Human Gene CNTN4 (ENST00000418658.6)
  Description: Homo sapiens contactin 4 (CNTN4), transcript variant 1, mRNA. (from RefSeq NM_175607)
RefSeq Summary (NM_175607): This gene encodes a member of the contactin family of immunoglobulins. Contactins are axon-associated cell adhesion molecules that function in neuronal network formation and plasticity. The encoded protein is a glycosylphosphatidylinositol-anchored neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Deletion or mutation of this gene may play a role in 3p deletion syndrome and autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011].
Gencode Transcript: ENST00000418658.6
Gencode Gene: ENSG00000144619.15
Transcript (Including UTRs)
   Position: hg38 chr3:2,098,866-3,057,959 Size: 959,094 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg38 chr3:2,571,504-3,056,220 Size: 484,717 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2021-01-14 15:32:12

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr3:2,098,866-3,057,959)mRNA (may differ from genome)Protein (1026 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Contactin-4; AltName: Full=Brain-derived immunoglobulin superfamily protein 2; Short=BIG-2; Flags: Precursor;
FUNCTION: Contactins mediate cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity. May be involved in synaptogenesis.
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor, GPI-anchor. Secreted (By similarity).
TISSUE SPECIFICITY: Mainly expressed in brain. Highly expressed in cerebellum and weakly expressed in corpus callosum, caudate nucleus, amygdala and spinal cord. Also expressed in testis, pancreas, thyroid, uterus, small intestine and kidney. Not expressed in skeletal muscle. Isoform 2 is weakly expressed in cerebral cortex.
INDUCTION: By retinoic acid, suggesting that it may act in response to differentiating agents.
DISEASE: Note=A chromosomal aberration involving CNTN4 has been found in a boy with characteristic physical features of 3p deletion syndrome (3PDS). Translocation t(3;10)(p26;q26). 3PDS is a rare contiguous gene disorder involving the loss of the telomeric portion of the short arm of chromosome 3 and characterized by developmental delay, growth retardation, and dysmorphic features.
SIMILARITY: Belongs to the immunoglobulin superfamily. Contactin family.
SIMILARITY: Contains 4 fibronectin type-III domains.
SIMILARITY: Contains 6 Ig-like C2-type (immunoglobulin-like) domains.

-  MalaCards Disease Associations
  MalaCards Gene Search: CNTN4
Diseases sorted by gene-association score: 3p- syndrome* (24), spinocerebellar ataxia type 16 (10), autism spectrum disorder (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.75 RPKM in Artery - Aorta
Total median expression: 88.98 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 -106.20339-0.313 Picture PostScript Text
3' UTR -360.001739-0.207 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

ModBase Predicted Comparative 3D Structure on Q8IWV2
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007155 cell adhesion
GO:0007158 neuron cell-cell adhesion
GO:0007399 nervous system development
GO:0007409 axonogenesis
GO:0007411 axon guidance
GO:0007413 axonal fasciculation
GO:0007420 brain development
GO:0031175 neuron projection development
GO:0045665 negative regulation of neuron differentiation
GO:0048167 regulation of synaptic plasticity

Cellular Component:
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030424 axon
GO:0031225 anchored component of membrane

-  Descriptions from all associated GenBank mRNAs
  AF549455 - Homo sapiens BIG-2 (BIG-2) mRNA, complete cds.
AK125460 - Homo sapiens cDNA FLJ43471 fis, clone OCBBF2037598, highly similar to Mus musculus axonal-associated cell adhesion molecule (Axcam).
AY090737 - Homo sapiens contactin 4 (CNTN4) mRNA, complete cds.
AK095729 - Homo sapiens cDNA FLJ38410 fis, clone FEBRA2009289, highly similar to Contactin-4 precursor.
BC013797 - Homo sapiens, clone IMAGE:4342649, mRNA.
AK097633 - Homo sapiens cDNA FLJ40314 fis, clone TESTI2030322, highly similar to Contactin-4 precursor.
AK314396 - Homo sapiens cDNA, FLJ95172, Homo sapiens contactin 4 (CNTN4), transcript variant 3, mRNA.
AK057278 - Homo sapiens cDNA FLJ32716 fis, clone TESTI2000808, highly similar to Contactin-4 precursor.
BC026119 - Homo sapiens contactin 4, mRNA (cDNA clone MGC:33615 IMAGE:4826091), complete cds.
KJ903893 - Synthetic construct Homo sapiens clone ccsbBroadEn_13287 CNTN4 gene, encodes complete protein.
JD358299 - Sequence 339323 from Patent EP1572962.
AF464063 - Homo sapiens contactin 4a (CNTN4) mRNA, complete cds; alternatively spliced.
JD523890 - Sequence 504914 from Patent EP1572962.
JD044582 - Sequence 25606 from Patent EP1572962.
JD524032 - Sequence 505056 from Patent EP1572962.
JD564205 - Sequence 545229 from Patent EP1572962.
JD557918 - Sequence 538942 from Patent EP1572962.
JD043829 - Sequence 24853 from Patent EP1572962.
JD333989 - Sequence 315013 from Patent EP1572962.
JD438410 - Sequence 419434 from Patent EP1572962.
JD200126 - Sequence 181150 from Patent EP1572962.
JD286301 - Sequence 267325 from Patent EP1572962.

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

Protein Q8IWV2 (Reactome details) participates in the following event(s):

R-HSA-8940388 GPLD1 hydrolyses GPI-anchors from proteins
R-HSA-163125 Post-translational modification: synthesis of GPI-anchored proteins
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B2RAX3, CNTN4_HUMAN, ENST00000418658.1, ENST00000418658.2, ENST00000418658.3, ENST00000418658.4, ENST00000418658.5, NM_175607, Q8IWV2, Q8IX14, Q8TC35, uc003bpc.1, uc003bpc.2, uc003bpc.3, uc003bpc.4, uc003bpc.5
UCSC ID: ENST00000418658.6
RefSeq Accession: NM_175607
Protein: Q8IWV2 (aka CNTN4_HUMAN)
CCDS: CCDS43041.1

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