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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

COL3A1 Gene

protein-coding GIFtS: 70
GCID: GC02P189803

collagen, type III, alpha 1

(Previous names: Ehlers-Danlos syndrome type IV, autosomal dominant )
(Previous symbol: EDS4A)

Explore 53 diseases affiliated with
COL3A1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Collagen, Type III, Alpha 1¹ ²
EDS4A¹ ²
Ehlers-Danlos Syndrome Type IV, Autosomal Dominant¹ ²
Alpha1 (III) Collagen²
Collagen Alpha-1(III) Chain²
Collagen, Fetal²

External Ids:	HGNC: 2201¹	Entrez Gene: 1281²	Ensembl: ENSG00000168542⁷	OMIM: 120180⁵	UniProtKB: P02461³

Export aliases for COL3A1 gene to outside databases

Previous GC identifers: GC02P187975 GC02P188522 GC02P190041 GC02P189664 GC02P189547 GC02P181698

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for COL3A1:

This gene encodes the pro-alpha1 chains of type III collagen, a fibrillar collagen that is found in extensible

connective tissues such as skin, lung, uterus, intestine and the vascular system, frequently in association with type

I collagen. Mutations in this gene are associated with Ehlers-Danlos syndrome types IV, and with aortic and arterial

aneurysms. Two transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this

gene. (provided by R. Dalgleish, Feb 2008)

UniProtKB/Swiss-Prot: CO3A1_HUMAN, P02461

Function: Collagen type III occurs in most soft connective tissues along with type I collagen

Gene Wiki entry for COL3A1 (Collagen, type III, alpha 1)

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000002.11 NC_018913.1 NT_005403.17

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the COL3A1 gene promoter:
Pbx1a Bach2 FOXD1 Nkx2-5 POU3F2 (N-Oct-5a) POU3F2 (N-Oct-5b) POU3F2 NF-kappaB NF-kappaB1 Hlf
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: COL3A1 promoter sequence

Search SABiosciences Chromatin IP Primers for COL3A1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat COL3A1

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

Entrez Gene cytogenetic band: 2q31 Ensembl cytogenetic band: 2q32.2 HGNC cytogenetic band: 2q32.2

COL3A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL3A1 gene location

GeneLoc information about chromosome 2 GeneLoc Exon Structure

GeneLoc location for GC02P189803: view genomic region (about GC identifiers)

Start:	189,839,046 bp from pter	End:	189,877,472 bp from pter
Size:	38,427 bases	Orientation:	plus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CO3A1_HUMAN, P02461 (See protein sequence)

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

Size: 1466 amino acids; 138564 Da

Subunit: Trimers of identical alpha 1(III) chains. The chains are linked to each other by interchain disulfide bonds.

Trimers are also cross-linked via hydroxylysines

Subcellular location: Secreted, extracellular space, extracellular matrix (By similarity)

6 PDB 3D structures from and Proteopedia for COL3A1:

2V53 (3D)

3DMW (3D)

4AE2 (3D)

4AEJ (3D)

4AK3 (3D)

4GYX (3D)

Secondary accessions: D3DPH4 P78429 Q15112 Q16403 Q53S91 Q541P8 Q6LDB3 Q6LDJ2 Q6LDJ3 Q7KZ56 Q8N6U4

Q9UC88 Q9UC89 Q9UC90 Q9UC91

Alternative splicing: 2 isoforms: P02461-1 P02461-2 (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for COL3A1: NX_P02461

Post-translational modifications:

Proline residues at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the

chains¹

O-linked glycan consists of a Glc-Gal disaccharide bound to the oxygen atom of a post-translationally added hydroxyl

group¹

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_P02461

COL3A1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_000081.1

ENSEMBL proteins:

ENSP00000304408 ENSP00000415346 ENSP00000315243

Reactome Protein details: P02461
Human Recombinant Protein Products:

	EMD Millipore Purified and/or Recombinant COL3A1 Protein
	R&D Systems Recombinant & Natural Proteins for COL3A1 (Collagen III alpha 1/COL3A1)
	Browse recombinant and purified proteins available from Enzo Life Sciences
	OriGene Purified Protein: COL3A1 OriGene Protein Over-expression Lysate: COL3A1 OriGene Custom Protein Services for COL3A1
	GenScript Custom Purified and Recombinant Proteins Services for COL3A1
	Novus Biologicals COL3A1 Proteins
	Browse Sino Biological Recombinant Proteins
	ProSpec Recombinant Protein for COL3A1
	Browse Proteins at Uscn

Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	TAS	--
GO:0005581	collagen	--	--
GO:0005586	collagen type III	NAS	1672129
GO:0005615	extracellular space	NAS	9036918
GO:0005788	endoplasmic reticulum lumen	TAS	--

COL3A1 for ontologies About GeneDecksing

COL3A1 Antibody Products:

	EMD Millipore Mono- and Polyclonal Antibodies for the study of COL3A1
	Browse R&D Systems for Antibodies
	OriGene Antibodies: COL3A1 OriGene Custom Antibody Services for COL3A1
	GenScript Custom Superior Antibodies Services for COL3A1
	Novus Biologicals COL3A1 Antibodies
	Abcam antibodies for COL3A1
	Browse Antibodies at Uscn
	ThermoFisher Antibodies for COL3A1

Assay Products for COL3A1:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	Browse R&D Systems for biochemical assays
	GenScript Custom Assay Services for COL3A1
	Browse Enzo Life Sciences for kits & assays
	Browse ELISAs and CLIAs at Uscn

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

COL3A1 for domains About GeneDecksing

3 InterPro domains/families:

IPR000885 Fib_collagen_C

IPR001007 VWF_C

IPR008160 Collagen

Graphical View of Domain Structure for InterPro Entry P02461

ProtoNet protein and cluster: P02461

4 Blocks protein families:

IPB000885 Fibrillar collagen

IPB001007 von Willebrand factor

IPB008160 Collagen triple helix repeat

IPB008161 Collagen helix repeat

UniProtKB/Swiss-Prot: CO3A1_HUMAN, P02461

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

Similarity: Belongs to the fibrillar collagen family

Similarity: Contains 1 fibrillar collagen NC1 domain

Similarity: Contains 1 VWFC domain

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: CO3A1_HUMAN, P02461

Function: Collagen type III occurs in most soft connective tissues along with type I collagen

Genatlas biochemistry entry for COL3A1:

collagen type III,alpha 1,fibril forming,putative down-regulated c-Myc target gene,

miRNA Products:		miRTarBase miRNAs that target COL3A1: hsa-mir-29b (MIRT005567), hsa-mir-29c (MIRT000927)

		OriGene 3'-UTR Clone: COL3A1 Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat COL3A1
		8/21 QIAGEN miScript miRNA Assays for microRNAs that regulate COL3A1 (see all 21):
		hsa-miR-520d-5p hsa-let-7d hsa-miR-202 hsa-miR-29a hsa-miR-29c hsa-miR-767-5p hsa-let-7c hsa-miR-380*

		SwitchGear 3'UTR luciferase reporter plasmid: COL3A1 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for COL3A1 (see all 7) OriGene shRNA RFP: COL3A1 OriGene siRNA: COL3A1
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat COL3A1

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for COL3A1

Clone Products:		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for COL3A1 (see all 3) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for COL3A1 OriGene custom cloning services � gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector: COL3A1 (NM_000090)
		Browse Sino Biological Human cDNA Clones
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL3A1
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL3A1

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for COL3A1
		Search LifeMap BioReagents cell lines for COL3A1

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL3A1

Gene Ontology (GO): 5/6 molecular function terms (GO ID links to tree view) (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005178	integrin binding	NAS	14970208
GO:0005201	extracellular matrix structural constituent	IMP	7487954
GO:0005515	protein binding	IPI	2839553
GO:0046332	SMAD binding	IEA	--
GO:0046872	metal ion binding	IEA	--

COL3A1 for ontologies About GeneDecksing

2 GenomeRNAi human phenotypes for COL3A1:

Increased gamma-H2AX phosphory

Synthetic lethal with imatinib

Animal Models:
Mouse knock-out Col3a1^tm1Jae for COL3A1
9 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Col3a1):

cardiovascular system	digestive/alimentary	growth/size	homeostasis/metabolism	integument
liver/biliary system	mortality/aging	muscle	respiratory system

COL3A1 for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways - 5/21 super-pathways (see all 21) About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Integrin Pathway

Integrin Pathway	1.00	UPA-UPAR Pathway	0.51
FAK1 Signaling	0.67	Transendothelial Migration of Leukocytes	0.38
GnRH Signaling	0.56	Inhibition of Angiogenesis by TSP1	0.37

