Human Gene COL5A1 (ENST00000371817.8_7) from GENCODE V47lift37
  Description: collagen type V alpha 1 chain, transcript variant 1 (from RefSeq NM_000093.5)
Gencode Transcript: ENST00000371817.8_7
Gencode Gene: ENSG00000130635.17_15
Transcript (Including UTRs)
   Position: hg19 chr9:137,533,649-137,736,689 Size: 203,041 Total Exon Count: 66 Strand: +
Coding Region
   Position: hg19 chr9:137,534,034-137,734,149 Size: 200,116 Coding Exon Count: 66 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:137,533,649-137,736,689)mRNA (may differ from genome)Protein (1838 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CO5A1_HUMAN
DESCRIPTION: RecName: Full=Collagen alpha-1(V) chain; Flags: Precursor;
FUNCTION: Type V collagen is a member of group I collagen (fibrillar forming collagen). It is a minor connective tissue component of nearly ubiquitous distribution. Type V collagen binds to DNA, heparan sulfate, thrombospondin, heparin, and insulin.
SUBUNIT: Trimers of two alpha 1(V) and one alpha 2(V) chains in most tissues and trimers of one alpha 1(V), one alpha 2(V), and one alpha 3(V) chains in placenta. Interacts with CSPG4.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix (By similarity).
DOMAIN: The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity).
PTM: Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
PTM: Sulfated on 40% of tyrosines.
DISEASE: Defects in COL5A1 are a cause of Ehlers-Danlos syndrome type 1 (EDS1) [MIM:130000]; also known as Ehlers-Danlos syndrome gravis or severe classic type Ehlers-Danlos syndrome. EDS is a connective tissue disorder characterized by hyperextensible skin, atrophic cutaneous scars due to tissue fragility and joint hyperlaxity. EDS1 is the severe form of classic Ehlers-Danlos syndrome.
DISEASE: Defects in COL5A1 are a cause of Ehlers-Danlos syndrome type 2 (EDS2) [MIM:130010]; also known as Ehlers-Danlos syndrome mitis or mild classic type Ehlers Danlos syndrome.
SIMILARITY: Belongs to the fibrillar collagen family.
SIMILARITY: Contains 1 fibrillar collagen NC1 domain.
SIMILARITY: Contains 1 laminin G-like domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL5A1";

-  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: COL5A1
Diseases sorted by gene-association score: ehlers-danlos syndrome, classic type* (894), ehlers-danlos syndrome type ii* (869), type i ehlers-danlos syndrome* (450), ehlers-danlos syndrome, type iv* (247), ehlers-danlos syndrome, classic type, col5a1-related* (200), ehlers-danlos syndrome (42), nail-patella syndrome (25), hypomelanosis of ito (16), tendinopathy (13), autoimmune lymphoproliferative syndrome, type iib (11), hypermobility syndrome (11), duodenal atresia (10), brittle cornea syndrome 2 (10), tuberous sclerosis-1 (9), corneal dystrophy, subepithelial mucinous (7), hereditary hemorrhagic telangiectasia (7), connective tissue disease (6), carpal tunnel syndrome, familial (6), nerve compression syndrome (6), collagen disease (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 86.06 RPKM in Cervix - Ectocervix
Total median expression: 804.29 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 -200.70385-0.521 Picture PostScript Text
3' UTR -769.702540-0.303 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
IPR008160 - Collagen
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR000885 - Fib_collagen_C
IPR001791 - Laminin_G

Pfam Domains:
PF01391 - Collagen triple helix repeat (20 copies)
PF01410 - Fibrillar collagen C-terminal domain

SCOP Domains:
49899 - Concanavalin A-like lectins/glucanases
56496 - Fibrinogen C-terminal domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1A89 - Model 1A9A - Model


ModBase Predicted Comparative 3D Structure on P20908
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005178 integrin binding
GO:0005201 extracellular matrix structural constituent
GO:0005515 protein binding
GO:0008201 heparin binding
GO:0043394 proteoglycan binding
GO:0046872 metal ion binding
GO:0048407 platelet-derived growth factor binding

