Cdhr1 (cadherin-related family member 1) - Rat Genome Database

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Gene: Cdhr1 (cadherin-related family member 1) Rattus norvegicus
Analyze
Symbol: Cdhr1
Name: cadherin-related family member 1
RGD ID: 620420
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion; photoreceptor cell morphogenesis; and photoreceptor cell outer segment organization. Predicted to act upstream of or within photoreceptor cell maintenance. Predicted to be located in photoreceptor outer segment membrane. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in cone-rod dystrophy 15. Orthologous to human CDHR1 (cadherin related family member 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: KIAA1775; MT-protocadherin; Pcdh21; photoreceptor cadherin; prCAD; protocadherin 21; protocadherin-21
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
GRCr81612,863,696 - 12,883,579 (-)NCBIGRCr8
mRatBN7.21612,843,436 - 12,863,321 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1612,843,437 - 12,863,396 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1612,787,727 - 12,807,565 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01613,932,462 - 13,952,306 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01612,780,219 - 12,800,039 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01614,328,161 - 14,348,049 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1614,328,160 - 14,348,046 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01614,230,682 - 14,250,567 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41613,284,018 - 13,303,854 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11613,284,016 - 13,303,852 (-)NCBI
Celera1613,101,611 - 13,121,487 (-)NCBICelera
Cytogenetic Map16p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Identification of three novel non-classical cadherin genes through comprehensive analysis of large cDNAs. Nakajima D, etal., Brain Res Mol Brain Res 2001 Oct 19;94(1-2):85-95.
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:11738025   PMID:18654668   PMID:20805371   PMID:23044944  


Genomics

Comparative Map Data
Cdhr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81612,863,696 - 12,883,579 (-)NCBIGRCr8
mRatBN7.21612,843,436 - 12,863,321 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1612,843,437 - 12,863,396 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1612,787,727 - 12,807,565 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01613,932,462 - 13,952,306 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01612,780,219 - 12,800,039 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01614,328,161 - 14,348,049 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1614,328,160 - 14,348,046 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01614,230,682 - 14,250,567 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41613,284,018 - 13,303,854 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11613,284,016 - 13,303,852 (-)NCBI
Celera1613,101,611 - 13,121,487 (-)NCBICelera
Cytogenetic Map16p14NCBI
CDHR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381084,194,537 - 84,219,621 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1084,194,537 - 84,219,621 (+)EnsemblGRCh38hg38GRCh38
GRCh371085,954,293 - 85,979,377 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361085,944,497 - 85,967,102 (+)NCBINCBI36Build 36hg18NCBI36
Build 341085,944,496 - 85,967,099NCBI
Celera1079,949,917 - 79,974,886 (+)NCBICelera
Cytogenetic Map10q23.1NCBI
HuRef1079,799,950 - 79,824,856 (+)NCBIHuRef
CHM1_11086,236,160 - 86,261,144 (+)NCBICHM1_1
T2T-CHM13v2.01085,073,058 - 85,098,147 (+)NCBIT2T-CHM13v2.0
Cdhr1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391436,799,806 - 36,820,304 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1436,799,814 - 36,820,304 (-)EnsemblGRCm39 Ensembl
GRCm381437,077,849 - 37,098,347 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1437,077,857 - 37,098,347 (-)EnsemblGRCm38mm10GRCm38
MGSCv371437,891,035 - 37,911,497 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361435,989,090 - 36,009,703 (-)NCBIMGSCv36mm8
Celera1433,288,873 - 33,309,346 (-)NCBICelera
Cytogenetic Map14BNCBI
cM Map1421.29NCBI
Cdhr1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555103,708,723 - 3,728,926 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555103,709,206 - 3,727,448 (+)NCBIChiLan1.0ChiLan1.0
CDHR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2896,176,577 - 96,198,587 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11096,181,920 - 96,203,907 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01080,610,079 - 80,632,084 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11084,180,049 - 84,204,163 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1084,179,704 - 84,204,747 (+)Ensemblpanpan1.1panPan2
CDHR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1432,435,364 - 32,459,181 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl432,439,148 - 32,459,192 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha432,423,793 - 32,444,614 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0432,753,737 - 32,774,756 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl432,753,554 - 32,775,779 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1432,616,386 - 32,637,362 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0432,808,625 - 32,829,652 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0433,305,337 - 33,326,219 (+)NCBIUU_Cfam_GSD_1.0
Cdhr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721346,259,115 - 46,283,067 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936767805,558 - 827,712 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936767805,910 - 829,838 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDHR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1485,429,952 - 85,455,822 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11485,429,506 - 85,455,823 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21492,234,667 - 92,259,011 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CDHR1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1947,611,969 - 47,638,846 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl947,613,257 - 47,636,794 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660487,788,707 - 7,813,916 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cdhr1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248412,820,546 - 2,839,005 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248412,820,543 - 2,838,998 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cdhr1
114 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:631
Count of miRNA genes:313
Interacting mature miRNAs:378
Transcripts:ENSRNOT00000018630
Prediction methods:Microtar, Miranda, 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
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760916039848Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16285170915884239Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 9 49 112 65 65 35 25 35 6 188 91 93 45 58 30

