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    CTNNA2 catenin alpha 2 [ Homo sapiens (human) ]

    Gene ID: 1496, updated on 3-May-2024

    Summary

    Official Symbol
    CTNNA2provided by HGNC
    Official Full Name
    catenin alpha 2provided by HGNC
    Primary source
    HGNC:HGNC:2510
    See related
    Ensembl:ENSG00000066032 MIM:114025; AllianceGenome:HGNC:2510
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CAPR; CTNR; CAP-R; CT114; CDCBM9
    Summary
    Enables actin filament binding activity. Involved in negative regulation of Arp2/3 complex-mediated actin nucleation; regulation of neuron migration; and regulation of neuron projection development. Located in cytoplasm. Implicated in complex cortical dysplasia with other brain malformations. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in brain (RPKM 26.7), testis (RPKM 6.2) and 1 other tissue See more
    Orthologs
    NEW
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    Genomic context

    Location:
    2p12
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (79185377..80648780)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (79185703..80649017)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (79412503..80875905)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374823 Neighboring gene regenerating family member 1 gamma, pseudogene Neighboring gene regenerating family member 3 alpha Neighboring gene NANOG hESC enhancer GRCh37_chr2:79620883-79621450 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_59361 Neighboring gene CTNNA2 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr2:79779842-79780343 Neighboring gene GNA13 pseudogene 1 Neighboring gene RNA, U6 small nuclear 561, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:80009037-80009662 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:80009663-80010286 Neighboring gene microRNA 4264 Neighboring gene NANOG hESC enhancer GRCh37_chr2:80204933-80205434 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:80235029-80235530 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:80235531-80236030 Neighboring gene microRNA 8080 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:80363322-80363951 Neighboring gene MPRA-validated peak3752 silencer Neighboring gene uncharacterized LOC107985903 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:80458363-80459016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:80530694-80531319 Neighboring gene uncharacterized LOC107985904 Neighboring gene RBM7 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr2:80557197-80557699 Neighboring gene uncharacterized LOC105374824 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:80591811-80592596 Neighboring gene NANOG hESC enhancer GRCh37_chr2:80592898-80593415 Neighboring gene leucine rich repeat transmembrane neuronal 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:80688730-80689234 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:80689235-80689740 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:80709895-80710095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16097 Neighboring gene NANOG hESC enhancer GRCh37_chr2:81005685-81006186 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:81101296-81102149 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:81103634-81104173 Neighboring gene uncharacterized LOC105374827 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:81147049-81147550 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:81420933-81421434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:81421435-81421934 Neighboring gene ANKRD11 pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Cortical dysplasia, complex, with other brain malformations 9
    MedGen: C4748540 OMIM: 618174 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies protein quantitative trait loci (pQTLs).
    EBI GWAS Catalog
    Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
    EBI GWAS Catalog
    Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry.
    EBI GWAS Catalog
    Genome-wide association study of orthostatic hypotension and supine-standing blood pressure changes in two korean populations.
    EBI GWAS Catalog
    Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
    EBI GWAS Catalog
    Variants in the 1q21 risk region are associated with a visual endophenotype of autism and schizophrenia.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 and alpha-catenin co-localize in gp160 and GST-alpha-catenin expressing cells; the leucine zipper-like domain (gp160 residues 791-824) of gp41 interacts strongly with the carboxy terminus (residues 795-906) of alpha-catenin PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp686H02198

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables actin filament binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables beta-catenin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cadherin binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables structural constituent of cytoskeleton NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in axonogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in brain morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell-cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cytoskeleton organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in dendrite morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of Arp2/3 complex-mediated actin nucleation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in prepulse inhibition ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in radial glia guided migration of Purkinje cell ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of neuron projection development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of synapse structural plasticity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in actin cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in adherens junction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of catenin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    catenin alpha-2
    Names
    alpha-N-catenin
    alpha-catenin-related protein
    cadherin-associated protein, related
    cancer/testis antigen 114
    catenin (cadherin-associated protein), alpha 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001164883.2NP_001158355.1  catenin alpha-2 isoform 2