Biological Process:
GO:0001568 blood vessel development
GO:0003007 heart morphogenesis
GO:0007155 cell adhesion
GO:0016477 cell migration
GO:0030198 extracellular matrix organization
GO:0030199 collagen fibril organization
GO:0032964 collagen biosynthetic process
GO:0035313 wound healing, spreading of epidermal cells
GO:0035989 tendon development
GO:0043588 skin development
GO:0045112 integrin biosynthetic process
GO:0048592 eye morphogenesis
GO:0051128 regulation of cellular component organization
GO:0097435 supramolecular fiber organization
GO:1903225 negative regulation of endodermal cell differentiation

Cellular Component:
GO:0005576 extracellular region
GO:0005581 collagen trimer
GO:0005588 collagen type V trimer
GO:0005604 basement membrane
GO:0005788 endoplasmic reticulum lumen
GO:0031012 extracellular matrix


-  Descriptions from all associated GenBank mRNAs
  LF205606 - JP 2014500723-A/13109: Polycomb-Associated Non-Coding RNAs.
AB371583 - Homo sapiens COL5A1 mRNA for collagen type V alpha 1, complete cds, clone: HP06504-ARe79B07.
M76729 - Human pro-alpha-1 (V) collagen mRNA, complete cds.
D90279 - Homo sapiens mRNA for collagen alpha 1(V) chain, complete cds.
E07265 - cDNA encoding human collagen V.
AB209864 - Homo sapiens mRNA for Pro-alpha-1 type V collagen variant protein.
MA441183 - JP 2018138019-A/13109: Polycomb-Associated Non-Coding RNAs.
LF211800 - JP 2014500723-A/19303: Polycomb-Associated Non-Coding RNAs.
JD159563 - Sequence 140587 from Patent EP1572962.
LF346471 - JP 2014500723-A/153974: Polycomb-Associated Non-Coding RNAs.
JD215991 - Sequence 197015 from Patent EP1572962.
JD440594 - Sequence 421618 from Patent EP1572962.
JD340954 - Sequence 321978 from Patent EP1572962.
JD206452 - Sequence 187476 from Patent EP1572962.
JD340120 - Sequence 321144 from Patent EP1572962.
JD340138 - Sequence 321162 from Patent EP1572962.
AK057231 - Homo sapiens cDNA FLJ32669 fis, clone TESTI1000125.
LF346479 - JP 2014500723-A/153982: Polycomb-Associated Non-Coding RNAs.
LF346480 - JP 2014500723-A/153983: Polycomb-Associated Non-Coding RNAs.
LF346481 - JP 2014500723-A/153984: Polycomb-Associated Non-Coding RNAs.
LF346485 - JP 2014500723-A/153988: Polycomb-Associated Non-Coding RNAs.
LF346486 - JP 2014500723-A/153989: Polycomb-Associated Non-Coding RNAs.
LF346487 - JP 2014500723-A/153990: Polycomb-Associated Non-Coding RNAs.
LF346488 - JP 2014500723-A/153991: Polycomb-Associated Non-Coding RNAs.
LF346489 - JP 2014500723-A/153992: Polycomb-Associated Non-Coding RNAs.
LF346490 - JP 2014500723-A/153993: Polycomb-Associated Non-Coding RNAs.
LF346491 - JP 2014500723-A/153994: Polycomb-Associated Non-Coding RNAs.
LF346492 - JP 2014500723-A/153995: Polycomb-Associated Non-Coding RNAs.
MA582048 - JP 2018138019-A/153974: Polycomb-Associated Non-Coding RNAs.
MA582056 - JP 2018138019-A/153982: Polycomb-Associated Non-Coding RNAs.
MA582057 - JP 2018138019-A/153983: Polycomb-Associated Non-Coding RNAs.
