Cldn4 (claudin 4) - Rat Genome Database
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Gene: Cldn4 (claudin 4) Rattus norvegicus
Analyze
Symbol: Cldn4
Name: claudin 4
RGD ID: 1307932
Description: Predicted to have chloride channel activity. Involved in circadian rhythm; female pregnancy; and response to progesterone. Localizes to several cellular components, including apicolateral plasma membrane; basal plasma membrane; and lateral plasma membrane. Biomarker of peptic esophagitis. Human ortholog(s) of this gene implicated in ovarian cancer and pancreatic cancer. Orthologous to human CLDN4 (claudin 4); PARTICIPATES IN hepatitis C pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2-acetamidofluorene; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: claudin-4; LOC304407
Orthologs:
Homo sapiens (human) : CLDN4 (claudin 4)  HGNC  Alliance
Mus musculus (house mouse) : Cldn4 (claudin 4)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Cldn4 (claudin 4)
Pan paniscus (bonobo/pygmy chimpanzee) : CLDN4 (claudin 4)
Canis lupus familiaris (dog) : CLDN4 (claudin 4)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Cldn4 (claudin 4)
Sus scrofa (pig) : CLDN4 (claudin 4)
Chlorocebus sabaeus (African green monkey) : CLDN4 (claudin 4)
Heterocephalus glaber (naked mole-rat) : Cldn4 (claudin 4)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01224,761,210 - 24,763,008 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1224,761,210 - 24,763,005 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01226,761,480 - 26,763,278 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41222,816,134 - 22,817,932 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11222,686,996 - 22,688,792 (+)NCBI
Celera1223,512,667 - 23,514,465 (+)NCBICelera
Cytogenetic Map12q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-acetamidofluorene  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP,ISO)
anthocyanin  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (EXP,ISO)
deoxynivalenol  (ISO)
diallyl disulfide  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
dibenziodolium  (EXP)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
ethanol  (ISO)
flavonoids  (ISO)
folic acid  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
genistein  (ISO)
glutathione  (EXP)
L-methionine  (ISO)
leuprolide  (ISO)
manganese(II) chloride  (EXP)
megestrol acetate  (ISO)
melanins  (ISO)
mercury dibromide  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
Monobutylphthalate  (EXP)
N-acetyl-L-cysteine  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
naphthalene  (ISO)
nicotine  (ISO)
ochratoxin A  (ISO)
okadaic acid  (ISO)
panobinostat  (ISO)
patulin  (ISO)
pentanal  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosgene  (ISO)
phoxim  (EXP)
pirinixic acid  (ISO)
progesterone  (ISO)
propanal  (ISO)
quercetin  (EXP,ISO)
quercitrin  (ISO)
rottlerin  (ISO)
sanguinarine  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium chloride  (EXP)
sulforaphane  (ISO)
T-2 toxin  (ISO)
tacrolimus hydrate  (EXP)
tamoxifen  (ISO)
testosterone  (ISO)
thalidomide  (ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vitamin E  (EXP)
vorinostat  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9892664   PMID:12477932   PMID:15602007   PMID:15775979   PMID:16103090   PMID:16520537   PMID:16670314   PMID:17964719   PMID:18036336   PMID:18774778   PMID:18855016   PMID:19447895  
PMID:20375010   PMID:20921420   PMID:21388515   PMID:21515662   PMID:22696678   PMID:23407391   PMID:23610556   PMID:23816505   PMID:23963446   PMID:25503106   PMID:28493961   PMID:29179201  
PMID:30734065  


