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COL12A1 Gene

protein-coding   GIFtS: 60
GCID: GC06M075850

Collagen, Type XII, Alpha 1

(Previous names: collagen, type XII, alpha 1-like)
(Previous symbol: COL12A1L)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Collagen, Type XII, Alpha 11 2     BA209D8.12
COL12A1L1 2 3     DJ234P15.12
Collagen Type XII Proteoglycan1 2     Collagen Alpha-1(XII) Chain2
Collagen, Type XII, Alpha 1-Like1     

External Ids:    HGNC: 21881   Entrez Gene: 13032   Ensembl: ENSG000001117997   OMIM: 1203205   UniProtKB: Q997153   

Export aliases for COL12A1 gene to outside databases

Previous GC identifers: GC06M075743 GC06M075789 GC06M072993


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for COL12A1 Gene:
This gene encodes the alpha chain of type XII collagen, a member of the FACIT (fibril-associated collagens with
interrupted triple helices) collagen family. Type XII collagen is a homotrimer found in association with type I
collagen, an association that is thought to modify the interactions between collagen I fibrils and the
surrounding matrix. Alternatively spliced transcript variants encoding different isoforms have been identified.
(provided by RefSeq, Jul 2008)

GeneCards Summary for COL12A1 Gene:
COL12A1 (collagen, type XII, alpha 1) is a protein-coding gene. Diseases associated with COL12A1 include exostosis, and esophagitis. GO annotations related to this gene include extracellular matrix structural constituent conferring tensile strength. An important paralog of this gene is VWA1.

UniProtKB/Swiss-Prot: COCA1_HUMAN, Q99715
Function: Type XII collagen interacts with type I collagen-containing fibrils, the COL1 domain could be associated
with the surface of the fibrils, and the COL2 and NC3 domains may be localized in the perifibrillar matrix (By
similarity)

Gene Wiki entry for COL12A1 (Collagen, type XII, alpha 1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000006.12  NT_025741.16  NC_018917.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL12A1 gene promoter:
         C/EBPbeta   AML1a   ATF-2   HTF   AP-2gamma   LCR-F1   E47   Ik-2   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOL12A1 promoter sequence
   Search Chromatin IP Primers for COL12A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL12A1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6q12-q13   Ensembl cytogenetic band:  6q14.1   HGNC cytogenetic band: 6q12-q13

COL12A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL12A1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M075850:  view genomic region     (about GC identifiers)

Start:
75,794,042 bp from pter      End:
75,915,767 bp from pter
Size:
121,726 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: COCA1_HUMAN, Q99715 (See protein sequence)
Recommended Name: Collagen alpha-1(XII) chain precursor  
Size: 3063 amino acids; 333147 Da
Subunit: Trimer of identical chains each containing 190 kDa of non-triple-helical sequences
Secondary accessions: O43853 Q15955 Q5VYK1 Q5VYK2 Q71UR3 Q99716
Alternative splicing: 3 isoforms:  Q99715-1   Q99715-2   Q99715-4   

Explore the universe of human proteins at neXtProt for COL12A1: NX_Q99715

Explore proteomics data for COL12A1 at MOPED

Post-translational modifications: 

  • The triple-helical tail is stabilized by disulfide bonds at each end (By similarity)1
  • Hydroxylation on proline residues within the sequence motif, GXPG, is most likely to be 4-hydroxy as this fits the
    requirement for 4-hydroxylation in vertebrates (By similarity)1
  • Isoform 1 O-glycosylation; glycosaminoglycan of chondroitin-sulfate type (By similarity)1
  • Glycosylation2 at Asn700, Ser798, Ser889, Ser981, Thr1099, Thr1106, Thr1120, Thr1124, Thr1748, Thr1749,
                                 Asn1763, Asn2206, Thr2295, Thr2299, Thr2303, Thr2309, Asn2528, Asn2679
  • Modification sites at PhosphoSitePlus

  • See COL12A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_004361.3  NP_542376.2  

