Human Gene COL18A1 (uc002zhg.3)
  Description: Homo sapiens collagen, type XVIII, alpha 1 (COL18A1), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr21:46,825,097-46,933,634 Size: 108,538 Total Exon Count: 42 Strand: +
Coding Region
   Position: hg19 chr21:46,825,146-46,932,312 Size: 107,167 Coding Exon Count: 42 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:46,825,097-46,933,634)mRNA (may differ from genome)Protein (1336 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMalacardsMGIPubMed
TreefamUniProtKBWikipedia

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): COL18A1
CDC HuGE Published Literature: COL18A1
Positive Disease Associations: breast cancer , Diabetes Mellitus, Type 2|Obesity , endometriosis , Socioeconomic Factors
Related Studies:
  1. breast cancer
    Lourenco, G. J. et al. 2006, A high risk of occurrence of sporadic breast cancer in individuals with the 104NN polymorphism of the COL18A1 gene, Breast Cancer Res Treat 2006. [PubMed 16807676]
  2. breast cancer
    Balasubramanian, S. P. et al. 2007, Endostatin gene variation and protein levels in breast cancer susceptibility and severity, BMC Cancer 2007 7(1) 107. [PubMed 17587451]
    The Endostatin 4349A allele is associated with$$$ invasive breast cancer.
  3. Diabetes Mellitus, Type 2|Obesity
    Flavia I V Errera , et al. An Acad Bras Cienc. 2008 80(1):167-77, COL18A1 is highly expressed during human adipocyte differentiation and the SNP c.1136C > T in its "frizzled" motif is associated with obesity in diabetes type 2 patients., An Acad Bras Cienc. 2008 80(1):167-77. [PubMed 18345385]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: COL18A1
Diseases sorted by gene-association score: knobloch syndrome, type 1* (1368), knobloch syndrome (62), occipital encephalocele (27), encephalocele (19), pigment dispersion syndrome (16), alveolar capillary dysplasia with misalignment of pulmonary veins (13), vitreoretinal degeneration (11), alveolar capillary dysplasia (9), myopia (7), retinal detachment (6), peliosis hepatis (5), pleuropneumonia (5), miles-carpenter syndrome (4), connective tissue disease (2), macular degeneration, age-related, 1 (1)
* = Manually curated disease association

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

+  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: 217.01 RPKM in Artery - Tibial
Total median expression: 2191.47 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 -14.0049-0.286 Picture PostScript Text
3' UTR -563.421322-0.426 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
IPR016186 - C-type_lectin-like
IPR016187 - C-type_lectin_fold
IPR008160 - Collagen
IPR010515 - Collagenase_NC10/endostatin
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR001791 - Laminin_G

Pfam Domains:
PF01391 - Collagen triple helix repeat (20 copies)
PF06482 - Collagenase NC10 and Endostatin
PF13385 - Concanavalin A-like lectin/glucanases superfamily

SCOP Domains:
49899 - Concanavalin A-like lectins/glucanases
56436 - C-type lectin-like

ModBase Predicted Comparative 3D Structure on D3DSM4
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005198 structural molecule activity

