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    COL13A1 collagen, type XIII, alpha 1 [ Homo sapiens ]

    Gene ID: 1305, updated on 11-May-2012
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    Summary

    Official Symbol
    COL13A1provided by HGNC
    Official Full Name
    collagen, type XIII, alpha 1provided by HGNC
    Primary source
    HGNC:2190
    See related
    Ensembl:ENSG00000197467; HPRD:00383; MIM:120350; Vega:OTTHUMG00000018394
    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
    COLXIIIA1; FLJ42485
    Summary
    This gene encodes the alpha chain of one of the nonfibrillar collagens. The function of this gene product is not known, however, it has been detected at low levels in all connective tissue-producing cells so it may serve a general function in connective tissues. Unlike most of the collagens, which are secreted into the extracellular matrix, collagen XIII contains a transmembrane domain and the protein has been localized to the plasma membrane. The transcripts for this gene undergo complex and extensive splicing involving at least eight exons. Like other collagens, collagen XIII is a trimer; it is not known whether this trimer is composed of one or more than one alpha chain isomer. A number of alternatively spliced transcript variants have been described, but the full length nature of some of them has not been determined. [provided by RefSeq, Jul 2008]
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    Genomic context

    Location :
    10q22
    Sequence :
    Chromosome: 10; NC_000010.10 (71561644..71718904)
    See COL13A1 in Epigenomics, MapViewer

    Chromosome 10 - NC_000010.10Genomic Context describing neighboring genes Neighboring gene chromosome 10 open reading frame 35 Neighboring gene ribosomal protein L5 pseudogene 26 Neighboring gene H2A histone family, member Y2 Neighboring gene apoptosis-inducing factor, mitochondrion-associated, 2 Neighboring gene trypsin domain containing 1

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    Genomic regions, transcripts, and products

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details
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    Bibliography

    Related articles in PubMed

    1. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. Chalasani N, et al. Gastroenterology, 2010 Nov. PMID 20708005.
    2. Association of genetic variants with hemorrhagic stroke in Japanese individuals. Yoshida T, et al. Int J Mol Med, 2010 Apr. PMID 20198315.
    3. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. Oguri M, et al. Am J Hypertens, 2010 Jan. PMID 19851296.
    4. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. Grupe A, et al. Am J Hum Genet, 2006 Jan. PMID 16385451.
    5. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. Choy KW, et al. Physiol Genomics, 2006 Mar 13. PMID 16368877.

    See all (22) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    3. two widely separated coiled-coil domains of type XIII and related collagens function as independent oligomerization domains participating in the folding of distinct areas of the molecule.
      Title: Type XIII collagen and some other transmembrane collagens contain two separate coiled-coil motifs, which may function as independent oligomerization domains.
    4. The type XIII collagen ectodomain is a 150-nm rod and capable of binding to fibronectin, nidogen-2, perlecan, and heparin.
      Title: The type XIII collagen ectodomain is a 150-nm rod and capable of binding to fibronectin, nidogen-2, perlecan, and heparin.
    Submit: New GeneRIF Correction
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    Phenotypes

    Review eQTL and phenotype association data in this region using PheGenI

    Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease.

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    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    Collagen, type XIII, alpha 1 Collagen, type XIII, alpha 1 COL13A1    HPRD  PubMed  
    Collagen, type XIII, alpha 1 P02751 FN1    HPRD  PubMed  
    Collagen, type XIII, alpha 1 P98160 HSPG2    HPRD  PubMed  
    Collagen, type XIII, alpha 1 P56199 ITGA1    HPRD  PubMed  
    Collagen, type XIII, alpha 1 P14543 NID1    HPRD  PubMed  
    Collagen, type XIII, alpha 1 Q14112 NID2    HPRD  PubMed  
    Collagen, type XIII, alpha 1 P09486 SPARC    HPRD  PubMed  
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    General gene information

    Markers

    Genotypes

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    extracellular matrix structural constituent NAS
    Non-traceable Author Statement
    more info
    		  
    heparin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    cell-cell adhesion IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    cell-matrix adhesion IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    endochondral ossification ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    morphogenesis of a branching structure ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    multicellular organismal development IEA
    Inferred from Electronic Annotation
    more info
    		  
    ossification IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    collagen IEA
    Inferred from Electronic Annotation
    more info
    		  
    collagen type XIII TAS
    Traceable Author Statement
    more info
    		 PubMed 
    integral to membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
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    General protein information

