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Aliases for COLEC12 Gene

Aliases for COLEC12 Gene

  • Collectin Subfamily Member 12 2 3 5
  • Scavenger Receptor With C-Type Lectin 3 4
  • Nurse Cell Scavenger Receptor 2 3 4
  • Collectin Placenta Protein 1 3 4
  • SCARA4 3 4
  • HCL-P1 3 4
  • CLP1 3 4
  • NSR2 3 4
  • SRCL 3 4
  • Scavenger Receptor Class A, Member 4 3
  • Scavenger Receptor Class A Member 4 4
  • Collectin Sub-Family Member 12 3
  • Collectin-12 3
  • CL-P1 4

External Ids for COLEC12 Gene

Previous GeneCards Identifiers for COLEC12 Gene

  • GC18M000603
  • GC18M000306

Summaries for COLEC12 Gene

Entrez Gene Summary for COLEC12 Gene

  • This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. This protein is a scavenger receptor, a cell surface glycoprotein that displays several functions associated with host defense. It can bind to carbohydrate antigens on microorganisms, facilitating their recognition and removal. It also mediates the recognition, internalization, and degradation of oxidatively modified low density lipoprotein by vascular endothelial cells. [provided by RefSeq, Oct 2011]

GeneCards Summary for COLEC12 Gene

COLEC12 (Collectin Subfamily Member 12) is a Protein Coding gene. Among its related pathways are Vesicle-mediated transport and Binding and Uptake of Ligands by Scavenger Receptors. GO annotations related to this gene include scavenger receptor activity and signaling pattern recognition receptor activity. An important paralog of this gene is SCARA3.

UniProtKB/Swiss-Prot for COLEC12 Gene

  • Scavenger receptor that displays several functions associated with host defense. Promotes binding and phagocytosis of Gram-positive, Gram-negative bacteria and yeast. Mediates the recognition, internalization and degradation of oxidatively modified low density lipoprotein (oxLDL) by vascular endothelial cells. Binds to several carbohydrates including Gal-type ligands, D-galactose, L- and D-fucose, GalNAc, T and Tn antigens in a calcium-dependent manner and internalizes specifically GalNAc in nurse-like cells. Binds also to sialyl Lewis X or a trisaccharide and asialo-orosomucoid (ASOR). May also play a role in the clearance of amyloid beta in Alzheimer disease.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COLEC12 Gene

Genomics for COLEC12 Gene

Regulatory Elements for COLEC12 Gene

Enhancers for COLEC12 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
GH18F000331 1 FANTOM5 Ensembl ENCODE 15.5 +168.3 168302 2.9 CTCF IKZF1 RAD21 ZKSCAN1 COLEC12 CLUL1 ENSG00000264514 GC18P000404
GH18F000469 0.2 Ensembl 12.3 +31.5 31529 0.4 ZNF335 CTCF ZBTB8A RAD21 COLEC12 THOC1 CLUL1 CETN1 GC18P000435
GH18F000471 0.2 Ensembl 12.3 +31.0 31029 0.2 ZNF335 COLEC12 THOC1 CLUL1 CETN1 GC18P000435
GH18F000474 0.9 Ensembl ENCODE 12.3 +25.1 25143 2.4 ELF3 CTCF SAP130 ZNF792 JUN TEAD4 ETS1 ZNF7 RARA TEAD3 COLEC12 THOC1 CLUL1 CETN1 USP14 GC18P000435
GH18F000470 1.3 Ensembl ENCODE 12.3 +29.2 29229 1.8 JUND ZNF316 CEBPB MAFG FOS PRDM1 MAFK COLEC12 THOC1 CLUL1 CETN1 GC18P000435
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around COLEC12 on UCSC Golden Path with GeneCards custom track

Promoters for COLEC12 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000521209 629 1801 PKNOX1 DMAP1 FEZF1 GLI4 ZNF2 GLIS2 FOS KLF7 ZNF263 SP3

Genomic Location for COLEC12 Gene

Chromosome:
18
Start:
316,740 bp from pter
End:
500,729 bp from pter
Size:
183,990 bases
Orientation:
Minus strand

