gene Mutation Database (HGMD)
CLEC11A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLEC11A

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLEC11A Gene

Disorders for CLEC11A Gene

MalaCards: The human disease database

(1) MalaCards diseases for CLEC11A Gene - From: GCD

Disorder Aliases PubMed IDs
chronic granulomatous disease
  • bridges-good syndrome
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CLEC11A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CLEC11A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLEC11A Gene

Publications for CLEC11A Gene

  1. Association study between keratinocyte-derived growth factor gene polymorphisms and susceptibility to vitiligo vulgaris in a Taiwanese population: potential involvement of stem cell factor. (PMID: 19416273) Lan CC … Yu HS (The British journal of dermatology 2009) 3 23 41
  2. Stem cell growth factor: in situ hybridization analysis on the gene expression, molecular characterization and in vitro proliferative activity of a recombinant preparation on primitive hematopoietic progenitor cells. (PMID: 11920266) Hiraoka A … Sugimoto S (The hematology journal : the official journal of the European Haematology Association 2001) 3 4 23
  3. Molecular cloning of a new secreted sulfated mucin-like protein with a C-type lectin domain that is expressed in lymphoblastic cells. (PMID: 9442024) Bannwarth S … Lefebvre JC (The Journal of biological chemistry 1998) 2 3 4
  4. Isolation and characterization of a cDNA for human mouse, and rat full-length stem cell growth factor, a new member of C-type lectin superfamily. (PMID: 9705843) Mio H … Hiraoka A (Biochemical and biophysical research communications 1998) 3 4 23
  5. Cloning, expression, and characterization of a cDNA encoding a novel human growth factor for primitive hematopoietic progenitor cells. (PMID: 9207134) Hiraoka A … Shimizu S (Proceedings of the National Academy of Sciences of the United States of America 1997) 2 3 23

Products for CLEC11A Gene

  • Boster Bio Antibodies for CLEC11A
  • Boster Bio ELISA Kits for CLEC11A

Sources for CLEC11A Gene