    Preferred Names
    collagen alpha-1(XIII) chain
    Names
    collagen alpha-1(XIII) chain
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    NCBI Reference Sequences (RefSeq)

    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_001130103.1 → NP_001123575.1  collagen alpha-1(XIII) chain isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC025426, AI741175, AJ293624, AL138925, BY796799, CN297094
      Consensus CDS
      CCDS44419.1
      UniProtKB/Swiss-Prot
      Q5TAT6
      Related
      ENSP00000381949, OTTHUMP00000019731, ENST00000398978, OTTHUMT00000048468
      Conserved Domains (1) summary
      pfam01391
      Location:315 – 377
      Blast Score: 92
      Collagen; Collagen triple helix repeat (20 copies)

    2. NM_080798.3 → NP_542988.3  collagen alpha-1(XIII) chain isoform 21

      Status: REVIEWED

      Description
      Transcript Variant: This variant (21) does not contain exons 3B, 4, 5, 12, and 29, based on the exon numbering used in PMID: 1894651. Isoform 21 lacks three internal segments, compared to isoform 1.
      Source sequence(s)
      AC024601, AC025426, AL138925
      Consensus CDS
      CCDS44427.2
      Related
      ENSP00000428057, OTTHUMP00000227634, ENST00000520267, OTTHUMT00000380458
      Conserved Domains (1) summary
      pfam01391
      Location:258 – 320
      Blast Score: 92
      Collagen; Collagen triple helix repeat (20 copies)

    3. NM_080800.3 → NP_542990.3  collagen alpha-1(XIII) chain isoform 11

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) does not contain exon 12 and 33, based on the exon numbering used in PMID: 1894651. Isoform 11 lacks two internal segments, compared to isoform 1.
      Source sequence(s)
      AC024601, AC025426, AL138925
      Consensus CDS
      CCDS44425.2
      UniProtKB/Swiss-Prot
      Q5TAT6
      Related
      ENSP00000428342, OTTHUMP00000227636, ENST00000522165, OTTHUMT00000380460
      Conserved Domains (1) summary
      pfam01391
      Location:296 – 358
      Blast Score: 90
      Collagen; Collagen triple helix repeat (20 copies)

    4. NM_080801.3 → NP_542991.3  collagen alpha-1(XIII) chain isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) does not contain exon 13, based on the exon numbering used in PMID: 1894651. Isoform 5 lacks an internal 22 aa compared to isoform 1.
      Source sequence(s)
      AC024601, AC025426, AL138925
      Consensus CDS
      CCDS44424.2
      UniProtKB/Swiss-Prot
      Q5TAT6
      Related
      ENSP00000346553, OTTHUMP00000019732, ENST00000354547, OTTHUMT00000048469
      Conserved Domains (1) summary
      pfam01391
      Location:293 – 355
      Blast Score: 89
      Collagen; Collagen triple helix repeat (20 copies)

    5. NM_080802.3 → NP_542992.3  collagen alpha-1(XIII) chain isoform 15

      Status: REVIEWED

      Description
      Transcript Variant: This variant (15) does not contain exons 13, 29, and 33, based on the exon numbering used in PMID: 1894651. Isoform 15 lacks three internal segments, compared to isoform 1.
      Source sequence(s)
      AC024601, AC025426, AL138925
      Consensus CDS
      CCDS44423.2
      UniProtKB/Swiss-Prot
      Q5TAT6
      Related
      ENSP00000430061, OTTHUMP00000227635, ENST00000517713, OTTHUMT00000380459
      Conserved Domains (1) summary
      pfam01391
      Location:293 – 355
      Blast Score: 94
      Collagen; Collagen triple helix repeat (20 copies)

    6. NM_080805.3 → NP_542995.3  collagen alpha-1(XIII) chain isoform 19

      Status: REVIEWED

      Description
      Transcript Variant: This variant (19) does not contain exons 4, 5, 13, 29, 33, and 37, based on the exon numbering used in PMID: 1894651. Isoform 19 lacks five internal segments, compared to isoform 1.
      Source sequence(s)
      AC024601, AC025426, AL138925
      Consensus CDS
      CCDS44428.2
      UniProtKB/TrEMBL
      E7EWL8
      Related
      ENSP00000430173, OTTHUMP00000227637, ENST00000520133, OTTHUMT00000380461
      Conserved Domains (1) summary
      pfam01391
      Location:264 – 326
      Blast Score: 104
      Collagen; Collagen triple helix repeat (20 copies)

    RefSeqs of Annotated Genomes: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000010.10 Reference GRCh37.p5 Primary Assembly

      Range
      71561644..71718904
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000142.1 Alternate HuRef

      Range
      65553122..65710673
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_005203.3: Suppressed sequence

      Description
      NM_005203.3: This RefSeq was permanently suppressed because currently there is not sufficient full-length data to support this transcript.

    2. NM_080799.2: Suppressed sequence

      Description
      NM_080799.2: This RefSeq was permanently suppressed because currently there is not sufficient full-length data to support this transcript.

    3. NM_080803.2: Suppressed sequence

      Description
      NM_080803.2: This RefSeq was permanently suppressed because currently there is not sufficient full-length data to support this transcript.

    4. NM_080804.2: Suppressed sequence

      Description
      NM_080804.2: This RefSeq was permanently suppressed because currently there is not sufficient full-length data to support this transcript.

    5. NM_080806.2: Suppressed sequence

      Description
      NM_080806.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.

    6. NM_080807.2: Suppressed sequence

      Description
      NM_080807.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.

    7. NM_080808.2: Suppressed sequence

      Description
      NM_080808.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.

    8. NM_080809.2: Suppressed sequence

      Description
      NM_080809.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.

    9. NM_080810.2: Suppressed sequence

      Description
      NM_080810.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.

    10. NM_080811.2: Suppressed sequence

      Description
      NM_080811.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.

    11. NM_080812.2: Suppressed sequence

      Description
      NM_080812.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.

    12. NM_080813.2: Suppressed sequence

      Description
      NM_080813.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.

    13. NM_080814.2: Suppressed sequence

      Description
      NM_080814.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.

    14. NM_080815.2: Suppressed sequence

      Description
      NM_080815.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
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    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AC024601.9 (115142..167292) None
    genomic AC025426.11 None
    genomic AF071009.1 AAD48082.1
    genomic AL138925.17 CAI15450.1
      CAI15451.2
      CAI15452.1
    genomic CH471083.1 EAW54333.1
      EAW54334.1
      EAW54335.1
      EAW54336.1
      EAW54337.1
      EAW54338.1
      EAW54339.1
      EAW54340.1
      EAW54341.1
      EAW54342.1
      EAW54343.1
      EAW54344.1
      EAW54345.1
      EAW54346.1
      EAW54347.1
      EAW54348.1
      EAW54349.1
      EAW54350.1
      EAW54351.1
      EAW54352.1
      EAW54353.1
      EAW54354.1
      EAW54355.1
      EAW54356.1
      EAW54357.1
      EAW54358.1
      EAW54359.1
      EAW54360.1
      EAW54361.1
      EAW54362.1
      EAW54363.1
      EAW54364.1
      EAW54365.1
      EAW54366.1
      EAW54367.1
      EAW54368.1
      EAW54369.1
      EAW54370.1
    genomic M20795.1 AAA51987.1
    genomic M20796.1 AAA51987.1
    genomic M20797.1 AAA51987.1
    genomic M20798.1 AAA51987.1
    genomic M20799.1 AAA51987.1
    genomic M20800.1 AAA51987.1
    genomic M20801.1 AAA51987.1
    genomic M20802.1 AAA51987.1
    genomic M20803.1 AAA51987.1
      AAA51988.1
      AAA51989.1
      AAA51990.1
      AAA51991.1
    genomic M20804.1 AAA51987.1
    genomic M20805.1 AAA51990.1
    genomic M69008.1 AAA52754.1
    mRNA AI741175.1 None
    mRNA AJ293624.1 CAC00688.1
    mRNA AK124476.1 None
    mRNA BC136385.1 AAI36386.1
    mRNA BC139913.1 None
    mRNA BM744248.1 None
    mRNA BY796799.2 None
    mRNA CN297094.1 None
    mRNA M15524.1 AAA52048.1
    mRNA M33653.1 AAA52047.1
    mRNA M59217.1 AAA51685.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5TAT6.1 GenPept UniProtKB/Swiss-Prot:Q5TAT6
    Q9UP45 GenPept UniProtKB/TrEMBL:Q9UP45
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    Additional Links

    Gene LinkOut

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

    Chemical Information
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