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COL13A1 collagen type XIII alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 1305, updated on 23-May-2018
Official Symbol
COL13A1provided by HGNC
Official Full Name
collagen type XIII alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2190
See related
Ensembl:ENSG00000197467 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
CMS19; COLXIIIA1
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]
Expression
Broad expression in prostate (RPKM 4.3), lung (RPKM 4.0) and 19 other tissues See more
Orthologs
See COL13A1 in Genome Data Viewer
Location:
10q22.1
Exon count:
43
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (69801835..69959148)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (71561644..71718904)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378346 Neighboring gene uncharacterized LOC105378347 Neighboring gene ribosomal protein L5 pseudogene 26 Neighboring gene uncharacterized LOC107984242 Neighboring gene uncharacterized LOC102723350 Neighboring gene H2A histone family member Y2 Neighboring gene HNF4 motif-containing MPRA enhancer 70

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Myasthenic syndrome, congenital, 19 Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis.
NHGRI GWA Catalog
Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease.
NHGRI GWA Catalog
Parkinson disease loci in the mid-western Amish.
NHGRI GWA Catalog
  • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
    Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
  • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
    Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
  • Collagen degradation, organism-specific biosystem (from REACTOME)
    Collagen degradation, organism-specific biosystemCollagen fibril diameter and spatial organisation are dependent on the species, tissue type and stage of development (Parry 1988). The lengths of collagen fibrils in mature tissues are largely unknow...
  • Collagen formation, organism-specific biosystem (from REACTOME)
    Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
  • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
    Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
    Integrin cell surface interactions, organism-specific biosystemThe extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength...
  • Protein digestion and absorption, organism-specific biosystem (from KEGG)
    Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Protein digestion and absorption, conserved biosystem (from KEGG)
    Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ42485

Gene Ontology Provided by GOA

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell adhesion IEP
Inferred from Expression Pattern
more info
PubMed 
cell-matrix adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-matrix adhesion IPI
Inferred from Physical Interaction
more info
PubMed 
collagen catabolic process TAS
Traceable Author Statement
more info
 
endochondral ossification ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
morphogenesis of a branching structure IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
morphogenesis of a branching structure ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cell-cell junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell junction IEA
Inferred from Electronic Annotation
more info
 
collagen type XIII trimer TAS
Traceable Author Statement
more info
PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
collagen alpha-1(XIII) chain
Names
collagen, type XIII, alpha 1

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_046344.1 RefSeqGene

    Range
    5001..162261
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130103.1NP_001123575.1  collagen alpha-1(XIII) chain isoform 1

    See identical proteins and their annotated locations for NP_001123575.1

    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
    ENSP00000381949.3, OTTHUMP00000019731, ENST00000398978.7, OTTHUMT00000048468
    Conserved Domains (1) summary
    pfam01391
    Location:643702
    Collagen; Collagen triple helix repeat (20 copies)
  2. NM_001320951.1NP_001307880.1  collagen alpha-1(XIII) chain isoform 22

    Status: REVIEWED

    Source sequence(s)
    AC024601, AC025426, AI741175, AL138925, BY796799, HY104799
    Conserved Domains (1) summary
    pfam01391
    Location:588645
    Collagen; Collagen triple helix repeat (20 copies)
  3. NM_080798.3NP_542988.3  collagen alpha-1(XIII) chain isoform 21

    See identical proteins and their annotated locations for NP_542988.3

    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
    UniProtKB/Swiss-Prot
    Q5TAT6
    Related
    ENSP00000428057.1, OTTHUMP00000227634, ENST00000520267.5, OTTHUMT00000380458
    Conserved Domains (1) summary
    pfam01391
    Location:571630
    Collagen; Collagen triple helix repeat (20 copies)
  4. NM_080800.3NP_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
    ENSP00000428342.1, OTTHUMP00000227636, ENST00000522165.5, OTTHUMT00000380460
    Conserved Domains (1) summary
    pfam01391
    Location:594651
    Collagen; Collagen triple helix repeat (20 copies)
  5. NM_080801.3NP_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
    ENSP00000346553.3, OTTHUMP00000019732, ENST00000354547.7, OTTHUMT00000048469
    Conserved Domains (1) summary
    pfam01391
    Location:621680
    Collagen; Collagen triple helix repeat (20 copies)
  6. NM_080802.3NP_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
    ENSP00000430061.1, OTTHUMP00000227635, ENST00000517713.5, OTTHUMT00000380459
    Conserved Domains (1) summary
    pfam01391
    Location:576633
    Collagen; Collagen triple helix repeat (20 copies)
  7. NM_080805.3NP_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/Swiss-Prot
    Q5TAT6
    Related
    ENSP00000430173.1, OTTHUMP00000227637, ENST00000520133.5, OTTHUMT00000380461
    Conserved Domains (1) summary
    pfam01391
    Location:547603
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p12 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    69801835..69959148
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011539292.3XP_011537594.1  collagen alpha-1(XIII) chain isoform X1