MA582058 - JP 2018138019-A/153984: Polycomb-Associated Non-Coding RNAs.
MA582062 - JP 2018138019-A/153988: Polycomb-Associated Non-Coding RNAs.
MA582063 - JP 2018138019-A/153989: Polycomb-Associated Non-Coding RNAs.
MA582064 - JP 2018138019-A/153990: Polycomb-Associated Non-Coding RNAs.
MA582065 - JP 2018138019-A/153991: Polycomb-Associated Non-Coding RNAs.
MA582066 - JP 2018138019-A/153992: Polycomb-Associated Non-Coding RNAs.
MA582067 - JP 2018138019-A/153993: Polycomb-Associated Non-Coding RNAs.
MA582068 - JP 2018138019-A/153994: Polycomb-Associated Non-Coding RNAs.
MA582069 - JP 2018138019-A/153995: Polycomb-Associated Non-Coding RNAs.
MA447377 - JP 2018138019-A/19303: Polycomb-Associated Non-Coding RNAs.
LF346496 - JP 2014500723-A/153999: Polycomb-Associated Non-Coding RNAs.
LF346497 - JP 2014500723-A/154000: Polycomb-Associated Non-Coding RNAs.
LF346498 - JP 2014500723-A/154001: Polycomb-Associated Non-Coding RNAs.
LF346499 - JP 2014500723-A/154002: Polycomb-Associated Non-Coding RNAs.
LF346501 - JP 2014500723-A/154004: Polycomb-Associated Non-Coding RNAs.
LF346502 - JP 2014500723-A/154005: Polycomb-Associated Non-Coding RNAs.
LF346503 - JP 2014500723-A/154006: Polycomb-Associated Non-Coding RNAs.
LF346504 - JP 2014500723-A/154007: Polycomb-Associated Non-Coding RNAs.
LF346505 - JP 2014500723-A/154008: Polycomb-Associated Non-Coding RNAs.
LF346506 - JP 2014500723-A/154009: Polycomb-Associated Non-Coding RNAs.
LF346508 - JP 2014500723-A/154011: Polycomb-Associated Non-Coding RNAs.
LF346509 - JP 2014500723-A/154012: Polycomb-Associated Non-Coding RNAs.
LF346510 - JP 2014500723-A/154013: Polycomb-Associated Non-Coding RNAs.
LF346511 - JP 2014500723-A/154014: Polycomb-Associated Non-Coding RNAs.
LF346512 - JP 2014500723-A/154015: Polycomb-Associated Non-Coding RNAs.
LF346513 - JP 2014500723-A/154016: Polycomb-Associated Non-Coding RNAs.
LF346514 - JP 2014500723-A/154017: Polycomb-Associated Non-Coding RNAs.
LF346515 - JP 2014500723-A/154018: Polycomb-Associated Non-Coding RNAs.
LF346516 - JP 2014500723-A/154019: Polycomb-Associated Non-Coding RNAs.
LF346517 - JP 2014500723-A/154020: Polycomb-Associated Non-Coding RNAs.
LF346518 - JP 2014500723-A/154021: Polycomb-Associated Non-Coding RNAs.
BC008760 - Homo sapiens collagen, type V, alpha 1, mRNA (cDNA clone IMAGE:3343931), complete cds.
LF346519 - JP 2014500723-A/154022: Polycomb-Associated Non-Coding RNAs.
LF346522 - JP 2014500723-A/154025: Polycomb-Associated Non-Coding RNAs.
LF346523 - JP 2014500723-A/154026: Polycomb-Associated Non-Coding RNAs.
LF346524 - JP 2014500723-A/154027: Polycomb-Associated Non-Coding RNAs.
LF346525 - JP 2014500723-A/154028: Polycomb-Associated Non-Coding RNAs.
LF205607 - JP 2014500723-A/13110: Polycomb-Associated Non-Coding RNAs.
LF346528 - JP 2014500723-A/154031: Polycomb-Associated Non-Coding RNAs.
LF346529 - JP 2014500723-A/154032: Polycomb-Associated Non-Coding RNAs.
AK127662 - Homo sapiens cDNA FLJ45760 fis, clone MESTC1000147, highly similar to Collagen alpha 1(V) chain precursor.
