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CTXN3 Gene

protein-coding   GIFtS: 39
GCID: GC05P127013

Cortexin 3

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Cortexin 31 2
Kidney And Brain-Expressed Protein2 3
KABE2 3
cortexin-32

External Ids:    HGNC: 311101   Entrez Gene: 6132122   Ensembl: ENSG000002052797   UniProtKB: Q4LDR23   

Export aliases for CTXN3 gene to outside databases

Previous GC identifers: GC05U900493 GC05P122176


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for CTXN3 Gene:
CTXN3 (cortexin 3) is a protein-coding gene. An important paralog of this gene is CTXN2.


(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)
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RefSeq DNA sequence at NCBI GenBank:
NC_000005.9  NC_018916.2  NT_034772.7  
Regulatory elements:
   Regulatory transcription factor binding sites in the CTXN3 gene promoter:
         Nkx3-1   Nkx3-1 v4   CUTL1   Nkx3-1 v1   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   RORalpha1   Nkx3-1 v2   Nkx3-1 v3   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CTXN3


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

Entrez Gene cytogenetic band: 5q23.2   Ensembl cytogenetic band:  5q23.2   HGNC cytogenetic band: 5q23.2

CTXN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CTXN3 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P127013:  view genomic region     (about GC identifiers)

Start:
126,984,713 bp from pter      End:
126,994,322 bp from pter
Size:
9,610 bases      Orientation:
plus strand

(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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
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UniProtKB/Swiss-Prot: CTXN3_HUMAN, Q4LDR2 (See protein sequence)
Recommended Name: Cortexin-3  
Size: 81 amino acids; 8933 Da
Secondary accessions: B2RV32 D3DQ82

Explore the universe of human proteins at neXtProt for CTXN3: NX_Q4LDR2

REFSEQ proteins (2 alternative transcripts): 
NP_001041717.1  NP_001120857.1  

ENSEMBL proteins: 
 ENSP00000368758   ENSP00000378732  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR020066 Cortexin

Graphical View of Domain Structure for InterPro Entry Q4LDR2

ProtoNet protein and cluster: Q4LDR2

UniProtKB/Swiss-Prot: CTXN3_HUMAN, Q4LDR2
Similarity: Belongs to the cortexin family


Find genes that share domains with CTXN3           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for CTXN3

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(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
CTXN3_HUMAN, Q4LDR2: Membrane; Single-pass membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
plasma membrane3
cytosol1
extracellular1
golgi apparatus1
mitochondrion1

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane IEA--
GO:0031224intrinsic component of membrane ----

Find genes that share ontologies with CTXN3           About GenesLikeMe


(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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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CTXN3
Interactions:

    Search GeneGlobe Interaction Network for CTXN3

(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 Tocris compounds for CTXN3



(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,
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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for CTXN3 gene (2 alternative transcripts): 
NM_001048252.2  NM_001127385.1  

Unigene Cluster for CTXN3:

Cortexin 3
Hs.66194  [show with all ESTs]
Unigene Representative Sequence: NM_001048252
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000379445(uc003kul.4) ENST00000514851 ENST00000395322(uc003kum.4)

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Additional mRNA sequence: 

AB219764.1 AB219832.1 BC071790.1 BC147012.1 

2 DOTS entries:

DT.453800  DT.101967156 

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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CTXN3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TGTAGAGGTA
CTXN3 Expression
About this image


CTXN3 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 4) fully expand
 
 Kidney (Urinary System)
         Metanephros
 
 Intermediate Mesoderm (Gastrulation Derivatives)
         Mesonephros
 
 Head Mesenchyme (Muscoskeletal System)
         Frontonasal Process
 
 Ovary (Reproductive System)
CTXN3 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.66194
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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)
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This gene was present in the common ancestor of chordates.