    ENSEMBL proteins: 
     ENSP00000399812   ENSP00000325146   ENSP00000305147   ENSP00000412864   ENSP00000421216  
     ENSP00000423423   ENSP00000393217  
    Reactome Protein details: Q99715

    COL12A1 Human Recombinant Protein Products:

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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

    COL12A1 Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse R&D Systems for Antibodies
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    Novus Biologicals COL12A1 Antibodies
    Abcam antibodies for COL12A1
    Browse Antibodies at Cloud-Clone Corp.
    Search ThermoFisher Antibodies for COL12A1
    LSBio Antibodies in human, mouse, rat for COL12A1

    COL12A1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for COL12A1
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    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    FN3: Fibronectin type III domain containing
    COLPG: Proteoglycans / Extracellular Matrix : Collagen proteoglycans
    COLLAGEN: Collagens

    Selected InterPro protein domains (see all 7):
     IPR003961 Fibronectin_type3
     IPR013320 ConA-like_subgrp
     IPR001791 Laminin_G
     IPR013783 Ig-like_fold
     IPR008160 Collagen

    Graphical View of Domain Structure for InterPro Entry Q99715

    ProtoNet protein and cluster: Q99715

    4 Blocks protein domains:
    IPB002035 Von Willebrand factor type A domain signature
    IPB003129 Thrombospondin
    IPB003962 Fibronectin type III repeat signature
    IPB008160 Collagen triple helix repeat


    UniProtKB/Swiss-Prot: COCA1_HUMAN, Q99715
    Similarity: Belongs to the fibril-associated collagens with interrupted helices (FACIT) family
    Similarity: Contains 4 collagen-like domains
    Similarity: Contains 18 fibronectin type-III domains
    Similarity: Contains 1 laminin G-like domain
    Similarity: Contains 4 VWFA domains


    COL12A1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: COCA1_HUMAN, Q99715
    Function: Type XII collagen interacts with type I collagen-containing fibrils, the COL1 domain could be associated
    with the surface of the fibrils, and the COL2 and NC3 domains may be localized in the perifibrillar matrix (By
    similarity)

         Genatlas biochemistry entry for COL12A1:
    collagen,type XII,alpha 1,extracellular matrix protein,fibril associated collagen with interrupted triple helices
    (FACIT),with two splice variants 330.8,203.2kDa,respectively,expressed in collagen I-containing tissues

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0030020extracellular matrix structural constituent conferring tensile strength NAS1427837
         
    COL12A1 for ontologies           About GeneDecksing


    Phenotypes:
         4 MGI mutant phenotypes (inferred from 1 allele(MGI details for Col12a1):
     growth/size/body  limbs/digits/tail  mortality/aging  skeleton 

    COL12A1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Col12a1tm1Debi for COL12A1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COL12A1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for COL12A1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for COL12A1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COL12A1

    miRNA
    Products:
        
    miRTarBase miRNAs that target COL12A1:
    hsa-mir-1 (MIRT024050), hsa-mir-375 (MIRT020009), hsa-mir-124-3p (MIRT023070), hsa-mir-9-5p (MIRT021464)

    Block miRNA regulation of human, mouse, rat COL12A1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate COL12A1 (see all 36):
    hsa-miR-300 hsa-miR-199a-3p hsa-miR-15a hsa-miR-449a hsa-miR-3171 hsa-miR-124 hsa-miR-1244 hsa-miR-424
    SwitchGear 3'UTR luciferase reporter plasmidCOL12A1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for COL12A1
    Predesigned siRNA for gene silencing in human, mouse, rat COL12A1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for COL12A1

    Clone
    Products:
         
    OriGene clones in human, mouse for COL12A1 (see all 9)
    OriGene ORF clones in mouse, rat for COL12A1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): COL12A1 (NM_004370)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL12A1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL12A1

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for COL12A1
    ESI BIO PureStem Progenitor for COL12A1: 
    PureStem 4D20.8, NCr-fac Progenitor
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL12A1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    COCA1_HUMAN, Q99715: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    endoplasmic reticulum4
    golgi apparatus1
    lysosome1
    nucleus1
    plasma membrane1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005595collagen type XII NAS1427837
    GO:0005615extracellular space IDA--
    GO:0005788endoplasmic reticulum lumen TAS--
    GO:0031012colocalizes with extracellular matrix IDA--

