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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
    NEW
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    Try the new Transcript table

    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)

    NEW Try the new Transcript table

    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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