      See identical proteins and their annotated locations for NP_001158355.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two consecutive exons in the 3' coding region but maintains the reading frame compared to variant 1. The resulting isoform (2) lacks an internal segment near the C-terminus compared to isoform 3.
      Source sequence(s)
      AK295181, BC052996, DA313393
      Consensus CDS
      CCDS54371.1
      UniProtKB/Swiss-Prot
      P26232
      Related
      ENSP00000486160.1, ENST00000629316.2
      Conserved Domains (1) summary
      pfam01044
      Location:81821
      Vinculin; Vinculin family
    2. NM_001282597.3NP_001269526.1  catenin alpha-2 isoform 3

      See identical proteins and their annotated locations for NP_001269526.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) encodes the longest isoform (3).
      Source sequence(s)
      AC008067, AC010975, AC011741, AC011746, AC096573, AC096753, AC104780, FJ695201
      Consensus CDS
      CCDS62944.1
      UniProtKB/Swiss-Prot
      B3KXE5, B7Z2W7, B7Z352, B7Z898, P26232, Q4ZFW1, Q53R26, Q53R33, Q53T67, Q53T71, Q53TM8, Q7Z3L1, Q7Z3Y0
      Related
      ENSP00000384638.4, ENST00000402739.9
      Conserved Domains (1) summary
      pfam01044
      Location:81914
      Vinculin; Vinculin family
    3. NM_001282598.2NP_001269527.1  catenin alpha-2 isoform 4

      See identical proteins and their annotated locations for NP_001269527.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has an alternate 5' terminal exon that includes an upstream in-frame AUG start codon, and lacks an in-frame exon in the 3' coding region, compared to variant 3. The resulting isoform (4) is longer at the N-terminus but lacks an internal segment near the C-terminus compared to isoform 3.
      Source sequence(s)
      AC010975, AK303035, BC052996
      UniProtKB/Swiss-Prot
      P26232
      Conserved Domains (1) summary
      pfam01044
      Location:115900
      Vinculin; Vinculin family
    4. NM_001282599.2NP_001269528.1  catenin alpha-2 isoform 5

      See identical proteins and their annotated locations for NP_001269528.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and has multiple coding region differences compared to variant 3. These differences include translation initiation at an alternate AUG start codon. The resulting isoform (5) has a shorter and distinct N-terminus and lacks an internal segment near the C-terminus compared to isoform 3.
      Source sequence(s)
      BC052996, BX537769
      Consensus CDS
      CCDS62945.1
      UniProtKB/TrEMBL
      A0A0A0MRI5
      Related
      ENSP00000341500.3, ENST00000343114.7
      Conserved Domains (1) summary
      pfam01044
      Location:32545
      Vinculin; Vinculin family
    5. NM_001282600.2NP_001269529.1  catenin alpha-2 isoform 6

      See identical proteins and their annotated locations for NP_001269529.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) has an alternate exon in the 5' UTR and has multiple coding region differences compared to variant 3. These differences include translation initiation at a downstream AUG start codon. The resulting isoform (6) is shorter at the N-terminus and lacks an internal segment near the C-terminus compared to isoform 3.
      Source sequence(s)
      BC052996, BI599815, HQ589336
      Consensus CDS
      CCDS74531.1
      UniProtKB/TrEMBL
      A0A0A0MRI5, F6KRI5
      Related
      ENSP00000444675.2, ENST00000541047.5
      Conserved Domains (1) summary
      pfam01044
      Location:1498
      Vinculin; Vinculin family
    6. NM_001320810.2NP_001307739.1  catenin alpha-2 isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and coding sequence compared to variant 3. This difference includes translation initiation at a downstream AUG start codon. The resulting isoform (7) is shorter at the N-terminus compared to isoform 3.
      Source sequence(s)
      AC008067, BI599815, BX648368, M94151
      UniProtKB/TrEMBL
      A0A0A0MRI5
      Related
      ENSP00000355398.5, ENST00000361291.8
      Conserved Domains (1) summary
      pfam01044
      Location:1546
      Vinculin; Vinculin family
    7. NM_001399737.1NP_001386666.1  catenin alpha-2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) lacks an in-frame exon in the 3' coding region compared to variant 3 and differs in the 5' UTR. The resulting isoform (1) lacks an internal segment near the C-terminus compared to isoform 3. Variants 1 and 8 encode the same isoform (1).
      Source sequence(s)
      AC008067, AC010975, AC011741, AC011746, AC011754, AC018733, AC096573, AC096753, AC104780, FJ695201
      Consensus CDS
      CCDS42703.2
      Related
      ENSP00000418191.1, ENST00000466387.5
      Conserved Domains (1) summary
      pfam01044
      Location:81866
      Vinculin; Vinculin family
    8. NM_004389.4NP_004380.2  catenin alpha-2 isoform 1

