Cdh16 (cadherin 16) - Rat Genome Database

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Gene: Cdh16 (cadherin 16) Rattus norvegicus
Analyze
Symbol: Cdh16
Name: cadherin 16
RGD ID: 1311638
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion. Predicted to act upstream of or within calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules. Predicted to be located in basolateral plasma membrane. Predicted to be active in plasma membrane. Orthologous to human CDH16 (cadherin 16); INTERACTS WITH acrylamide; amitrole; atrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cadherin-16; LOC307614
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr819367,202 - 377,710 (+)NCBIGRCr8
mRatBN7.219360,824 - 371,008 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl19360,824 - 371,007 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx19348,915 - 359,097 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0191,115,720 - 1,125,902 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.019390,913 - 401,095 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.019568,329 - 578,513 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl19568,287 - 578,520 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.019562,589 - 572,773 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.419279,359 - 289,543 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.119279,358 - 289,542 (+)NCBI
Celera19357,030 - 367,220 (+)NCBICelera
Cytogenetic Map19p14NCBI
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. CDH16/Ksp-cadherin is expressed in the developing thyroid gland and is strongly down-regulated in thyroid carcinomas. Calì G, etal., Endocrinology. 2012 Jan;153(1):522-34. doi: 10.1210/en.2011-1572. Epub 2011 Oct 25.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15023525   PMID:23533145   PMID:27780871  


Genomics

Comparative Map Data
Cdh16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr819367,202 - 377,710 (+)NCBIGRCr8
mRatBN7.219360,824 - 371,008 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl19360,824 - 371,007 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx19348,915 - 359,097 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0191,115,720 - 1,125,902 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.019390,913 - 401,095 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.019568,329 - 578,513 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl19568,287 - 578,520 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.019562,589 - 572,773 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.419279,359 - 289,543 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.119279,358 - 289,542 (+)NCBI
Celera19357,030 - 367,220 (+)NCBICelera
Cytogenetic Map19p14NCBI
CDH16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381666,908,122 - 66,918,885 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1666,908,122 - 66,918,917 (-)EnsemblGRCh38hg38GRCh38
GRCh371666,942,025 - 66,952,788 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361665,499,526 - 65,510,267 (-)NCBINCBI36Build 36hg18NCBI36
Build 341665,499,525 - 65,510,267NCBI
Celera1651,450,284 - 51,461,025 (-)NCBICelera
Cytogenetic Map16q22.1NCBI
HuRef1652,816,134 - 52,826,996 (-)NCBIHuRef
CHM1_11668,349,034 - 68,359,895 (-)NCBICHM1_1
T2T-CHM13v2.01672,702,422 - 72,713,185 (-)NCBIT2T-CHM13v2.0
Cdh16
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398105,328,547 - 105,351,028 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8105,328,543 - 105,351,028 (-)EnsemblGRCm39 Ensembl
GRCm388104,601,915 - 104,624,396 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8104,601,911 - 104,624,396 (-)EnsemblGRCm38mm10GRCm38
MGSCv378107,138,047 - 107,148,161 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368107,503,276 - 107,513,390 (-)NCBIMGSCv36mm8
Celera8108,846,745 - 108,856,860 (-)NCBICelera
Cytogenetic Map8D3NCBI
cM Map853.04NCBI
Cdh16
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543323,413,349 - 23,423,323 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543323,413,904 - 23,423,324 (-)NCBIChiLan1.0ChiLan1.0
CDH16
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21876,408,051 - 76,418,829 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11682,320,586 - 82,331,361 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01647,223,506 - 47,234,305 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11666,325,345 - 66,336,573 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1666,325,615 - 66,335,657 (-)Ensemblpanpan1.1panPan2
CDH16
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1582,398,443 - 82,417,807 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl582,398,541 - 82,408,061 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha582,387,135 - 82,406,493 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0582,835,051 - 82,854,428 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl582,835,148 - 82,844,668 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1582,658,232 - 82,677,589 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0582,345,049 - 82,364,362 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0582,984,014 - 83,003,379 (+)NCBIUU_Cfam_GSD_1.0
Cdh16
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934942,419,995 - 42,428,117 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493647517,161,228 - 17,169,113 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDH16
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl627,589,184 - 27,598,987 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1627,589,183 - 27,599,002 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CDH16
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1552,607,436 - 52,618,645 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl552,607,396 - 52,618,310 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604723,295,627 - 23,306,554 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cdh16
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474619,590,445 - 19,602,672 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474619,590,590 - 19,600,101 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cdh16
21 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:181
Count of miRNA genes:135
Interacting mature miRNAs:147
Transcripts:ENSRNOT00000016419
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
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat

Markers in Region
RH132708  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.219370,691 - 370,898 (+)MAPPERmRatBN7.2
Rnor_6.019578,197 - 578,403NCBIRnor6.0
Rnor_5.019572,457 - 572,663UniSTSRnor5.0
RGSC_v3.419289,227 - 289,433UniSTSRGSC3.4
Celera19366,904 - 367,110UniSTS
Cytogenetic Map19p14UniSTS


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

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 35 19
Low 14 3 1 2 1 2 20 6
Below cutoff 29 29 15 14 15 8 9 12 2 5 8

Sequence


RefSeq Acc Id: ENSRNOT00000016419   ⟹   ENSRNOP00000016419
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl19360,824 - 371,007 (+)Ensembl
Rnor_6.0 Ensembl19568,287 - 578,520 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094878   ⟹   ENSRNOP00000078051
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl19361,685 - 371,007 (+)Ensembl
RefSeq Acc Id: NM_001012055   ⟹   NP_001012055
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819367,274 - 377,458 (+)NCBI
mRatBN7.219360,824 - 371,008 (+)NCBI
Rnor_6.019568,329 - 578,513 (+)NCBI
Rnor_5.019562,589 - 572,773 (+)NCBI
RGSC_v3.419279,359 - 289,543 (+)RGD
Celera19357,030 - 367,220 (+)RGD
Sequence:
RefSeq Acc Id: XM_063277975   ⟹   XP_063134045
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819367,239 - 377,710 (+)NCBI
RefSeq Acc Id: XM_063277976   ⟹   XP_063134046
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819367,202 - 377,710 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001012055 (Get FASTA)   NCBI Sequence Viewer  
  XP_063134045 (Get FASTA)   NCBI Sequence Viewer  
  XP_063134046 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH81996 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016419
  ENSRNOP00000016419.4
  ENSRNOP00000078051.1
RefSeq Acc Id: NP_001012055   ⟸   NM_001012055
- Peptide Label: precursor
- UniProtKB: Q66H67 (UniProtKB/TrEMBL),   A6JXU7 (UniProtKB/TrEMBL),   G3V7L4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016419   ⟸   ENSRNOT00000016419
RefSeq Acc Id: ENSRNOP00000078051   ⟸   ENSRNOT00000094878
RefSeq Acc Id: XP_063134046   ⟸   XM_063277976
- Peptide Label: isoform X2
- UniProtKB: A6JXU7 (UniProtKB/TrEMBL),   G3V7L4 (UniProtKB/TrEMBL),   A0A8I5Y838 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134045   ⟸   XM_063277975
- Peptide Label: isoform X1
- UniProtKB: A6JXU7 (UniProtKB/TrEMBL),   G3V7L4 (UniProtKB/TrEMBL)
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V7L4-F1-model_v2 AlphaFold G3V7L4 1-830 view protein structure

Transcriptome

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

Promoters
RGD ID:13700907
Promoter ID:EPDNEW_R11431
Type:initiation region
Name:Cdh16_1
Description:cadherin 16
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.019568,308 - 568,368EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311638 AgrOrtholog
BioCyc Gene G2FUF-6656 BioCyc
Ensembl Genes ENSRNOG00000012222 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016419 ENTREZGENE
  ENSRNOT00000016419.7 UniProtKB/TrEMBL
  ENSRNOT00000094878.1 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7130691 IMAGE-MGC_LOAD
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
KEGG Report rno:307614 UniProtKB/TrEMBL
MGC_CLONE MGC:94217 IMAGE-MGC_LOAD
NCBI Gene 307614 ENTREZGENE
PANTHER CADHERIN 16, KSP-CADHERIN UniProtKB/TrEMBL
  CADHERIN-23 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
PhenoGen Cdh16 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012222 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A0A8I5Y838 ENTREZGENE, UniProtKB/TrEMBL
  A6JXU7 ENTREZGENE, UniProtKB/TrEMBL
  G3V7L4 ENTREZGENE, UniProtKB/TrEMBL
  Q66H67 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Cdh16  cadherin 16  Cdh16_predicted  cadherin 16 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Cdh16_predicted  cadherin 16 (predicted)      Symbol and Name status set to approved 70820 APPROVED