Sequence


Ensembl Acc Id: ENSRNOT00000018630   ⟹   ENSRNOP00000018631
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1612,843,437 - 12,863,396 (-)Ensembl
Rnor_6.0 Ensembl1614,328,160 - 14,348,046 (-)Ensembl
RefSeq Acc Id: NM_053572   ⟹   NP_446024
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81612,863,696 - 12,883,579 (-)NCBI
mRatBN7.21612,843,436 - 12,863,321 (-)NCBI
Rnor_6.01614,328,161 - 14,348,049 (-)NCBI
Rnor_5.01614,230,682 - 14,250,567 (-)NCBI
RGSC_v3.41613,284,018 - 13,303,854 (-)RGD
Celera1613,101,611 - 13,121,487 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446024 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAB61906 (Get FASTA)   NCBI Sequence Viewer  
  EDL90897 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018631.5
GenBank Protein Q91XU7 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_446024   ⟸   NM_053572
- Peptide Label: precursor
- UniProtKB: Q91XU7 (UniProtKB/Swiss-Prot),   A6K9J0 (UniProtKB/TrEMBL),   A0A8L2Q9B0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000018631   ⟸   ENSRNOT00000018630
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q91XU7-F1-model_v2 AlphaFold Q91XU7 1-859 view protein structure

Transcriptome

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

Promoters
RGD ID:13699966
Promoter ID:EPDNEW_R10488
Type:single initiation site
Name:Cdhr1_1
Description:cadherin-related family member 1
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_6.01614,348,062 - 14,348,122EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620420 AgrOrtholog
BioCyc Gene G2FUF-11994 BioCyc
Ensembl Genes ENSRNOG00000013330 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018630.6 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:93662 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 93662 ENTREZGENE
PANTHER CADHERIN-23 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CADHERIN-RELATED FAMILY MEMBER 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cdhr1 PhenoGen
PRINTS CADHERIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013330 RatGTEx
SMART SM00112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49313 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2Q9B0 ENTREZGENE, UniProtKB/TrEMBL
  A6K9J0 ENTREZGENE, UniProtKB/TrEMBL
  CDHR1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Cdhr1  cadherin-related family member 1  Pcdh21  protocadherin 21  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-25 Pcdh21  protocadherin 21  Pcdh21  MT-protocadherin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Pcdh21  MT-protocadherin  KIAA1775    Symbol and Name updated 1299863 APPROVED
2002-08-07 KIAA1775  MT-protocadherin      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains large protein with six cadherin domains 633048
gene_expression expressed exclusively in the olfactory bulb of the rat brain 633048