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COL23A1 Gene

protein-coding GIFtS: 49

GC05M177597

collagen, type XXIII, alpha 1
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

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

Aliases
DKFZp434K0621 ^¹, ²

Descriptions
collagen, type XXIII, alpha 1 ^²
procollagen, type XXIII, alpha 1 ^²

External Ids
HGNC: 22990¹
Entrez Gene: 91522²
UniProtKB: Q86Y22³
Ensembl: ENSG00000050767⁷

Search outside databases for aliases for COL23A1 gene

Previous GC identifers: GC05M177733 GC05M177778

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

EntrezGene summary for COL23A1:

COL23A1 is a member of the transmembrane collagens, a subfamily of the nonfibrillar collagens that

contain a single pass hydrophobic transmembrane domain (Banyard et al., 2003 [PubMed

12644459]).[supplied by OMIM]

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the COL23A1 gene

Entrez Gene cytogenetic band: 5q35.3 Ensembl cytogenetic band: 5q35.3 HGNC cytogenetic band: 5q35.3

COL23A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 5 GeneLoc Exon Structure

GeneLoc location for GC05M177597: (about GC identifiers)

Start:	177,597,225 bp from pter
End:	177,950,162 bp from pter
Size:	352,938 bases
Orientation:	minus strand

RefSeq DNA sequence:

NC_000005.8 NT_023133.12

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: CONA1_HUMAN, Q86Y22 (See protein sequence)

Recommended Name: Collagen alpha-1(XXIII) chain

Size: 540 amino acids; 51944 Da

Subunit: Homotrimer (By similarity)

Subcellular location: Cell membrane; Single-pass type II membrane protein; Extracellular side (By

similarity)

Secondary accessions: Q8IVR4 Q9NT93

Alternative splicing: 2 isoforms: Q86Y22-1 Q86Y22-2

Post-translational modifications:

Undergoes proteolytic cleavage by furin protease to yield a 60 kDa soluble form that forms an

homotrimer and exhibits a low affinity interaction with heparin (By similarity)¹

REFSEQ proteins: NP_775736.2

ENSEMBL proteins:

ENSP00000375069 ENSP00000385092

Human Recombinant Proteins

	Browse Drug Discovery Central at Invitrogen for human recombinant proteins
	Browse Purified and Recombinant Proteins at Millipore
	Browse Human Recombinant Proteins at Sigma-Aldrich
	R&D Systems Recombinant & Natural Proteins for COL23A1 (Collagen XXIII alpha 1)
	Browse recombinant and purified proteins available from Enzo Life Sciences
	Recombinant Proteins from Abcam (COL23A1)
	Human Recombinant Proteins from Abnova (COL23A1)

Browse Origene for full length recombinant human proteins expressed in human HEK293 cells

2 Gene Ontology (GO) cellular component terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005886	plasma membrane	IEA	--
GO:0016021	integral to membrane	IEA	--

About this table

Antibodies for COL23A1:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Sigma-Aldrich Antibodies for COL23A1
	Browse R&D Systems for Antibodies
	Antibodies from Abcam (COL23A1), each with their Abpromise^SM
	Monoclonal and Polyclonal Antibodies from Abnova (COL23A1)
	Novus Biologicals Antibodies for COL23A1

Assays for COL23A1:

	Browse Invitrogen for biochemical assays
	Browse Kits and Assays available from Millipore
	Browse R&D Systems for biochemical assays
	Browse biochemical assays available from Enzo Life Sciences

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

Graphical View of Domain Structure for InterPro Entry Q86Y22

ProtoNet protein and cluster: Q86Y22

2 Blocks protein families:

IPB008160 Collagen triple helix repeat

IPB008161 Collagen helix repeat

UniProtKB/Swiss-Prot: CONA1_HUMAN, Q86Y22

Similarity: Contains 5 collagen-like domains

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (COL23A1)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (COL23A1)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_173465

Applied Biosystems Silencer® siRNAs for COL23A1

Sigma-Aldrich siRNA for COL23A1

Browse shRNA at Sigma-Aldrich

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for COL23A1
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_173465
Myc/DDK tagged cDNA clone in CMV expression vector: NM_173465
untagged cDNA clone in CMV expression vector: NM_173465

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_173465

1 Gene Ontology (GO) molecular function term (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005515	protein binding	IPI	15231747

About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

1 Interacting protein for COL23A1 (Q86Y22¹) via UniProtKB, MINT, and/or STRING
Interactant Interaction Details
GeneCard External ID(s)
LSM8 O95777¹ EBI-373279, EBI-347779
About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for COL23A1

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (COL23A1)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (COL23A1)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_173465

