Cux1 (cut-like homeobox 1) - Rat Genome Database

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Gene: Cux1 (cut-like homeobox 1) Rattus norvegicus
Analyze
Symbol: Cux1
Name: cut-like homeobox 1
RGD ID: 620618
Description: Exhibits protein-macromolecule adaptor activity. Involved in retrograde transport, vesicle recycling within Golgi. Localizes to Golgi membrane. Orthologous to human CUX1 (cut like homeobox 1); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CCAAT displacement protein; CDP; CDP2; cut (Drosophila)-like 1; cut-like 1; cut-like 1 (Drosophila); Cutl1; homeobox protein cut-like 1; homeobox protein cux-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21220,107,062 - 20,425,868 (+)NCBI
Rnor_6.0 Ensembl1223,151,180 - 23,445,074 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01223,150,886 - 23,470,095 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01225,151,301 - 25,470,445 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41221,223,919 - 21,516,938 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11221,468,508 - 21,506,811 (+)NCBI
Celera1221,874,658 - 22,194,905 (+)NCBICelera
Cytogenetic Map12q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-butoxyethanol  (ISO)
4-hydroxynon-2-enal  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (EXP,ISO)
bisphenol A  (EXP)
butanal  (ISO)
cadmium dichloride  (ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dichloromethane  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
hydrogen peroxide  (ISO)
L-methionine  (ISO)
methamphetamine  (EXP)
methapyrilene  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
pirinixic acid  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
Soman  (EXP)
succimer  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
topotecan  (EXP)
Tributyltin oxide  (EXP)
trichostatin A  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zearalenone  (ISO)
zebularine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

References

Additional References at PubMed
PMID:1363085   PMID:11839809   PMID:15656993   PMID:15994318   PMID:18829740   PMID:18836447   PMID:20473291   PMID:20485671   PMID:20510857   PMID:25100583   PMID:27250217   PMID:27986613  


Genomics

Comparative Map Data
Cux1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21220,107,062 - 20,425,868 (+)NCBI
Rnor_6.0 Ensembl1223,151,180 - 23,445,074 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01223,150,886 - 23,470,095 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01225,151,301 - 25,470,445 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41221,223,919 - 21,516,938 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11221,468,508 - 21,506,811 (+)NCBI
Celera1221,874,658 - 22,194,905 (+)NCBICelera
Cytogenetic Map12q12NCBI
CUX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7101,815,904 - 102,283,958 (+)EnsemblGRCh38hg38GRCh38
GRCh387101,815,991 - 102,283,958 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh377101,459,287 - 101,927,250 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367101,246,012 - 101,713,970 (+)NCBINCBI36hg18NCBI36
Celera796,467,441 - 96,936,259 (+)NCBI
Cytogenetic Map7q22.1NCBI
HuRef796,049,661 - 96,517,462 (+)NCBIHuRef
CHM1_17101,389,393 - 101,855,391 (+)NCBICHM1_1
CRA_TCAGchr7v27100,817,571 - 101,284,708 (+)NCBI
Cux1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395136,276,989 - 136,596,438 (-)NCBIGRCm39mm39
GRCm39 Ensembl5136,276,989 - 136,596,344 (-)Ensembl
GRCm385136,248,135 - 136,567,590 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5136,248,135 - 136,567,490 (-)EnsemblGRCm38mm10GRCm38
MGSCv375136,724,005 - 137,043,301 (-)NCBIGRCm37mm9NCBIm37
MGSCv365136,532,762 - 136,851,867 (-)NCBImm8
Celera5133,264,708 - 133,588,225 (-)NCBICelera
Cytogenetic Map5G2NCBI
cM Map575.96NCBI
Cux1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545615,276,959 - 15,638,004 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545615,292,562 - 15,636,835 (-)NCBIChiLan1.0ChiLan1.0
CUX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17107,191,108 - 107,609,940 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7107,191,124 - 107,609,940 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0793,954,599 - 94,432,697 (+)NCBIMhudiblu_PPA_v0panPan3
CUX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.167,820,154 - 8,108,236 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl67,820,764 - 8,195,631 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha69,514,914 - 9,882,633 (-)NCBI
ROS_Cfam_1.067,640,261 - 8,004,747 (-)NCBI
UMICH_Zoey_3.167,624,228 - 7,961,118 (-)NCBI
UNSW_CanFamBas_1.067,572,159 - 7,599,430 (-)NCBI
UNSW_CanFamBas_1.067,599,495 - 7,936,098 (-)NCBI
UU_Cfam_GSD_1.067,735,793 - 8,100,353 (-)NCBI
Cux1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344132,239,671 - 132,550,554 (-)NCBI
SpeTri2.0NW_0049365431,482,606 - 1,781,294 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CUX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl39,317,114 - 9,669,998 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.139,317,145 - 9,669,999 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.239,324,555 - 9,427,871 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CUX1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12810,901,529 - 11,370,834 (-)NCBI
ChlSab1.1 Ensembl2810,937,512 - 11,370,702 (-)Ensembl
Cux1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474015,289,616 - 15,664,090 (-)NCBI