Collagen formation

Collagen formation	1.00	Extracellular matrix organization	0.54
Collagen biosynthesis and modifying enzymes	0.74	Secretion of collagens	0.49
Assembly of collagen fibrils and other multimeric structures	0.65

Rho Family GTPases

Rho Family GTPases	1.00	MAPK Signaling	0.51
ERK Signaling	0.61	ILK Signaling	0.45
Molecular Mechanisms of Cancer	0.51

Cell adhesion_ECM remodeling

	Cell adhesion ECM remodeling	1.00			Metalloproteases in connective tissue degradation	0.31
	Cell adhesion_ECM remodeling	1.00

NCAM signaling for neurite out-growth

NCAM signaling for neurite out-growth

1.00

NCAM1 interactions

0.62

Pathway sources
See GeneCards unified pathways
Show all pathways

2 EMD Millipore Pathways for COL3A1

	Cell adhesion ECM remodeling
	Metalloproteases in connective tissue degradation

5/15 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for COL3A1 (see all 15)

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

1 GeneGo (Thomson Reuters) Pathway for COL3A1

Cell adhesion ECM remodeling

3 BioSystems Pathways for COL3A1

	Focal Adhesion
	Endothelins
	Inflammatory Response Pathway

5/18 Reactome Pathways for COL3A1 (see all 18)

	Developmental Biology
	Formation of collagen fibrils
	Assembly of collagen fibrils and other multimeric structures
	Gelatin degradation by MMP19
	Extracellular matrix organization

1 PharmGKB Pathway for COL3A1

Platelet Aggregation Inhibitor Pathway, Pharmacodynamics

4 Kegg Pathways (Kegg details for COL3A1):

	Focal adhesion
	ECM-receptor interaction
	Protein digestion and absorption
	Amoebiasis

COL3A1 for pathways About GeneDecksing

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for COL3A1

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

5/86 Interacting proteins for COL3A1 (P02461^{2, 3} ENSP00000304408⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 86)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
SPARC	P09486³, ENSP00000231061⁴	I2D: score=4 STRING: ENSP00000231061
CAPN1	P07384³, ENSP00000279247⁴	I2D: score=3 STRING: ENSP00000279247
DDR1	Q08345³, ENSP00000406091⁴	I2D: score=2 STRING: ENSP00000406091
HTRA1	Q92743³, ENSP00000357980⁴	I2D: score=1 STRING: ENSP00000357980
PCOLCE	Q15113³, ENSP00000223061⁴	I2D: score=2 STRING: ENSP00000223061

About this table

Gene Ontology (GO): 5/20 biological process terms (GO ID links to tree view) (see all 20): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001501	skeletal system development	IEA	--
GO:0001568	blood vessel development	IEA	--
GO:0007160	cell-matrix adhesion	IDA	16912226
GO:0007179	transforming growth factor beta receptor signaling pathway	IDA	16360482
GO:0007229	integrin-mediated signaling pathway	IMP	14970208

COL3A1 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

COL3A1 for compounds About GeneDecksing

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for COL3A1

1 DrugBank Compound for COL3A1 About this table

Compound	Synonyms	CAS #	Type	Actions	PubMed Ids
Collagenase	--	9001-12-1	target	--	17016423 2145268 17139284

8 Novoseek chemical compound relationships for COL3A1 gene About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
nppa	68.3	2	14993121 (1), 15582321 (1)
procollagen	51.4	2	9076960 (1), 17487505 (1)
nppb	38.7	2	14993121 (1), 15582321 (1)
ribonucleic acid	12.1	2	16360482 (1), 15582321 (1)
thymidine	0	2	19741209 (1), 8918626 (1)
aspartate	0	1	11168790 (1)
glutamate	0	2	1352273 (1), 8098182 (1)
cyclosporin a	0	8	10831628 (5), 9636386 (1)

Search CenterWatch for drugs/clinical trials and news about COL3A1 / CO3A1

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for COL3A1 gene:

NM_000090.3

Unigene Cluster for COL3A1:

Collagen, type III, alpha 1

Hs.443625 [show with all ESTs]

