Patj (PATJ, crumbs cell polarity complex component) - Rat Genome Database

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Gene: Patj (PATJ, crumbs cell polarity complex component) Rattus norvegicus
Analyze
Symbol: Patj
Name: PATJ, crumbs cell polarity complex component
RGD ID: 1565362
Description: Predicted to be involved in several processes, including establishment of apical/basal cell polarity; positive regulation of epithelial cell migration; and tight junction assembly. Part of protein-containing complex. Orthologous to human PATJ (PATJ crumbs cell polarity complex component); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; amitriptyline.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: InaD-like 2; InaD-like 2 (Drosophila); inaD-like protein; Inadl; Inadl2; LOC313382; PDZ domain protein; PDZ domain protein (Drosophila inaD-like); RGD1565362; similar to channel-interacting pdz domain protein isoform 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: PatjTn(sb-T2/Bart3)2.343Mcwi  
Genetic Models: F344-PatjTn(sb-T2/Bart3)2.343Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25113,061,985 - 113,364,807 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5113,062,118 - 113,364,807 (+)Ensembl
Rnor_6.05117,038,548 - 117,340,308 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5117,052,260 - 117,340,336 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05120,981,525 - 121,281,044 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45118,806,744 - 119,131,114 (+)NCBIRGSC3.4rn4RGSC3.4
Celera5111,633,199 - 111,931,738 (+)NCBICelera
Cytogenetic Map5q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acrolein  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amitriptyline  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
atrazine  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
butanal  (ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
dibenzo[a,l]pyrene  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (ISO)
finasteride  (EXP)
flutamide  (EXP)
formaldehyde  (ISO)
fulvestrant  (ISO)
gentamycin  (EXP)
mercury dibromide  (ISO)
mercury dichloride  (ISO)
methapyrilene  (ISO)
morphine  (ISO)
Muraglitazar  (EXP)
N-methyl-N-nitrosourea  (ISO)
nicotine  (ISO)
Nor-9-carboxy-delta9-THC  (ISO)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
pentanal  (ISO)
phenylmercury acetate  (ISO)
potassium dichromate  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium dichromate  (EXP)
Tesaglitazar  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:11964389   PMID:14758363   PMID:15225788   PMID:18596123   PMID:19056867   PMID:20152177   PMID:22006950   PMID:22337881   PMID:23533145   PMID:25636444  