Biological Process:
GO:0007155 cell adhesion

Cellular Component:
GO:0005581 collagen trimer
GO:0031012 extracellular matrix


-  Descriptions from all associated GenBank mRNAs
  AK130835 - Homo sapiens cDNA FLJ27325 fis, clone TMS08226, highly similar to Collagen alpha 1(XVIII) chain precursor.
AF018082 - Homo sapiens type XVIII collagen (COL18A1) mRNA, alternatively spliced, short form, complete cds.
BC063833 - Homo sapiens collagen, type XVIII, alpha 1, mRNA (cDNA clone MGC:74745 IMAGE:6181818), complete cds.
AB590554 - Synthetic construct DNA, clone: pFN21AB7280, Homo sapiens COL18A1 gene for collagen, type XVIII, alpha 1, without stop codon, in Flexi system.
AF018081 - Homo sapiens type XVIII collagen (COL18A1) mRNA, alternatively spliced, long form, complete cds.
BC033715 - Homo sapiens, Similar to collagen, type XVIII, alpha 1, clone IMAGE:4425380, mRNA, partial cds.
L22548 - Human collagen type XVIII alpha 1 (COL18A1) mRNA, partial cds.
LF208796 - JP 2014500723-A/16299: Polycomb-Associated Non-Coding RNAs.
MA444373 - JP 2018138019-A/16299: Polycomb-Associated Non-Coding RNAs.
LF322972 - JP 2014500723-A/130475: Polycomb-Associated Non-Coding RNAs.
LF322970 - JP 2014500723-A/130473: Polycomb-Associated Non-Coding RNAs.
LF322969 - JP 2014500723-A/130472: Polycomb-Associated Non-Coding RNAs.
LF322968 - JP 2014500723-A/130471: Polycomb-Associated Non-Coding RNAs.
AK098216 - Homo sapiens cDNA FLJ40897 fis, clone UTERU2002964, highly similar to Homo sapiens type XVIII collagen (COL18A1) mRNA.
LF322967 - JP 2014500723-A/130470: Polycomb-Associated Non-Coding RNAs.
LF322966 - JP 2014500723-A/130469: Polycomb-Associated Non-Coding RNAs.
AF416592 - Homo sapiens collagen XVIII mRNA, partial cds.
AF184060 - Homo sapiens type XVIII collagen mRNA, complete cds.
AF282883 - Homo sapiens multi-functional protein MFP mRNA, complete cds.
LF322965 - JP 2014500723-A/130468: Polycomb-Associated Non-Coding RNAs.
LF322964 - JP 2014500723-A/130467: Polycomb-Associated Non-Coding RNAs.
AF333246 - Homo sapiens endostatin-like mRNA, partial sequence.
AF333247 - Homo sapiens endostatin variant mRNA, partial cds.
LF322962 - JP 2014500723-A/130465: Polycomb-Associated Non-Coding RNAs.
LF322961 - JP 2014500723-A/130464: Polycomb-Associated Non-Coding RNAs.
JD476237 - Sequence 457261 from Patent EP1572962.
LF322960 - JP 2014500723-A/130463: Polycomb-Associated Non-Coding RNAs.
JD521207 - Sequence 502231 from Patent EP1572962.
JD299138 - Sequence 280162 from Patent EP1572962.
JD053129 - Sequence 34153 from Patent EP1572962.
JD113251 - Sequence 94275 from Patent EP1572962.
JD399517 - Sequence 380541 from Patent EP1572962.
JD380362 - Sequence 361386 from Patent EP1572962.
JD487185 - Sequence 468209 from Patent EP1572962.
JD510226 - Sequence 491250 from Patent EP1572962.
JD151701 - Sequence 132725 from Patent EP1572962.
JD208023 - Sequence 189047 from Patent EP1572962.
JD214562 - Sequence 195586 from Patent EP1572962.
LF322959 - JP 2014500723-A/130462: Polycomb-Associated Non-Coding RNAs.
JD452002 - Sequence 433026 from Patent EP1572962.
JD392898 - Sequence 373922 from Patent EP1572962.
JD544146 - Sequence 525170 from Patent EP1572962.
LF322958 - JP 2014500723-A/130461: Polycomb-Associated Non-Coding RNAs.
JD525095 - Sequence 506119 from Patent EP1572962.
JD500210 - Sequence 481234 from Patent EP1572962.
JD132130 - Sequence 113154 from Patent EP1572962.
JD148703 - Sequence 129727 from Patent EP1572962.
JD371443 - Sequence 352467 from Patent EP1572962.
JD386173 - Sequence 367197 from Patent EP1572962.
JD376611 - Sequence 357635 from Patent EP1572962.
JD543826 - Sequence 524850 from Patent EP1572962.
JD455286 - Sequence 436310 from Patent EP1572962.
JD350650 - Sequence 331674 from Patent EP1572962.
JD508224 - Sequence 489248 from Patent EP1572962.
LF322957 - JP 2014500723-A/130460: Polycomb-Associated Non-Coding RNAs.
JD538266 - Sequence 519290 from Patent EP1572962.
JD404362 - Sequence 385386 from Patent EP1572962.
LF322956 - JP 2014500723-A/130459: Polycomb-Associated Non-Coding RNAs.
LF322955 - JP 2014500723-A/130458: Polycomb-Associated Non-Coding RNAs.
MA558549 - JP 2018138019-A/130475: Polycomb-Associated Non-Coding RNAs.
MA558547 - JP 2018138019-A/130473: Polycomb-Associated Non-Coding RNAs.
MA558546 - JP 2018138019-A/130472: Polycomb-Associated Non-Coding RNAs.
MA558545 - JP 2018138019-A/130471: Polycomb-Associated Non-Coding RNAs.
MA558544 - JP 2018138019-A/130470: Polycomb-Associated Non-Coding RNAs.
MA558543 - JP 2018138019-A/130469: Polycomb-Associated Non-Coding RNAs.
MA558542 - JP 2018138019-A/130468: Polycomb-Associated Non-Coding RNAs.
MA558541 - JP 2018138019-A/130467: Polycomb-Associated Non-Coding RNAs.
MA558539 - JP 2018138019-A/130465: Polycomb-Associated Non-Coding RNAs.
MA558538 - JP 2018138019-A/130464: Polycomb-Associated Non-Coding RNAs.
MA558537 - JP 2018138019-A/130463: Polycomb-Associated Non-Coding RNAs.
MA558536 - JP 2018138019-A/130462: Polycomb-Associated Non-Coding RNAs.
MA558535 - JP 2018138019-A/130461: Polycomb-Associated Non-Coding RNAs.
MA558534 - JP 2018138019-A/130460: Polycomb-Associated Non-Coding RNAs.
MA558533 - JP 2018138019-A/130459: Polycomb-Associated Non-Coding RNAs.
MA558532 - JP 2018138019-A/130458: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: D3DSM4, D3DSM4_HUMAN, hCG_1647196, NM_130445, NP_569712
UCSC ID: uc002zhg.3
RefSeq Accession: NM_130445
Protein: D3DSM4 CCDS: CCDS42971.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_130445.2
exon count: 42CDS single in 3' UTR: no RNA size: 5398
ORF size: 4020CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 8020.00frame shift in genome: no % Coverage: 99.70
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.