Unigene Representative Sequence: NM_000090

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

ENST00000304636(uc002uqj.1) ENST00000470167 ENST00000450867 ENST00000467886

ENST00000487010 ENST00000317840(uc010frw.1)

miRNA Products:		OriGene 3'-UTR Clone: COL3A1 Browse OriGene MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat COL3A1
		8/21 QIAGEN miScript miRNA Assays for microRNAs that regulate COL3A1 (see all 21):
		hsa-miR-520d-5p hsa-let-7d hsa-miR-202 hsa-miR-29a hsa-miR-29c hsa-miR-767-5p hsa-let-7c hsa-miR-380*

		SwitchGear 3'UTR luciferase reporter plasmid: COL3A1 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for COL3A1 (see all 7) OriGene shRNA RFP: COL3A1 OriGene siRNA: COL3A1
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat COL3A1

Clone Products:		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for COL3A1 (see all 3) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for COL3A1 OriGene custom cloning services � gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector: COL3A1 (NM_000090)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL3A1
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL3A1

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		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat COL3A1
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat COL3A1

Additional cDNA sequence:

AK021531.1 AK091853.1 AK308010.1 BC028178.1 BX649097.1 M13146.1 M59227.1 S79877.1

X01655.1 X06700.1 X07240.1 X14420.1

24/53 DOTS entries (see all 53):

DT.100893398 DT.87024767 DT.95126490 DT.100893393 DT.99969260 DT.100046024 DT.95126542 DT.97761863

DT.100893402 DT.99975383 DT.100893410 DT.95196532 DT.92471487 DT.100893395 DT.40239493 DT.101974976

DT.40124083 DT.97814164 DT.95126654 DT.120985447 DT.100741033 DT.100762161 DT.100893411 DT.120985475

24/1770 AceView cDNA sequences (see all 1770):

BQ181913 H89012 BM702152 AA347957 CA413816 AU119414 NM_000090 BU628046

H89890 AI754852 CB215260 AI827248 BM667293 CA422262 CA412948 AW002774

CF995759 AA319923 BQ573699 AA338118 BQ024609 AI571615 CA415296 CA415007

GeneLoc Exon Structure

5/8 Alternative Splicing Database (ASD) splice patterns (SP) for COL3A1 (see all 8) About this scheme

ExUns:	1a	·	1b	·	1c	·	1d	^	2a	·	2b	·	2c	^	3	^	4	^	5	^	6	^	7	^	8	^	9	^	10	^	11	^	12	^	13	^	14	^	15	^	16	^	17	^	18	^	19	^	20	^	21	^
SP1:
SP2:
SP3:															-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-
SP4:
SP5:											-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-

ExUns:	22	^	23	^	24	^	25	^	26	^	27	^	28	^	29	^	30	^	31a	·	31b	^	32	^	33	^	34	^	35	^	36	^	37a	·	37b	^	38a	·	38b	^	39	^	40	^	41	^	42	^	43	^	44	^
SP1:																																							-
SP2:							-		-		-		-		-		-		-																				-
SP3:	-		-		-		-		-		-		-		-		-		-
SP4:
SP5:	-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-

ExUns:	45	^	46	^	47	^	48a	·	48b	·	48c	^	49	^	50a	·	50b	^	51a	·	51b	^	52a	·	52b	·	52c	·	52d
SP1:							-
SP2:							-
SP3:
SP4:
SP5:	-		-		-		-		-

ECgene alternative splicing isoforms for COL3A1

(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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

COL3A1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GATCAGGCCA

About this image

COL3A1 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

10/17 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 17)

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Bone

Facial Sutures

Facial Presumptive Suture Cells

Selective marker (cell-identifying gene)

Bone

Facial Sutures

Facial Suture Cells

Bone

Rostral Sutures

Rostral Presumptive Suture Cells

Bone

Rostral Sutures

Rostral Suture Cells

Bone

Limb

Autopod Synovial Joint

Central Intermediate Lamina Cells

Cartilage

Limb

Autopod Synovial Joint

Interzone Cells

Cartilage

Limb

Stylopod Synovial Joint

Central Intermediate Lamina Cells

Cartilage

Limb

Stylopod Synovial Joint

Interzone Cells

Cartilage

Limb

Zeugopod Synovial Joint

Central Intermediate Lamina Cells

Cartilage

Limb

Zeugopod Synovial Joint

Interzone Cells

Cartilage

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 10/14 LifeMap Cells (see all 14)

Name

Category

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PureStem™ mesenchymal progenitor MEL2 (Embryonic Progenitor Cell)

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PureStem™ mesenchymal progenitor 7SMOO32 (Embryonic Progenitor Cell)

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PureStem™ mesenchymal progenitor E15 (Embryonic Progenitor Cell)

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PureStem™ progenitor EN13 (Embryonic Progenitor Cell)

Connective tissue progenitor cells (Generation of connec...)