Genomic View for COLEC12 Gene

Genes around COLEC12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COLEC12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COLEC12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COLEC12 Gene

Proteins for COLEC12 Gene

  • Protein details for COLEC12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5KU26-COL12_HUMAN
    Recommended name:
    Collectin-12
    Protein Accession:
    Q5KU26
    Secondary Accessions:
    • Q6P9F2
    • Q8TCR2
    • Q8WZA4
    • Q9BY85
    • Q9BYH7

    Protein attributes for COLEC12 Gene

    Size:
    742 amino acids
    Molecular mass:
    81515 Da
    Quaternary structure:
    • The extracellular domain forms a stable trimer. The extracellular domain interacts with fibrillar beta amyloid peptide.
    SequenceCaution:
    • Sequence=BAB39148.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for COLEC12 Gene

neXtProt entry for COLEC12 Gene

Post-translational modifications for COLEC12 Gene

  • Glycosylation at Asn 67, Asn 159, Asn 168, and Asn 271
  • Modification sites at PhosphoSitePlus

Other Protein References for COLEC12 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for COLEC12 Gene

Domains & Families for COLEC12 Gene

Suggested Antigen Peptide Sequences for COLEC12 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q5KU26

UniProtKB/Swiss-Prot:

COL12_HUMAN :
  • Contains 1 C-type lectin domain.
Domain:
  • Contains 1 C-type lectin domain.
  • Contains 3 collagen-like domains.
genes like me logo Genes that share domains with COLEC12: view

Function for COLEC12 Gene

Molecular function for COLEC12 Gene

UniProtKB/Swiss-Prot Function:
Scavenger receptor that displays several functions associated with host defense. Promotes binding and phagocytosis of Gram-positive, Gram-negative bacteria and yeast. Mediates the recognition, internalization and degradation of oxidatively modified low density lipoprotein (oxLDL) by vascular endothelial cells. Binds to several carbohydrates including Gal-type ligands, D-galactose, L- and D-fucose, GalNAc, T and Tn antigens in a calcium-dependent manner and internalizes specifically GalNAc in nurse-like cells. Binds also to sialyl Lewis X or a trisaccharide and asialo-orosomucoid (ASOR). May also play a role in the clearance of amyloid beta in Alzheimer disease.

Gene Ontology (GO) - Molecular Function for COLEC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005044 scavenger receptor activity TAS 11162630
GO:0005534 galactose binding NAS 11564734
GO:0008329 signaling pattern recognition receptor activity IDA 11564734
GO:0030169 low-density lipoprotein particle binding IDA 11564734
GO:0030246 carbohydrate binding IEA --
genes like me logo Genes that share ontologies with COLEC12: view

Phenotypes for COLEC12 Gene

genes like me logo Genes that share phenotypes with COLEC12: view

Animal Model Products

  • Taconic Biosciences Mouse Models for COLEC12

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for COLEC12 Gene

Localization for COLEC12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COLEC12 Gene

Membrane; Single-pass type II membrane protein. Note=Forms clusters on the cell surface.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COLEC12 Gene COMPARTMENTS Subcellular localization image for COLEC12 gene
Compartment Confidence
extracellular 5
plasma membrane 5
cytosol 1
endoplasmic reticulum 1
golgi apparatus 1
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for COLEC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005581 collagen trimer IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane TAS 11162630
GO:0030666 endocytic vesicle membrane TAS --
genes like me logo Genes that share ontologies with COLEC12: view

Pathways & Interactions for COLEC12 Gene

genes like me logo Genes that share pathways with COLEC12: view

Pathways by source for COLEC12 Gene

Interacting Proteins for COLEC12 Gene

STRING Interaction Network Preview (showing 3 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000383115%0d%0a9606.ENSP00000326514%0d%0a9606.ENSP00000370395%0d%0a9606.ENSP00000221566%0d%0a
Selected Interacting proteins: ENSP00000383115 Q5KU26-COL12_HUMAN for COLEC12 Gene via STRING IID

Gene Ontology (GO) - Biological Process for COLEC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006898 receptor-mediated endocytosis TAS --
GO:0006910 phagocytosis, recognition IDA 11564734
GO:0006952 defense response TAS 11162630
GO:0006955 immune response IEA --
GO:0009756 carbohydrate mediated signaling NAS 11564734
genes like me logo Genes that share ontologies with COLEC12: view