LF346530 - JP 2014500723-A/154033: Polycomb-Associated Non-Coding RNAs.
LF346532 - JP 2014500723-A/154035: Polycomb-Associated Non-Coding RNAs.
BC032405 - Homo sapiens collagen, type V, alpha 1, mRNA (cDNA clone IMAGE:5209850), with apparent retained intron.
JD544081 - Sequence 525105 from Patent EP1572962.
LF346533 - JP 2014500723-A/154036: Polycomb-Associated Non-Coding RNAs.
JD164655 - Sequence 145679 from Patent EP1572962.
JD116296 - Sequence 97320 from Patent EP1572962.
JD104646 - Sequence 85670 from Patent EP1572962.
JD214632 - Sequence 195656 from Patent EP1572962.
LF346534 - JP 2014500723-A/154037: Polycomb-Associated Non-Coding RNAs.
JD321339 - Sequence 302363 from Patent EP1572962.
JD104502 - Sequence 85526 from Patent EP1572962.
LF346535 - JP 2014500723-A/154038: Polycomb-Associated Non-Coding RNAs.
LF346536 - JP 2014500723-A/154039: Polycomb-Associated Non-Coding RNAs.
LF346537 - JP 2014500723-A/154040: Polycomb-Associated Non-Coding RNAs.
LF346538 - JP 2014500723-A/154041: Polycomb-Associated Non-Coding RNAs.
AK122763 - Homo sapiens cDNA FLJ16299 fis, clone PLACE6017578.
LF346539 - JP 2014500723-A/154042: Polycomb-Associated Non-Coding RNAs.
LF346540 - JP 2014500723-A/154043: Polycomb-Associated Non-Coding RNAs.
LF346541 - JP 2014500723-A/154044: Polycomb-Associated Non-Coding RNAs.
LF346542 - JP 2014500723-A/154045: Polycomb-Associated Non-Coding RNAs.
LF346543 - JP 2014500723-A/154046: Polycomb-Associated Non-Coding RNAs.
LF346544 - JP 2014500723-A/154047: Polycomb-Associated Non-Coding RNAs.
LF346545 - JP 2014500723-A/154048: Polycomb-Associated Non-Coding RNAs.
LF346546 - JP 2014500723-A/154049: Polycomb-Associated Non-Coding RNAs.
MA582073 - JP 2018138019-A/153999: Polycomb-Associated Non-Coding RNAs.
MA582074 - JP 2018138019-A/154000: Polycomb-Associated Non-Coding RNAs.
MA582075 - JP 2018138019-A/154001: Polycomb-Associated Non-Coding RNAs.
MA582076 - JP 2018138019-A/154002: Polycomb-Associated Non-Coding RNAs.
MA582078 - JP 2018138019-A/154004: Polycomb-Associated Non-Coding RNAs.
MA582079 - JP 2018138019-A/154005: Polycomb-Associated Non-Coding RNAs.
MA582080 - JP 2018138019-A/154006: Polycomb-Associated Non-Coding RNAs.
MA582081 - JP 2018138019-A/154007: Polycomb-Associated Non-Coding RNAs.
MA582082 - JP 2018138019-A/154008: Polycomb-Associated Non-Coding RNAs.
MA582083 - JP 2018138019-A/154009: Polycomb-Associated Non-Coding RNAs.
MA582085 - JP 2018138019-A/154011: Polycomb-Associated Non-Coding RNAs.
MA582086 - JP 2018138019-A/154012: Polycomb-Associated Non-Coding RNAs.
MA582087 - JP 2018138019-A/154013: Polycomb-Associated Non-Coding RNAs.
MA582088 - JP 2018138019-A/154014: Polycomb-Associated Non-Coding RNAs.
MA582089 - JP 2018138019-A/154015: Polycomb-Associated Non-Coding RNAs.
MA582090 - JP 2018138019-A/154016: Polycomb-Associated Non-Coding RNAs.
MA582091 - JP 2018138019-A/154017: Polycomb-Associated Non-Coding RNAs.
MA582092 - JP 2018138019-A/154018: Polycomb-Associated Non-Coding RNAs.
