Human Gene COL8A1 (ENST00000273342.8) from GENCODE V44
  Description: Macromolecular component of the subendothelium. Major component of the Descemet's membrane (basement membrane) of corneal endothelial cells. Also component of the endothelia of blood vessels. Necessary for migration and proliferation of vascular smooth muscle cells and thus, has a potential role in the maintenance of vessel wall integrity and structure, in particular in atherogenesis. (from UniProt P27658)
RefSeq Summary (NM_020351): This gene encodes one of the two alpha chains of type VIII collagen. The gene product is a short chain collagen and a major component of the basement membrane of the corneal endothelium. The type VIII collagen fibril can be either a homo- or a heterotrimer. Alternatively spliced transcript variants encoding the same protein have been observed. [provided by RefSeq, Dec 2011].
Gencode Transcript: ENST00000273342.8
Gencode Gene: ENSG00000144810.16
Transcript (Including UTRs)
   Position: hg38 chr3:99,638,596-99,796,733 Size: 158,138 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr3:99,790,683-99,796,136 Size: 5,454 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:99,638,596-99,796,733)mRNA (may differ from genome)Protein (744 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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HPRDLynxMalacardsMGIneXtProtPubMed
ReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CO8A1_HUMAN
DESCRIPTION: RecName: Full=Collagen alpha-1(VIII) chain; AltName: Full=Endothelial collagen; Contains: RecName: Full=Vastatin; Flags: Precursor;
FUNCTION: Macromolecular component of the subendothelium. Major component of the Descemet's membrane (basement membrane) of corneal endothelial cells. Also component of the endothelia of blood vessels. Necessary for migration and proliferation of vascular smooth muscle cells and thus, has a potential role in the maintenance of vessel wall integrity and structure, in particular in atherogenesis.
FUNCTION: Vastatin, the C-terminal fragment comprising the NC1 domain, inhibits aortic endothelial cell proliferation and causes cell apoptosis.
SUBUNIT: Homotrimers, or heterotrimers in association with alpha 2(VIII) type collagens. Four homotrimers can form a tetrhedron stabilized by central interacting C-terminal NC1 trimers.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix, basement membrane.
TISSUE SPECIFICITY: Expressed primarily in the subendothelium of large blood vessels. Also expressed in arterioles and venules in muscle, heart, kidney, spleen, umbilical cord, liver and lung and is also found in connective tissue layers around hair follicles, around nerve bundles in muscle, in the dura of the optic nerve, in cornea and sclera, and in the perichondrium of cartilaginous tissues. In the kidney, expressed in mesangial cells, glomerular endothelial cells, and tubular epithelial cells. Also expressed in mast cells, and in astrocytes during the repair process. Expressed in Descemet's membrane. Specifically expressed in peritoneal fibroblasts and mesothelial cells.
INDUCTION: Up-regulated during vascular injury, in atherosclerosis and in diabetes.
PTM: Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
PTM: Proteolytically cleaved by neutrophil elastase, in vitro. Proteolytic processing produces the C-terminal NC1 domain fragment, vastatin.
MISCELLANEOUS: Four consecutive Gly-Pro-Pro triplets are present at the C-terminus of the triple-helical region. These may provide the high thermal stability of this region.
SIMILARITY: Contains 1 C1q domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: COL8A1
Diseases sorted by gene-association score: corneal dystrophy (6), macular degeneration, age-related, 1 (2), fuchs' endothelial dystrophy (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 83.37 RPKM in Artery - Tibial
Total median expression: 408.73 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -57.60197-0.292 Picture PostScript Text
3' UTR -120.90597-0.203 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001073 - C1q
IPR008160 - Collagen
IPR008983 - Tumour_necrosis_fac-like

Pfam Domains:
PF00386 - C1q domain
PF01391 - Collagen triple helix repeat (20 copies)

ModBase Predicted Comparative 3D Structure on P27658
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0001525 angiogenesis
GO:0007155 cell adhesion
GO:0010811 positive regulation of cell-substrate adhesion
GO:0030198 extracellular matrix organization
GO:0035987 endodermal cell differentiation
GO:0048593 camera-type eye morphogenesis
GO:0050673 epithelial cell proliferation

