Human Gene CNTNAP1 (ENST00000264638.9_4) from GENCODE V47lift37
  Description: contactin associated protein 1 (from RefSeq NM_003632.3)
Gencode Transcript: ENST00000264638.9_4
Gencode Gene: ENSG00000108797.12_7
Transcript (Including UTRs)
   Position: hg19 chr17:40,834,549-40,852,011 Size: 17,463 Total Exon Count: 24 Strand: +
Coding Region
   Position: hg19 chr17:40,834,848-40,850,928 Size: 16,081 Coding Exon Count: 24 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:40,834,549-40,852,011)mRNA (may differ from genome)Protein (1384 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CNTP1_HUMAN
DESCRIPTION: RecName: Full=Contactin-associated protein 1; Short=Caspr; Short=Caspr1; AltName: Full=Neurexin IV; AltName: Full=Neurexin-4; AltName: Full=p190; Flags: Precursor;
FUNCTION: Seems to play a role in the formation of functional distinct domains critical for saltatory conduction of nerve impulses in myelinated nerve fibers. Seems to demarcate the paranodal region of the axo-glial junction. In association with contactin may have a role in the signaling between axons and myelinating glial cells.
SUBUNIT: Interacts with contactin in cis form.
INTERACTION: P16333:NCK1; NbExp=2; IntAct=EBI-1751903, EBI-389883;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Potential).
TISSUE SPECIFICITY: Predominantly expressed in brain. Weak expression detected in ovary, pancreas, colon, lung, heart, intestine and testis.
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.

-  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: CNTNAP1
Diseases sorted by gene-association score: lethal congenital contracture syndrome 7* (1229), hypomyelination neuropathy-arthrogryposis syndrome* (350), autoimmune neuropathy (16), autoimmune disease of central nervous system (16), childhood pilocytic astrocytoma (7), polyhydramnios (6), charcot-marie-tooth disease, type 2e (5), distal arthrogryposis (1)
* = 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: 77.76 RPKM in Brain - Cerebellum
Total median expression: 724.34 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 -73.00299-0.244 Picture PostScript Text
3' UTR -353.901083-0.327 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
IPR003585 - Neurexin-like

Pfam Domains:
PF00054 - Laminin G domain
PF00754 - F5/8 type C 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 P78357
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005070 SH3/SH2 adaptor activity
GO:0005515 protein binding
GO:0017124 SH3 domain binding
GO:0038023 signaling receptor activity

Biological Process:
GO:0002175 protein localization to paranode region of axon
GO:0007010 cytoskeleton organization
GO:0007155 cell adhesion
GO:0007165 signal transduction
GO:0009967 positive regulation of signal transduction
GO:0019227 neuronal action potential propagation
GO:0022010 central nervous system myelination
GO:0022011 myelination in peripheral nervous system
GO:0030913 paranodal junction assembly
GO:0031175 neuron projection development
GO:0048812 neuron projection morphogenesis
GO:0050884 neuromuscular process controlling posture
GO:0050885 neuromuscular process controlling balance
GO:0071205 protein localization to juxtaparanode region of axon

Cellular Component:
GO:0005887 integral component of plasma membrane
GO:0008076 voltage-gated potassium channel complex
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030424 axon
GO:0033010 paranodal junction
GO:0033270 paranode region of axon
GO:0043209 myelin sheath


-  Descriptions from all associated GenBank mRNAs
  U87223 - Homo sapiens contactin associated protein (Caspr) mRNA, complete cds.
JD544351 - Sequence 525375 from Patent EP1572962.
JD477829 - Sequence 458853 from Patent EP1572962.
JD404330 - Sequence 385354 from Patent EP1572962.
JD472755 - Sequence 453779 from Patent EP1572962.
BC171797 - Homo sapiens cDNA clone IMAGE:9054451, containing frame-shift errors.
JD178138 - Sequence 159162 from Patent EP1572962.
JD192231 - Sequence 173255 from Patent EP1572962.
AB384696 - Synthetic construct DNA, clone: pF1KB1311, Homo sapiens CNTNAP1 gene for contactin-associated protein 1 precursor, complete cds, without stop codon, in Flexi system.
BC160132 - Synthetic construct Homo sapiens clone IMAGE:100064164, MGC:193247 contactin associated protein 1 (CNTNAP1) mRNA, encodes complete protein.
L77576 - Homo sapiens (clone SEL13) 17q YAC (26F3) RNA.
L77577 - Homo sapiens (clone SEL23) 17q YAC (26F3) RNA.
L77605 - Homo sapiens (clone SEL273) 17q YAC (303G8) RNA.
JD387591 - Sequence 368615 from Patent EP1572962.
JD400591 - Sequence 381615 from Patent EP1572962.
JD159821 - Sequence 140845 from Patent EP1572962.
JD196930 - Sequence 177954 from Patent EP1572962.
JD401379 - Sequence 382403 from Patent EP1572962.
JD157217 - Sequence 138241 from Patent EP1572962.
JD078700 - Sequence 59724 from Patent EP1572962.
JD259773 - Sequence 240797 from Patent EP1572962.
JD063775 - Sequence 44799 from Patent EP1572962.
JD342908 - Sequence 323932 from Patent EP1572962.
JD317165 - Sequence 298189 from Patent EP1572962.
JD288918 - Sequence 269942 from Patent EP1572962.
JD157307 - Sequence 138331 from Patent EP1572962.
JD265116 - Sequence 246140 from Patent EP1572962.
JD190308 - Sequence 171332 from Patent EP1572962.

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

Protein P78357 (Reactome details) participates in the following event(s):

R-HSA-373733 Neurofascin binds contactin-1:CASPR complex
R-HSA-447043 Neurofascin interactions
R-HSA-373760 L1CAM interactions
R-HSA-422475 Axon guidance
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: CASPR, CNTP1_HUMAN, ENST00000264638.1, ENST00000264638.2, ENST00000264638.3, ENST00000264638.4, ENST00000264638.5, ENST00000264638.6, ENST00000264638.7, ENST00000264638.8, NM_003632, NRXN4, P78357, uc317htt.1, uc317htt.2
UCSC ID: ENST00000264638.9_4
RefSeq Accession: NM_003632.3
Protein: P78357 (aka CNTP1_HUMAN or CTA1_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.