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Set Analyses:

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COL18A1 Gene

protein-coding GIFtS: 69
GCID: GC21P046825

Collagen, Type XVIII, Alpha 1

(Previous names: Knobloch syndrome, type 1)
(Previous symbol: KNO)

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, ¹⁵RNAdb, and/or ¹¹Nature:405,311-319 and CroW21)
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Aliases
Collagen, Type XVIII, Alpha 1¹ ²		Human Type XVIII Collagen11
KNO¹ ²		KS²
endostatin¹ ²		Antiangiogenic Agent²
KNO1² ⁵		Collagen Alpha-1(XVIII) Chain²
Knobloch Syndrome, Type 1¹		Multi-Functional Protein MFP²

External Ids:	HGNC: 2195¹	Entrez Gene: 80781²	Ensembl: ENSG00000182871⁷	OMIM: 120328⁵	UniProtKB: P39060³

Export aliases for COL18A1 gene to outside databases

Previous GC identifers: GC21P043334 GC21P045681 GC21P045649 GC21P032201

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for COL18A1 Gene:

This gene encodes the alpha chain of type XVIII collagen. This collagen is one of the multiplexins, extracellular

matrix proteins that contain multiple triple-helix domains (collagenous domains) interrupted by non-collagenous

domains. The proteolytically produced C-terminal fragment of type XVIII collagen is endostatin, a potent

antiangiogenic protein. Mutations in this gene are associated with Knobloch syndrome. The main features of this

syndrome involve retinal abnormalities, so type XVIII collagen may play an important role in retinal structure

and in neural tube closure. Alternatively spliced transcript variants encoding different isoforms have been found

for this gene. (provided by RefSeq, Sep 2008)

GeneCards Summary for COL18A1 Gene:

COL18A1 (collagen, type XVIII, alpha 1) is a protein-coding gene. Diseases associated with COL18A1 include encephalocele, and knobloch syndrome type i. GO annotations related to this gene include structural molecule activity and identical protein binding. An important paralog of this gene is COL15A1.

UniProtKB/Swiss-Prot: COIA1_HUMAN, P39060

Function: COLA18A probably plays a major role in determining the retinal structure as well as in the closure of

the neural tube

Function: Endostatin potently inhibits endothelial cell proliferation and angiogenesis. May inhibit angiogenesis

by binding to the heparan sulfate proteoglycans involved in growth factor signaling

Gene Wiki entry for COL18A1 (Collagen, type XVIII, alpha 1) Gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics, Whole Chromsome Sequence According to Nature (Cited Here with Permission):405,311-319 and CroW21)
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RefSeq DNA sequence:

NC_000021.9 NC_018932.2 NT_011512.12

Regulatory elements:

Regulatory transcription factor binding sites in the COL18A1 gene promoter:
p53 STAT3 NF-kappaB NF-kappaB1 ATF
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: COL18A1 promoter sequence

Search Chromatin IP Primers for COL18A1

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL18A1

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 21q22.3 Ensembl cytogenetic band: 21q22.3 HGNC cytogenetic band: 21q22.3
Nature(405: 311-319) cytogenetic band: 21q22.3

COL18A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL18A1 gene location

GeneLoc information about chromosome 21 GeneLoc Exon Structure

(about GC identifiers)

GC21P046825:	GeneLoc	Nature:405,311-319
Start:	46,825,052 bp from pter	32,384,934 bp from centromere
End:	46,933,634 bp from pter	32,443,158 bp from centromere
Size:	108,583 bases	58,225 bases
Orientation:	plus strand	plus strand

Whole chromosome sequencing:
cDNA sequence:	AF018081
genomic clones:	P310E12 BAC-53I10

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: COIA1_HUMAN, P39060 (See protein sequence)

Recommended Name: Collagen alpha-1(XVIII) chain precursor

Size: 1754 amino acids; 178188 Da

3 PDB 3D structures from and Proteopedia for COL18A1:

1BNL (3D)

3HON (3D)

3HSH (3D)

Secondary accessions: A8MVI4 Q58EX6 Q6RZ39 Q6RZ40 Q6RZ41 Q8N4S4 Q8WXI5 Q96T70 Q9UK38 Q9Y6Q7

Q9Y6Q8

Alternative promoter usage, Alternative splicing: 3 isoforms: P39060-3 P39060-1 P39060-2 (Produced by alternative promoter usage)

Explore the universe of human proteins at neXtProt for COL18A1: NX_P39060

Explore proteomics data for COL18A1 at MOPED

Post-translational modifications:

Prolines at the third position of the tripeptide repeating unit (G-X-Y) of the triple-helical regions are

hydroxylated¹

Glycosylation² at Asn68, Asn129, Asn164, Asn691, Thr1292, Ser1304, Thr1332

Modification sites at PhosphoSitePlus

See COL18A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts):

NP_085059.2 NP_569712.2

ENSEMBL proteins:

ENSP00000383191 ENSP00000347665 ENSP00000339118 ENSP00000415692 ENSP00000352798

Reactome Protein details: P39060

COL18A1 Human Recombinant Protein Products:

	EMD Millipore Purified and/or Recombinant COL18A1 Protein
	R&D Systems Recombinant & Natural Proteins for COL18A1 (Endostatin)
	Enzo Life Sciences proteins for COL18A1
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	GenScript Purified and Recombinant Proteins for COL18A1
	Novus Biologicals COL18A1 Proteins
	Browse Sino Biological Recombinant Proteins Browse Sino Biological Cell Lysates
	ProSpec Recombinant Protein for COL18A1
	Browse Proteins at Cloud-Clone Corp.

COL18A1 Antibody Products:

	EMD Millipore Mono- and Polyclonal Antibodies for the study of COL18A1
	R&D Systems Antibodies for COL18A1 (Endostatin)
	OriGene Antibodies for COL18A1 OriGene Custom Antibody Services for COL18A1
	Novus Biologicals COL18A1 Antibodies
	Abcam antibodies for COL18A1 (P39059, P39060)
	Browse Antibodies at Cloud-Clone Corp.
	ThermoFisher Antibody for COL18A1
	LSBio Antibodies in human, mouse, rat for COL18A1

COL18A1 Assay Products:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Assay Services for COL18A1
	R&D Systems ELISAs for COL18A1 (Endostatin) (see all)
	GenScript Custom Assay Services for COL18A1
	Browse Enzo Life Sciences for kits & assays
	Browse ELISAs at Cloud-Clone Corp. Browse CLIAs at Cloud-Clone Corp.

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:

COLLAGEN: Collagens

Selected InterPro protein domains (see all 9):

IPR026917 COL18A1

IPR001791 Laminin_G

IPR020067 Frizzled_dom

IPR016187 C-type_lectin_fold

IPR010515 Collagenase_NC10/endostatin

Graphical View of Domain Structure for InterPro Entry P39060

ProtoNet protein and cluster: P39060

5 Blocks protein domains:

IPB001791 Laminin G

IPB003129 Thrombospondin

IPB008160 Collagen triple helix repeat

IPB008161 Collagen helix repeat

IPB010515 Collagenase NC10 and endostatin

UniProtKB/Swiss-Prot: COIA1_HUMAN, P39060

Similarity: Belongs to the multiplexin collagen family

Similarity: Contains 1 FZ (frizzled) domain

Similarity: Contains 1 laminin G-like domain

COL18A1 for domains About GeneDecksing

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: COIA1_HUMAN, P39060

Function: COLA18A probably plays a major role in determining the retinal structure as well as in the closure of

the neural tube

Function: Endostatin potently inhibits endothelial cell proliferation and angiogenesis. May inhibit angiogenesis

by binding to the heparan sulfate proteoglycans involved in growth factor signaling

Genatlas biochemistry entry for COL18A1:

collagen,type XVIII,alpha 1,multiplexin family with interrupted helical domain

Gene Ontology (GO): 4 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005198	structural molecule activity	IEA	--
GO:0005515	protein binding	IPI	17615292
GO:0042802	identical protein binding	IPI	16269408
GO:0046872	metal ion binding	IEA	--

COL18A1 for ontologies About GeneDecksing

Phenotypes:
9 MGI mutant phenotypes (inferred from 4 alleles) (MGI details for Col18a1):

cardiovascular system	craniofacial	homeostasis/metabolism	nervous system	other
renal/urinary system	skeleton	tumorigenesis	vision/eye

COL18A1 for phenotypes About GeneDecksing

Animal Models:
MGI mouse knock-outs for COL18A1: Col18a1^{tm1(KOMP)Vlcg} Col18a1^tm1Hms

inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COL18A1

inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for COL18A1

genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for COL18A1

genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COL18A1

miRNA Products:		miRTarBase miRNAs that target COL18A1: hsa-mir-92a-3p (MIRT049203), hsa-mir-877-3p (MIRT037044)