MA582093 - JP 2018138019-A/154019: Polycomb-Associated Non-Coding RNAs.
MA582094 - JP 2018138019-A/154020: Polycomb-Associated Non-Coding RNAs.
MA582095 - JP 2018138019-A/154021: Polycomb-Associated Non-Coding RNAs.
MA582096 - JP 2018138019-A/154022: Polycomb-Associated Non-Coding RNAs.
MA582099 - JP 2018138019-A/154025: Polycomb-Associated Non-Coding RNAs.
MA582100 - JP 2018138019-A/154026: Polycomb-Associated Non-Coding RNAs.
MA582101 - JP 2018138019-A/154027: Polycomb-Associated Non-Coding RNAs.
MA582102 - JP 2018138019-A/154028: Polycomb-Associated Non-Coding RNAs.
MA582105 - JP 2018138019-A/154031: Polycomb-Associated Non-Coding RNAs.
MA582106 - JP 2018138019-A/154032: Polycomb-Associated Non-Coding RNAs.
MA582107 - JP 2018138019-A/154033: Polycomb-Associated Non-Coding RNAs.
MA582109 - JP 2018138019-A/154035: Polycomb-Associated Non-Coding RNAs.
MA582110 - JP 2018138019-A/154036: Polycomb-Associated Non-Coding RNAs.
MA582111 - JP 2018138019-A/154037: Polycomb-Associated Non-Coding RNAs.
MA582112 - JP 2018138019-A/154038: Polycomb-Associated Non-Coding RNAs.
MA582113 - JP 2018138019-A/154039: Polycomb-Associated Non-Coding RNAs.
MA582114 - JP 2018138019-A/154040: Polycomb-Associated Non-Coding RNAs.
MA582115 - JP 2018138019-A/154041: Polycomb-Associated Non-Coding RNAs.
MA582116 - JP 2018138019-A/154042: Polycomb-Associated Non-Coding RNAs.
MA582117 - JP 2018138019-A/154043: Polycomb-Associated Non-Coding RNAs.
MA582118 - JP 2018138019-A/154044: Polycomb-Associated Non-Coding RNAs.
MA582119 - JP 2018138019-A/154045: Polycomb-Associated Non-Coding RNAs.
MA582120 - JP 2018138019-A/154046: Polycomb-Associated Non-Coding RNAs.
MA582121 - JP 2018138019-A/154047: Polycomb-Associated Non-Coding RNAs.
MA582122 - JP 2018138019-A/154048: Polycomb-Associated Non-Coding RNAs.
MA582123 - JP 2018138019-A/154049: Polycomb-Associated Non-Coding RNAs.
MA441184 - JP 2018138019-A/13110: Polycomb-Associated Non-Coding RNAs.

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

Protein P20908 (Reactome details) participates in the following event(s):

R-HSA-8944223 Association of procollagen type V
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-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-2002440 Removal of fibrillar collagen C-propeptides
R-HSA-2022073 Procollagen triple helix formation
R-HSA-2002428 Removal of fibrillar collagen N-propeptides
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: A0A087WXW9, CO5A1_HUMAN, ENST00000371817.1, ENST00000371817.2, ENST00000371817.3, ENST00000371817.4, ENST00000371817.5, ENST00000371817.6, ENST00000371817.7, NM_000093, P20908, Q15094, Q5SUX4, uc318jkr.1, uc318jkr.2
UCSC ID: ENST00000371817.8_7
RefSeq Accession: NM_000093.5
Protein: P20908 (aka CO5A1_HUMAN or CA15_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene COL5A1:
eds (Classic Ehlers-Danlos Syndrome)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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