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Cdh6 cadherin 6 [ Rattus norvegicus (Norway rat) ]

Gene ID: 25409, updated on 10-Jul-2024

Summary

Official Symbol
Cdh6provided by RGD
Official Full Name
cadherin 6provided by RGD
Primary source
RGD:2322
See related
EnsemblRapid:ENSRNOG00000013535 AllianceGenome:RGD:2322
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
KCAD
Summary
Predicted to enable cadherin binding activity and calcium ion binding activity. Involved in female gonad development. Predicted to be located in cell junction; nucleoplasm; and plasma membrane. Predicted to be part of catenin complex. Predicted to be active in adherens junction. Orthologous to human CDH6 (cadherin 6). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Kidney (RPKM 159.8), Brain (RPKM 87.5) and 6 other tissues See more
Orthologs
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Genomic context

See Cdh6 in Genome Data Viewer
Location:
2q16
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (63801630..63952309, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (62079139..62225298, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (63100723..63246618, complement)

Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene similar to human chromosome 5 open reading frame 22 Neighboring gene drosha ribonuclease III Neighboring gene uncharacterized LOC103695100 Neighboring gene 60S ribosomal protein L7a pseudogene Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

General gene information

Markers

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables beta-catenin binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables cadherin binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within Notch signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in adherens junction organization IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules TAS
Traceable Author Statement
more info
PubMed 
involved_in cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cell morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cell-cell adhesion mediated by cadherin IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cell-cell junction assembly IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in female gonad development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
involved_in multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in synaptic membrane adhesion IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in synaptic membrane adhesion IEA
Inferred from Electronic Annotation
more info
 
involved_in synaptic membrane adhesion ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of catenin complex IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cell junction ISO
Inferred from Sequence Orthology
more info
 
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
is_active_in glutamatergic synapse ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 
is_active_in synapse ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
cadherin-6
Names
K-cadherin
cadherin 6, type 2, K-cadherin
kidney cadherin

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.

mRNA and Protein(s)

  1. NM_012927.2NP_037059.2  cadherin-6 precursor

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000002
    UniProtKB/Swiss-Prot
    P55280
    UniProtKB/TrEMBL
    A6KJN4, F1LQP8
    Related
    ENSRNOP00000018246.8, ENSRNOT00000018246.9
    Conserved Domains (3) summary
    cd11304
    Location:163264
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:79157
    CA; Cadherin repeats
    pfam01049
    Location:637783
    Cadherin_C; Cadherin cytoplasmic region

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086020.1 Reference GRCr8

    Range
    63801630..63952309 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063281354.1XP_063137424.1  cadherin-6 isoform X1

    UniProtKB/Swiss-Prot
    P55280
    UniProtKB/TrEMBL
    A6KJN4, F1LQP8
  2. XM_063281355.1XP_063137425.1  cadherin-6 isoform X2