No data available for SIGNOR curated interactions for COLEC12 Gene

Drugs & Compounds for COLEC12 Gene

(1) Drugs for COLEC12 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0

(4) Additional Compounds for COLEC12 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
D-Galactose
  • (+)-Galactose
  • 5abp
  • 8abp
  • alpha D-Galactose
  • alpha-D-Galactopyranose
59-23-4
Lewis X trisaccharide
  • 3-Fucosyl-N-acetyllactosamine
  • FAL
  • Lewis X
  • Lewis X trisaccharide
  • Lex
71208-06-5
genes like me logo Genes that share compounds with COLEC12: view

Transcripts for COLEC12 Gene

Unigene Clusters for COLEC12 Gene

Collectin sub-family member 12:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COLEC12 Gene

No ASD Table

Relevant External Links for COLEC12 Gene

GeneLoc Exon Structure for
COLEC12
ECgene alternative splicing isoforms for
COLEC12

Expression for COLEC12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COLEC12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for COLEC12 Gene

This gene is overexpressed in Placenta (16.6) and Cerebrospinal fluid (15.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for COLEC12 Gene



NURSA nuclear receptor signaling pathways regulating expression of COLEC12 Gene:

COLEC12

SOURCE GeneReport for Unigene cluster for COLEC12 Gene:

Hs.464422

mRNA Expression by UniProt/SwissProt for COLEC12 Gene:

Q5KU26-COL12_HUMAN
Tissue specificity: Expressed in perivascular macrophages. Expressed in plaques-surrounding reactive astrocytes and in perivascular astrocytes associated with cerebral amyloid angiopathy (CAA) in the temporal cortex of Alzheimer patient (at protein level). Strongly expressed in placenta. Moderately expressed in heart, skeletal muscle, small intestine and lung. Weakly expressed in brain, colon, thymus and kidney. Expressed in nurse-like cells. Expressed in reactive astrocytes and vascular/perivascular cells in the brain of Alzheimer patient.
genes like me logo Genes that share expression patterns with COLEC12: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for COLEC12 Gene

Orthologs for COLEC12 Gene

This gene was present in the common ancestor of animals.

Orthologs for COLEC12 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COLEC12 34 35
  • 99.37 (n)
dog
(Canis familiaris)
Mammalia COLEC12 34 35
  • 91.11 (n)
oppossum
(Monodelphis domestica)
Mammalia COLEC12 35
  • 89 (a)
OneToOne
cow
(Bos Taurus)
Mammalia COLEC12 34 35
  • 88.36 (n)
rat
(Rattus norvegicus)
Mammalia Colec12 34
  • 87.87 (n)
mouse
(Mus musculus)
Mammalia Colec12 34 16 35
  • 87.69 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia COLEC12 35
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves COLEC12 34 35
  • 76.03 (n)
lizard
(Anolis carolinensis)
Reptilia COLEC12 35
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia colec12 34
  • 67.31 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.19955 34
zebrafish
(Danio rerio)
Actinopterygii colec12 34 35
  • 57.06 (n)
idibd2826 34
worm
(Caenorhabditis elegans)
Secernentea col-118 35
  • 29 (a)
ManyToMany
col-187 35
  • 29 (a)
ManyToMany
col-148 35
  • 27 (a)
ManyToMany
col-89 35
  • 26 (a)
ManyToMany
col-149 35
  • 25 (a)
ManyToMany
col-150 35
  • 25 (a)
ManyToMany
col-176 35
  • 25 (a)
ManyToMany
col-10 35
  • 24 (a)
ManyToMany
col-126 35
  • 24 (a)
ManyToMany
col-127 35
  • 24 (a)
ManyToMany
col-144 35
  • 24 (a)
ManyToMany
col-145 35
  • 24 (a)
ManyToMany
col-61 35
  • 23 (a)
ManyToMany
col-177 35
  • 19 (a)
ManyToMany
Species where no ortholog for COLEC12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 squirt (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)
  • wheat (Triticum aestivum)

