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CTNND2 catenin delta 2 [ Homo sapiens (human) ]

Gene ID: 1501, updated on 27-Nov-2024

Summary

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Official Symbol
CTNND2provided by HGNC
Official Full Name
catenin delta 2provided by HGNC
Primary source
HGNC:HGNC:2516
See related
Ensembl:ENSG00000169862 MIM:604275; AllianceGenome:HGNC:2516
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GT24; NPRAP
Summary
This gene encodes an adhesive junction associated protein of the armadillo/beta-catenin superfamily and is implicated in brain and eye development and cancer formation. The protein encoded by this gene promotes the disruption of E-cadherin based adherens junction to favor cell spreading upon stimulation by hepatocyte growth factor. This gene is overexpressed in prostate adenocarcinomas and is associated with decreased expression of tumor suppressor E-cadherin in this tissue. This gene resides in a region of the short arm of chromosome 5 that is deleted in Cri du Chat syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2013]
Expression
Biased expression in brain (RPKM 42.1) and spleen (RPKM 2.8) See more
Orthologs
mouse all
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Genomic context

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See CTNND2 in Genome Data Viewer
Location:
5p15.2
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (10971836..11904446, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (10909469..11841846, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (10971948..11904558, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized CTD-2154B17.1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15930 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:10761404-10762249 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:10904846-10905500 Neighboring gene death associated protein Neighboring gene DAP divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22383 Neighboring gene uncharacterized LOC105374654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10987709-10988210 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22384 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:11022334-11023533 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:11065447-11066374 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:11069015-11069605 Neighboring gene RNA, U6 small nuclear 429, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr5:11141031-11141205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22385 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_80752 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:11385794-11386750 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:11466555-11466731 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:11528941-11529462 Neighboring gene NANOG hESC enhancer GRCh37_chr5:11700418-11700919 Neighboring gene NANOG hESC enhancer GRCh37_chr5:11797120-11797650 Neighboring gene Sharpr-MPRA regulatory region 1238 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:12237819-12238658 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:12320809-12321309 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:12321906-12322765 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:12322922-12323820 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:12323821-12324717 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:12330269-12331254 Neighboring gene uncharacterized LOC105374656 Neighboring gene uncharacterized LOC105374655 Neighboring gene RNA, U6 small nuclear 679, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. δ-Catenin (CTNND2) missense mutation in familial cortical myoclonic tremor and epilepsy. van Rootselaar AF, et al. Neurology, 2017 Dec 5. PMID 29127138
  2. Severe manifestation of Rauch-Azzarello syndrome associated with biallelic deletion of CTNND2. Pauly M, et al. Clin Genet, 2024 Aug. PMID 38604781
  3. Increased nucleotide polymorphic changes in the 5'-untranslated region of delta-catenin (CTNND2) gene in prostate cancer. Wang T, et al. Oncogene, 2009 Jan 29. PMID 18978817, Free PMC Article
  4. δ-Catenin promotes tumorigenesis and metastasis of lung adenocarcinoma. Huang F, et al. Oncol Rep, 2018 Feb. PMID 29251319
  5. p120-Catenin is essential for N-cadherin-mediated formation of proper junctional structure, thereby establishing cell polarity in epithelial cells. Ozaki C, et al. Cell Struct Funct, 2010. PMID 20859058