Genomics

Comparative Map Data
Patj
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25113,061,985 - 113,364,807 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5113,062,118 - 113,364,807 (+)Ensembl
Rnor_6.05117,038,548 - 117,340,308 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5117,052,260 - 117,340,336 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05120,981,525 - 121,281,044 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45118,806,744 - 119,131,114 (+)NCBIRGSC3.4rn4RGSC3.4
Celera5111,633,199 - 111,931,738 (+)NCBICelera
Cytogenetic Map5q33NCBI
PATJ
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38161,742,480 - 62,163,915 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl161,742,477 - 62,178,675 (+)EnsemblGRCh38hg38GRCh38
GRCh37162,208,152 - 62,629,587 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36161,980,737 - 62,402,180 (+)NCBINCBI36hg18NCBI36
Celera160,496,772 - 60,918,615 (+)NCBI
Cytogenetic Map1p31.3NCBI
HuRef160,320,895 - 60,742,543 (+)NCBIHuRef
CHM1_1162,323,629 - 62,744,942 (+)NCBICHM1_1
Patj
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39498,283,803 - 98,607,840 (+)NCBIGRCm39mm39
GRCm39 Ensembl498,284,022 - 98,607,840 (+)Ensembl
GRCm38498,395,560 - 98,719,603 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl498,395,785 - 98,719,603 (+)EnsemblGRCm38mm10GRCm38
MGSCv37498,062,517 - 98,386,294 (+)NCBIGRCm37mm9NCBIm37
MGSCv36497,887,844 - 98,211,621 (+)NCBImm8
Celera496,759,588 - 97,075,177 (+)NCBICelera
Cytogenetic Map4C6NCBI
Patj
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542327,409,623 - 27,629,731 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542327,408,334 - 27,637,065 (-)NCBIChiLan1.0ChiLan1.0
PATJ
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1162,832,424 - 63,233,073 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl162,832,424 - 63,247,074 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0160,993,316 - 61,416,043 (+)NCBIMhudiblu_PPA_v0panPan3
PATJ
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1547,913,433 - 48,268,043 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl547,914,284 - 48,256,861 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha547,973,462 - 48,335,754 (-)NCBI
ROS_Cfam_1.0548,097,120 - 48,453,049 (-)NCBI
ROS_Cfam_1.0 Ensembl548,097,122 - 48,452,964 (-)Ensembl
UMICH_Zoey_3.1548,051,707 - 48,405,688 (-)NCBI
UNSW_CanFamBas_1.0547,998,363 - 48,352,502 (-)NCBI
UU_Cfam_GSD_1.0548,260,886 - 48,617,091 (-)NCBI
Patj
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505875,084,131 - 75,401,322 (+)NCBI
SpeTri2.0NW_00493652215,136 - 233,484 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PATJ
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6150,245,497 - 150,605,544 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16150,248,714 - 150,605,565 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26138,472,898 - 138,557,009 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PATJ
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12070,910,594 - 71,300,877 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2070,910,447 - 71,301,424 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603346,104,468 - 46,515,476 (+)NCBIVero_WHO_p1.0
Patj
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474231,510,784 - 31,725,256 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D5Rat25  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25113,060,909 - 113,061,097 (+)MAPPERmRatBN7.2
Rnor_6.05117,037,089 - 117,037,276NCBIRnor6.0
Rnor_5.05120,979,996 - 120,980,183UniSTSRnor5.0
RGSC_v3.45118,805,536 - 118,805,723UniSTSRGSC3.4
RGSC_v3.45118,805,535 - 118,805,723RGDRGSC3.4
RGSC_v3.15118,810,762 - 118,810,949RGD
Celera5111,631,991 - 111,632,178UniSTS
RH 3.4 Map5789.6RGD
RH 3.4 Map5789.6UniSTS
SHRSP x BN Map561.5499RGD
SHRSP x BN Map561.5499UniSTS
Cytogenetic Map5q33UniSTS
RH143216  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25113,364,282 - 113,364,390 (+)MAPPERmRatBN7.2
Rnor_6.05117,339,784 - 117,339,891NCBIRnor6.0
Rnor_5.05121,280,905 - 121,281,012UniSTSRnor5.0
RGSC_v3.45119,131,961 - 119,132,068UniSTSRGSC3.4
Celera5111,931,214 - 111,931,321UniSTS
RH 3.4 Map5794.9UniSTS
Cytogenetic Map5q33UniSTS
RH142079  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25113,362,916 - 113,363,115 (+)MAPPERmRatBN7.2
Rnor_6.05117,338,418 - 117,338,616NCBIRnor6.0
Rnor_5.05121,279,539 - 121,279,737UniSTSRnor5.0
RGSC_v3.45119,130,595 - 119,130,793UniSTSRGSC3.4
Celera5111,929,848 - 111,930,046UniSTS
RH 3.4 Map958.2UniSTS
Cytogenetic Map5q33UniSTS
AU049786  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25113,246,624 - 113,246,759 (+)MAPPERmRatBN7.2
Rnor_6.05117,222,689 - 117,222,823NCBIRnor6.0
Rnor_5.05121,165,800 - 121,165,934UniSTSRnor5.0
RGSC_v3.45119,007,905 - 119,008,039UniSTSRGSC3.4
Celera5111,814,675 - 111,814,791UniSTS
Cytogenetic Map5q33UniSTS
UniSTS:234969  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25113,335,953 - 113,336,240 (+)MAPPERmRatBN7.2
Rnor_6.05117,311,488 - 117,311,774NCBIRnor6.0
Rnor_5.05121,252,809 - 121,253,095UniSTSRnor5.0
RGSC_v3.45119,103,292 - 119,103,578UniSTSRGSC3.4
Celera5111,903,153 - 111,903,439UniSTS
Cytogenetic Map5q33UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)579584860124584860Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)579584860124584860Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)590067849128034027Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
1582212Livw2Liver weight QTL 23.50.0004liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)599016066119085810Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
7794743Bp373Blood pressure QTL 3730.0058arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5112175546116047089Rat


Genetic Models
This gene Patj is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:615
Count of miRNA genes:253
Interacting mature miRNAs:312
Transcripts:ENSRNOT00000010112, ENSRNOT00000010211, ENSRNOT00000057943, ENSRNOT00000065197
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.