		Block miRNA regulation of human, mouse, rat COL18A1 using miScript Target Protectors
		6 qRT-PCR Assays for microRNAs that regulate COL18A1:
		hsa-miR-9 hsa-miR-526b hsa-miR-516a-3p hsa-miR-516b* hsa-miR-578 hsa-miR-3159
		SwitchGear 3'UTR luciferase reporter plasmid: COL18A1 3' UTR sequence

Inhib. RNA Products:		OriGene RNAi products in human, mouse, rat for COL18A1
		Predesigned siRNA for gene silencing in human, mouse, rat COL18A1

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for COL18A1

Clone Products:		OriGene clones in human, mouse for COL18A1 (see all 12) OriGene ORF clones in mouse, rat for COL18A1 OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector (see all 2): COL18A1 (NM_030582)
		Browse Sino Biological Human cDNA Clones
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL18A1
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL18A1

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for COL18A1
		Browse ESI BIO Cell Lines and PureStem Progenitors for COL18A1

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL18A1

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot

COIA1_HUMAN, P39060: Secreted, extracellular space, extracellular matrix (By similarity)

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
endoplasmic reticulum	4
extracellular	4
plasma membrane	3
cytoskeleton	1
cytosol	1
golgi apparatus	1
lysosome	1
mitochondrion	1
nucleus	1
vacuole	1

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Gene Ontology (GO): Selected cellular component terms (see all 7): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	TAS	--
GO:0005581	collagen	IEA	--
GO:0005604	basement membrane	IEA	--
GO:0005615	extracellular space	IDA	--
GO:0005788	endoplasmic reticulum lumen	TAS	--

COL18A1 for ontologies About GeneDecksing

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for COL18A1 About (see all 12)

See pathways by source

SuperPath

Contained pathways About

Collagen biosynthesis and modifying enzymes

Collagen biosynthesis and modifying enzymes	0.75	Intrinsic Prothrombin Activation Pathway	0.39
Collagen formation	0.75	Blood Coagulation Cascade	0.38
Assembly of collagen fibrils and other multimeric structures	0.62

Integrin Pathway

FAK1 Signaling	0.67	UPA-UPAR Pathway	0.56
Integrin Pathway	0.67	Inhibition of Angiogenesis by TSP1	0.50
GnRH Signaling	0.56	Transendothelial Migration of Leukocytes	0.38

ERK Signaling

Rho Family GTPases	0.61	Molecular Mechanisms of Cancer	0.51
ERK Signaling	0.61	ILK Signaling	0.49
MAPK Signaling	0.58

Degradation of the extracellular matrix

	Degradation of the extracellular matrix	0.43			Extracellular matrix organization	0.34
	Collagen degradation	0.43

Phospholipase-C Pathway

Phospholipase-C Pathway

0.56

PTEN Pathway

0.56

Pathways by source See SuperPaths
Show all pathways

Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL18A1 (see all 15)

	MAPK Signaling
	Molecular Mechanisms of Cancer
	PTEN Pathway
	Transendothelial Migration of Leukocytes
	UPA-UPAR Pathway

2 BioSystems Pathways for COL18A1

	FOXA1 transcription factor network
	Direct p53 effectors

Selected Reactome Pathways for COL18A1 (see all 6)

	Laminin interactions
	Integrin cell surface interactions
	Collagen biosynthesis and modifying enzymes
	Assembly of collagen fibrils and other multimeric structures
	Collagen degradation

1 Kegg Pathway (Kegg details for COL18A1):

Protein digestion and absorption

COL18A1 for pathways About GeneDecksing

Pathway & Disease-focused RT² Profiler PCR Arrays including COL18A1:

Endothelial Cell Biology in human mouse rat

Angiogenic Growth Factors in human mouse rat

Apoptosis 384HT in human mouse rat

Angiogenesis in human mouse rat

Interactions:

GeneGlobe Interaction Network for COL18A1

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for COL18A1 (P39060^{1, 3} ENSP00000352798⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 66)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
TECPR1	Q7Z6L1³, ENSP00000404923⁴	I2D: score=3 STRING: ENSP00000404923
KDR	P35968³, ENSP00000263923⁴	I2D: score=1 STRING: ENSP00000263923
TGM2	P21980¹, ENSP00000355330⁴	EBI-2566375,EBI-727668 STRING: ENSP00000355330
NCL	P19338¹, ENSP00000318195⁴	EBI-2566375,EBI-346967 STRING: ENSP00000318195
APP	P05067¹	EBI-2566375,EBI-821758