See all (95) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CTNND2 moderates the pace of synaptic maturation and links human evolution to synaptic neoteny.
    Title: CTNND2 moderates the pace of synaptic maturation and links human evolution to synaptic neoteny.
  2. Severe manifestation of Rauch-Azzarello syndrome associated with biallelic deletion of CTNND2.
    Title: Severe manifestation of Rauch-Azzarello syndrome associated with biallelic deletion of CTNND2.
  3. microRNA-218-5p plays a protective role in eosinophilic airway inflammation via targeting delta-catenin, a novel catenin in asthma.
    Title: microRNA-218-5p plays a protective role in eosinophilic airway inflammation via targeting δ-catenin, a novel catenin in asthma.
  4. A child with autism, behavioral issues, and dysmorphic features found to have a tandem duplication within CTNND2 by mate-pair sequencing.
    Title: A child with autism, behavioral issues, and dysmorphic features found to have a tandem duplication within CTNND2 by mate-pair sequencing.
  5. Intratumor delta-catenin heterogeneity driven by genomic rearrangement dictates growth factor dependent prostate cancer progression.
    Title: Intratumor δ-catenin heterogeneity driven by genomic rearrangement dictates growth factor dependent prostate cancer progression.
  6. EIF3J-AS1 promotes CTNND2 expression via sponging miR-122-5p. Hypoxia-induced EIF3J-AS1 facilitates hepatocellular carcinoma progression via regulating CTNND2.
    Title: Hypoxia-induced lncRNA EIF3J-AS1 accelerates hepatocellular carcinoma progression via targeting miR-122-5p/CTNND2 axis.
  7. The increase in invasive capacity induced by bevacizumab therapy was associated with upregulation of delta-catenin expression in invasive tumor cells. This finding suggests that delta-catenin is related to tumor invasion and migration.
    Title: δ-Catenin Promotes Bevacizumab-Induced Glioma Invasion.
  8. These results add further insights into the epigenetic regulation of insulin sensitivity and associated complications, pointing the CTNND2 and LPL genes as potential underlying epigenetic biomarkers for future risk of insulin-related diseases.
    Title: Insulin Sensitivity Is Associated with Lipoprotein Lipase (LPL) and Catenin Delta 2 (CTNND2) DNA Methylation in Peripheral White Blood Cells in Non-Diabetic Young Women.
  9. Data provide evidence that delta-catenin may serve an important role in the malignancy of lung adenocarcinoma through activation of canonical Wnt signaling and cancer stem cell maintenance.
    Title: δ-Catenin promotes tumorigenesis and metastasis of lung adenocarcinoma.
  10. Gene Ontology analysis revealed that neuronal differentiation-related genes were enriched among targets that were co-regulated by REST and TRIM28, while the level of CTNND2 was increased by the knockdown of REST and TRIM28. Consistently, during neuronal differentiation, the level of CTNND2 increased while those of REST and TRIM28 decreased, suggesting that CTNND2 expression may be co-regulated by both.
    Title: Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation.
Submit: New GeneRIF Correction See all GeneRIFs (37)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2021-10-12)

ClinGen Genome Curation PagePubMed
Triplosensitivity

No evidence available (Last evaluated 2021-10-12)

ClinGen Genome Curation Page

EBI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
EBI GWAS Catalog
Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
EBI GWAS Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
EBI GWAS Catalog
Genome-wide association studies reveal genetic variants in CTNND2 for high myopia in Singapore Chinese.
EBI GWAS Catalog
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
EBI GWAS Catalog
Genome-wide association study of lung function decline in adults with and without asthma.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables beta-catenin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables cadherin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in cell adhesion TAS
Traceable Author Statement
more info
 PubMed 
involved_in cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in dendritic spine morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in dendritic spine morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of canonical Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in signal transduction TAS
Traceable Author Statement
more info
 PubMed 
involved_in synapse organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in perikaryon IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in postsynaptic density IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
catenin delta-2
Names
T-cell delta-catenin
catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)
neurojungin

NCBI Reference Sequences (RefSeq)

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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.

Genomic

  1. NG_023544.2 RefSeqGene

    Range
    4553..937163
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001288715.1 → NP_001275644.1  catenin delta-2 isoform 2

    See identical proteins and their annotated locations for NP_001275644.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region, uses a downstream start codon, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AB013805, AC010626, AI680877, AK226124, DC332925, U52351, U52828
    Consensus CDS
    CCDS75228.1
    UniProtKB/TrEMBL
    A0A994J5I1, E7EPC8
    Related
    ENSP00000426510.1, ENST00000511377.5
    Conserved Domains (6) summary
    smart00185
    Location:490 → 530
    ARM; Armadillo/beta-catenin-like repeats
    pfam00514
    Location:743 → 784
    Arm; Armadillo/beta-catenin-like repeat
    sd00043
    Location:461 → 486
    ARM; armadillo repeat [structural motif]
    cl25496
    Location:164 → 292
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl27106
    Location:459 → 632
    PLN03200; cellulose synthase-interactive protein; Provisional
    cl28033
    Location:72 → 443
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region