Cellular Component:
GO:0005576 extracellular region
GO:0005581 collagen trimer
GO:0005591 collagen type VIII trimer
GO:0005604 basement membrane
GO:0005788 endoplasmic reticulum lumen
GO:0031012 extracellular matrix


-  Descriptions from all associated GenBank mRNAs
  BC013581 - Homo sapiens collagen, type VIII, alpha 1, mRNA (cDNA clone MGC:9568 IMAGE:3875911), complete cds.
AY550974 - Homo sapiens cell proliferation-inducing protein 41 mRNA, complete cds.
AK311449 - Homo sapiens cDNA, FLJ18491.
AF170702 - Homo sapiens smooth muscle cell-expressed and macrophage conditioned medium-induced protein smag-64 mRNA, complete cds.
JD071606 - Sequence 52630 from Patent EP1572962.
JD198936 - Sequence 179960 from Patent EP1572962.
JD043488 - Sequence 24512 from Patent EP1572962.
JD190680 - Sequence 171704 from Patent EP1572962.
CU680628 - Synthetic construct Homo sapiens gateway clone IMAGE:100017479 5' read COL8A1 mRNA.
KJ890948 - Synthetic construct Homo sapiens clone ccsbBroadEn_00342 COL8A1 gene, encodes complete protein.
AB384777 - Synthetic construct DNA, clone: pF1KB3288, Homo sapiens COL8A1 gene for collagen alpha-1(VIII) chain precursor, complete cds, without stop codon, in Flexi system.
DQ893873 - Synthetic construct Homo sapiens clone IMAGE:100008333; FLH165161.01L; RZPDo839G09157D collagen, type VIII, alpha 1 (COL8A1) gene, encodes complete protein.
BT009917 - Homo sapiens collagen, type VIII, alpha 1 mRNA, complete cds.
X57527 - Human COL8A1 mRNA for alpha 1(VIII) collagen.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P27658 (Reactome details) participates in the following event(s):

R-HSA-8944218 Association of procollagen type VIII
R-HSA-2002460 P4HB binds Collagen chains
R-HSA-8948230 P3HB binds 4-Hyp-collagen propeptides
R-HSA-1650808 Prolyl 4-hydroxylase converts collagen prolines to 4-hydroxyprolines
R-HSA-1980233 Collagen prolyl 3-hydroxylase converts 4-Hyp collagen to 3,4-Hyp collagen
R-HSA-8948219 PLOD3 binds Lysyl hydroxylated collagen propeptides
R-HSA-8948228 COLGALT1,COLGALT2 bind Lysyl hydroxylated collagen propeptides
R-HSA-2022073 Procollagen triple helix formation
R-HSA-1981104 Procollagen lysyl hydroxylases convert collagen lysines to 5-hydroxylysines
R-HSA-1981120 Galactosylation of collagen propeptide hydroxylysines by procollagen galactosyltransferases 1, 2.
R-HSA-1981128 Galactosylation of collagen propeptide hydroxylysines by PLOD3
R-HSA-1981157 Glucosylation of collagen propeptide hydroxylysines
R-HSA-2213207 Formation of collagen networks
R-HSA-8948216 Collagen chain trimerization
R-HSA-1650814 Collagen biosynthesis and modifying enzymes
R-HSA-1474290 Collagen formation
R-HSA-1474244 Extracellular matrix organization
R-HSA-2022090 Assembly of collagen fibrils and other multimeric structures

-  Other Names for This Gene
  Alternate Gene Symbols: AY550974, C3orf7, CO8A1_HUMAN, D3DN42, ENST00000273342.1, ENST00000273342.2, ENST00000273342.3, ENST00000273342.4, ENST00000273342.5, ENST00000273342.6, ENST00000273342.7, P27658, Q53XI6, Q96D07, uc003dth.1, uc003dth.2
UCSC ID: ENST00000273342.8
RefSeq Accession: NM_020351
Protein: P27658 (aka CO8A1_HUMAN or CA18_HUMAN)
CCDS: CCDS2934.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.