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Gene Ontology (GO): Selected biological process terms (see all 15): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001525	angiogenesis	IEA	--
GO:0001886	endothelial cell morphogenesis	IEA	--
GO:0007155	cell adhesion	IEA	--
GO:0007601	visual perception	TAS	10942434
GO:0008284	positive regulation of cell proliferation	IEA	--

COL18A1 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for COL18A1 (COIA1)

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for COL18A1 gene (3 alternative transcripts):

NM_030582.3 NM_130445.2 NM_130444.2

Unigene Cluster for COL18A1:

Collagen, type XVIII, alpha 1

Hs.517356 [show with all ESTs]

Unigene Representative Sequence: AF018081

7 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000400337(uc002zhg.3) ENST00000355480(uc002zhi.3) ENST00000342220(uc002zhj.3 uc002zhk.3)

ENST00000459895 ENST00000423214 ENST00000473212 ENST00000359759

miRNA Products:		Block miRNA regulation of human, mouse, rat COL18A1 using miScript Target Protectors
		6 qRT-PCR Assays for microRNAs that regulate COL18A1:
		hsa-miR-9 hsa-miR-526b hsa-miR-516a-3p hsa-miR-516b* hsa-miR-578 hsa-miR-3159
		SwitchGear 3'UTR luciferase reporter plasmid: COL18A1 3' UTR sequence

Inhib. RNA Products:		OriGene RNAi products in human, mouse, rat for COL18A1
		Predesigned siRNA for gene silencing in human, mouse, rat COL18A1

Clone Products:		OriGene clones in human, mouse for COL18A1 (see all 12) OriGene ORF clones in mouse, rat for COL18A1 OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector (see all 2): COL18A1 (NM_030582)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL18A1
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL18A1

Primer Products:		OriGene qSTAR qPCR primer pairs in human, mouse for COL18A1
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat COL18A1
		QuantiTect SYBR Green Assays in human, mouse, rat COL18A1
		QuantiFast Probe-based Assays in human, mouse, rat COL18A1

Additional mRNA sequence:

AF018081.1 AF018082.1 AF184060.1 AF333246.1 AF333247.1 AF416592.1 AK098216.1 AK130835.1

AK311062.1 BC033715.1 BC063833.1

19 DOTS entries:

DT.447571 DT.92001135 DT.91912586 DT.95302146 DT.121139495 DT.101985460 DT.100039632 DT.99986442

DT.95220877 DT.92436231 DT.100034049 DT.100039626 DT.40116647 DT.100039627 DT.95090195 DT.95349603

DT.100798481 DT.91744920 DT.99955859

Selected AceView cDNA sequences (see all 195):

BG106854 AA350510 AA350511 AA470378 BU680493 AI076853 AK127669 AA350512

R86040 AA913825 AI814596 T28473 AA069352 AI738703 BU502539 BE881571

AI858077 AI970756 AA743360 AI763165 AI660746 AA731506 BQ003811 AI074505

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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COL18A1 expression in normal human tissues (normalized intensities) COL18A1 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: TAATCCTCAA

About this image

COL18A1 expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database
selected tissues (see all 11) fully expand


Brain (Nervous System) fully expand to see all 4 entries
Midbrain tegmentum

Neural Tube (Nervous System) fully expand to see all 3 entries
Metencephalon

Kidney (Urinary System) fully expand to see all 2 entries
Ureteric Bud Cells Ureteric Bud
Metanephros

Thymus (Hematopoietic System)
Thymus

Epithelial Cells
Mature Retinal Pigmented Epithelium Cells Retinal Pigmented Epithelium

COL18A1 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

COL18A1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.517356

UniProtKB/Swiss-Prot: COIA1_HUMAN, P39060

Tissue specificity: Present in multiple organs with highest levels in liver, lung and kidney

Pathway & Disease-focused RT² Profiler PCR Arrays including COL18A1:

Endothelial Cell Biology in human mouse rat

Angiogenic Growth Factors in human mouse rat

Apoptosis 384HT in human mouse rat

Angiogenesis in human mouse rat

Primer Products:		OriGene qSTAR qPCR primer pairs in human, mouse for COL18A1
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat COL18A1
		QuantiTect SYBR Green Assays in human, mouse, rat COL18A1
		QuantiFast Probe-based Assays in human, mouse, rat COL18A1