Evolution for COLEC12 Gene

ENSEMBL:
Gene Tree for COLEC12 (if available)
TreeFam:
Gene Tree for COLEC12 (if available)

Paralogs for COLEC12 Gene

Paralogs for COLEC12 Gene

(5) SIMAP similar genes for COLEC12 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with COLEC12: view

Variants for COLEC12 Gene

Sequence variations from dbSNP and Humsavar for COLEC12 Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs1006487 -- 341,466(-) ATCTA(G/T)CTAGC intron-variant
rs10459985 -- 414,547(+) gagcc(A/G)agatc intron-variant
rs10459986 -- 414,876(+) GTGAG(G/T)GTGGC intron-variant
rs10460012 -- 412,927(+) acaat(A/G)acaaa intron-variant
rs10460013 -- 412,941(+) taaaa(C/G)agcag intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COLEC12 Gene

Variant ID Type Subtype PubMed ID
dgv3301n100 CNV gain 25217958
dgv3306n100 CNV loss 25217958
dgv3307n100 CNV gain 25217958
dgv5810n54 CNV gain 21841781
dgv594e214 CNV gain 21293372
esv3554937 CNV deletion 23714750
esv3582928 CNV loss 25503493
esv3582929 CNV loss 25503493
esv3582930 CNV loss 25503493
esv3641472 CNV loss 21293372
esv3641473 CNV gain 21293372
esv3641484 CNV gain 21293372
esv3641486 CNV loss 21293372
esv3641488 CNV gain 21293372
esv3641490 CNV loss 21293372
esv3641491 CNV loss 21293372
esv3641492 CNV loss 21293372
esv3641495 CNV gain 21293372
esv3893055 CNV gain 25118596
esv3893056 CNV gain 25118596
nsv1064150 CNV gain 25217958
nsv1066129 CNV gain 25217958
nsv1066337 CNV gain 25217958
nsv1066822 CNV gain 25217958
nsv1070858 CNV deletion 25765185
nsv1109117 CNV deletion 24896259
nsv1138591 CNV deletion 24896259
nsv2177 CNV insertion 18451855
nsv457977 CNV gain 19166990
nsv475138 CNV novel sequence insertion 20440878
nsv477785 CNV novel sequence insertion 20440878
nsv482935 CNV loss 15286789
nsv510444 OTHER sequence alteration 20534489
nsv517980 CNV loss 19592680
nsv518642 CNV gain 19592680
nsv522804 CNV loss 19592680
nsv576227 CNV gain 21841781
nsv576228 CNV loss 21841781
nsv576235 CNV gain 21841781
nsv576236 CNV gain 21841781
nsv576238 CNV loss 21841781
nsv576239 CNV gain 21841781

Variation tolerance for COLEC12 Gene

Residual Variation Intolerance Score: 75.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.03; 92.12% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COLEC12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
COLEC12

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COLEC12 Gene

Disorders for COLEC12 Gene

Relevant External Links for COLEC12

Genetic Association Database (GAD)
COLEC12
Human Genome Epidemiology (HuGE) Navigator
COLEC12
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COLEC12

No disorders were found for COLEC12 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for COLEC12 Gene

Publications for COLEC12 Gene

  1. Molecular cloning and functional characterization of a human scavenger receptor with C-type lectin (SRCL), a novel member of a scavenger receptor family. (PMID: 11162630) Nakamura K. … Nakamura T. (Biochem. Biophys. Res. Commun. 2001) 2 3 4 22 64
  2. Selective binding of the scavenger receptor C-type lectin to Lewis X trisaccharide and related glycan ligands. (PMID: 15845541) Coombs P.J. … Taylor M.E. (J. Biol. Chem. 2005) 3 4 22 64
  3. Haplotype analysis of the human collectin placenta 1 (hCL-P1) gene. (PMID: 12601552) Ohmori H. … Hata A. (J. Hum. Genet. 2003) 3 4 22 64
  4. The membrane-type collectin CL-P1 is a scavenger receptor on vascular endothelial cells. (PMID: 11564734) Ohtani K. … Wakamiya N. (J. Biol. Chem. 2001) 3 4 22 64
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64

Products for COLEC12 Gene

Sources for COLEC12 Gene

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