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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

CCDC3 Gene

protein-coding GIFtS: 39
GCID: GC10M012938

coiled-coil domain containing 3

Search for CCDC3
in

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
Coiled-Coil Domain Containing 3¹ ²
Fat/Vessel-Derived Secretory Protein² ³
DKFZp761F241¹
Coiled-Coil Domain-Containing Protein 3²
Favine³
Favine³

External Ids:	HGNC: 23813¹	Entrez Gene: 83643²	Ensembl: ENSG00000151468⁷	UniProtKB: Q9BQI4³

Export aliases for CCDC3 gene to outside databases

Previous GC identifers: GC10M012943 GC10M012978

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

Gene Wiki entry for CCDC3

(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_000010.10 NC_018921.1 NT_008705.16

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the CCDC3 gene promoter:
AML1a NCX/Ncx MyoD STAT5A YY1 AREB6 Pax-3 POU2F1 POU2F1a En-1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: CCDC3 promoter sequence

Search SABiosciences Chromatin IP Primers for CCDC3

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CCDC3

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

Entrez Gene cytogenetic band: 10p13 Ensembl cytogenetic band: 10p13 HGNC cytogenetic band: 10p14

CCDC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC3 gene location

GeneLoc information about chromosome 10 GeneLoc Exon Structure

GeneLoc location for GC10M012938: view genomic region (about GC identifiers)

Start:	12,938,625 bp from pter	End:	13,141,652 bp from pter
Size:	203,028 bases	Orientation:	minus 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: CCDC3_HUMAN, Q9BQI4 (See protein sequence)

Recommended Name: Coiled-coil domain-containing protein 3 precursor

Size: 270 amino acids; 30731 Da

Subunit: Homodimer (By similarity)

Subcellular location: Secreted (By similarity)

Secondary accessions: Q5VYV8

Explore the universe of human proteins at neXtProt for CCDC3: NX_Q9BQI4

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9BQI4

CCDC3 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_113643.1

ENSEMBL proteins:

ENSP00000368116 ENSP00000368102

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Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	IEA	--
GO:0005783	endoplasmic reticulum	IDA	--

CCDC3 for ontologies About GeneDecksing

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

ProtoNet protein and cluster: Q9BQI4

(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: CCDC3_HUMAN, Q9BQI4

Induction: Up-regulated by pioglitazone and down-regulated by TNF in HUVEC

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(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

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for CCDC3

(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

Browse Small Molecules at EMD Millipore

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Search CenterWatch for drugs/clinical trials and news about CCDC3

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
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About This Section

REFSEQ mRNAs for CCDC3 gene:

NM_031455.3

Unigene Cluster for CCDC3:

Coiled-coil domain containing 3

Hs.498720 [show with all ESTs]

Unigene Representative Sequence: AK095792

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

ENST00000378839(uc009xjb.1 uc001ilr.2 uc009xjc.1 uc009xjd.1)

ENST00000378825(uc001ilq.1)

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Additional cDNA sequence:

AF190154.1 AK024578.1 AK095792.1 AK123393.1 AK124195.1 AK307203.1 AK307304.1 AL136562.1

BC051334.1

5 DOTS entries:

DT.452185 DT.101979320 DT.100751472 DT.95157924 DT.121250123

24/136 AceView cDNA sequences (see all 136):

BF594160 F25081 AI619787 AA709346 AW662224 BU726400 W81358 AI369042

AI582141 BF725142 AW439377 AA045504 AI921755 AI669775 AI924580 BE549983

T47013 AI690473 AA988084 BM712203 AA058939 BM705580 R67634 BP381775

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™, 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

CCDC3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GAAGCTACAC

About this image

CCDC3 expression in embryonic tissues and stem cells

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

7 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Kidney

S-shaped Body

Kidney Endothelial Cells

Endothelium

Neural Ectoderm

Brain

Brain

Mesencephalic Floor Plate

Neural Tube

Metencephalon

Neural Tube

Spinal Cord

Spinal Floor Plate

Spinal Cord

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 3 LifeMap Cells

Name

Category

PureStem™ progenitor E69 (Embryonic Progenitor Cell)

PureStem™ progenitor T36 (Embryonic Progenitor Cell)

Definitive endoderm-like cells (A scalable, suspensi...)

See CCDC3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CCDC3

SOURCE GeneReport for Unigene cluster: Hs.498720

UniProtKB/Swiss-Prot: CCDC3_HUMAN, Q9BQI4

Tissue specificity: Expressed in umbilical vein endothelial cells (HUVEC), and at lower levels in aortic smooth muscle

cells (HASMC)

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In Situ
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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 chordates.

