Colec12 collectin sub-family member 12 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Colec12provided by RGD
Official Full Name: collectin sub-family member 12provided by RGD
Primary source: RGD:735039
See related: Ensembl:ENSRNOG00000016366 AllianceGenome:RGD:735039
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable low-density lipoprotein particle binding activity; pattern recognition receptor activity; and scavenger receptor activity. Predicted to be involved in several processes, including cellular response to exogenous dsRNA; positive regulation of cell adhesion molecule production; and toll-like receptor 3 signaling pathway. Predicted to act upstream of or within immune response. Predicted to be integral component of membrane. Predicted to be part of collagen trimer. Orthologous to human COLEC12 (collectin subfamily member 12). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 395.8), Uterus (RPKM 227.1) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 18p13

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	18	NC_086036.1 (1005787..1193455)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	18	NC_051353.1 (732950..920620)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	18	NC_005117.4 (867048..1054047)

Chromosome 18 - NC_086036.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The molecular docking revealed that S-allyl-mercapto-glutathione interacting with Colec12, MARCO (class A), and SCARB1 (class B) scavenger receptors in in vitro tests demonstrates a direct stimulation of immunoglobulin secretion by S-allylmercaptoglutathione (GSSA) in CD19+ B lymphocytes.
Title: New Aspects Towards a Molecular Understanding of the Allicin Immunostimulatory Mechanism via Colec12, MARCO, and SCARB1 Receptors.

Submit: New GeneRIF Correction

General gene information

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Markers

D18Chm30 (e-PCR)
- UniSTS:518196

D18MIT12 (e-PCR)
- UniSTS:120225

D2Rat367 (e-PCR), detects polymorphism
- UniSTS:227501

d18rat114 (e-PCR)
- UniSTS:121289

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
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
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
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
NOT involved_in cellular response to exogenous dsRNA	ISO Inferred from Sequence Orthology more info
involved_in cellular response to exogenous dsRNA	ISO Inferred from Sequence Orthology more info
involved_in defense response to bacterium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within immune response	ISO Inferred from Sequence Orthology more info
involved_in phagocytosis, recognition	ISO Inferred from Sequence Orthology more info
involved_in phagocytosis, recognition	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_positive_effect plasma membrane raft organization	ISO Inferred from Sequence Orthology 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 membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collectin-12

Names: CL-P1; collectin placenta protein 1; nurse cell scavenger receptor 2

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_001025721.1 → NP_001020892.1 collectin-12

See identical proteins and their annotated locations for NP_001020892.1

Status: PROVISIONAL

Source sequence(s)

BC097495

UniProtKB/Swiss-Prot

Q4V885, Q76LC3

UniProtKB/TrEMBL

A6KND5

Related

ENSRNOP00000059663.1, ENSRNOT00000065494.2

Conserved Domains (3) 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)

cl02193
Location:157 → 317

VirB5_like; VirB5 protein family