Position Markers
D12Got43  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01223,262,102 - 23,262,260NCBIRnor6.0
Rnor_5.01225,262,452 - 25,262,610UniSTSRnor5.0
RGSC_v3.41221,333,262 - 21,333,421RGDRGSC3.4
RGSC_v3.41221,333,263 - 21,333,421UniSTSRGSC3.4
RGSC_v3.11221,322,875 - 21,323,033RGD
Celera1221,987,007 - 21,987,165UniSTS
RH 3.4 Map12301.61UniSTS
RH 3.4 Map12301.61RGD
Cytogenetic Map12q12UniSTS
RH133068  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01223,161,758 - 23,161,963NCBIRnor6.0
Rnor_5.01225,162,108 - 25,162,313UniSTSRnor5.0
RGSC_v3.41221,233,257 - 21,233,462UniSTSRGSC3.4
Celera1221,885,471 - 21,885,676UniSTS
RH 3.4 Map12294.7UniSTS
Cytogenetic Map12q12UniSTS
RH130111  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01223,453,948 - 23,454,129NCBIRnor6.0
Rnor_5.01225,454,298 - 25,454,479UniSTSRnor5.0
RGSC_v3.41221,525,112 - 21,525,293UniSTSRGSC3.4
Celera1222,178,758 - 22,178,939UniSTS
RH 3.4 Map12298.5UniSTS
Cytogenetic Map12q12UniSTS
BE120355  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01223,452,384 - 23,452,552NCBIRnor6.0
Rnor_5.01225,452,734 - 25,452,902UniSTSRnor5.0
RGSC_v3.41221,523,548 - 21,523,716UniSTSRGSC3.4
Celera1222,177,194 - 22,177,362UniSTS
RH 3.4 Map12299.2UniSTS
Cytogenetic Map12q12UniSTS
BF411168  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01223,381,291 - 23,381,516NCBIRnor6.0
Rnor_5.01225,381,641 - 25,381,866UniSTSRnor5.0
RGSC_v3.41221,452,456 - 21,452,681UniSTSRGSC3.4
Celera1222,106,150 - 22,106,375UniSTS
RH 3.4 Map12299.4UniSTS
Cytogenetic Map12q12UniSTS
BF412746  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01223,332,802 - 23,332,895NCBIRnor6.0
Rnor_5.01225,333,152 - 25,333,245UniSTSRnor5.0
RGSC_v3.41221,403,967 - 21,404,060UniSTSRGSC3.4
Celera1222,057,668 - 22,057,761UniSTS
RH 3.4 Map12297.6UniSTS
Cytogenetic Map12q12UniSTS
AU047743  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01223,359,247 - 23,359,412NCBIRnor6.0
Rnor_5.01225,359,597 - 25,359,762UniSTSRnor5.0
RGSC_v3.41221,430,412 - 21,430,577UniSTSRGSC3.4
Celera1222,084,106 - 22,084,271UniSTS
Cytogenetic Map12q12UniSTS
RH139585  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01223,469,604 - 23,469,810NCBIRnor6.0
Rnor_5.01225,469,954 - 25,470,160UniSTSRnor5.0
RGSC_v3.41221,540,768 - 21,540,974UniSTSRGSC3.4
Celera1222,194,414 - 22,194,620UniSTS
Cytogenetic Map12q12UniSTS
AU049974  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01223,220,199 - 23,220,406NCBIRnor6.0
Rnor_5.01225,220,549 - 25,220,756UniSTSRnor5.0
RGSC_v3.41221,291,342 - 21,291,549UniSTSRGSC3.4
Celera1221,943,391 - 21,943,598UniSTS
Cytogenetic Map12q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123758197Rat
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
61443Btemp2Thermal response to stress QTL 23.30.000094body temperature trait (VT:0005535)core body temperature (CMO:0001036)121711477023839390Rat
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:490
Count of miRNA genes:212
Interacting mature miRNAs:250
Transcripts:ENSRNOT00000001928, ENSRNOT00000044841, ENSRNOT00000059486, ENSRNOT00000075031
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 42 32 16 19 16 8 11 74 35 41 11 8
Low 1 25 25 25
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053860 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_001070410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003751160 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003751161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003752579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003752580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006221329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006221330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006221331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006221332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249202 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249203 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769168 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_347163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC091536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC091618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U09229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000059486   ⟹   ENSRNOP00000056243
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1223,151,180 - 23,445,074 (+)Ensembl
RefSeq Acc Id: NM_053860   ⟹   NP_446312
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,107,311 - 20,409,127 (+)NCBI
RefSeq Acc Id: XM_001070410   ⟹   XP_001070410
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,874,660 - 22,178,164 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003751160   ⟹   XP_003751208
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,107,062 - 20,409,127 (+)NCBI
Rnor_6.01223,150,886 - 23,453,354 (+)NCBI
Rnor_5.01225,151,301 - 25,470,445 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003751161   ⟹   XP_003751209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,107,063 - 20,409,127 (+)NCBI
Rnor_6.01223,150,888 - 23,453,354 (+)NCBI
Rnor_5.01225,151,301 - 25,470,445 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003752579   ⟹   XP_003752627
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,874,724 - 22,194,905 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003752580   ⟹   XP_003752628