    Related
    ENSP00000496051.1, ENST00000645393.1
    Conserved Domains (1) summary
    pfam01391
    Location:654713
    Collagen; Collagen triple helix repeat (20 copies)
  2. XM_017015676.2XP_016871165.1  collagen alpha-1(XIII) chain isoform X2

  3. XM_017015677.2XP_016871166.1  collagen alpha-1(XIII) chain isoform X4

  4. XM_011539293.3XP_011537595.1  collagen alpha-1(XIII) chain isoform X3

    Conserved Domains (1) summary
    pfam01391
    Location:639698
    Collagen; Collagen triple helix repeat (20 copies)
  5. XM_024447815.1XP_024303583.1  collagen alpha-1(XIII) chain isoform X5

    Conserved Domains (1) summary
    pfam01391
    Location:331388
    Collagen; Collagen triple helix repeat (20 copies)
  6. XM_011539295.3XP_011537597.1  collagen alpha-1(XIII) chain isoform X7

    Conserved Domains (1) summary
    pfam01391
    Location:609666
    Collagen; Collagen triple helix repeat (20 copies)
  7. XM_017015679.2XP_016871168.1  collagen alpha-1(XIII) chain isoform X8

  8. XM_017015687.2XP_016871176.1  collagen alpha-1(XIII) chain isoform X16

  9. XM_017015680.2XP_016871169.1  collagen alpha-1(XIII) chain isoform X9

  10. XM_017015682.2XP_016871171.1  collagen alpha-1(XIII) chain isoform X11

  11. XM_011539294.3XP_011537596.1  collagen alpha-1(XIII) chain isoform X6

    Conserved Domains (1) summary
    pfam01391
    Location:633692
    Collagen; Collagen triple helix repeat (20 copies)
  12. XM_017015681.2XP_016871170.1  collagen alpha-1(XIII) chain isoform X10

  13. XM_017015689.2XP_016871178.1  collagen alpha-1(XIII) chain isoform X18

  14. XM_017015691.2XP_016871180.1  collagen alpha-1(XIII) chain isoform X20

  15. XM_017015685.2XP_016871174.1  collagen alpha-1(XIII) chain isoform X14

  16. XM_017015686.2XP_016871175.1  collagen alpha-1(XIII) chain isoform X15

  17. XM_017015693.2XP_016871182.1  collagen alpha-1(XIII) chain isoform X22

  18. XM_017015688.2XP_016871177.1  collagen alpha-1(XIII) chain isoform X17

  19. XM_017015684.2XP_016871173.1  collagen alpha-1(XIII) chain isoform X13

  20. XM_017015683.2XP_016871172.1  collagen alpha-1(XIII) chain isoform X12

  21. XM_017015692.2XP_016871181.1  collagen alpha-1(XIII) chain isoform X21

  22. XM_024447816.1XP_024303584.1  collagen alpha-1(XIII) chain isoform X23

    Conserved Domains (1) summary
    pfam01391
    Location:547604
    Collagen; Collagen triple helix repeat (20 copies)
  23. XM_024447817.1XP_024303585.1  collagen alpha-1(XIII) chain isoform X25

    Conserved Domains (1) summary
    pfam01391
    Location:494552
    Collagen; Collagen triple helix repeat (20 copies)
  24. XM_017015690.2XP_016871179.1  collagen alpha-1(XIII) chain isoform X19

  25. XM_024447818.1XP_024303586.1  collagen alpha-1(XIII) chain isoform X26

    Conserved Domains (1) summary
    pfam01391
    Location:556612
    Collagen; Collagen triple helix repeat (20 copies)
  26. XM_017015694.2XP_016871183.1  collagen alpha-1(XIII) chain isoform X24

  27. XM_017015695.2XP_016871184.1  collagen alpha-1(XIII) chain isoform X27

  28. XM_017015697.2XP_016871186.1  collagen alpha-1(XIII) chain isoform X28

RNA

  1. XR_001747024.2 RNA Sequence

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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