Human Gene CNTN2 (uc009xbi.3)
  Description: Homo sapiens contactin 2 (axonal) (CNTN2), mRNA.
RefSeq Summary (NM_005076): This gene encodes a member of the contactin family of proteins, part of the immunoglobulin superfamily of cell adhesion molecules. The encoded glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein plays a role in the proliferation, migration, and axon guidance of neurons of the developing cerebellum. A mutation in this gene may be associated with adult myoclonic epilepsy. [provided by RefSeq, Sep 2016].
Transcript (Including UTRs)
   Position: hg19 chr1:205,027,309-205,031,463 Size: 4,155 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr1:205,027,632-205,031,237 Size: 3,606 Coding Exon Count: 5 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:205,027,309-205,031,463)mRNA (may differ from genome)Protein (296 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMalacardsMGIPubMedWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CNTN2
CDC HuGE Published Literature: CNTN2
Positive Disease Associations: Stroke , Waist Circumference
Related Studies:
  1. Stroke
    , , . [PubMed 0]
  2. Waist Circumference
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: CNTN2
Diseases sorted by gene-association score: epilepsy, myoclonic, familial adult, 5* (1050), benign adult familial myoclonic epilepsy* (247), tropical spastic paraparesis (34), adult t-cell leukemia (25), myelopathy, htlv-1-associated (21), human t-cell leukemia virus type 1 (14), t-cell leukemia (12), demyelinating polyneuropathy (11), van der woude syndrome (10), chronic inflammatory demyelinating polyneuropathy (9), multifocal motor neuropathy (9), tremor (8), human t-cell leukemia virus type 2 (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 94.83 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 399.76 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -126.40323-0.391 Picture PostScript Text
3' UTR -97.10226-0.430 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  CR749495 - Homo sapiens mRNA; cDNA DKFZp781D102 (from clone DKFZp781D102).
X67734 - H.sapiens mRNA for transient axonal glycoprotein (tag-1).
X68274 - Homo sapiens mRNA for TAG-1/axonin-1 precursor (TAG-1 gene).
BC129986 - Homo sapiens contactin 2 (axonal), mRNA (cDNA clone MGC:157722 IMAGE:40128240), complete cds.
AK289985 - Homo sapiens cDNA FLJ75250 complete cds, highly similar to Homo sapiens contactin 2 (axonal) (CNTN2), mRNA.
KJ897638 - Synthetic construct Homo sapiens clone ccsbBroadEn_07032 CNTN2 gene, encodes complete protein.
AB384410 - Synthetic construct DNA, clone: pF1KSDB6001, Homo sapiens CNTN2 gene for contactin-2 precursor, complete cds, without stop codon, in Flexi system.
AB587327 - Synthetic construct DNA, clone: pF1KB7012, Homo sapiens CNTN2 gene for contactin 2, without stop codon, in Flexi system.
AK309108 - Homo sapiens cDNA, FLJ99149.
AK124736 - Homo sapiens cDNA FLJ42746 fis, clone BRAWH3000166, highly similar to Contactin-2 precursor.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04514 - Cell adhesion molecules (CAMs)

-  Other Names for This Gene
  Alternate Gene Symbols: AK309108
UCSC ID: uc009xbi.3
RefSeq Accession: NM_005076

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK309108.1
exon count: 5CDS single in 3' UTR: no RNA size: 1238
ORF size: 891CDS single in intron: no Alignment % ID: 99.92
txCdsPredict score: 1708.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 334# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.