Human Gene CTNNA1 (uc003ldh.3)
  Description: Homo sapiens catenin (cadherin-associated protein), alpha 1, 102kDa (CTNNA1), mRNA.
RefSeq Summary (NM_001903): This gene encodes a member of the catenin family of proteins that play an important role in cell adhesion process by connecting cadherins located on the plasma membrane to the actin filaments inside the cell. The encoded mechanosensing protein contains three vinculin homology domains and undergoes conformational changes in response to cytoskeletal tension, resulting in the reconfiguration of cadherin-actin filament connections. Certain mutations in this gene cause butterfly-shaped pigment dystrophy. [provided by RefSeq, May 2016].
Transcript (Including UTRs)
   Position: hg19 chr5:138,089,107-138,270,723 Size: 181,617 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr5:138,117,614-138,269,778 Size: 152,165 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:138,089,107-138,270,723)mRNA (may differ from genome)Protein (906 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CTNA1_HUMAN
DESCRIPTION: RecName: Full=Catenin alpha-1; AltName: Full=Alpha E-catenin; AltName: Full=Cadherin-associated protein; AltName: Full=Renal carcinoma antigen NY-REN-13;
FUNCTION: Associates with the cytoplasmic domain of a variety of cadherins. The association of catenins to cadherins produces a complex which is linked to the actin filament network, and which seems to be of primary importance for cadherins cell-adhesion properties. Can associate with both E- and N-cadherins. Originally believed to be a stable component of E-cadherin/catenin adhesion complexes and to mediate the linkage of cadherins to the actin cytoskeleton at adherens junctions. In contrast, cortical actin was found to be much more dynamic than E-cadherin/catenin complexes and CTNNA1 was shown not to bind to F-actin when assembled in the complex suggesting a different linkage between actin and adherens junctions components. The homodimeric form may regulate actin filament assembly and inhibit actin branching by competing with the Arp2/3 complex for binding to actin filaments. May play a crucial role in cell differentiation.
SUBUNIT: Monomer and homodimer; the monomer preferentially binds to CTNNB1 and the homodimer to actin. Binds MLLT4 and F-actin. Possible component of an E-cadherin/ catenin adhesion complex together with E-cadherin/CDH1 and beta-catenin/CTNNB1 or gamma- catenin/JUP; the complex is located to adherens junctions. The stable association of CTNNA1 is controversial as CTNNA1 was shown not to bind to F-actin when assembled in the complex. Alternatively, the CTNNA1-containing complex may be linked to F- actin by other proteins such as LIMA1. Interacts with ARHGAP21 and with AJUBA. Interacts with LIMA1 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton. Cell junction, adherens junction. Cell membrane; Peripheral membrane protein; Cytoplasmic side. Cell junction. Note=Found at cell-cell boundaries and probably at cell-matrix boundaries.
TISSUE SPECIFICITY: Expressed ubiquitously in normal tissues.
PTM: Sumoylated.
SIMILARITY: Belongs to the vinculin/alpha-catenin family.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/ctnna1/";

-  Primer design for this transcript
 

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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): CTNNA1
CDC HuGE Published Literature: CTNNA1
Positive Disease Associations: Blood Pressure , Carotid Stenosis
Related Studies:
  1. Blood Pressure
    Daniel Levy et al. BMC medical genetics 2007, Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness., BMC medical genetics. [PubMed 17903302]
    These results of genome-wide association testing for blood pressure and arterial stiffness phenotypes in an unselected community-based sample of adults may aid in the identification of the genetic basis of hypertension and arterial disease, help identify high risk individuals, and guide novel therapies for hypertension. Additional studies are needed to replicate any associations identified in these analyses.
  2. Carotid Stenosis
    Christopher J O'Donnell et al. BMC medical genetics 2007, Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903303]
    The results from this GWAS generate hypotheses regarding several SNPs that may be associated with SCA phenotypes in multiple arterial beds. Given the number of tests conducted, subsequent independent replication in a staged approach is essential to identify genetic variants that may be implicated in atherosclerosis.