Orthologs for CCDC3 gene from 5/11 species (see all 11) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Ccdc3^{1 , 5}	coiled-coil domain containing 3^{1, 5}	88.22(n)¹ 91.35(a)¹		2 (3.25 cM)⁵ 74186¹ NM_028804.1¹ NP_083080.1¹ 5137776⁵
chicken (Gallus gallus)	Aves	CCDC3¹	coiled-coil domain containing 3	75.95(n) 79.61(a)		769832 XM_003640333.1 XP_003640381.1
lizard (Anolis carolinensis)	Reptilia	CCDC3⁶	--	79(a)	1 ↔ 1	GL343349.1(82165-89277)
tropical clawed frog (Xenopus tropicalis)	Amphibia	Str.19636²	Transcribed sequence with moderate similarity to protein more	77.44(n)		BX781788.1
zebrafish (Danio rerio)	Actinopterygii	ccdc3¹	coiled-coil domain containing 3	68.68(n) 68.95(a)		560952 NM_001025510.1 NP_001020681.1

ENSEMBL Gene Tree for CCDC3 (if available)
TreeFam Gene Tree for CCDC3 (if available)

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

(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 10 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs10531955^1,2	C,	--	12938122(+)	`TTATG-/TGAGT TGAGT`	1	--	int¹		1		CSA	2
rs10565819^1,2	C	--	12938123(+)	`GAGTT-/GAGTT TGGAA`	1	--	int¹		1		NA	2
rs199903446^1,2		--	12938125(+)	`GTGAG-/TTTGAG`	1	--	int¹		0	--	--	--	--
rs80301986^1,2	C,F,	--	12938228(+)	`CATCAA/GGGTCG`	1	--	int¹		1		EA	120
rs73584054^1,2	C,	--	12938419(+)	`TGCAGG/CTGTGT`	1	--	int¹		1		WA	118
rs187519788^1,2		--	12938541(+)	`CCCCCA/CAGAGG`	1	--	int¹		0	--	--	--	--
rs200556020^1,2		--	12938724(+)	`ACATT-/ACCCTT`	1	--	ut3¹		0	--	--	--	--
rs3232^1,2	C,F,A,H,	--	12938754(+)	`GGGGGC/TGCAAA`	1	--	ut3¹ ese³		24		EA MN NA NS WA	3478
rs140678982^1,2	C,	--	12938900(+)	`TTCTG-/TCCAGT`	1	--	ut3¹		0	--	--	--	--
rs115893438^1,2	C,F,	--	12938927(+)	`TCCCCC/TGTGGA`	1	--	ut3¹		1		WA	118

HapMap Linkage Disequilibrium report for CCDC3 (12938625 - 13141652 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for CCDC3: --

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

(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 CCDC3 gene, integrated from 9 sources (see all 11):
(articles sorted by number of sources associating them with CCDC3)

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

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)^{1, 2} Wiemann S.... Poustka A. (2001)
Hundreds of variants clustered in genomic loci and bi ological pathways affect human height. (PubMed id 20881960)¹ Lango Allen H....Hirschhorn J.N. (2010)
Identification of a new secretory factor, CCDC3/Favin e, in adipocytes and endothelial cells. (PubMed id 20043878)² Kobayashi S....Shimomura I. (2010)
The LIFEdb database in 2006. (PubMed id 16381901)¹ Mehrle A....Wiemann S. (2006)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)¹ Ota T.... Sugano S. (2004)
The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)² Deloukas P.... Rogers J. (2004)
From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)¹ Wiemann S....Poustka A. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)
Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. (PubMed id 11256614)¹ Simpson J.C.... Wiemann S. (2000)

(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, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 83643	HGNC: 23813	AceView: CCDC3	Ensembl:ENSG00000151468	euGenes: HUgn83643
ECgene: CCDC3	H-InvDB: CCDC3

(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 CCDC3	Pharmacogenomics, SNPs, Pathways

Intellectual Property for CCDC3 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for CCDC3 gene:
Search GeneIP for patents involving CCDC3

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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About This Section


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GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 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

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes Disease genes CCDC3 gene at Home site.

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CCDC3 Gene

coiled-coil domain containing 3

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CCDC3 Gene

coiled-coil domain containing 3

Aliasesfor CCDC3 gene

Summariesfor CCDC3 gene

Genomic Viewsfor CCDC3 gene

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Protein Domains /Familiesfor CCDC3 gene

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for CCDC3 gene

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for CCDC3 gene

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for CCDC3 gene

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for CCDC3 gene

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