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

Gene ID: 140792, updated on 23-Jun-2021

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
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
S; Sc; CL-; SRCL; CL-P1; Scara4
Expression
Broad expression in bladder adult (RPKM 21.0), lung adult (RPKM 20.6) and 26 other tissues See more
Orthologs
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Genomic context

See Colec12 in Genome Data Viewer
Location:
18; 18 A1
Exon count:
11
Annotation release Status Assembly Chr Location
109 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)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 18 NC_000084.5 (9707646..9877993)

Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene centrin 1 Neighboring gene kinectin 1 pseudogene Neighboring gene 60S ribosomal protein L24-like Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene predicted gene, 23350 Neighboring gene cell division cycle associated 7 pseudogene Neighboring gene developmental pluripotency associated 4 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2) 
  • Endonuclease-mediated (1) 

General gene information

Markers

Homology

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 ISO
Inferred from Sequence Orthology
more info
 
enables signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
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 positive regulation of cell adhesion molecule production 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 collagen-containing extracellular matrix HDA PubMed 
located_in integral component of membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

  1. NM_130449.2NP_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
    Q8K4Q8
    Related
    ENSMUSP00000157132.2, ENSMUST00000234965.2
    Conserved Domains (5) summary
    cd03590
    Location:607732
    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:454563
    Collagen; Collagen triple helix repeat (20 copies)
    COG3883
    Location:48280
    CwlO1; Uncharacterized N-terminal domain of peptidoglycan hydrolase CwlO [Function unknown]
    cl01416
    Location:286359
    Fimbrial; Fimbrial protein
    cl02193
    Location:157317
    VirB5_like; VirB5 protein family

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000084.7 Reference GRCm39 C57BL/6J

    Range
    9707648..9877995
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (3) summary
    cd03590
    Location:543668
    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:390499
    Collagen; Collagen triple helix repeat (20 copies)
    PRK11281
    Location:21347
    PRK11281; mechanosensitive channel MscK
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