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL18A1

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for COL18A1 gene from Selected species (see all 14) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Col18a1^{1 , 5}	collagen, type XVIII, alpha 1^{1, 5}	75.59(n)¹ 75.49(a)¹		10 (39.72 cM)⁵ 12822¹ NM_001109991.1¹ NP_001103461.1¹ 77052178⁵
chicken (Gallus gallus)	Aves	COL18A1¹	collagen, type XVIII, alpha 1	67.21(n) 68.86(a)		373978 NM_204164.1 NP_989495.1
lizard (Anolis carolinensis)	Reptilia	COL18A1⁶	collagen, type XVIII, alpha 1	56(a)	1 ↔ 1	1(90395003-90458517)
African clawed frog (Xenopus laevis)	Amphibia	AB047066.1²	--	74.53(n)		AB047066.1
zebrafish (Danio rerio)	Actinopterygii	AJ494837.1²	--	75.34(n)		360140 AJ494837.1
fruit fly (Drosophila melanogaster)	Insecta	mp⁶	multiplexin	29(a)	1 → many	3L(6991943-7046528)
worm (Caenorhabditis elegans)	Secernentea	cle-1³	cle-1 isoform A	33(a)		I(8714046-8732339) --

ENSEMBL Gene Tree for COL18A1 (if available)
TreeFam Gene Tree for COL18A1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for COL18A1 gene

COL15A1²

1 SIMAP similar gene for COL18A1 using alignment to 6 protein entries: COIA1_HUMAN (see all proteins):

COLQ

COL18A1 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Polymorphic Variants from UniProtKB/Swiss-Prot

COIA1_HUMAN, P39060: There is an association between a polymorphism in position 1675 and prostate cancer. Heterozygous

Asn-1675 individuals have a 2.5 times increased chance of developing prostate cancer as compared with homozygous

Asp-1675 individuals

SNP ID	Valid	Clinical significance	Chr 21 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs12483377^1,2,,4	C,F,H	pathogenic¹	46931109(+)	`CCTTTG/AACGGC`	4	/N /D	mis¹ ese³		31		NA NS EA MN EU	3505
rs191134880^1,2		--	46823185(+)	`CCCTGC/TCCCAG`	1	--	us2k¹		0	--	--	--	--
rs146727184^1,2		--	46823307(+)	`ATGGGG/TTGGGT`	1	--	us2k¹		0	--	--	--	--
rs140367398^1,2	C	--	46823339(+)	`GGCAGA/GTGAGA`	1	--	us2k¹		0	--	--	--	--
rs12482579^1,2	H	--	46823369(+)	`CTGCAC/GTGCAG`	1	--	us2k¹		4		NS EA	416
rs78601909^1,2	C,F	--	46823375(+)	`TGCAGG/CGTTAA`	1	--	us2k¹		2		CSA WA	120
rs75884265^1,2	C,F	--	46823382(+)	`TTAATG/TGACAG`	1	--	us2k¹		2		CSA WA	120
rs183317419^1,2		--	46823512(+)	`ACAGAA/CACACA`	1	--	us2k¹		0	--	--	--	--
rs139693353^1,2	C	--	46823544(+)	`GAGAG-/ACAT GCACACACATG`	1	--	us2k¹		0	--	--	--	--
rs186851250^1,2		--	46823702(+)	`TGTGCA/GATGAC`	1	--	us2k¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for COL18A1 (46825052 - 46933634 bp)

Structural Variations
Database of Genomic Variants (DGV) Selected variations for COL18A1 (see all 74): About this table

Variant ID	Type	Subtype	PubMed ID
esv2723773	CNV	Deletion	23290073
esv2723784	CNV	Deletion	23290073
esv2723770	CNV	Deletion	23290073
dgv764e201	CNV	Deletion	23290073
esv2660971	CNV	Deletion	23128226
esv2570683	CNV	Deletion	19546169
esv2723753	CNV	Deletion	23290073
esv2723765	CNV	Deletion	23290073
esv2723781	CNV	Deletion	23290073
esv2723771	CNV	Deletion	23290073

Human Gene Mutation Database (HGMD): COL18A1

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing COL18A1

DNA2.0 Custom Variant and Variant Library Synthesis for COL18A1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 120328
OMIM disorders: 267750
UniProtKB/Swiss-Prot: COIA1_HUMAN, P39060

Knobloch syndrome 1 (KNO1) [MIM:267750]: A developmental disorder primarily characterized by typical eye

abnormalities, including high myopia, cataracts, dislocated lens, vitreoretinal degeneration, and retinal

detachment, with occipital skull defects, which can range from occipital encephalocele to occult cutis aplasia.