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 10 8 13 8 11 31 17 11
Low 43 47 33 6 33 8 11 63 4 24 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010211   ⟹   ENSRNOP00000010211
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5113,062,118 - 113,364,807 (+)Ensembl
Rnor_6.0 Ensembl5117,052,260 - 117,340,336 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094178   ⟹   ENSRNOP00000092161
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5113,062,118 - 113,332,082 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095175   ⟹   ENSRNOP00000079221
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5113,062,118 - 113,364,807 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101438   ⟹   ENSRNOP00000077045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5113,062,118 - 113,364,807 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103328   ⟹   ENSRNOP00000097148
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5113,207,165 - 113,363,205 (+)Ensembl
RefSeq Acc Id: NM_080398   ⟹   NP_536323
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25113,062,118 - 113,364,807 (+)NCBI
Rnor_6.05117,038,630 - 117,340,308 (+)NCBI
Celera5111,633,199 - 111,931,738 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008763915   ⟹   XP_008762137
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25113,062,054 - 113,182,942 (+)NCBI
Rnor_6.05117,038,616 - 117,159,681 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008763916   ⟹   XP_008762138
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25113,207,170 - 113,364,422 (+)NCBI
Rnor_6.05117,181,442 - 117,339,923 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039109186   ⟹   XP_038965114
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25113,062,054 - 113,364,422 (+)NCBI
RefSeq Acc Id: XM_039109187   ⟹   XP_038965115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25113,061,985 - 113,364,422 (+)NCBI
RefSeq Acc Id: XM_039109188   ⟹   XP_038965116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25113,062,054 - 113,364,422 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_008762137   ⟸   XM_008763915
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008762138   ⟸   XM_008763916
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: NP_536323   ⟸   NM_080398
- UniProtKB: F1MAD2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000010211   ⟸   ENSRNOT00000010211
RefSeq Acc Id: XP_038965115   ⟸   XM_039109187
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038965114   ⟸   XM_039109186
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038965116   ⟸   XM_039109188
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000077045   ⟸   ENSRNOT00000101438
RefSeq Acc Id: ENSRNOP00000092161   ⟸   ENSRNOT00000094178
RefSeq Acc Id: ENSRNOP00000079221   ⟸   ENSRNOT00000095175
RefSeq Acc Id: ENSRNOP00000097148   ⟸   ENSRNOT00000103328
Protein Domains
L27   PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1MAD2-F1-model_v2 AlphaFold F1MAD2 1-1836 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565362 AgrOrtholog
BioCyc Gene G2FUF-40588 BioCyc
Ensembl Genes ENSRNOG00000007551 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000010211 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000079221 ENTREZGENE
  ENSRNOP00000092161 ENTREZGENE
  ENSRNOP00000097148 ENTREZGENE
Ensembl Transcript ENSRNOT00000010211 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000094178 ENTREZGENE
  ENSRNOT00000095175 ENTREZGENE
  ENSRNOT00000103328 ENTREZGENE
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot
InterPro L27_2 UniProtKB/Swiss-Prot
  L27_dom UniProtKB/Swiss-Prot
  L27_dom_sf UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  PDZ_sf UniProtKB/Swiss-Prot
KEGG Report rno:140581 UniProtKB/Swiss-Prot
NCBI Gene Inadl ENTREZGENE
Pfam L27_2 UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
PhenoGen Patj PhenoGen
PROSITE L27 UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
SMART L27 UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
Superfamily-SCOP SSF101288 UniProtKB/Swiss-Prot
  SSF50156 UniProtKB/Swiss-Prot
UniProt F1MAD2 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-07-18 Inadl  InaD-like (Drosophila)  Inadl2  InaD-like 2 (Drosophila)  Data Merged 737654 APPROVED
2008-03-20 Inadl2  InaD-like 2 (Drosophila)  Inadl  InaD-like (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-20 Inadl  InaD-like (Drosophila)  RGD1565362_predicted  similar to channel-interacting PDZ domain protein isoform 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565362_predicted  similar to channel-interacting PDZ domain protein isoform 1 (predicted)  LOC313382  similar to channel-interacting PDZ domain protein isoform 1  Symbol and Name status set to approved 1299863 APPROVED
2005-01-20 Inadl  InaD-like (Drosophila)    PDZ domain protein (Drosophila inaD-like)  Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function may participate in TRPC3 protein mediated 1alpha,25(OH)(2)D(3) modulation of CCE in muscle and osteoblastic cells 1304343