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    COL12A1 collagen type XII alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1303, updated on 14-Nov-2024

    Summary

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    Official Symbol
    COL12A1provided by HGNC
    Official Full Name
    collagen type XII alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2188
    See related
    Ensembl:ENSG00000111799 MIM:120320; AllianceGenome:HGNC:2188
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    UCMD2; BTHLM2; EDSMYP; COL12A1L; BA209D8.1; DJ234P15.1
    Summary
    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]
    Expression
    Broad expression in endometrium (RPKM 41.5), ovary (RPKM 33.4) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See COL12A1 in Genome Data Viewer
    Location:
    6q13-q14.1
    Exon count:
    68
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (75084326..75206053, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (76261502..76383203, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (75794042..75915769, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928516 Neighboring gene uncharacterized LOC105377858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:75490962-75491462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:75491463-75491963 Neighboring gene Sharpr-MPRA regulatory region 6905 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94546 Neighboring gene NUP50 pseudogene 4 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94569 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94572 Neighboring gene NANOG hESC enhancer GRCh37_chr6:75674378-75674954 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:75794417-75794939 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:75828643-75829842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24756 Neighboring gene small nucleolar RNA, C/D box 156 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:75918738-75918943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24757 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24758 Neighboring gene uncharacterized LOC124901344 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:75981645-75982844 Neighboring gene cytochrome c oxidase subunit 7A2 Neighboring gene transmembrane protein 30A

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Whole exome sequencing identifies a novel variant in the COL12A1 gene in a family with Ullrich congenital muscular dystrophy 2.
      Title: Whole exome sequencing identifies a novel variant in the COL12A1 gene in a family with Ullrich congenital muscular dystrophy 2.
    2. PABPC1 promotes cell proliferation and metastasis in pancreatic adenocarcinoma by regulating COL12A1 expression.
      Title: PABPC1 promotes cell proliferation and metastasis in pancreatic adenocarcinoma by regulating COL12A1 expression.
    3. Epigenetic dysregulation-mediated COL12A1 upregulation predicts worse outcome in intrahepatic cholangiocarcinoma patients.
      Title: Epigenetic dysregulation-mediated COL12A1 upregulation predicts worse outcome in intrahepatic cholangiocarcinoma patients.
    4. Temporal profiling of the breast tumour microenvironment reveals collagen XII as a driver of metastasis.
      Title: Temporal profiling of the breast tumour microenvironment reveals collagen XII as a driver of metastasis.
    5. Collagen XII mediated cellular and extracellular mechanisms regulate establishment of tendon structure and function.
      Title: Collagen XII mediated cellular and extracellular mechanisms regulate establishment of tendon structure and function.
    6. Role of collagen XII in skin homeostasis and repair.
      Title: Role of collagen XII in skin homeostasis and repair.
    7. Bioinformatics analysis identified MMP14 and COL12A1 as immune-related biomarkers associated with pancreatic adenocarcinoma prognosis.
      Title: Bioinformatics analysis identified MMP14 and COL12A1 as immune-related biomarkers associated with pancreatic adenocarcinoma prognosis.
    8. COL12A1 Single Nucleotide Polymorphisms rs240736 and rs970547 Are Not Associated with Temporomandibular Joint Disc Displacement without Reduction.
      Title: COL12A1 Single Nucleotide Polymorphisms rs240736 and rs970547 Are Not Associated with Temporomandibular Joint Disc Displacement without Reduction.
    9. Integrated bioinformatics analysis of expression and gene regulation network of COL12A1 in colorectal cancer.
      Title: Integrated bioinformatics analysis of expression and gene regulation network of COL12A1 in colorectal cancer.
    10. A novel mutation in the COL12A1 gene.
      Title: A novel mutation in the COL12A1 gene.
    Submit: New GeneRIF Correction See all GeneRIFs (30)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Bethlem myopathy 2
    MedGen: C4225313 OMIM: 616471 GeneReviews: Not available
    		not available
    Ullrich congenital muscular dystrophy 2
    MedGen: C4225314 OMIM: 616470 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in collagen fibril organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in endodermal cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endodermal cell differentiation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of collagen type XII trimer NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    colocalizes_with collagen-containing extracellular matrix HDA PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region HDA PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular space HDA PubMed 
    located_in extracellular vesicle HDA PubMed 

    General protein information

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    Preferred Names
    collagen alpha-1(XII) chain
    Names
    collagen type XII proteoglycan
    collagen, type XII, alpha 1

    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.

