Cdh24 (cadherin 24) - Rat Genome Database

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Gene: Cdh24 (cadherin 24) Rattus norvegicus
Analyze
Symbol: Cdh24
Name: cadherin 24
RGD ID: 1560161
Description: Predicted to enable several functions, including alpha-catenin binding activity; beta-catenin binding activity; and delta-catenin binding activity. Predicted to be involved in several processes, including calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; cell-cell adhesion mediated by cadherin; and cell-cell junction organization. Predicted to act upstream of or within cell-cell adhesion. Predicted to be located in cell-cell junction. Predicted to be part of catenin complex. Predicted to be active in adherens junction. Orthologous to human CDH24 (cadherin 24); INTERACTS WITH 6-propyl-2-thiouracil; amitrole; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cadherin 24, type 2; cadherin-24; cadherin-like 24; LOC498515; RGD1560161; similar to Cadherin-like 24
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81532,061,588 - 32,071,323 (-)NCBIGRCr8
mRatBN7.21528,091,578 - 28,101,330 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1528,091,637 - 28,101,340 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01533,277,845 - 33,287,546 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1533,278,713 - 33,285,779 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01537,162,640 - 37,172,757 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41532,710,204 - 32,717,270 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1527,669,781 - 27,679,490 (-)NCBICelera
Cytogenetic Map15p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12734196  


Genomics

Comparative Map Data
Cdh24
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81532,061,588 - 32,071,323 (-)NCBIGRCr8
mRatBN7.21528,091,578 - 28,101,330 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1528,091,637 - 28,101,340 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01533,277,845 - 33,287,546 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1533,278,713 - 33,285,779 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01537,162,640 - 37,172,757 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41532,710,204 - 32,717,270 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1527,669,781 - 27,679,490 (-)NCBICelera
Cytogenetic Map15p13NCBI
CDH24
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381423,047,067 - 23,057,520 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1423,047,062 - 23,057,538 (-)EnsemblGRCh38hg38GRCh38
GRCh371423,516,276 - 23,526,729 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361422,586,709 - 22,594,875 (-)NCBINCBI36Build 36hg18NCBI36
Build 341422,586,708 - 22,594,875NCBI
Celera143,378,962 - 3,389,437 (-)NCBICelera
Cytogenetic Map14q11.2NCBI
HuRef143,633,349 - 3,643,699 (-)NCBIHuRef
CHM1_11423,514,900 - 23,525,377 (-)NCBICHM1_1
T2T-CHM13v2.01417,247,688 - 17,258,139 (-)NCBIT2T-CHM13v2.0
Cdh24
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391454,868,688 - 54,878,853 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1454,868,688 - 54,878,821 (-)EnsemblGRCm39 Ensembl
GRCm381454,631,231 - 54,642,067 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1454,631,231 - 54,641,364 (-)EnsemblGRCm38mm10GRCm38
MGSCv371455,250,829 - 55,260,201 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361453,585,436 - 53,595,523 (-)NCBIMGSCv36mm8
Celera1452,420,388 - 52,429,748 (-)NCBICelera
Cytogenetic Map14C2NCBI
cM Map1427.87NCBI
Cdh24
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540937,249,531 - 37,256,603 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540937,249,377 - 37,257,420 (+)NCBIChiLan1.0ChiLan1.0
CDH24
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21524,479,600 - 24,490,032 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11423,696,087 - 23,706,518 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0143,866,958 - 3,877,393 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11421,963,975 - 21,974,369 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1421,964,897 - 21,972,528 (-)Ensemblpanpan1.1panPan2
CDH24
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.183,359,452 - 3,369,590 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl83,359,875 - 3,367,942 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha83,308,149 - 3,318,203 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.083,467,319 - 3,477,376 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl83,467,250 - 3,475,742 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.183,158,726 - 3,168,781 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.083,219,964 - 3,230,010 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.083,482,028 - 3,492,086 (-)NCBIUU_Cfam_GSD_1.0
Cdh24
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864035,113,156 - 35,123,474 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367221,265,219 - 1,275,920 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367221,265,583 - 1,276,443 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDH24
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl775,990,220 - 76,001,130 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1775,990,185 - 76,001,133 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2781,327,040 - 81,351,723 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CDH24
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12923,416,449 - 23,427,764 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2923,417,354 - 23,426,738 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605922,990,284 - 23,000,750 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cdh24
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248209,485,919 - 9,494,990 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248209,484,779 - 9,494,891 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cdh24
49 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:83
Count of miRNA genes:78
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000036150
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151448116528469888Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat

Markers in Region
AI073030  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21528,102,205 - 28,102,399 (+)MAPPERmRatBN7.2
Rnor_6.01533,288,463 - 33,288,656NCBIRnor6.0
Rnor_5.01537,173,258 - 37,173,451UniSTSRnor5.0
RGSC_v3.41532,719,954 - 32,720,147UniSTSRGSC3.4
Celera1527,680,407 - 27,680,600UniSTS
Cytogenetic Map15p13UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 10 4 4 4 66 18 28
Low 3 23 50 34 15 34 1 1 8 15 11 11 1
Below cutoff 10 3 3 4 3 6 9 2 2 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000036150   ⟹   ENSRNOP00000037678
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1528,091,637 - 28,101,340 (-)Ensembl
Rnor_6.0 Ensembl1533,278,713 - 33,285,779 (-)Ensembl
RefSeq Acc Id: NM_001427281   ⟹   NP_001414210
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81532,061,588 - 32,071,283 (-)NCBI
RefSeq Acc Id: XM_039093832   ⟹   XP_038949760
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81532,064,005 - 32,071,323 (-)NCBI
mRatBN7.21528,093,995 - 28,101,330 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001414210 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949760 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM14184 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037678.3
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000037678   ⟸   ENSRNOT00000036150
RefSeq Acc Id: XP_038949760   ⟸   XM_039093832
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001414210   ⟸   NM_001427281
- Peptide Label: precursor
- UniProtKB: A6KGV5 (UniProtKB/TrEMBL),   D3ZTI3 (UniProtKB/TrEMBL)
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZTI3-F1-model_v2 AlphaFold D3ZTI3 1-781 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560161 AgrOrtholog
BioCyc Gene G2FUF-13787 BioCyc
Ensembl Genes ENSRNOG00000013503 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000036150.4 UniProtKB/TrEMBL
Gene3D-CATH 4.10.900.10 UniProtKB/TrEMBL
  Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_cytoplasmic-dom UniProtKB/TrEMBL
  Catenin_binding_dom UniProtKB/TrEMBL
KEGG Report rno:498515 UniProtKB/TrEMBL
NCBI Gene 498515 ENTREZGENE
PANTHER CADHERIN-24 UniProtKB/TrEMBL
  PTHR24027 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
PhenoGen Cdh24 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013503 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A6KGV5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZTI3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-20 Cdh24  cadherin 24  Cdh24  cadherin 24, type 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-07-29 Cdh24  cadherin 24, type 2  Cdh24  cadherin-like 24  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Cdh24  cadherin-like 24  RGD1560161_predicted  similar to Cadherin-like 24 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560161_predicted  similar to Cadherin-like 24 (predicted)  LOC498515  similar to Cadherin-like 24  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498515  similar to Cadherin-like 24      Symbol and Name status set to provisional 70820 PROVISIONAL