Sigma-Aldrich siRNA for COL23A1

Browse shRNA at Sigma-Aldrich

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_173465

REFSEQ mRNAs for COL23A1 gene:

NM_173465.3

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_173465

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_173465
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_173465
                                 untagged cDNA clone in CMV expression vector: NM_173465

Additional cDNA sequence:

AL137461.1 AY158895.1 AY898961.1

5 DOTS entries:

DT.100740250 DT.406862 DT.75125190 DT.95249322 DT.91842038

2 AceView cDNA sequences:

BV191746 AI420126

highest scoring ESTs for COL23A1:

AI147035 AI420126 AY158895 AA323948 AA400449 AA746228 AA863140 AA873232 AI092311 AI126221

Unigene Cluster for COL23A1:

Collagen, type XXIII, alpha 1

Hs.660026 [show with all ESTs]

Unigene Representative Sequence: NM_173465

GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for COL23A1

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

About this scheme

ECgene alternative splicing isoforms for COL23A1

2 Ensembl transcripts including schematic representations:

ENST00000390654 ENST00000407622

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

COL23A1 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for COL23A1

¹ / ² / ³

3 probe-sets matching COL23A1 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
46106_at²^{, 3}	U95-B	1	1.00	1.00	1.00	1.00	AI147035	0.80	1.00	0.91	1
229168_at²^{, 3}	U133-B	1	1.00	1.00	--	--	AI690433	0.60	1.00	0.82	1
229168_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--

About this table

Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.660026

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for COL23A1 gene from 5 species

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	COL23A1¹	--	collagen, type XXIII, alpha 1	89.08(n) 90.17(a)	607556 XM_844285.1 XP_849378.1
cow (Bos taurus)	COL23A1¹	--	collagen, type XXIII, alpha 1	85.25(n) 86.25(a)	613347 XM_864013.2 XP_869106.2
rat (Rattus norvegicus)	Col23a1¹	--	collagen, type XXIII, alpha 1	85.19(n) 91.49(a)	353303 NM_181636.2 NP_853667.1
mouse (Mus musculus)	Col23a1^{1, 5}	11⁵	collagen, type XXIII, alpha 1^{1, 5}	85.38(n)¹ 91.3(a)¹	237759¹ NM_153393.1¹ NP_700442.1¹ AF410792⁵ AI429655⁵ (see all 12)
zebrafish (Danio rerio)	DKEYP-44A8.4¹	--	novel protein with Collagen triple helix repeat (2 more	61.18(n) 64.41(a)	567373 XM_690666.3 XP_695758.3

About this table Species with no ortholog for COL23A1

ENSEMBL Gene Tree for COL23A1

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

Paralogs for COL23A1 gene

COL25A1² COL13A1²

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/2941 NCBI SNPs in COL23A1 are shown (see all 2941 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 917)

AB	SNP ID	Valid	Chr 5 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
	rs1544926^1,2	A,C,F,H,O	177597948(-)	`CCTGCC/TCCCGC`	1	--	ut3¹		9		MN EU EA WA	1022
	rs596780^1,2	A,C,F,H,O	177951271(-)	`CTTGTA/GAGAGG`	1	--	ng3¹		9		NA EA EU WA	838
	rs890802^1,2	A,C,F,H,O	177615983(-)	`GAGGCA/GCGGAT`	1	T/A	mis¹ ese³		13		EA NA EU WA	1126
--	rs574103^1,2	A,C,F,O	177951340(-)	`ATACAT/AGCAGT`	1	--	ng3¹ tfbs³		9		NA EA NS	453
	rs7715762^1,2	A,C,F,H	177596903(+)	`aaatcG/Accatt`	1	--	ng5¹		4		EU EA WA	420
	rs13741^1,2	A,C,F,H	177597606(-)	`TGTCGG/AGGATG`	1	--	ut3¹		5		MN EU EA WA	497
--	rs721143^1,2	A,C,O	177951637(-)	`CAAGTA/CAGTCA`	1	--	ng3¹		0	--	--	--	--
--	rs721144^1,2	A,C	177951757(-)	`TGCTTC/TGGCCT`	1	--	ng3¹		0	--	--	--	--
	rs1967419^1,2	A,C	177950301(-)	`GCTCCA/GGCCAG`	1	--	ng3¹ tfbs³		0	--	--	--	--
--	rs721142^1,2	A,C	177951814(-)	`CCAGGG/TTTCCC`	1	--	ng3¹		0	--	--	--	--

About this table

HapMap Linkage Disequilibrium images for COL23A1 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 610043