  2. NM_001288716.1 → NP_001275645.1  catenin delta-2 isoform 3

    See identical proteins and their annotated locations for NP_001275645.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding region, uses a downstream start codon, and lacks two alternate exons in the 5' coding region, compared to variant 1. The resulting protein (isoform 3) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC010626, AF035302, AI680877, AK299300, DB571461, DC332925
    Consensus CDS
    CCDS75227.1
    UniProtKB/TrEMBL
    B3KXF4, B4DJU1, B4DRK2
    Related
    ENSP00000426887.1, ENST00000503622.5
    Conserved Domains (4) summary
    smart00185
    Location:244 → 284
    ARM; Armadillo/beta-catenin-like repeats
    PLN03200
    Location:213 → 386
    PLN03200; cellulose synthase-interactive protein; Provisional
    sd00043
    Location:215 → 240
    ARM; armadillo repeat [structural motif]
    pfam00514
    Location:288 → 329
    Arm; Armadillo/beta-catenin-like repeat

  3. NM_001288717.2 → NP_001275646.1  catenin delta-2 isoform 4

    See identical proteins and their annotated locations for NP_001275646.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate internal exon and uses a downstream start codon, compared to variant 1. The resulting protein (isoform 4) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC010626, AC127460, AI680877, AK226124, AK296232, U52351, U52828
    UniProtKB/TrEMBL
    B3KXF4, B4DJU1
    Conserved Domains (4) summary
    smart00185
    Location:148 → 188
    ARM; Armadillo/beta-catenin-like repeats
    PLN03200
    Location:117 → 290
    PLN03200; cellulose synthase-interactive protein; Provisional
    sd00043
    Location:119 → 144
    ARM; armadillo repeat [structural motif]
    pfam00514
    Location:401 → 441
    Arm; Armadillo/beta-catenin-like repeat

  4. NM_001332.4 → NP_001323.1  catenin delta-2 isoform 1

    See identical proteins and their annotated locations for NP_001323.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).
    Source sequence(s)
    AB013805, AC010626, AC127460, DC341093, U52351, U96136
    Consensus CDS
    CCDS3881.1
    UniProtKB/Swiss-Prot
    B0FTZ7, O00379, O15390, O43206, O43840, Q13589, Q9UM66, Q9UPM3, Q9UQB3
    Related
    ENSP00000307134.8, ENST00000304623.13
    Conserved Domains (5) summary
    smart00185
    Location:581 → 621
    ARM; Armadillo/beta-catenin-like repeats
    pfam00514
    Location:834 → 875
    Arm; Armadillo/beta-catenin-like repeat
    sd00043
    Location:552 → 577
    ARM; armadillo repeat [structural motif]
    cl27106
    Location:550 → 723
    PLN03200; cellulose synthase-interactive protein; Provisional
    cl28033
    Location:163 → 534
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region

  5. NM_001364128.2 → NP_001351057.1  catenin delta-2 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence, lacks two alternate exons, and contains another alternate in-frame exon compared to variant 1. The resulting isoform (6) is shorter at the N-terminus, lacks an alternate internal segment, and contains another alternate segment compared to isoform 1.
    Source sequence(s)
    AC003954, AC004648, AC005367, AC005610, AC010433, AC010626
    Consensus CDS
    CCDS93685.1
    UniProtKB/TrEMBL
    A0A994J5V2, B3KXF4, B4DJU1
    Related
    ENSP00000516315.1, ENST00000706271.1
    Conserved Domains (4) summary
    smart00185
    Location:244 → 284
    ARM; Armadillo/beta-catenin-like repeats
    PLN03200
    Location:213 → 386
    PLN03200; cellulose synthase-interactive protein; Provisional
    sd00043
    Location:215 → 240
    ARM; armadillo repeat [structural motif]
    pfam00514
    Location:288 → 329
    Arm; Armadillo/beta-catenin-like repeat