-  MalaCards Disease Associations
  MalaCards Gene Search: CTNNA1
Diseases sorted by gene-association score: macular dystrophy, patterned, 2* (1330), butterfly-shaped pigment dystrophy* (390), diffuse gastric cancer (20), gastric cancer risk after h. pylori infection* (10), acquired thrombocytopenia (9), gastric diffuse adenocarcinoma (6), lobular neoplasia (6), microinvasive gastric cancer (6), colorectal cancer (3), arrhythmogenic right ventricular cardiomyopathy (3), leber congenital amaurosis (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: 95.90 RPKM in Nerve - Tibial
Total median expression: 2639.11 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 -30.8095-0.324 Picture PostScript Text
3' UTR -250.90945-0.266 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
IPR001033 - Alpha_catenin
IPR006077 - Vinculin/catenin
IPR000633 - Vinculin_CS

Pfam Domains:
PF01044 - Vinculin family

SCOP Domains:
47220 - alpha-catenin/vinculin

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1H6G - X-ray MuPIT 4EHP - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P35221
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-  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 BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005198 structural molecule activity
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0017166 vinculin binding
GO:0042802 identical protein binding
GO:0045295 gamma-catenin binding
GO:0045296 cadherin binding
GO:0046982 protein heterodimerization activity
GO:0051015 actin filament binding

Biological Process:
GO:0001541 ovarian follicle development
GO:0007015 actin filament organization
GO:0007155 cell adhesion
GO:0007163 establishment or maintenance of cell polarity
GO:0007406 negative regulation of neuroblast proliferation
GO:0007568 aging
GO:0008584 male gonad development
GO:0014070 response to organic cyclic compound
GO:0016264 gap junction assembly
GO:0031103 axon regeneration
GO:0034332 adherens junction organization
GO:0034613 cellular protein localization
GO:0042127 regulation of cell proliferation
GO:0042475 odontogenesis of dentin-containing tooth
GO:0043066 negative regulation of apoptotic process
GO:0043297 apical junction assembly
GO:0043627 response to estrogen
GO:0045880 positive regulation of smoothened signaling pathway
GO:0051149 positive regulation of muscle cell differentiation
GO:0051291 protein heterooligomerization
GO:0071681 cellular response to indole-3-methanol
GO:0090136 epithelial cell-cell adhesion
GO:2000146 negative regulation of cell motility
GO:2001045 negative regulation of integrin-mediated signaling pathway
GO:2001240 negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
GO:2001241 positive regulation of extrinsic apoptotic signaling pathway in absence of ligand

