Cldnd2 (claudin domain containing 2) - Rat Genome Database

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Gene: Cldnd2 (claudin domain containing 2) Rattus norvegicus
Analyze
Symbol: Cldnd2
Name: claudin domain containing 2
RGD ID: 1566413
Description: Predicted to be located in membrane. Predicted to be active in plasma membrane. Orthologous to human CLDND2 (claudin domain containing 2); INTERACTS WITH bisphenol A; Cuprizon; 2-hydroxypropanoic acid (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: claudin domain-containing protein 2; LOC499140; RGD1566413; similar to hypothetical protein MGC33839
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81102,985,122 - 102,988,010 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1102,985,122 - 102,987,808 (+)EnsemblGRCr8
mRatBN7.2193,848,533 - 93,851,693 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl193,848,533 - 93,851,217 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx199,233,882 - 99,236,570 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01107,706,556 - 107,709,244 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01100,999,136 - 101,001,820 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0198,487,631 - 98,490,315 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl198,487,631 - 98,490,315 (-)Ensemblrn6Rnor6.0
Rnor_5.0199,564,436 - 99,567,120 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4193,816,749 - 93,819,433 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera188,125,644 - 88,128,328 (+)NCBICelera
Cytogenetic Map1q22NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View
COVID-19  (ISO)

Gene-Chemical Interaction 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

Genomics

Comparative Map Data
Cldnd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81102,985,122 - 102,988,010 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1102,985,122 - 102,987,808 (+)EnsemblGRCr8
mRatBN7.2193,848,533 - 93,851,693 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl193,848,533 - 93,851,217 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx199,233,882 - 99,236,570 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01107,706,556 - 107,709,244 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01100,999,136 - 101,001,820 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0198,487,631 - 98,490,315 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl198,487,631 - 98,490,315 (-)Ensemblrn6Rnor6.0
Rnor_5.0199,564,436 - 99,567,120 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4193,816,749 - 93,819,433 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera188,125,644 - 88,128,328 (+)NCBICelera
Cytogenetic Map1q22NCBI
CLDND2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381951,366,739 - 51,369,003 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1951,367,098 - 51,369,003 (-)Ensemblhg38GRCh38
GRCh371951,870,352 - 51,872,257 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361956,562,164 - 56,564,069 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1948,921,434 - 48,923,339 (-)NCBICelera
Cytogenetic Map19q13.41NCBI
HuRef1948,202,326 - 48,204,231 (-)NCBIHuRef
CHM1_11951,872,314 - 51,874,219 (-)NCBICHM1_1
T2T-CHM13v2.01954,455,382 - 54,457,884 (-)NCBIT2T-CHM13v2.0
Cldnd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39743,090,164 - 43,093,554 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl743,090,206 - 43,092,758 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38743,440,740 - 43,444,130 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl743,440,782 - 43,443,334 (+)Ensemblmm10GRCm38
MGSCv37750,696,186 - 50,698,690 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36743,308,708 - 43,311,254 (+)NCBIMGSCv36mm8
Celera738,907,481 - 38,909,985 (+)NCBICelera
Cytogenetic Map7B3NCBI
cM Map728.25NCBI
Cldnd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555581,030,594 - 1,032,198 (+)Ensembl
ChiLan1.0NW_0049555581,030,594 - 1,032,198 (+)NCBIChiLan1.0ChiLan1.0
CLDND2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22057,404,407 - 57,406,483 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11959,325,546 - 59,327,819 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01948,301,853 - 48,304,251 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11957,187,820 - 57,189,721 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1957,187,820 - 57,189,721 (-)EnsemblpanPan2panpan1.1
CLDND2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11105,609,654 - 105,612,128 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1105,610,511 - 105,628,125 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1105,181,541 - 105,184,832 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01106,118,385 - 106,121,675 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1106,119,990 - 106,121,672 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11105,790,033 - 105,793,322 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01105,430,882 - 105,434,162 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01106,226,423 - 106,229,713 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cldnd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934923,066,508 - 23,068,077 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493737838,874 - 39,940 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLDND2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl658,499,119 - 58,501,653 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1658,499,702 - 58,501,179 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2651,688,577 - 51,692,436 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLDND2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1644,286,708 - 44,288,857 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl644,286,753 - 44,288,181 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607324,335,901 - 24,337,456 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cldnd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248323,504,527 - 3,505,606 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Cldnd2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12156,034,693 - 156,037,338 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cldnd2
17 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:42
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000056490
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)187889942132889942Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1102780511182384005Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)192963855109494029Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1101228864146228864Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)187785026142582336Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183019780128019780Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)166404680111404680Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)193903998191260518Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)184107164115183752Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)191302413136302413Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)1102359314153680016Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)199645382182701046Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)199645382221502378Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)186622262131622262Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)158769992103769992Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)166077886111077886Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)198879955208479939Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of, or within a discrete space in an open field apparatus (CMO:0001514)192683681137683681Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)152891222109116986Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)186993904131993904Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)187558587132558587Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)192683681137683681Rat
737977Bp160Blood pressure QTL 1600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)197582336142582336Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1101594089146594089Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1100345976145345976Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)196717367160111531Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
12 5 17 68 34 41 17 66 17 1 161 99 8 52 29 52 24 8 8