Embryoid bodies (Generation of adipoc...)

Midbrain dopaminergic-like neurons (Generation of midbra...)

Trophoblast-like cells (Generation of tropho...)

Embryoid bodies (Two-step protocol fo...)

See COL3A1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for COL3A1

SOURCE GeneReport for Unigene cluster: Hs.443625

SABiosciences Expression via Pathway-Focused PCR Arrays including COL3A1 (see all 8):

Osteogenesis in human mouse rat

Fibrosis in human mouse rat

Extracellular Matrix & Adhesion Molecules in human mouse rat

Atherosclerosis in human mouse rat

Wound Healing in human mouse rat

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for COL3A1 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat COL3A1
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat COL3A1
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat COL3A1

In Situ
Assay Products:

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(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)
About This Section

This gene was present in the common ancestor of eukaryotes.

Orthologs for COL3A1 gene from 7/21 species (see all 21) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	COL3A1¹	collagen, type III, alpha 1	72.82(n) 74.71(a)		396340 NM_205380.2 NP_990711.2
lizard (Anolis carolinensis)	Reptilia	COL3A1⁶ -- (see all 3)	--	73(a) 7(a) (see all 3)	1 ↔ 1 possible ortholog (see all 3)	GL343290.1(1466689-1529674) 5(3529736-3603275)
African clawed frog (Xenopus laevis)	Amphibia	BC060753.1²	--	77.76(n)		BC060753.1
zebrafish (Danio rerio)	Actinopterygii	col6a3⁶ cmn⁶	calymmin	7(a)	possible ortholog possible ortholog	9(25017211-25027570) 12(14224584-14270293)
fruit fly (Drosophila melanogaster)	Insecta	pygo⁶	pygopus	9(a)	possible ortholog	3R(27401557-27406412)
worm (Caenorhabditis elegans)	Secernentea	bli-1⁶ col-44⁶ (see all 48)	COLlagen family member (col-44) (see all 48)	7(a) 33(a) (see all 48)	possible ortholog possible ortholog (see all 48)	II(10708901-10712066) X(13591428-13592391)
thale cress (Arabidopsis thaliana)	eudicotyledons	AT1G15830¹	hypothetical protein	45.83(n) 37.75(a)		838153 NM_101451.1 NP_173035.1

ENSEMBL Gene Tree for COL3A1 (if available)
TreeFam Gene Tree for COL3A1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for COL3A1 gene

COL4A6² COL19A1² COL11A2² COL4A5² COL24A1² COL4A4² COL5A3² COL1A1²

COL16A1² COL4A2² COL5A2² COL5A1² COL4A3² COL22A1² COL7A1² COL1A2²

COL27A1² COL2A1² COL4A1² COL11A1²

13 SIMAP similar genes for COL3A1 using alignment to 4 protein entries: CO3A1_HUMAN (see all proteins):

COL2A1 COL1A1 ECM2 COL5A2 COL1A2 COL7A1

SFTPD C1QTNF9 C1QTNF9B COL28A1 COL11A1 COL21A1

COL5A3

COL3A1 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 2 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs2271679^1,2	C,F,O,A,H,	non-pathogenic	181718627(+)	`CTTGTT/ATTTTC`	1	--	int¹ trp³		14		EA MN NS WA CSA NA	2553
rs1800255^1,2	C,F,H,	non-pathogenic	181723762(+)	`GTGGAA/GCTGGT`	2	T A	mis¹		35		EA MN NA NS CSA WA	9797
rs113485686^1,2	C,F	pathogenic	181725962(+)	`CCCCCG/AGACTT`	2	/R /G	mis¹		1		NS	962
rs112456072^1,2	C	pathogenic	181733335(+)	`TCCTGG/AACCTC`	2	/E /G	mis¹		1		NS	1134
rs41263773^1,2	C,F,	probable-non-pathogenic	181723705(+)	`CTGGTG/ACCCCT`	2	/T /A	mis¹		4		MN NA NS	4466
rs121912914^1,2	C	probable-pathogenic	181730808(+)	`TCCAGA/G/TCCCAC`	3	D G V	mis¹		0	--	--	--	--
rs114299724^1,2	C,F,	unknown	181721725(+)	`TTCCCT/CAACTG`	1	--	int¹		2		NA EU	1313
rs16830961^1,2	C,F,H,	--	181696738(+)	`AAACTA/GTGTTT`	1	--	us2k¹		10		NA NS EA WA	792
rs13009064^1,2	C,H	--	181697437(+)	`GAGAAA/GGATGA`	1	--	us2k¹ tfbs³ trp³		4		NS EA	416
rs17358566^1,2	C,F,H,	--	181697628(+)	`TCCACC/TGTAGA`	1	--	us2k¹		22		NA NS EA WA	2620

