Cdh12 (cadherin 12) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Cdh12 (cadherin 12) Rattus norvegicus
Analyze
Symbol: Cdh12
Name: cadherin 12
RGD ID: 1566350
Description: Predicted to enable beta-catenin binding activity and cadherin 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 be part of catenin complex. Predicted to be active in adherens junction. Orthologous to human CDH12 (cadherin 12); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cadherin-12; LOC301887; RGD1566350; similar to cadherin 12, type 2 preproprotein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8272,201,859 - 73,436,039 (+)NCBIGRCr8
mRatBN7.2270,474,679 - 71,705,369 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl270,475,043 - 71,700,572 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0271,310,228 - 72,540,063 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl272,006,099 - 72,540,263 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0291,039,561 - 92,271,682 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4272,175,690 - 72,598,944 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera266,295,278 - 67,494,155 (+)NCBICelera
Cytogenetic Map2q22NCBI
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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:15485826  


Genomics

Comparative Map Data
Cdh12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8272,201,859 - 73,436,039 (+)NCBIGRCr8
mRatBN7.2270,474,679 - 71,705,369 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl270,475,043 - 71,700,572 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0271,310,228 - 72,540,063 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl272,006,099 - 72,540,263 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0291,039,561 - 92,271,682 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4272,175,690 - 72,598,944 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera266,295,278 - 67,494,155 (+)NCBICelera
Cytogenetic Map2q22NCBI
CDH12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38521,750,673 - 22,853,344 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl521,750,673 - 22,853,344 (-)EnsemblGRCh38hg38GRCh38
GRCh37521,750,782 - 22,853,453 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36521,786,911 - 22,889,488 (-)NCBINCBI36Build 36hg18NCBI36
Build 34521,786,910 - 22,889,488NCBI
Celera521,615,397 - 22,740,089 (-)NCBICelera
Cytogenetic Map5p14.3NCBI
HuRef521,604,798 - 22,819,780 (-)NCBIHuRef
CHM1_1521,750,833 - 22,853,585 (-)NCBICHM1_1
T2T-CHM13v2.0521,857,991 - 22,961,025 (-)NCBIT2T-CHM13v2.0
Cdh12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391520,448,967 - 21,598,668 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1520,449,351 - 21,589,619 (+)EnsemblGRCm39 Ensembl
GRCm381520,448,878 - 21,598,421 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1520,449,265 - 21,589,533 (+)EnsemblGRCm38mm10GRCm38
MGSCv371521,041,207 - 21,519,288 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361521,056,177 - 21,534,258 (+)NCBIMGSCv36mm8
Celera1522,028,455 - 22,369,031 (+)NCBICelera
Cytogenetic Map15A2NCBI
cM Map158.25NCBI
Cdh12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554269,651,959 - 10,059,415 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554269,652,418 - 10,610,762 (-)NCBIChiLan1.0ChiLan1.0
CDH12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2487,502,309 - 88,605,663 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1585,655,954 - 86,759,309 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0588,532,493 - 88,636,522 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1594,143,751 - 94,269,418 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl594,160,742 - 94,268,811 (+)Ensemblpanpan1.1panPan2
CDH12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1482,501,335 - 83,124,378 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl482,875,494 - 83,123,473 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha481,810,642 - 82,766,572 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0482,774,803 - 83,742,031 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl483,327,616 - 83,741,351 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1482,308,589 - 83,268,674 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0482,561,447 - 83,521,372 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0483,263,631 - 84,299,820 (+)NCBIUU_Cfam_GSD_1.0
Cdh12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213214,331,894 - 215,268,682 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936775516,237 - 789,589 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936775515,504 - 789,575 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDH12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl169,985,126 - 10,384,663 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1169,985,759 - 10,975,489 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21610,811,499 - 11,212,363 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDH12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1421,183,585 - 22,272,005 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660646,125,823 - 7,234,642 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Cdh12
9748 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:19
Count of miRNA genes:17
Interacting mature miRNAs:17
Transcripts:ENSRNOT00000034044
Prediction methods:Microtar, Miranda, Rnahybrid
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
1578777Stresp15Stress response QTL 1520.05blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)259846005104846005Rat
6480225Gdil1Gastrointestinal dilation QTL 1enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)25666087974786777Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
631500Bp99Blood pressure QTL 992.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)259324719102755241Rat
10755436Coatc8Coat color QTL 80.02431coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23502311780023117Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23064806575648065Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243162366111362592Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)243162366111362592Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
5684996Bmd85Bone mineral density QTL 854.70.024tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)259324377103795077Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240067944102785628Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
631208Bw1Body weight QTL15.09mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)24317101783575226Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
5684990Bmd82Bone mineral density QTL 822.8tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)259324377103795077Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
7411551Bw131Body weight QTL 13129.60.001body mass (VT:0001259)body weight gain (CMO:0000420)267942638112942638Rat
1558648Smcn1Smooth muscle cell number QTL 10.039blood vessel smooth muscle cell quantity (VT:0010525)aorta smooth muscle cell count per unit vessel length (CMO:0001646)259134147127460910Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354592Rf50Renal function QTL 503.5urine output (VT:0003620)timed urine volume (CMO:0000260)25382274774786777Rat
2306903Bp336Blood pressure QTL 3360.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)264366971109366971Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23513484188029593Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
1582246Cm60Cardiac mass QTL 605.8heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)25760561276539510Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)259324377141596857Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat


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 13
Low 55 4 10
Below cutoff 3 17 29 13 18 13 4 4 4 15 19 10 4

Sequence


RefSeq Acc Id: ENSRNOT00000034044   ⟹   ENSRNOP00000032511
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl270,475,043 - 71,700,572 (+)Ensembl
Rnor_6.0 Ensembl272,006,099 - 72,540,263 (+)Ensembl
RefSeq Acc Id: NM_001427475   ⟹   NP_001414404
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8272,886,532 - 73,436,039 (+)NCBI
RefSeq Acc Id: XM_017591412   ⟹   XP_017446901
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8272,201,859 - 73,436,039 (+)NCBI
mRatBN7.2270,474,679 - 71,705,369 (+)NCBI
Rnor_6.0271,310,228 - 72,540,063 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001414404 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446901 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL82601 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000032511
  ENSRNOP00000032511.4
RefSeq Acc Id: XP_017446901   ⟸   XM_017591412
- Peptide Label: isoform X1
- UniProtKB: F1M1A2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000032511   ⟸   ENSRNOT00000034044
RefSeq Acc Id: NP_001414404   ⟸   NM_001427475
- Peptide Label: precursor
- UniProtKB: F1M1A2 (UniProtKB/TrEMBL)
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M1A2-F1-model_v2 AlphaFold F1M1A2 1-794 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:1566350 AgrOrtholog
BioCyc Gene G2FUF-53990 BioCyc
Ensembl Genes ENSRNOG00000026392 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034044.6 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:301887 UniProtKB/TrEMBL
NCBI Gene 301887 ENTREZGENE
PANTHER CADHERIN-12 UniProtKB/TrEMBL
  PTHR24027 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
PhenoGen Cdh12 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000026392 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt F1M1A2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Cdh12  cadherin 12  RGD1566350_predicted  similar to cadherin 12, type 2 preproprotein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1566350_predicted  similar to cadherin 12, type 2 preproprotein (predicted)  LOC301887  similar to cadherin 12, type 2 preproprotein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC301887  similar to cadherin 12, type 2 preproprotein      Symbol and Name status set to provisional 70820 PROVISIONAL