Colec12 collectin sub-family member 12 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Colec12provided by MGI
Official Full Name: collectin sub-family member 12provided by MGI
Primary source: MGI:MGI:2152907
See related: Ensembl:ENSMUSG00000036103 AllianceGenome:MGI:2152907
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: SRCL; CL-P1; Scara4
Summary: Predicted to enable several functions, including low-density lipoprotein particle binding activity; pattern recognition receptor activity; and scavenger receptor activity. Acts upstream of or within immune response. Located in collagen-containing extracellular matrix. Is expressed in several structures, including gut; meninges; mesothelium; respiratory system; and skeleton. Orthologous to human COLEC12 (collectin subfamily member 12). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in bladder adult (RPKM 21.0), lung adult (RPKM 20.6) and 26 other tissues See more
Orthologs: human all
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Genomic context

Location:: 18 A1; 18 4.91 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	18	NC_000084.7 (9707648..9877995)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	18	NC_000084.6 (9707648..9877995)

Chromosome 18 - NC_000084.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CL-P1 is a novel receptor involved in myelin uptake by phagocytes and likely plays a role in multiple sclerosis lesion development.
Title: Scavenger receptor collectin placenta 1 is a novel receptor involved in the uptake of myelin by phagocytes.
Structural analysis of carbohydrate-recognition domain of SRCL in complex with Lewis(x) and mutagenesis show the basis for this specificity, which is analogous to how selectins and DC-SIGN bind to related fucosylated glycans [scavenger receptor C]
Title: Scavenger receptor C-type lectin binds to the leukocyte cell surface glycan Lewis(x) by a novel mechanism.
CL-P1 predominantly mediated phagocytosis for fungi in vascular endothelia.
Title: Scavenger receptor collectin placenta 1 (CL-P1) predominantly mediates zymosan phagocytosis by human vascular endothelial cells.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)
Targeted (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables carbohydrate binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables low-density lipoprotein particle binding	ISO Inferred from Sequence Orthology more info
enables low-density lipoprotein particle binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables pattern recognition receptor activity	ISO Inferred from Sequence Orthology more info
enables pattern recognition receptor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables scavenger receptor activity	IEA Inferred from Electronic Annotation more info
enables scavenger receptor activity	ISO Inferred from Sequence Orthology more info
enables signaling receptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cellular response to exogenous dsRNA	IEA Inferred from Electronic Annotation more info
involved_in cellular response to exogenous dsRNA	ISO Inferred from Sequence Orthology more info
involved_in defense response to bacterium	IEA Inferred from Electronic Annotation more info
involved_in defense response to bacterium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in phagocytosis, recognition	ISO Inferred from Sequence Orthology more info
involved_in phagocytosis, recognition	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in plasma membrane raft organization	IEA Inferred from Electronic Annotation more info
involved_in toll-like receptor 3 signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in toll-like receptor 3 signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed

General protein information

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Preferred Names: collectin-12

Names: collectin placenta protein 1; scavenger receptor with C-type lectin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_130449.2 → NP_569716.2 collectin-12

See identical proteins and their annotated locations for NP_569716.2

Status: VALIDATED

Source sequence(s)

AB078434, AK042772, AK141928

Consensus CDS

CCDS37732.1

UniProtKB/Swiss-Prot

Q3TYT8, Q8C979, Q8K4Q8, Q8VIF6

Related

ENSMUSP00000157132.2, ENSMUST00000234965.2

Conserved Domains (5) summary

cd03590
Location:607 → 732

CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)

pfam01391
Location:454 → 563

Collagen; Collagen triple helix repeat (20 copies)

COG3883
Location:48 → 280

CwlO1; Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO [Function unknown]

cl01416
Location:286 → 359

Fimbrial; Fimbrial protein

cl02193
Location:157 → 317

VirB5_like; VirB5 protein family

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000084.7 Reference GRCm39 C57BL/6J

Range

9707648..9877995

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006525640.4 → XP_006525703.1 collectin-12 isoform X1

Conserved Domains (3) summary

cd03590
Location:543 → 668

CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)

pfam01391
Location:390 → 499

Collagen; Collagen triple helix repeat (20 copies)

PRK11281
Location:21 → 347

PRK11281; mechanosensitive channel MscK