Human Gene COLEC12 (ENST00000400256.5_8) from GENCODE V47lift37

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Description: collectin subfamily member 12 (from RefSeq NM_130386.3)
Gencode Transcript: ENST00000400256.5_8
Gencode Gene: ENSG00000158270.12_10
Transcript (Including UTRs)
Position: hg19 chr18:316,737-500,701 Size: 183,965 Total Exon Count: 10 Strand: -
Coding Region
Position: hg19 chr18:320,045-500,514 Size: 180,470 Coding Exon Count: 10

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr18:316,737-500,701)			mRNA (may differ from genome)		Protein (742 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: COL12_HUMAN DESCRIPTION: RecName: Full=Collectin-12; AltName: Full=Collectin placenta protein 1; Short=CL-P1; Short=hCL-P1; AltName: Full=Nurse cell scavenger receptor 2; AltName: Full=Scavenger receptor class A member 4; AltName: Full=Scavenger receptor with C-type lectin; 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. SUBUNIT: The extracellular domain forms a stable trimer. The extracellular domain interacts with fibrillar beta amyloid peptide. SUBCELLULAR LOCATION: Membrane; Single-pass type II membrane protein. Note=Forms clusters on the cell surface. 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. SIMILARITY: Contains 1 C-type lectin domain. SIMILARITY: Contains 3 collagen-like domains. SEQUENCE CAUTION: Sequence=BAB39148.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact;

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: COLEC12 Diseases sorted by gene-association score: leukoencephalopathy with vanishing white matter (1)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D000082 Acetaminophen D001564 Benzo(a)pyrene D002794 Choline D019324 beta-Naphthoflavone D015124 8-Bromo Cyclic Adenosine Monophosphate D016589 Astemizole D002104 Cadmium D019256 Cadmium Chloride D002117 Calcitriol D002922 Ciguatoxins more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 42.10 RPKM in Cervix - Ectocervix Total median expression: 452.02 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-104.90	187	-0.561	Picture	PostScript	Text
3' UTR	-1244.60	3308	-0.376	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR001304 - C-type_lectin
IPR016186 - C-type_lectin-like
IPR018378 - C-type_lectin_CS
IPR016187 - C-type_lectin_fold
IPR008160 - Collagen

Pfam Domains:
PF00059 - Lectin C-type domain
PF01391 - Collagen triple helix repeat (20 copies)

SCOP Domains:
56436 - C-type lectin-like
57997 - Tropomyosin
58104 - Methyl-accepting chemotaxis protein (MCP) signaling domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2OX8 - X-ray

ModBase Predicted Comparative 3D Structure on Q5KU26


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD	Ensembl

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0005044 scavenger receptor activity GO:0005534 galactose binding GO:0008329 signaling pattern recognition receptor activity GO:0030169 low-density lipoprotein particle binding GO:0030246 carbohydrate binding GO:0046872 metal ion binding Biological Process: GO:0006898 receptor-mediated endocytosis GO:0006910 phagocytosis, recognition GO:0006952 defense response GO:0006955 immune response GO:0009756 carbohydrate mediated signaling GO:0034138 toll-like receptor 3 signaling pathway GO:0045087 innate immune response GO:0050776 regulation of immune response GO:0051260 protein homooligomerization GO:0060355 positive regulation of cell adhesion molecule production GO:0071360 cellular response to exogenous dsRNA Cellular Component: GO:0005581 collagen trimer GO:0005886 plasma membrane GO:0016020 membrane GO:0016021 integral component of membrane GO:0030666 endocytic vesicle membrane