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
About This Section

7 PubMed articles for COL23A1 gene:

Type XXIII collagen, a new transmembrane collagen identified in metastatic tumor cells. (PubMed id 12644459)^{2, 3, 4} Banyard J.... Zetter B.R. (2003)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{3, 4} Gerhard D.S....Malek J. (2004)
Shedding of collagen XXIII is mediated by furin and depends on the plasma membrane microenvironment. (PubMed id 17627939)³ Veit G....Koch M. (2007)
The full-ORF clone resource of the German cDNA Consortium. (PubMed id 17974005)⁴ Bechtel S....Schupp I. (2007)
Expression of type XXIII collagen mRNA and protein. (PubMed id 16728390)³ Koch M....Gordon M.K. (2006)
A protein interaction framework for human mRNA degradation. (PubMed id 15231747)³ Lehner B. and Sanderson C.M. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)³ Strausberg R.L....Marra M.A. (2002)

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

		AND	OR
Aliases
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, and/or H-InvDB)
About This Section

Entrez Gene: 91522	HGNC: 22990	AceView: COL23A1.1	Ensembl:ENSG00000050767	euGenes: HUgn91522
ECgene: COL23A1	H-InvDB: COL23A1

(According to HUGE)
About This Section

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

Licensable Technologies for COL23A1
(Available from WIS Yeda, Salk, Tufts)

About This Section

(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section

Products for COL23A1:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for COL23A1-related products

	Millipore Custom Antibody & Bulk Services
	Millipore Preclinical / Clinical Development Services
	Millipore Immunoassay Services
	Millipore Target Screening & Profiling Services

	Predesigned and custom siRNAs for COL23A1		Antibodies for COL23A1
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Browse shRNAs at Sigma-Aldrich		Browse small molecules at Sigma-Aldrich
	"Your Favorite Gene" Pathways		feedback

	Antibodies		Primer Pairs
	Cell Culture Products		ELISAs
	Flow Cytometry Kits		Protease Activity Assays & Reagents
	Cell Selection/Detection Kits & Reagents		ELISA/Assay Development Kits & Reagents
	Multiplex/Array Assay Kits & Reagents		ELISpot Kits & Development Modules
	Recombinant & Natural Proteins

	Recombinant Proteins (COL23A1)
	Antibodies (COL23A1)
	Chimera RNAi (COL23A1)
	Custom Service for Mouse Mab
	Custom Service for Rabbit Pab from Full-length Protein

Search for Antibodies & Assays

	Recombinant Proteins (COL23A1)
	Antibodies (COL23A1)

Search OriGene for COL23A1

Search Tocris compounds for COL23A1

Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies

Antibodies for COL23A1

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COL23A1 Gene

protein-coding GIFtS: 49

Aliases &
Descriptions
for COL23A1

Summaries
for COL23A1

Genomic Location
for COL23A1

Proteins
for COL23A1

Protein Domains/
Families
for COL23A1

Gene Function
for COL23A1

Pathways & Interactions
for COL23A1

Drugs & Compounds
for COL23A1

Transcripts
for COL23A1

Expression
for COL23A1

Orthologs
for COL23A1

Paralogs
for COL23A1

SNPs/Variants
for COL23A1

Disorders & Mutations
for COL23A1

Medical News
for COL23A1

Publications
for COL23A1

Search for COL23A1

Genome Databases showing COL23A1

Other Databases showing COL23A1

Specialized Databases showing COL23A1

Licensable Technologies
for COL23A1

Services
for COL23A1

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

COL23A1 Gene

protein-coding GIFtS: 49

Aliases & Descriptionsfor COL23A1

Summariesfor COL23A1

Genomic Locationfor COL23A1

Proteinsfor COL23A1

Protein Domains/Familiesfor COL23A1

Gene Functionfor COL23A1

Pathways & Interactionsfor COL23A1

Drugs & Compoundsfor COL23A1

Transcriptsfor COL23A1

Expression for COL23A1

Orthologsfor COL23A1

Paralogsfor COL23A1

SNPs/Variantsfor COL23A1

Disorders & Mutationsfor COL23A1

Medical Newsfor COL23A1

Publicationsfor COL23A1

Search for COL23A1

Genome Databases showing COL23A1

Other Databases showing COL23A1

Specialized Databases showing COL23A1

Licensable Technologiesfor COL23A1

Servicesfor COL23A1

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for COL23A1

Summaries
for COL23A1

Genomic Location
for COL23A1

Proteins
for COL23A1

Protein Domains/
Families
for COL23A1

Gene Function
for COL23A1

Pathways & Interactions
for COL23A1

Drugs & Compounds
for COL23A1

Transcripts
for COL23A1

Expression
for COL23A1

Orthologs
for COL23A1

Paralogs
for COL23A1

SNPs/Variants
for COL23A1

Disorders & Mutations
for COL23A1

Medical News
for COL23A1

Publications
for COL23A1

Licensable Technologies
for COL23A1

Services
for COL23A1