Sequence


Ensembl Acc Id: ENSRNOT00000056490   ⟹   ENSRNOP00000053327
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1102,985,122 - 102,987,808 (+)Ensembl
mRatBN7.2 Ensembl193,848,533 - 93,851,217 (+)Ensembl
Rnor_6.0 Ensembl198,487,631 - 98,490,315 (-)Ensembl
RefSeq Acc Id: NM_001109143   ⟹   NP_001102613
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81102,985,122 - 102,987,808 (+)NCBI
mRatBN7.2193,848,533 - 93,851,217 (+)NCBI
Rnor_6.0198,487,631 - 98,490,315 (-)NCBI
Rnor_5.0199,564,436 - 99,567,120 (-)NCBI
RGSC_v3.4193,816,749 - 93,819,433 (+)RGD
Celera188,125,644 - 88,128,328 (+)RGD
Sequence:
RefSeq Acc Id: XM_039087376   ⟹   XP_038943304
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81102,985,982 - 102,988,010 (+)NCBI
mRatBN7.2193,848,578 - 93,851,693 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102613 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943304 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07556 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000053327
  ENSRNOP00000053327.2
RefSeq Acc Id: NP_001102613   ⟸   NM_001109143
- UniProtKB: D3ZQB5 (UniProtKB/TrEMBL),   A6JAH8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000053327   ⟸   ENSRNOT00000056490
RefSeq Acc Id: XP_038943304   ⟸   XM_039087376
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZQB5-F1-model_v2 AlphaFold D3ZQB5 1-167 view protein structure

Transcriptome

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

Promoters
RGD ID:13689983
Promoter ID:EPDNEW_R508
Type:initiation region
Name:Cldnd2_1
Description:claudin domain containing 2
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_6.0198,490,270 - 98,490,330EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566413 AgrOrtholog
BioCyc Gene G2FUF-59850 BioCyc
Ensembl Genes ENSRNOG00000037333 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056490 ENTREZGENE
  ENSRNOT00000056490.4 UniProtKB/TrEMBL
Gene3D-CATH 1.20.140.150 UniProtKB/TrEMBL
InterPro PMP-22/EMP/MP20 UniProtKB/TrEMBL
  PMP22/EMP/MP20/Claudin UniProtKB/TrEMBL
KEGG Report rno:499140 UniProtKB/TrEMBL
NCBI Gene 499140 ENTREZGENE
PANTHER CLAUDIN DOMAIN-CONTAINING PROTEIN 2 UniProtKB/TrEMBL
  EPITHELIAL MEMBRANE PROTEIN-RELATED UniProtKB/TrEMBL
Pfam PMP22_Claudin UniProtKB/TrEMBL
PhenoGen Cldnd2 PhenoGen
RatGTEx ENSRNOG00000037333 RatGTEx
UniProt A6JAH8 ENTREZGENE, UniProtKB/TrEMBL
  D3ZQB5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Cldnd2  claudin domain containing 2  RGD1566413_predicted  similar to hypothetical protein MGC33839 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1566413_predicted  similar to hypothetical protein MGC33839 (predicted)  LOC499140  similar to hypothetical protein MGC33839  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499140  similar to hypothetical protein MGC33839      Symbol and Name status set to provisional 70820 PROVISIONAL