RNA

  1. NR_109988.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC010626, AC127460, AK299300, DC341093, EU328348

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    10971836..11904446 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009074.2 → XP_016864563.1  catenin delta-2 isoform X4

    UniProtKB/TrEMBL
    E9PHB5
    Conserved Domains (4) summary
    smart00185
    Location:335 → 375
    ARM; Armadillo/beta-catenin-like repeats
    PLN03200
    Location:304 → 477
    PLN03200; cellulose synthase-interactive protein; Provisional
    sd00043
    Location:306 → 331
    ARM; armadillo repeat [structural motif]
    pfam00514
    Location:379 → 420
    Arm; Armadillo/beta-catenin-like repeat

  2. XM_017009072.2 → XP_016864561.1  catenin delta-2 isoform X3

    UniProtKB/TrEMBL
    E9PHB5
    Related
    ENSP00000421093.1, ENST00000513588.5
    Conserved Domains (4) summary
    smart00185
    Location:335 → 375
    ARM; Armadillo/beta-catenin-like repeats
    PLN03200
    Location:304 → 477
    PLN03200; cellulose synthase-interactive protein; Provisional
    sd00043
    Location:306 → 331
    ARM; armadillo repeat [structural motif]
    pfam00514
    Location:379 → 420
    Arm; Armadillo/beta-catenin-like repeat

  3. XM_005248251.4 → XP_005248308.1  catenin delta-2 isoform X1

    See identical proteins and their annotated locations for XP_005248308.1

    Conserved Domains (4) summary
    cd00020
    Location:544 → 666
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    pfam00514
    Location:834 → 875
    Arm; Armadillo/beta-catenin-like repeat
    pfam17052
    Location:1054 → 1113
    CAF20; Cap associated factor
    sd00043
    Location:552 → 577
    ARM; armadillo repeat [structural motif]

  4. XM_011513967.3 → XP_011512269.1  catenin delta-2 isoform X2

    See identical proteins and their annotated locations for XP_011512269.1

    UniProtKB/TrEMBL
    A0A994J5I1
    Conserved Domains (4) summary
    cd00020
    Location:453 → 575
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    pfam00514
    Location:743 → 784
    Arm; Armadillo/beta-catenin-like repeat
    pfam17052
    Location:963 → 1022
    CAF20; Cap associated factor
    sd00043
    Location:461 → 486
    ARM; armadillo repeat [structural motif]

  5. XM_005248253.2 → XP_005248310.1  catenin delta-2 isoform X2

    See identical proteins and their annotated locations for XP_005248310.1

    UniProtKB/TrEMBL
    A0A994J5I1
    Conserved Domains (4) summary
    cd00020
    Location:453 → 575
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    pfam00514
    Location:743 → 784
    Arm; Armadillo/beta-catenin-like repeat
    pfam17052
    Location:963 → 1022
    CAF20; Cap associated factor
    sd00043
    Location:461 → 486
    ARM; armadillo repeat [structural motif]

  6. XM_047416777.1 → XP_047272733.1  catenin delta-2 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    10909469..11841846 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351724.1 → XP_054207699.1  catenin delta-2 isoform X4

  2. XM_054351723.1 → XP_054207698.1  catenin delta-2 isoform X3

  3. XM_054351719.1 → XP_054207694.1  catenin delta-2 isoform X1

  4. XM_054351720.1 → XP_054207695.1  catenin delta-2 isoform X6

  5. XM_054351722.1 → XP_054207697.1  catenin delta-2 isoform X2

  6. XM_054351721.1 → XP_054207696.1  catenin delta-2 isoform X2

  7. XM_054351725.1 → XP_054207700.1  catenin delta-2 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UQB3.3 GenPept UniProtKB/Swiss-Prot:Q9UQB3

Gene LinkOut

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Chemical Information
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