    COL12A1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for COL12A1 About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.75
    Intrinsic Prothrombin Activation Pathway0.39
    Collagen formation0.75
    Blood Coagulation Cascade0.38
    2Integrin Pathway
    FAK1 Signaling0.67
    UPA-UPAR Pathway0.56
    Integrin Pathway0.67
    Inhibition of Angiogenesis by TSP10.50
    GnRH Signaling0.56
    Transendothelial Migration of Leukocytes0.38
    3ERK Signaling
    Rho Family GTPases0.61
    Molecular Mechanisms of Cancer0.51
    ERK Signaling0.61
    ILK Signaling0.49
    MAPK Signaling0.58
    4Degradation of the extracellular matrix
    Degradation of the extracellular matrix0.43
    Extracellular matrix organization0.34
    Collagen degradation0.43
    5Phospholipase-C Pathway
    Phospholipase-C Pathway0.56
    PTEN Pathway0.56

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL12A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    2 Reactome Pathways for COL12A1
        Collagen biosynthesis and modifying enzymes
    Collagen degradation


    1 Kegg Pathway  (Kegg details for COL12A1):
        Protein digestion and absorption


    COL12A1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL12A1: 
              Extracellular Matrix & Adhesion Molecules in human mouse rat
              Neurotoxicity in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for COL12A1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for COL12A1 (Q997153 ENSP000003251464) via UniProtKB, MINT, STRING, and/or I2D (see all 43)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PXNP490233I2D: score=1 
    TLN1Q9Y4903I2D: score=1 
    COL10A1ENSP000002432224STRING: ENSP00000243222
    COL11A1ENSP000003511634STRING: ENSP00000351163
    COL13A1ENSP000003486954STRING: ENSP00000348695
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001501skeletal system development TAS3476925
    GO:0007155cell adhesion IEA--
    GO:0022617extracellular matrix disassembly TAS--
    GO:0030198extracellular matrix organization TAS--
    GO:0030199collagen fibril organization NAS1427837

    COL12A1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for COL12A1 (COCA1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for COL12A1 gene (2 alternative transcripts): 
    NM_004370.5  NM_080645.2  

    Unigene Cluster for COL12A1:

    Collagen, type XII, alpha 1
    Hs.101302  [show with all ESTs]
    Unigene Representative Sequence: NM_004370
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000425443 ENST00000322507(uc021zbv.1 uc021zbw.1 uc003phs.3 uc003pht.3)
    ENST00000345356 ENST00000416123(uc003phu.1) ENST00000483888 ENST00000511023
    ENST00000493109 ENST00000419671 ENST00000474564 ENST00000486533
    miRNA
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    Block miRNA regulation of human, mouse, rat COL12A1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate COL12A1 (see all 36):
    hsa-miR-300 hsa-miR-199a-3p hsa-miR-15a hsa-miR-449a hsa-miR-3171 hsa-miR-124 hsa-miR-1244 hsa-miR-424
    SwitchGear 3'UTR luciferase reporter plasmidCOL12A1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat COL12A1
    Clone
    Products:
         
    OriGene clones in human, mouse for COL12A1 (see all 9)
    OriGene ORF clones in mouse, rat for COL12A1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): COL12A1 (NM_004370)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL12A1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL12A1
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for COL12A1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL12A1
      QuantiTect SYBR Green Assays in human, mouse, rat COL12A1
      QuantiFast Probe-based Assays in human, mouse, rat COL12A1

    Additional mRNA sequence: 

    AJ420501.1 AK022029.1 AK057081.1 AK307558.1 AL359627.1 BC034534.1 BC034715.1 BC050587.1 
    BC146868.1 U68139.1 U73778.1 U73779.1 

    10 DOTS entries:

    DT.87017023  DT.100762402  DT.100762401  DT.91746276  DT.95221237  DT.40232173  DT.91664852  DT.121407384 
    DT.70101412  DT.91938419 