      See identical proteins and their annotated locations for NP_004380.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks an in-frame exon in the 3' coding region compared to variant 3. The resulting isoform (1) lacks an internal segment near the C-terminus compared to isoform 3. Variants 1 and 8 encode the same isoform (1).
      Source sequence(s)
      BC040458, BC052996, DA313393
      Consensus CDS
      CCDS42703.2
      UniProtKB/Swiss-Prot
      P26232
      UniProtKB/TrEMBL
      Q49AD3
      Related
      ENSP00000419295.1, ENST00000496558.5
      Conserved Domains (1) summary
      pfam01044
      Location:81866
      Vinculin; Vinculin family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      79185377..80648780
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024452714.2XP_024308482.1  catenin alpha-2 isoform X1

      UniProtKB/Swiss-Prot
      B3KXE5, B7Z2W7, B7Z352, B7Z898, P26232, Q4ZFW1, Q53R26, Q53R33, Q53T67, Q53T71, Q53TM8, Q7Z3L1, Q7Z3Y0
      Conserved Domains (1) summary
      pfam01044
      Location:81914
      Vinculin; Vinculin family
    2. XM_011532556.3XP_011530858.1  catenin alpha-2 isoform X1

      See identical proteins and their annotated locations for XP_011530858.1

      UniProtKB/Swiss-Prot
      B3KXE5, B7Z2W7, B7Z352, B7Z898, P26232, Q4ZFW1, Q53R26, Q53R33, Q53T67, Q53T71, Q53TM8, Q7Z3L1, Q7Z3Y0
      Conserved Domains (1) summary
      pfam01044
      Location:81914
      Vinculin; Vinculin family
    3. XM_017003403.3XP_016858892.1  catenin alpha-2 isoform X2

      UniProtKB/Swiss-Prot
      P26232
      Conserved Domains (1) summary
      pfam01044
      Location:81866
      Vinculin; Vinculin family
    4. XM_047443447.1XP_047299403.1  catenin alpha-2 isoform X3

    5. XM_017003405.3XP_016858894.1  catenin alpha-2 isoform X4

    6. XM_024452715.2XP_024308483.1  catenin alpha-2 isoform X1

      UniProtKB/Swiss-Prot
      B3KXE5, B7Z2W7, B7Z352, B7Z898, P26232, Q4ZFW1, Q53R26, Q53R33, Q53T67, Q53T71, Q53TM8, Q7Z3L1, Q7Z3Y0
      Conserved Domains (1) summary
      pfam01044
      Location:81914
      Vinculin; Vinculin family
    7. XM_011532557.3XP_011530859.1  catenin alpha-2 isoform X5

      See identical proteins and their annotated locations for XP_011530859.1

      UniProtKB/TrEMBL
      A0A0A0MRI5
      Conserved Domains (1) summary
      pfam01044
      Location:1465
      Vinculin; Vinculin family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      79185703..80649017
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340643.1XP_054196618.1  catenin alpha-2 isoform X1

      UniProtKB/Swiss-Prot
      B3KXE5, B7Z2W7, B7Z352, B7Z898, P26232, Q4ZFW1, Q53R26, Q53R33, Q53T67, Q53T71, Q53TM8, Q7Z3L1, Q7Z3Y0
    2. XM_054340642.1XP_054196617.1  catenin alpha-2 isoform X1

      UniProtKB/Swiss-Prot
      B3KXE5, B7Z2W7, B7Z352, B7Z898, P26232, Q4ZFW1, Q53R26, Q53R33, Q53T67, Q53T71, Q53TM8, Q7Z3L1, Q7Z3Y0
    3. XM_054340644.1XP_054196619.1  catenin alpha-2 isoform X2

    4. XM_054340645.1XP_054196620.1  catenin alpha-2 isoform X3

    5. XM_054340646.1XP_054196621.1  catenin alpha-2 isoform X4

    6. XM_054340641.1XP_054196616.1  catenin alpha-2 isoform X1

      UniProtKB/Swiss-Prot
      B3KXE5, B7Z2W7, B7Z352, B7Z898, P26232, Q4ZFW1, Q53R26, Q53R33, Q53T67, Q53T71, Q53TM8, Q7Z3L1, Q7Z3Y0
    7. XM_054340647.1XP_054196622.1  catenin alpha-2 isoform X5