HapMap Linkage Disequilibrium report for COL3A1 (189839046 - 189877472 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for COL3A1: --
Human Gene Mutation Database (HGMD): COL3A1

Locus Specific Mutation Databases (LSDB): COL3A1

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing COL3A1

DNA2.0 Custom Variant and Variant Library Synthesis for COL3A1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

COL3A1 for disorders           About GeneDecksing

OMIM gene information: 120180
OMIM disorders: 130050  130020
UniProtKB/Swiss-Prot: CO3A1_HUMAN, P02461

Defects in COL3A1 are a cause of Ehlers-Danlos syndrome type 3 (EDS3) [MIM:130020]; also known as benign

hypermobility syndrome. EDS is a connective tissue disorder characterized by hyperextensible skin, atrophic cutaneous

scars due to tissue fragility and joint hyperlaxity. EDS3 is a form of Ehlers-Danlos syndrome characterized by marked

joint hyperextensibility without skeletal deformity

Defects in COL3A1 are the cause of Ehlers-Danlos syndrome type 4 (EDS4) [MIM:130050]. EDS is a connective

tissue disorder characterized by hyperextensible skin, atrophic cutaneous scars due to tissue fragility and joint

hyperlaxity. EDS4 is the most severe form of the disease. It is characterized by the joint and dermal manifestations

as in other forms of the syndrome, characteristic facial features (acrogeria) in most patients, and by proneness to

spontaneous rupture of bowel and large arteries. The vascular complications may affect all anatomical areas

Defects in COL3A1 are a cause of susceptibility to aortic aneurysm abdominal (AAA) [MIM:100070]. AAA is a

common multifactorial disorder characterized by permanent dilation of the abdominal aorta, usually due to degenerative

changes in the aortic wall. Histologically, AAA is characterized by signs of chronic inflammation, destructive

remodeling of the extracellular matrix, and depletion of vascular smooth muscle cells

20/53 diseases for COL3A1 (see all 53): About MalaCards

ehlers-danlos syndrome ehlers-danlos syndrome type iv acrogeria, gottron type familial thoracic aortic aneurysm and dissection

larsen-like syndrome loeys-dietz syndrome thoracic aortic aneurysm osteogenesis imperfecta

mitral valve prolapse diffuse large b-cell lymphoma aortic aneurysm patent ductus arteriosus

usual interstitial pneumonia connective tissue disease hiatus hernia b-cell lymphomas

intracranial aneurysm abdominal aortic aneurysm marfan syndrome uterine fibroid

3 diseases from the University of Copenhagen DISEASES database for COL3A1:

Ehlers-Danlos syndrome Loeys-Dietz syndrome Pneumothorax

10/19 Novoseek disease relationships for COL3A1 gene (see all 19) About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
eds iv	96.8	10	1757960 (1), 7833919 (1), 9036918 (1), 8411057 (1) (see all 10)
ehlers-danlos syndrome	95.9	54	1757960 (2), 8317500 (2), 7487954 (2), 11577371 (2) (see all 46)
ehlers-danlos syndrome, type ii	78.5	1	2049575 (1)
ehlers-danlos syndrome, type i	78.5	1	1684560 (1)
vascular rupture	76.6	1	8881656 (1)
connective tissue diseases	69.4	3	9546243 (1), 17053184 (1), 19751346 (1)
marfan syndrome	56.6	1	19639654 (1)
osteogenesis imperfecta	53.8	3	8950675 (1), 18272325 (1), 1905723 (1)
intracranial aneurysm	53.3	12	18642782 (3), 10436112 (2), 8255472 (1)
collagen fibril	52.6	1	9036918 (1)