Descriptions from all associated GenBank mRNAs


	LF385230 - JP 2014500723-A/192733: Polycomb-Associated Non-Coding RNAs. AB005145 - Homo sapiens CL-P1 mRNA for collectin placenta 1, complete cds. BC060789 - Homo sapiens collectin sub-family member 12, mRNA (cDNA clone MGC:71579 IMAGE:30344546), complete cds. AB038518 - Homo sapiens SRCL mRNA for scavenger receptor with C-type lectin type I, complete cds. AB052103 - Homo sapiens SRCL mRNA for scavenger receptor with C-type lectin type II, complete cds. AB034251 - Homo sapiens NSR2 mRNA for nurse cell scavenger receptor 2, complete cds. JF432431 - Synthetic construct Homo sapiens clone IMAGE:100073639 collectin sub-family member 12 (COLEC12) gene, encodes complete protein. KJ899665 - Synthetic construct Homo sapiens clone ccsbBroadEn_09059 COLEC12 gene, encodes complete protein. CU687424 - Synthetic construct Homo sapiens gateway clone IMAGE:100021245 5' read COLEC12 mRNA. MA620807 - JP 2018138019-A/192733: Polycomb-Associated Non-Coding RNAs. JD523077 - Sequence 504101 from Patent EP1572962. JD160900 - Sequence 141924 from Patent EP1572962. JD153059 - Sequence 134083 from Patent EP1572962. JD325885 - Sequence 306909 from Patent EP1572962. JD198357 - Sequence 179381 from Patent EP1572962. JD101956 - Sequence 82980 from Patent EP1572962. JD517227 - Sequence 498251 from Patent EP1572962. JD366201 - Sequence 347225 from Patent EP1572962. JD366202 - Sequence 347226 from Patent EP1572962. JD105183 - Sequence 86207 from Patent EP1572962. JD517226 - Sequence 498250 from Patent EP1572962. JD189767 - Sequence 170791 from Patent EP1572962. JD405182 - Sequence 386206 from Patent EP1572962. JD057123 - Sequence 38147 from Patent EP1572962. JD461273 - Sequence 442297 from Patent EP1572962. JD100390 - Sequence 81414 from Patent EP1572962. JD186577 - Sequence 167601 from Patent EP1572962. AL713657 - Homo sapiens mRNA; cDNA DKFZp547G1215 (from clone DKFZp547G1215). LF342640 - JP 2014500723-A/150143: Polycomb-Associated Non-Coding RNAs. JD092824 - Sequence 73848 from Patent EP1572962. LF342639 - JP 2014500723-A/150142: Polycomb-Associated Non-Coding RNAs. JD419833 - Sequence 400857 from Patent EP1572962. JD281786 - Sequence 262810 from Patent EP1572962. JD220147 - Sequence 201171 from Patent EP1572962. LF342638 - JP 2014500723-A/150141: Polycomb-Associated Non-Coding RNAs. JD338991 - Sequence 320015 from Patent EP1572962. JD245920 - Sequence 226944 from Patent EP1572962. JD359351 - Sequence 340375 from Patent EP1572962. LF342637 - JP 2014500723-A/150140: Polycomb-Associated Non-Coding RNAs. JD345368 - Sequence 326392 from Patent EP1572962. JD345367 - Sequence 326391 from Patent EP1572962. LF342636 - JP 2014500723-A/150139: Polycomb-Associated Non-Coding RNAs. JD355984 - Sequence 337008 from Patent EP1572962. LF342635 - JP 2014500723-A/150138: Polycomb-Associated Non-Coding RNAs. JD456176 - Sequence 437200 from Patent EP1572962. JD316810 - Sequence 297834 from Patent EP1572962. JD189856 - Sequence 170880 from Patent EP1572962. LF342634 - JP 2014500723-A/150137: Polycomb-Associated Non-Coding RNAs. JD450054 - Sequence 431078 from Patent EP1572962. JD369576 - Sequence 350600 from Patent EP1572962. LF342633 - JP 2014500723-A/150136: Polycomb-Associated Non-Coding RNAs. LF342632 - JP 2014500723-A/150135: Polycomb-Associated Non-Coding RNAs. LF342631 - JP 2014500723-A/150134: Polycomb-Associated Non-Coding RNAs. LF342630 - JP 2014500723-A/150133: Polycomb-Associated Non-Coding RNAs. LF342629 - JP 2014500723-A/150132: Polycomb-Associated Non-Coding RNAs. LF342628 - JP 2014500723-A/150131: Polycomb-Associated Non-Coding RNAs. LF342627 - JP 2014500723-A/150130: Polycomb-Associated Non-Coding RNAs. LF342626 - JP 2014500723-A/150129: Polycomb-Associated Non-Coding RNAs. LF342625 - JP 2014500723-A/150128: Polycomb-Associated Non-Coding RNAs. LF342623 - JP 2014500723-A/150126: Polycomb-Associated Non-Coding RNAs. MA578217 - JP 2018138019-A/150143: Polycomb-Associated Non-Coding RNAs. MA578216 - JP 2018138019-A/150142: Polycomb-Associated Non-Coding RNAs. MA578215 - JP 2018138019-A/150141: Polycomb-Associated Non-Coding RNAs. MA578214 - JP 2018138019-A/150140: Polycomb-Associated Non-Coding RNAs. MA578213 - JP 2018138019-A/150139: Polycomb-Associated Non-Coding RNAs. MA578212 - JP 2018138019-A/150138: Polycomb-Associated Non-Coding RNAs. MA578211 - JP 2018138019-A/150137: Polycomb-Associated Non-Coding RNAs. MA578210 - JP 2018138019-A/150136: Polycomb-Associated Non-Coding RNAs. MA578209 - JP 2018138019-A/150135: Polycomb-Associated Non-Coding RNAs. MA578208 - JP 2018138019-A/150134: Polycomb-Associated Non-Coding RNAs. MA578207 - JP 2018138019-A/150133: Polycomb-Associated Non-Coding RNAs. MA578206 - JP 2018138019-A/150132: Polycomb-Associated Non-Coding RNAs. MA578205 - JP 2018138019-A/150131: Polycomb-Associated Non-Coding RNAs. MA578204 - JP 2018138019-A/150130: Polycomb-Associated Non-Coding RNAs. MA578203 - JP 2018138019-A/150129: Polycomb-Associated Non-Coding RNAs. MA578202 - JP 2018138019-A/150128: Polycomb-Associated Non-Coding RNAs. MA578200 - JP 2018138019-A/150126: Polycomb-Associated Non-Coding RNAs. LF212724 - JP 2014500723-A/20227: Polycomb-Associated Non-Coding RNAs. JD458752 - Sequence 439776 from Patent EP1572962. JD407211 - Sequence 388235 from Patent EP1572962. MA448301 - JP 2018138019-A/20227: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q5KU26 (Reactome details) participates in the following event(s): R-HSA-2187261 COLEC12 (SCARA4) binds ligands R-HSA-8862090 PILRA binds PIANP, COLLEC12 trimer, NPDC1, CLEC4G R-HSA-3000480 Scavenging by Class A Receptors R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell R-HSA-2173782 Binding and Uptake of Ligands by Scavenger Receptors R-HSA-1280218 Adaptive Immune System R-HSA-5653656 Vesicle-mediated transport R-HSA-168256 Immune System

Other Names for This Gene


	Alternate Gene Symbols: CLP1, COL12_HUMAN, ENST00000400256.1, ENST00000400256.2, ENST00000400256.3, ENST00000400256.4, NM_130386, NSR2, Q5KU26, Q6P9F2, Q8TCR2, Q8WZA4, Q9BY85, Q9BYH7, SCARA4, SRCL, uc319aue.1, uc319aue.2 UCSC ID: ENST00000400256.5_8 RefSeq Accession: NM_130386.3 Protein: Q5KU26 (aka COL12_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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