Orthologs for CTXN3 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ctxn31 , 5 cortexin 31, 5 87.5(n)1
93.75(a)1
  18 (32.15 cM)5
6291471  NM_001134697.11  NP_001128169.11 
 574684865 
chicken
(Gallus gallus)
Aves LOC1008593281 cortexin-3-like 76.13(n)
79.01(a)
  100859328  XM_004949376.1  XP_004949433.1 
lizard
(Anolis carolinensis)
Reptilia CTXN36
cortexin 3
65(a)
1 ↔ 1
2(29781499-29781741)
tropical clawed frog
(Xenopus tropicalis)
Amphibia ctxn31 cortexin 3 69.66(n)
73.08(a)
  100216131  NM_001171688.2  NP_001165159.2 
zebrafish
(Danio rerio)
Actinopterygii LOC1003313021 cortexin-3-like 67.1(n)
71.43(a)
  100331302  XM_002663503.2  XP_002663549.1 


ENSEMBL Gene Tree for CTXN3 (if available)
TreeFam Gene Tree for CTXN3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for CTXN3 gene
CTXN22  CTXN12  
2 SIMAP similar genes for CTXN3 using alignment to 1 protein entry:     CTXN3_HUMAN:
CTXN2    CTXN1

Find genes that share paralogs with CTXN3           About GenesLikeMe



(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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Selected SNPs for CTXN3 (see all 277)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs65957871,2
C,F,A,H--126982737(+) TGTATC/TTGAGC 1 -- us2k119Minor allele frequency- T:0.19NS EA NA WA CSA 2340
rs1153321021,2
F--126982832(+) ATAAAG/AATTAT 1 -- us2k11Minor allele frequency- A:0.01WA 118
rs13823301,2
C,F,H--126982856(-) TAGATC/ACTATT 1 -- us2k1 tfbs36Minor allele frequency- A:0.21NS EA WA 528
rs1440284811,2
C--126982857(+) ATAGGA/TTCTAA 1 -- us2k10--------
rs1895496951,2
--126982872(+) AAATGA/TTCAAA 1 -- us2k10--------
rs1819404361,2
--126982882(+) ATGGAA/CCTTTG 1 -- us2k10--------
rs1849173151,2
--126983061(+) TAGTTC/TGGCTT 1 -- us2k10--------
rs1890492831,2
--126983104(+) TGGAGG/TGGTTA 1 -- us2k10--------
rs1148551971,2
F--126983131(+) AGCAAG/AGACAG 1 -- us2k11Minor allele frequency- A:0.05WA 118
rs1398072211,2
--126983151(+) AAATGC/TGCCAA 1 -- us2k10--------

HapMap Linkage Disequilibrium report for CTXN3 (126984713 - 126994322 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for CTXN3:    About this table    
Variant IDTypeSubtypePubMed ID
nsv830480CNV Loss17160897
nsv830479CNV Gain17160897

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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.)
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Find genes that share disorders with CTXN3           About GenesLikeMe

Genetic Association Database (GAD): CTXN3
Human Genome Epidemiology (HuGE) Navigator: CTXN3 (1 document)

Export disorders for CTXN3 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 CTXN3 gene, integrated from 10 sources (see all 12):
(articles sorted by number of sources associating them with CTXN3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A genome-wide association study of schizophrenia using brain activation as a quantitative phenotype. (PubMed id 19023125)1, 4 Potkin S.G....Macciardi F. (Schizophr Bull 2009)
  2. Association of CTXN3-SLC12A2 polymorphisms and schizophrenia in a Thai population. (PubMed id 22643131)1 Panichareon B....Sukhumsirichart W. (Behav Brain Funct 2012)
  3. Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness. (PubMed id 17903302)4 Levy D....Mitchell G.F. (BMC Med. Genet. 2007)
  4. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)
  5. Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project. (PubMed id 17903300)4 Fox C.S....Atwood L.D. (BMC Med. Genet. 2007)
  6. Genome-wide association of sleep and circadian phenotypes. (PubMed id 17903308)4 Gottlieb D.J....Wilk J.B. (BMC Med. Genet. 2007)
  7. Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. (PubMed id 17903301)4 Vasan R.S....Benjamin E.J. (BMC Med. Genet. 2007)
  8. In silico-initiated cloning and molecular characterization of cortexin 3, a novel human gene specifically expressed in the kidney and brain, and well conserved in vertebrates. (PubMed id 17786280)1 Wang H.T....Li B.G. (Int. J. Mol. Med. 2007)
  9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
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)
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Entrez Gene: 613212 HGNC: 31110 Ensembl:ENSG00000205279 euGenes: HUgn613212 ECgene: CTXN3
H-InvDB: CTXN3

(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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NameDescription
PharmGKB entry for CTXN3 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for CTXN3 gene:
Search GeneIP for patents involving CTXN3

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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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