Note=The disease is caused by mutations affecting the gene represented in this entry

Selected diseases for COL18A1 (see all 61): About MalaCards

encephalocele knobloch syndrome type i knobloch syndrome encephaloceles

occipital encephalocele funisitis vitreoretinal degeneration retinal detachment

hepatopulmonary syndrome bronchopulmonary dysplasia rhabdoid tumor cerebral malaria

retinitis traumatic brain injury brain injury myopia

clear cell renal cell carcinoma hypertriglyceridemia sporadic breast cancer idiopathic pulmonary fibrosis

1 disease from the University of Copenhagen DISEASES database for COL18A1:

Lung cancer

COL18A1 for disorders About GeneDecksing

Congresses - knowledge worth sharing:
Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

3 Novoseek inferred disease relationships for COL18A1 gene About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
knobloch syndrome	98.5	6	19390655 (2), 14695535 (1), 17546652 (1), 18484314 (1) (see all 5)
occipital encephalocele	81.6	1	15857886 (1)
tumors	0	1	20212451 (1)

Genetic Association Database (GAD): COL18A1
Human Genome Epidemiology (HuGE) Navigator: COL18A1 (19 documents)
Tumor Gene Database (TGDB): COL18A1

Export disorders for COL18A1 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for COL18A1 gene, integrated from 10 sources (see all 155):
(articles sorted by number of sources associating them with COL18A1)

Utopia: connect your pdf to the dynamic
world of online information

Collagen XVIII, containing an endogenous inhibitor of angiogenesis and tumor growth, plays a critical role in the maintenance of retinal structure and in neural tube closure. (PubMed id 10942434)^{1, 2, 3, 9} Sertie A.L....Passos-Bueno M.R. (Hum. Mol. Genet. 2000)
Cloning of cDNA and genomic DNA encoding human type XVIII collagen and localization of the alpha 1(XVIII) collagen gene to mouse chromosome 10 and human chromosome 21. (PubMed id 8188291)^{1, 2, 3, 9} Oh S.P....Olsen B.R. (Genomics 1994)
Knobloch syndrome: novel mutations in COL18A1, evidence for genetic heterogeneity, and a functionally impaired polymorphism in endostatin. (PubMed id 14695535)^{1, 2, 9} Menzel O.... Guipponi M. (Hum. Mutat. 2004)
A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS). (PubMed id 19961619)^{1, 4, 9} Castro-Giner F....de Cid R. (BMC Med. Genet. 2009)
A high risk of occurrence of sporadic breast cancer in individuals with the 104NN polymorphism of the COL18A1 gene. (PubMed id 16807676)^{1, 4, 9} LourenAso G.J....Lima C.S. (Breast Cancer Res. Treat. 2006)
CNS malformations in Knobloch syndrome with splice mutation in COL18A1 gene. (PubMed id 17546652)^{1, 3, 9} Keren B....Verloes A. (Am. J. Med. Genet. A 2007)
No evidence for locus heterogeneity in Knobloch syndrome. (PubMed id 23667181)^{1, 2} Aldahmesh M.A....Alkuraya F.S. (J. Med. Genet. 2013)
Genetic risk factors for hepatopulmonary syndrome in patients with advanced liver disease. (PubMed id 20346360)^{1, 4} Roberts K.E....Fallon M.B. (Gastroenterology 2010)
MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer. (PubMed id 20819778)^{1, 4} Zhang X....Wu X. (Carcinogenesis 2010)
Genetic susceptibility to distinct bladder cancer subphenotypes. (PubMed id 19692168)^{1, 4} Guey L.T....Malats N. (Eur. Urol. 2010)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 80781	HGNC: 2195	AceView: SLC19A1	Ensembl:ENSG00000182871	euGenes: HUgn80781
ECgene: COL18A1	Kegg: 80781	H-InvDB: COL18A1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for COL18A1	Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for COL18A1	Genetics and Cytogenetics in Oncology and Haematology
GeneReviews	http://www.ncbi.nlm.nih.gov/books/NBK1116/?term=COL18A1[genesymbol]

Intellectual Property for COL18A1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for COL18A1 gene:
Search GeneIP for patents involving COL18A1

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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	Regulatory tfbs in COL18A1 promoter

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COL18A1 Gene

Collagen, Type XVIII, Alpha 1

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COL18A1 Gene

Collagen, Type XVIII, Alpha 1

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