    Selected AceView cDNA sequences (see all 270):

    CA398208 BI767647 CA413826 AI567192 AI923317 N67161 AI753984 D62627 
    AI142490 BX507042 BM698169 BF590639 BM263377 CA418850 BQ183286 AI753354 
    BM672577 CA413988 AW956188 AI752931 CA412991 BQ004336 BM723821 CA415528 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    COL12A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTGTGTTGT
    COL12A1 Expression
    About this image


    COL12A1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 19) fully expand
     
     Tendon & Ligament (Muscoskeletal System)    fully expand to see all 4 entries
             Early Tenocyte Cells Limb Tendon Primordia
     
     Bone (Muscoskeletal System)    fully expand to see all 6 entries
             Notch-transfected mesenchymal stromal cells (SB623)
             HyStem+BMP4-induced 4D20.8 cells
     
     Cartilage (Muscoskeletal System)    fully expand to see all 5 entries
             HyStem+BMP4-induced 4D20.8 cells
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 4 entries
             Line H9 (Naive)
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Pre-Granulosa Cells Primordial Follicle
    COL12A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL12A1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.101302

    UniProtKB/Swiss-Prot: COCA1_HUMAN, Q99715
    Tissue specificity: Found in collagen I-containing tissues: both isoform 1 and isoform 2 appear in amnion,
    chorion, skeletal muscle, small intestine, and in cell culture of dermal fibroblasts, keratinocytes and
    endothelial cells. Only isoform 2 is found in lung, placenta, kidney and a squamous cell carcinoma cell line.
    Isoform 1 is also present in the corneal epithelial Bowman's membrane (BM) and the interfibrillar matrix of the
    corneal stroma, but it is not detected in the limbal BM

        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL12A1: 
              Extracellular Matrix & Adhesion Molecules in human mouse rat
              Neurotoxicity in human mouse rat

    Primer
    Products:
    OriGene qSTAR qPCR primer pairs in human, mouse for COL12A1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL12A1
    QuantiTect SYBR Green Assays in human, mouse, rat COL12A1
    QuantiFast Probe-based Assays in human, mouse, rat COL12A1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL12A1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for COL12A1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col12a11 , 5 collagen, type XII, alpha 11, 5 87.75(n)1
    92.32(a)1
      9 (43.82 cM)5
    128161  NM_007730.21  NP_031756.21 
     795989915 
    chicken
    (Gallus gallus)
    Aves COL12A11 collagen, type XII, alpha 1 75.96(n)
    78.8(a)
      395875  NM_205021.1  NP_990352.1 
    lizard
    (Anolis carolinensis)
    Reptilia COL12A16
    collagen, type XII, alpha 1
    77(a)
    1 ↔ 1
    1(201527135-201667719)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.237902 Xenopus laevis transcribed sequence with moderate similarity more 75.6(n)    CF519332.1 
    zebrafish
    (Danio rerio)
    Actinopterygii CF347657.12   -- 71.78(n)    CF347657.1 


    ENSEMBL Gene Tree for COL12A1 (if available)
    TreeFam Gene Tree for COL12A1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for COL12A1 gene
    VWA12  MATN42  COL14A12  MATN32  MATN22  VIT2  COCH2  COL20A12  
    VWA22  MATN12  
    4 SIMAP similar genes for COL12A1 using alignment to 6 protein entries:     COCA1_HUMAN (see all proteins):
    COL14A1    COL20A1    ITGA2    COL21A1

    COL12A1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for COL12A1
    PGOHUM00000239979