GeneTests: COL3A1

Ehlers-Danlos Syndrome, Vascular Type

Genetic Association Database (GAD): COL3A1
Human Genome Epidemiology (HuGE) Navigator: COL3A1 (25 documents)

Export disorders for COL3A1 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)
About This Section

PubMed articles for COL3A1 gene, integrated from 9 sources (see all 264):
(articles sorted by number of sources associating them with COL3A1)

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

A base substitution at a splice site in the COL3A1 gene causes exon skipping and generates abnormal type III procollagen in a patient with Ehlers-Danlos syndrome type IV. (PubMed id 2145268)^{1, 2, 7, 9} Cole W.G.... Bateman J.F. (1990)
Nucleotide and amino acid sequences of the entire human alpha 1 (III) collagen. (PubMed id 2780304)^{1, 2, 3} Janeczko R.A. and Ramirez F. (1989)
Analysis of the COL3A1 gene in patients with spontaneous cervical artery dissections. (PubMed id 12140670)^{1, 4, 9} von Pein F....Grond-Ginsbach C. (2002)
Association between COL3A1 collagen gene exon 31 polymorphism and risk of floppy mitral valve/mitral valve prolapse. (PubMed id 15193836)^{1, 4, 9} Chou H.T....Tsai F.J. (2004)
Parental somatic and germ-line mosaicism for a multiexon deletion with unusual endpoints in a type III collagen (COL3A1) allele produces Ehlers-Danlos syndrome type IV in the heterozygous offspring. (PubMed id 8317500)^{1, 2, 9} Milewicz D.M....Byers P.H. (1993)
Genomic organization of the human COL3A1 and COL5A2 genes: COL5A2 has evolved differently than the other minor fibrillar collagen genes. (PubMed id 11566270)^{1, 2, 9} Valkkila M....Ala-Kokko L. (2001)
Mutations in the COL3A1 gene result in the Ehlers-Danlos syndrome type IV and alterations in the size and distribution of the major collagen fibrils of the dermis. (PubMed id 9036918)^{1, 2, 9} Smith L.T.... Byers P.H. (1997)
Ehlers-Danlos syndrome type IV: unusual congenital anomalies in a mother and son with a COL3A1 mutation and a normal collagen III protein profile. (PubMed id 12694234)^{1, 2, 9} Kroes H.Y.... van Essen A.J. (2003)
Characterization of 11 new mutations in COL3A1 of individuals with Ehlers-Danlos syndrome type IV: preliminary comparison of RNase cleavage, EMC and DHPLC assays. (PubMed id 10923041)^{1, 2, 9} Giunta C. and Steinmann B. (2000)
Abnormal type III collagen produced by an exon-17-skipping mutation of the COL3A1 gene in Ehlers-Danlos syndrome type IV is not incorporated into the extracellular matrix. (PubMed id 7487954)^{1, 2, 9} Chiodo A.A.... Bateman J.F. (1995)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		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)
About This Section

Entrez Gene: 1281	HGNC: 2201	AceView: COL3A1	Ensembl:ENSG00000168542	euGenes: HUgn1281
ECgene: COL3A1	Kegg: 1281	H-InvDB: COL3A1

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for COL3A1	Pharmacogenomics, SNPs, Pathways
COL3A1	http://www.le.ac.uk/genetics/collagen/col3a1.html
GeneReviews	http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL3A1
Wikipedia	http://en.wikipedia.org/wiki/Type-III_collagen

Intellectual Property for COL3A1 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 COL3A1 gene:
Search GeneIP for patents involving COL3A1

GeneCards and IP:
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COL3A1 Gene

collagen, type III, alpha 1

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EHLERS-DANLOS SYNDROME, TYPE II
EDS IV
Coronary Artery Disease
Ehlers-Danlos Syndrome, Vascular Type
perforation
Intracranial Aneurysm
Osteogenesis Imperfecta
vascular rupture
EHLERS-DANLOS SYNDROME, TYPE I
genetic disorder
Sclerosis Systemic
Peritonitis
Ehlers-Danlos Syndrome
Rhabdomyosarcoma
Aneurysm
Connective Tissue Diseases
Collagen fibril
Pregnancy Complications
Marfan Syndrome
Myocardial Infarction

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COL3A1 Gene

collagen, type III, alpha 1

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