Human Gene CDON (ENST00000263577.11) from GENCODE V44
  Description: Homo sapiens cell adhesion associated, oncogene regulated (CDON), transcript variant 2, mRNA. (from RefSeq NM_016952)
RefSeq Summary (NM_016952): This gene encodes a cell surface receptor that is a member of the immunoglobulin superfamily. The encoded protein contains three fibronectin type III domains and five immunoglobulin-like C2-type domains. This protein is a member of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells and positively regulates myogenesis. [provided by RefSeq, Aug 2011].
Gencode Transcript: ENST00000263577.11
Gencode Gene: ENSG00000064309.16
Transcript (Including UTRs)
   Position: hg38 chr11:125,960,679-126,063,292 Size: 102,614 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg38 chr11:125,960,942-126,023,476 Size: 62,535 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:125,960,679-126,063,292)mRNA (may differ from genome)Protein (1264 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGImyGene2
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CDON_HUMAN
DESCRIPTION: RecName: Full=Cell adhesion molecule-related/down-regulated by oncogenes; Flags: Precursor;
FUNCTION: Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells (By similarity).
SUBUNIT: Part of a complex that contains BOC, CDON, NEO1, cadherins and CTNNB1. Interacts with NTN3 (By similarity). Interacts with PTCH1 (By similarity). Interacts with GAS1 (By similarity).
SUBCELLULAR LOCATION: Membrane; Single-pass membrane protein (Potential).
PTM: N-glycosylated (By similarity).
DISEASE: Defects in CDON are the cause of holoprosencephaly type 11 (HPE11) [MIM:614226]. HPE11 is a structural anomaly of the brain, in which the developing forebrain fails to correctly separate into right and left hemispheres. Holoprosencephaly is genetically heterogeneous and associated with several distinct facies and phenotypic variability.
SIMILARITY: Contains 3 fibronectin type-III domains.
SIMILARITY: Contains 5 Ig-like C2-type (immunoglobulin-like) domains.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: CDON
Diseases sorted by gene-association score: holoprosencephaly 11* (1229), cdon-related holoprosencephaly* (500), microform holoprosencephaly* (368), pituitary stalk interruption syndrome* (213), lobar holoprosencephaly* (111), alobar holoprosencephaly* (111), semilobar holoprosencephaly* (106), septopreoptic holoprosencephaly* (94), midline interhemispheric variant of holoprosencephaly* (94), holoprosencephaly (17), meesmann corneal dystrophy (8), duodenal obstruction (6), carpenter syndrome (6)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.86 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 146.44 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 -38.10128-0.298 Picture PostScript Text
3' UTR -47.00263-0.179 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.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003961 - Fibronectin_type3
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003599 - Ig_sub
IPR003598 - Ig_sub2

Pfam Domains:
PF00041 - Fibronectin type III domain
PF07679 - Immunoglobulin I-set domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3D1M - X-ray MuPIT 3N1F - X-ray MuPIT 3N1Q - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q4KMG0
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0001708 cell fate specification
GO:0001934 positive regulation of protein phosphorylation
GO:0002088 lens development in camera-type eye
GO:0007155 cell adhesion
GO:0007224 smoothened signaling pathway
GO:0007520 myoblast fusion
GO:0009952 anterior/posterior pattern specification
GO:0010172 embryonic body morphogenesis
GO:0014816 skeletal muscle satellite cell differentiation
GO:0021987 cerebral cortex development
GO:0043410 positive regulation of MAPK cascade
GO:0043497 regulation of protein heterodimerization activity
GO:0045663 positive regulation of myoblast differentiation
GO:0045664 regulation of neuron differentiation
GO:0045666 positive regulation of neuron differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048598 embryonic morphogenesis
GO:0048643 positive regulation of skeletal muscle tissue development
GO:0051057 positive regulation of small GTPase mediated signal transduction
GO:0051146 striated muscle cell differentiation
GO:0051149 positive regulation of muscle cell differentiation
GO:0060059 embryonic retina morphogenesis in camera-type eye
GO:2000179 positive regulation of neural precursor cell proliferation

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031012 extracellular matrix


-  Descriptions from all associated GenBank mRNAs
  AB209396 - Homo sapiens mRNA for surface glycoprotein, Ig superfamily member variant protein.
BC098583 - Homo sapiens Cdon homolog (mouse), mRNA (cDNA clone MGC:111524 IMAGE:30528009), complete cds.
AF004841 - Homo sapiens CDO mRNA, complete cds.
BC112362 - Homo sapiens cDNA clone IMAGE:40067963, containing frame-shift errors.
BC114435 - Homo sapiens Cdon homolog (mouse), mRNA (cDNA clone MGC:133089 IMAGE:40027264), complete cds.
JD300415 - Sequence 281439 from Patent EP1572962.
JD307656 - Sequence 288680 from Patent EP1572962.
JD326345 - Sequence 307369 from Patent EP1572962.
KJ905466 - Synthetic construct Homo sapiens clone ccsbBroadEn_15058 CDON gene, encodes complete protein.
AL832223 - Homo sapiens mRNA; cDNA DKFZp686M2136 (from clone DKFZp686M2136).
BX647207 - Homo sapiens mRNA; cDNA DKFZp686L1636 (from clone DKFZp686L1636).
DQ587066 - Homo sapiens piRNA piR-54178, complete sequence.
AK309694 - Homo sapiens cDNA, FLJ99735.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q4KMG0 (Reactome details) participates in the following event(s):

R-HSA-375138 CDO binds BOC
R-HSA-5632652 Hh-Npp binds CDON and PTCH
R-HSA-375140 CDO binds promyogenic cadherins
R-HSA-375141 Neogenin:Netrin-3 binds CDO complex
R-HSA-376121 Bnip2 interacts with CDO complex
R-HSA-376119 Interaction of Bnip-2 with Cdc42
R-HSA-376117 JLP interacts with CDO complex
R-HSA-449200 Interaction of ABL1 with CDO complex
R-HSA-448957 Interaction of p38 MAPK with JLP
R-HSA-375170 CDO in myogenesis
R-HSA-5632681 Ligand-receptor interactions
R-HSA-525793 Myogenesis
R-HSA-5632684 Hedgehog 'on' state
R-HSA-1266738 Developmental Biology
R-HSA-5358351 Signaling by Hedgehog
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: CDO, CDON_HUMAN, ENST00000263577.1, ENST00000263577.10, ENST00000263577.2, ENST00000263577.3, ENST00000263577.4, ENST00000263577.5, ENST00000263577.6, ENST00000263577.7, ENST00000263577.8, ENST00000263577.9, NM_016952, O14631, Q4KMG0, uc001qdc.1, uc001qdc.2, uc001qdc.3, uc001qdc.4, uc001qdc.5
UCSC ID: ENST00000263577.11
RefSeq Accession: NM_016952
Protein: Q4KMG0 (aka CDON_HUMAN)
CCDS: CCDS8468.1, CCDS58192.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CDON:
hpe-overview (Holoprosencephaly Overview)

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