Cellular Component:
GO:0001669 acrosomal vesicle
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005912 adherens junction
GO:0005913 cell-cell adherens junction
GO:0005915 zonula adherens
GO:0005925 focal adhesion
GO:0014704 intercalated disc
GO:0015629 actin cytoskeleton
GO:0016020 membrane
GO:0016342 catenin complex
GO:0016600 flotillin complex
GO:0030027 lamellipodium
GO:0030054 cell junction
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  LF385248 - JP 2014500723-A/192751: Polycomb-Associated Non-Coding RNAs.
AK300439 - Homo sapiens cDNA FLJ54547 complete cds, highly similar to Alpha-1 catenin (Cadherin-associated protein).
AK296708 - Homo sapiens cDNA FLJ54052 complete cds, highly similar to Alpha-1 catenin (Cadherin-associated protein).
D14705 - Homo sapiens mRNA for alpha-catenin, complete cds.
D13866 - Homo sapiens mRNA for alpha-catenin, complete cds.
AK094151 - Homo sapiens cDNA FLJ36832 fis, clone ASTRO2010799, highly similar to ALPHA-1 CATENIN.
BC000385 - Homo sapiens catenin (cadherin-associated protein), alpha 1, 102kDa, mRNA (cDNA clone MGC:8429 IMAGE:2821111), complete cds.
GQ900929 - Homo sapiens clone HEL-T-41 epididymis secretory sperm binding protein mRNA, complete cds.
AK304267 - Homo sapiens cDNA FLJ54047 complete cds, highly similar to Alpha-1 catenin (Cadherin-associated protein).
L23805 - Human alpha1(E)-catenin mRNA, complete cds.
U03100 - Human alpha2(E)-catenin mRNA, complete cds.
AB385159 - Synthetic construct DNA, clone: pF1KB5702, Homo sapiens CTNNA1 gene for catenin alpha-1, complete cds, without stop codon, in Flexi system.
DQ891250 - Synthetic construct clone IMAGE:100003880; FLH176824.01X; RZPDo839H09122D catenin (cadherin-associated protein), alpha 1, 102kDa (CTNNA1) gene, encodes complete protein.
DQ894435 - Synthetic construct Homo sapiens clone IMAGE:100008895; FLH176820.01L; RZPDo839H09121D catenin (cadherin-associated protein), alpha 1, 102kDa (CTNNA1) gene, encodes complete protein.
L22080 - Human alpha-catenin mRNA, partial cds.
AK308882 - Homo sapiens cDNA, FLJ98923.
MA620825 - JP 2018138019-A/192751: Polycomb-Associated Non-Coding RNAs.
LF343106 - JP 2014500723-A/150609: Polycomb-Associated Non-Coding RNAs.
LF343107 - JP 2014500723-A/150610: Polycomb-Associated Non-Coding RNAs.
LF343108 - JP 2014500723-A/150611: Polycomb-Associated Non-Coding RNAs.
LF343115 - JP 2014500723-A/150618: Polycomb-Associated Non-Coding RNAs.
LF343116 - JP 2014500723-A/150619: Polycomb-Associated Non-Coding RNAs.
MA578683 - JP 2018138019-A/150609: Polycomb-Associated Non-Coding RNAs.
MA578684 - JP 2018138019-A/150610: Polycomb-Associated Non-Coding RNAs.
MA578685 - JP 2018138019-A/150611: Polycomb-Associated Non-Coding RNAs.
MA578692 - JP 2018138019-A/150618: Polycomb-Associated Non-Coding RNAs.
MA578693 - JP 2018138019-A/150619: Polycomb-Associated Non-Coding RNAs.
LF343119 - JP 2014500723-A/150622: Polycomb-Associated Non-Coding RNAs.
LF343122 - JP 2014500723-A/150625: Polycomb-Associated Non-Coding RNAs.
HQ589335 - Homo sapiens catenin alpha 1 isoform CTNNA1b (CTNNA1) mRNA, complete cds.
BC031262 - Homo sapiens catenin (cadherin-associated protein), alpha 1, 102kDa, mRNA (cDNA clone MGC:39727 IMAGE:5274351), complete cds.
CU689138 - Synthetic construct Homo sapiens gateway clone IMAGE:100017395 5' read CTNNA1 mRNA.
KJ901365 - Synthetic construct Homo sapiens clone ccsbBroadEn_10759 CTNNA1 gene, encodes complete protein.
LF343145 - JP 2014500723-A/150648: Polycomb-Associated Non-Coding RNAs.
LF343146 - JP 2014500723-A/150649: Polycomb-Associated Non-Coding RNAs.
LF343147 - JP 2014500723-A/150650: Polycomb-Associated Non-Coding RNAs.
AK055751 - Homo sapiens cDNA FLJ31189 fis, clone KIDNE2000383, moderately similar to ALPHA-1 CATENIN.
LF343150 - JP 2014500723-A/150653: Polycomb-Associated Non-Coding RNAs.
LF343151 - JP 2014500723-A/150654: Polycomb-Associated Non-Coding RNAs.
LF343152 - JP 2014500723-A/150655: Polycomb-Associated Non-Coding RNAs.
LF343153 - JP 2014500723-A/150656: Polycomb-Associated Non-Coding RNAs.
JD394982 - Sequence 376006 from Patent EP1572962.
JD549892 - Sequence 530916 from Patent EP1572962.
LF343154 - JP 2014500723-A/150657: Polycomb-Associated Non-Coding RNAs.
LF343155 - JP 2014500723-A/150658: Polycomb-Associated Non-Coding RNAs.
JD092706 - Sequence 73730 from Patent EP1572962.
JD095782 - Sequence 76806 from Patent EP1572962.
JD264120 - Sequence 245144 from Patent EP1572962.
LF343156 - JP 2014500723-A/150659: Polycomb-Associated Non-Coding RNAs.
JD429499 - Sequence 410523 from Patent EP1572962.
JD290043 - Sequence 271067 from Patent EP1572962.
LF343157 - JP 2014500723-A/150660: Polycomb-Associated Non-Coding RNAs.
AK022326 - Homo sapiens cDNA FLJ12264 fis, clone MAMMA1001600.
MA578696 - JP 2018138019-A/150622: Polycomb-Associated Non-Coding RNAs.
MA578699 - JP 2018138019-A/150625: Polycomb-Associated Non-Coding RNAs.
MA578722 - JP 2018138019-A/150648: Polycomb-Associated Non-Coding RNAs.
MA578723 - JP 2018138019-A/150649: Polycomb-Associated Non-Coding RNAs.
MA578724 - JP 2018138019-A/150650: Polycomb-Associated Non-Coding RNAs.
MA578727 - JP 2018138019-A/150653: Polycomb-Associated Non-Coding RNAs.
MA578728 - JP 2018138019-A/150654: Polycomb-Associated Non-Coding RNAs.
MA578729 - JP 2018138019-A/150655: Polycomb-Associated Non-Coding RNAs.
MA578730 - JP 2018138019-A/150656: Polycomb-Associated Non-Coding RNAs.
MA578731 - JP 2018138019-A/150657: Polycomb-Associated Non-Coding RNAs.
MA578732 - JP 2018138019-A/150658: Polycomb-Associated Non-Coding RNAs.
MA578733 - JP 2018138019-A/150659: Polycomb-Associated Non-Coding RNAs.
MA578734 - JP 2018138019-A/150660: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04520 - Adherens junction
hsa04530 - Tight junction
hsa04670 - Leukocyte transendothelial migration
hsa05100 - Bacterial invasion of epithelial cells
hsa05200 - Pathways in cancer
hsa05213 - Endometrial cancer
hsa05412 - Arrhythmogenic right ventricular cardiomyopathy (ARVC)