    Genomic

    1. NG_042181.1 RefSeqGene

      Range
      4855..126582
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001424113.1 → NP_001411042.1  collagen alpha-1(XII) chain isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) encodes the longest isoform (3).
      Source sequence(s)
      AL080250, AL096771, AL354664
      Related
      ENSP00000421216.1, ENST00000483888.6

    2. NM_001424114.1 → NP_001411043.1  collagen alpha-1(XII) chain isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080250, AL096771, AL354664

    3. NM_001424115.1 → NP_001411044.1  collagen alpha-1(XII) chain isoform 5 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080250, AL096771, AL354664

    4. NM_001424116.1 → NP_001411045.1  collagen alpha-1(XII) chain isoform 6 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080250, AL096771

    5. NM_004370.6 → NP_004361.3  collagen alpha-1(XII) chain long isoform precursor

      See identical proteins and their annotated locations for NP_004361.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (long) represents a transcript that encodes an isoform longer than that of the short isoform.
      Source sequence(s)
      AI752603, AL080250, AL096771, AL354664, BP286308, DA661773, U73778
      Consensus CDS
      CCDS43482.1
      UniProtKB/Swiss-Prot
      O43853, Q15955, Q5VYK1, Q5VYK2, Q71UR3, Q99715, Q99716
      UniProtKB/TrEMBL
      D6RGG3
      Related
      ENSP00000325146.8, ENST00000322507.13
      Conserved Domains (6) summary
      pfam01391
      Location:2765 → 2891
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:1474 → 1548
      FN3; Fibronectin type 3 domain
      smart00210
      Location:2520 → 2712
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:2118 → 2197
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd01482
      Location:1198 → 1361
      vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
      pfam00041
      Location:1754 → 1834
      fn3; Fibronectin type III domain

    6. NM_080645.3 → NP_542376.2  collagen alpha-1(XII) chain short isoform precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (short) lacks multiple exons in the 5' coding region compared to the long variant. The encoded isoform (short) is shorter but has identical N-and C-termini compared to the long isoform.
      Source sequence(s)
      AI752603, AL080250, AL096771, DA661773, U73778
      Consensus CDS
      CCDS43481.1
      UniProtKB/TrEMBL
      B9EJB8
      Related
      ENSP00000305147.9, ENST00000345356.10
      Conserved Domains (6) summary
      pfam01391
      Location:1705 → 1733
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:310 → 384
      FN3; Fibronectin type 3 domain
      smart00210
      Location:1356 → 1548
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:954 → 1033
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd01482
      Location:34 → 197
      vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
      pfam00041
      Location:590 → 670
      fn3; Fibronectin type III domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      75084326..75206053 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535435.2 → XP_011533737.1  collagen alpha-1(XII) chain isoform X3

      UniProtKB/TrEMBL
      D6RGG3
      Conserved Domains (6) summary
      pfam01391
      Location:2674 → 2800
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:1383 → 1457
      FN3; Fibronectin type 3 domain
      smart00210
      Location:2429 → 2621
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:2027 → 2106
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd01482
      Location:1107 → 1270
      vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
      pfam00041
      Location:1663 → 1743
      fn3; Fibronectin type III domain

    2. XM_047418186.1 → XP_047274142.1  collagen alpha-1(XII) chain isoform X6

    3. XM_047418184.1 → XP_047274140.1  collagen alpha-1(XII) chain isoform X1

    4. XM_017010252.3 → XP_016865741.1  collagen alpha-1(XII) chain isoform X2

      UniProtKB/TrEMBL
      D6RGG3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      76261502..76383203 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354234.1 → XP_054210209.1  collagen alpha-1(XII) chain isoform X3

    2. XM_054354232.1 → XP_054210207.1  collagen alpha-1(XII) chain isoform X1

    3. XM_054354237.1 → XP_054210212.1  collagen alpha-1(XII) chain isoform X6

    4. XM_054354233.1 → XP_054210208.1  collagen alpha-1(XII) chain isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99715.2 GenPept UniProtKB/Swiss-Prot:Q99715

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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