Human Gene CNTNAP4 (ENST00000611870.5_10) from GENCODE V47lift37
  Description: contactin associated protein family member 4, transcript variant 14 (from RefSeq NR_136216.2)
Gencode Transcript: ENST00000611870.5_10
Gencode Gene: ENSG00000152910.19_14
Transcript (Including UTRs)
   Position: hg19 chr16:76,311,299-76,594,654 Size: 283,356 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg19 chr16:76,311,561-76,592,580 Size: 281,020 Coding Exon Count: 25 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:76,311,299-76,594,654)mRNA (may differ from genome)Protein (1305 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CNTP4_HUMAN
DESCRIPTION: RecName: Full=Contactin-associated protein-like 4; AltName: Full=Cell recognition molecule Caspr4; Flags: Precursor;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Potential).
SIMILARITY: Belongs to the neurexin family.
SIMILARITY: Contains 2 EGF-like domains.
SIMILARITY: Contains 1 F5/8 type C domain.
SIMILARITY: Contains 1 fibrinogen C-terminal domain.
SIMILARITY: Contains 4 laminin G-like domains.
SEQUENCE CAUTION: Sequence=BAB21854.2; Type=Erroneous initiation;

-  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


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

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -48.60262-0.185 Picture PostScript Text
3' UTR -473.402074-0.228 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
IPR000421 - Coagulation_fac_5/8-C_type_dom
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR000742 - EG-like_dom
IPR002181 - Fibrinogen_a/b/g_C
IPR008979 - Galactose-bd-like
IPR001791 - Laminin_G

Pfam Domains:
PF00054 - Laminin G domain
PF02210 - Laminin G domain

SCOP Domains:
49785 - Galactose-binding domain-like
49899 - Concanavalin A-like lectins/glucanases
56496 - Fibrinogen C-terminal domain-like
57196 - EGF/Laminin

ModBase Predicted Comparative 3D Structure on Q9C0A0
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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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007155 cell adhesion
GO:0032225 regulation of synaptic transmission, dopaminergic
GO:0032228 regulation of synaptic transmission, GABAergic
GO:2000821 regulation of grooming behavior

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030425 dendrite
GO:0042734 presynaptic membrane
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  AB051550 - Homo sapiens KIAA1763 mRNA for KIAA1763 protein.
AB385503 - Synthetic construct DNA, clone: pF1KA1763, Homo sapiens CNTNAP4 gene for contactin-associated protein-like 4 precursor, complete cds, without stop codon, in Flexi system.
BC141550 - Synthetic construct Homo sapiens clone IMAGE:100014525, MGC:175303 contactin associated protein-like 4 (CNTNAP4) mRNA, encodes complete protein.
AB100092 - Homo sapiens mRNA for hypothetical protein, complete cds, clone:pFCP176316.
AB100094 - Homo sapiens mRNA for hypothetical protein, complete cds, clone:pFCP176350.
AF463518 - Homo sapiens cell recognition protein CASPR4 (CASPR4) mRNA, complete cds.
AB100093 - Homo sapiens mRNA for hypothetical protein, complete cds, clone:pFCP176318.
AK057327 - Homo sapiens cDNA FLJ32765 fis, clone TESTI2001852, weakly similar to Homo sapiens contactin associated protein (Caspr) mRNA.
BC017266 - Homo sapiens contactin associated protein-like 4, mRNA (cDNA clone IMAGE:4544528), partial cds.
AK054786 - Homo sapiens cDNA FLJ30224 fis, clone BRACE2001834.
JD447503 - Sequence 428527 from Patent EP1572962.
JD503471 - Sequence 484495 from Patent EP1572962.
JD278594 - Sequence 259618 from Patent EP1572962.
JD372526 - Sequence 353550 from Patent EP1572962.
JD095767 - Sequence 76791 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CASPR4, CNTP4_HUMAN, E9PFZ6, ENST00000611870.1, ENST00000611870.2, ENST00000611870.3, ENST00000611870.4, KIAA1763, NR_136216, Q86YZ7, Q9C0A0, uc327npq.1, uc327npq.2
UCSC ID: ENST00000611870.5_10
RefSeq Accession: NR_136210.2
Protein: Q9C0A0 (aka CNTP4_HUMAN or CTA4_HUMAN)

-  Gene Model Information
  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.