BioCarta from NCI Cancer Genome Anatomy Project
h_cell2cellPathway - Cell to Cell Adhesion Signaling

Reactome (by CSHL, EBI, and GO)

Protein P35221 (Reactome details) participates in the following event(s):

R-HSA-419002 Interaction of cadherin with Beta/gamma catenin, alpha catenin and p120 catenin
R-HSA-5672304 IQGAP1 binds CDH1:CTTNB1:CTTNA1 and MEN1
R-HSA-5357477 PAK1-3 phosphorylates VE-cadherin
R-HSA-375140 CDO binds promyogenic cadherins
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-418990 Adherens junctions interactions
R-HSA-5626467 RHO GTPases activate IQGAPs
R-HSA-5218920 VEGFR2 mediated vascular permeability
R-HSA-421270 Cell-cell junction organization
R-HSA-195258 RHO GTPase Effectors
R-HSA-4420097 VEGFA-VEGFR2 Pathway
R-HSA-446728 Cell junction organization
R-HSA-375170 CDO in myogenesis
R-HSA-194315 Signaling by Rho GTPases
R-HSA-194138 Signaling by VEGF
R-HSA-1500931 Cell-Cell communication
R-HSA-525793 Myogenesis
R-HSA-162582 Signal Transduction
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: CTNA1_HUMAN, NM_001903, NP_001894, P35221, Q12795
UCSC ID: uc003ldh.3
RefSeq Accession: NM_001903
Protein: P35221 (aka CTNA1_HUMAN)
CCDS: CCDS34243.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001903.2
exon count: 18CDS single in 3' UTR: no RNA size: 3778
ORF size: 2721CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5642.00frame shift in genome: no % Coverage: 99.55
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# 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.