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for COL12A1 (see all 2593)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs600590951,2
    C,F--75793685(+) CTAGCA/CATTAA 2 -- ds50011Minor allele frequency- C:0.16EA 120
    rs1920489931,2
    --75793713(+) GTATGC/GTATAG 2 -- ds50010--------
    rs94431511,2
    C,F,H--75793899(+) TCACCG/ATATCA 2 -- ds50016Minor allele frequency- A:0.11NS EA CSA WA 538
    rs595964141,2
    C--75794016(+) AGGCC-/CTTCAA 2 -- ds50010--------
    rs1378563531,2
    --75794033(+) AGAAAC/TATGCC 2 -- ds50010--------
    rs585403341,2
    C,F--75794237(+) TACAAC/TACAAA 2 -- ut311Minor allele frequency- T:0.50WA 2
    rs1860216101,2
    C--75794343(+) GTTGAG/TGCACT 2 -- ut310--------
    rs1434405121,2
    --75794398(+) TATACC/GAGCAT 2 -- ut310--------
    rs1460819051,2
    C--75794434(+) TAGAAA/GAGGAA 2 -- ut310--------
    rs734620551,2
    C,F--75794709(+) CAAAGG/ACAAAA 2 -- ut312Minor allele frequency- A:0.08WA 120

    HapMap Linkage Disequilibrium report for COL12A1 (75794042 - 75915767 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for COL12A1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv886181CNV Loss21882294
    nsv830697CNV Gain+Loss17160897

    Human Gene Mutation Database (HGMD): COL12A1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL12A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL12A1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 120320    OMIM disorders: --

    5 diseases for COL12A1:    
    About MalaCards
    exostosis    esophagitis    adenocarcinoma    squamous cell carcinoma
    endotheliitis

    1 disease from the University of Copenhagen DISEASES database for COL12A1:
    Exostosis

    COL12A1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): COL12A1
    Human Genome Epidemiology (HuGE) Navigator: COL12A1 (3 documents)

    Export disorders for COL12A1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for COL12A1 gene, integrated from 10 sources (see all 32):
    (articles sorted by number of sources associating them with COL12A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete primary structure of two splice variants of collagen XII, and assignment of alpha 1(XII) collagen (COL12A1), alpha 1(IX) collagen (COL9A1), and alpha 1(XIX) collagen (COL19A1) to human chromosome 6q12-q13. (PubMed id 9143499)1, 2, 3, 9 Gerecke D.R.... Burgeson R.E. (Genomics 1997)
    2. The COL12A1 and COL14A1 genes and Achilles tendon injuries. (PubMed id 17960519)1, 4, 9 September A.V....Collins M. (Int J Sports Med 2008)
    3. The mouse alpha 1(XII) and human alpha 1(XII)-like collagen genes are localized on mouse chromosome 9 and human chromosome 6. (PubMed id 1427837)1, 2, 9 Oh S.P....Olsen B.R. (Genomics 1992)
    4. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PubMed id 20453000)1, 4 Liu C.Y....Christiani D.C. (Carcinogenesis 2010)
    5. The association between the COL12A1 gene and anterior cruciate ligament ruptures. (PubMed id 19443461)1, 4 Posthumus M....Collins M. (Br J Sports Med 2010)
    6. The chick and human collagen alpha1(XII) gene promoter -- activity of highly conserved regions around the first exon and in the first intron. (PubMed id 9826181)1, 2 Chiquet M.... Koch M. (Eur. J. Biochem. 1998)
    7. Type XII collagen contributes to diversities in human corneal and limbal extracellular matrices. (PubMed id 9344363)1, 2 Wessel H.... SundarRaj N. (Invest. Ophthalmol. Vis. Sci. 1997)
    8. No association between COL3A1, COL6A1 or COL12A1 gene variants and range of motion. (PubMed id 23013106)1 O'connell K....Collins M. (J Sports Sci 2013)
    9. Association of type XI collagen genes with chronic Achilles tendinopathy in independent populations from South Africa and Australia. (PubMed id 23624467)1 Hay M....Collins M. (Br J Sports Med 2013)
    10. Collagen XII and XIV, new partners of cartilage oligomeric matrix protein in the skin extracellular matrix suprastructure. (PubMed id 22573329)1 Agarwal P....Eckes B. (J. Biol. Chem. 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1303 HGNC: 2188 AceView: COL12A1 Ensembl:ENSG00000111799 euGenes: HUgn1303
    ECgene: COL12A1 Kegg: 1303 H-InvDB: COL12A1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for COL12A1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for COL12A1 gene:
    Search GeneIP for patents involving COL12A1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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