Genomics

Comparative Map Data
Cldn4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01224,761,210 - 24,763,008 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1224,761,210 - 24,763,005 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01226,761,480 - 26,763,278 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41222,816,134 - 22,817,932 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11222,686,996 - 22,688,792 (+)NCBI
Celera1223,512,667 - 23,514,465 (+)NCBICelera
Cytogenetic Map12q12NCBI
CLDN4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl773,799,542 - 73,832,693 (+)EnsemblGRCh38hg38GRCh38
GRCh38773,830,996 - 73,832,690 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37773,245,193 - 73,247,015 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36772,883,129 - 72,884,951 (+)NCBINCBI36hg18NCBI36
Build 34772,689,843 - 72,691,665NCBI
Celera768,723,847 - 68,725,669 (+)NCBI
Cytogenetic Map7q11.23NCBI
HuRef769,128,478 - 69,130,300 (+)NCBIHuRef
CHM1_1773,390,573 - 73,392,403 (+)NCBICHM1_1
CRA_TCAGchr7v2772,578,265 - 72,580,087 (+)NCBI
Cldn4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395134,973,977 - 134,975,788 (-)NCBI
GRCm385134,945,123 - 134,946,934 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5134,945,119 - 134,946,934 (-)EnsemblGRCm38mm10GRCm38
MGSCv375135,420,993 - 135,422,804 (-)NCBIGRCm37mm9NCBIm37
MGSCv365135,229,754 - 135,231,542 (-)NCBImm8
Celera5131,955,947 - 131,957,758 (-)NCBICelera
Cytogenetic Map5G2NCBI
cM Map574.9NCBI
Cldn4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545613,962,497 - 13,963,126 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545613,961,743 - 13,965,498 (-)NCBIChiLan1.0ChiLan1.0
CLDN4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1780,981,237 - 80,985,320 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl780,983,832 - 80,984,461 (+)Ensemblpanpan1.1panPan2
CLDN4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl66,493,513 - 6,494,145 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.166,492,706 - 6,506,750 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cldn4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365432,984,797 - 2,986,563 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLDN4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl311,039,706 - 11,053,925 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1311,039,711 - 11,053,930 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2310,776,896 - 10,788,804 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLDN4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl289,242,909 - 9,243,538 (-)Ensembl
ChlSab1.1289,242,054 - 9,244,972 (-)NCBI
Cldn4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474014,033,848 - 14,035,854 (-)NCBI

Position Markers
RH136879  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01224,762,647 - 24,762,803NCBIRnor6.0
Rnor_5.01226,762,917 - 26,763,073UniSTSRnor5.0
RGSC_v3.41222,817,571 - 22,817,727UniSTSRGSC3.4
Celera1223,514,104 - 23,514,260UniSTS
Cytogenetic Map12q12UniSTS
RH 3.4 Map12310.01UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12130749723Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12895459327911196Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121017588931975590Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)121025689031723732Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)121176499537522089Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121312721127285590Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721131723688Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721150320041Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121441977552716770Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121502198652716770Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121571460935964508Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121571460941291738Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121590890052716770Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121590890052716770Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121718558044098244Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121796086538409001Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121834247752716770Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121834247752716770Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121872904352716770Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121875259352716770Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101875259352716770Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)122265070227190240Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)122265070245946937Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265070248598906Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)122265070252716770Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265072141291738Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)122287629743799153Rat
631521Pia12Pristane induced arthritis QTL 128.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122324124626710128Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:88
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000002003
Prediction methods: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.


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 3 2 31 14
Low 4 27 18 14 18 1 1 11 4 19 11 1
Below cutoff 21 28 21 5 21 6 7 44 7 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002003   ⟹   ENSRNOP00000002003
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1224,761,210 - 24,763,005 (+)Ensembl
RefSeq Acc Id: NM_001012022   ⟹   NP_001012022
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01224,761,210 - 24,763,008 (+)NCBI
Rnor_5.01226,761,480 - 26,763,278 (+)NCBI
RGSC_v3.41222,816,134 - 22,817,932 (+)RGD
Celera1223,512,667 - 23,514,465 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001012022   ⟸   NM_001012022
- UniProtKB: Q5XIT8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002003   ⟸   ENSRNOT00000002003

Transcriptome

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

Promoters
RGD ID:13698564
Promoter ID:EPDNEW_R9089
Type:single initiation site
Name:Cldn4_1
Description:claudin 4
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_6.01224,761,218 - 24,761,278EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 26762176 26762177 C G snv COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 22816830 22816831 C G snv FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307932 AgrOrtholog
Ensembl Genes ENSRNOG00000001476 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002003 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002003 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7130270 IMAGE-MGC_LOAD
InterPro Claudin UniProtKB/TrEMBL
  Claudin4 UniProtKB/TrEMBL
  Claudin_CS UniProtKB/TrEMBL
  PMP22/EMP/MP20/Claudin UniProtKB/TrEMBL
KEGG Report rno:304407 UniProtKB/TrEMBL
MGC_CLONE MGC:94208 IMAGE-MGC_LOAD
NCBI Gene 304407 ENTREZGENE
PANTHER Claudin UniProtKB/TrEMBL
Pfam PMP22_Claudin UniProtKB/TrEMBL
PhenoGen Cldn4 PhenoGen
PRINTS CLAUDIN4 UniProtKB/TrEMBL
PROSITE CLAUDIN UniProtKB/TrEMBL
UniGene Rn.6830 ENTREZGENE
UniProt Q5XIT8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Cldn4  claudin 4  Cldn4_predicted  claudin 4 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Cldn4_predicted  claudin 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED