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

    Gene ID: 1303, updated on 3-Dec-2024

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    General protein information

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

    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.

    Genomic

    1. NG_042181.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001424113.1NP_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
      UniProtKB/TrEMBL
      D6RGG3
      Related
      ENSP00000421216.1, ENST00000483888.6
    2. NM_001424114.1NP_001411043.1  collagen alpha-1(XII) chain isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080250, AL096771, AL354664
      UniProtKB/TrEMBL
      D6RGG3
    3. NM_001424115.1NP_001411044.1  collagen alpha-1(XII) chain isoform 5 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080250, AL096771, AL354664
      UniProtKB/TrEMBL
      D6RGG3
    4. NM_001424116.1NP_001411045.1  collagen alpha-1(XII) chain isoform 6 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080250, AL096771
      UniProtKB/TrEMBL
      B9EJB8
    5. NM_004370.6NP_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:27652891
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:14741548
      FN3; Fibronectin type 3 domain
      smart00210
      Location:25202712
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:21182197
      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:11981361
      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:17541834
      fn3; Fibronectin type III domain
    6. NM_080645.3NP_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:17051733
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:310384
      FN3; Fibronectin type 3 domain
      smart00210
      Location:13561548
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:9541033
      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:34197
      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:590670
      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_011535435.2XP_011533737.1  collagen alpha-1(XII) chain isoform X3

      UniProtKB/TrEMBL
      D6RGG3
      Conserved Domains (6) summary
      pfam01391
      Location:26742800
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:13831457
      FN3; Fibronectin type 3 domain
      smart00210
      Location:24292621
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:20272106
      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:11071270
      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:16631743
      fn3; Fibronectin type III domain
    2. XM_047418186.1XP_047274142.1  collagen alpha-1(XII) chain isoform X6

      UniProtKB/TrEMBL
      B9EJB8
    3. XM_047418184.1XP_047274140.1  collagen alpha-1(XII) chain isoform X1

      UniProtKB/TrEMBL
      D6RGG3
    4. XM_017010252.3XP_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_054354234.1XP_054210209.1  collagen alpha-1(XII) chain isoform X3

      UniProtKB/TrEMBL
      D6RGG3
    2. XM_054354232.1XP_054210207.1  collagen alpha-1(XII) chain isoform X1

      UniProtKB/TrEMBL
      D6RGG3
    3. XM_054354237.1XP_054210212.1  collagen alpha-1(XII) chain isoform X6

      UniProtKB/TrEMBL
      B9EJB8
    4. XM_054354233.1XP_054210208.1  collagen alpha-1(XII) chain isoform X2

      UniProtKB/TrEMBL
      D6RGG3