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,874,658 - 22,178,164 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006221329   ⟹   XP_006221391
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,876,192 - 22,178,164 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006221330   ⟹   XP_006221392
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,876,192 - 22,178,164 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006221331   ⟹   XP_006221393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,876,192 - 22,178,164 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006221332   ⟹   XP_006221394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,876,192 - 22,178,164 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249202   ⟹   XP_006249264
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,108,619 - 20,409,127 (+)NCBI
Rnor_6.01223,152,420 - 23,453,354 (+)NCBI
Rnor_5.01225,151,301 - 25,470,445 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249203   ⟹   XP_006249265
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01223,152,420 - 23,453,354 (+)NCBI
Rnor_5.01225,151,301 - 25,470,445 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249204   ⟹   XP_006249266
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,108,619 - 20,409,127 (+)NCBI
Rnor_6.01223,152,420 - 23,453,354 (+)NCBI
Rnor_5.01225,151,301 - 25,470,445 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249206   ⟹   XP_006249268
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,107,104 - 20,425,868 (+)NCBI
Rnor_6.01223,150,952 - 23,470,095 (+)NCBI
Rnor_5.01225,151,301 - 25,470,445 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760260   ⟹   XP_008758482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,874,659 - 22,178,164 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760271   ⟹   XP_008758493
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,876,192 - 22,194,905 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760274   ⟹   XP_008758496
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,876,192 - 22,194,905 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760277   ⟹   XP_008758499
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1221,874,723 - 22,194,905 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769165   ⟹   XP_008767387
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01223,150,887 - 23,453,354 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769166   ⟹   XP_008767388
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,108,619 - 20,425,868 (+)NCBI
Rnor_6.01223,152,420 - 23,470,095 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769167   ⟹   XP_008767389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,108,619 - 20,425,868 (+)NCBI
Rnor_6.01223,152,420 - 23,470,095 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769168   ⟹   XP_008767390
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,107,102 - 20,425,868 (+)NCBI
Rnor_6.01223,150,951 - 23,470,095 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039089023   ⟹   XP_038944951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,108,619 - 20,409,127 (+)NCBI
RefSeq Acc Id: XM_347163   ⟹   XP_347164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21220,108,619 - 20,409,127 (+)NCBI
Rnor_6.01223,152,420 - 23,453,354 (+)NCBI
Rnor_5.01225,151,301 - 25,470,445 (+)NCBI
RGSC_v3.41221,223,919 - 21,516,938 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: XP_001070410   ⟸   XM_001070410
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_347164   ⟸   XM_347163
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_003751208   ⟸   XM_003751160
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_003751209   ⟸   XM_003751161
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_003752627   ⟸   XM_003752579
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_003752628   ⟸   XM_003752580
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006221391   ⟸   XM_006221329
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006221393   ⟸   XM_006221331
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006221392   ⟸   XM_006221330
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006221394   ⟸   XM_006221332
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006249268   ⟸   XM_006249206
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006249265   ⟸   XM_006249203
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006249264   ⟸   XM_006249202
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006249266   ⟸   XM_006249204
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008758482   ⟸   XM_008760260
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_008758499   ⟸   XM_008760277
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_008758493   ⟸   XM_008760271
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_008758496   ⟸   XM_008760274
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_008767387   ⟸   XM_008769165
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_008767390   ⟸   XM_008769168
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_008767388   ⟸   XM_008769166
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008767389   ⟸   XM_008769167
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: ENSRNOP00000056243   ⟸   ENSRNOT00000059486
RefSeq Acc Id: NP_446312   ⟸   NM_053860
RefSeq Acc Id: XP_038944951   ⟸   XM_039089023
- Peptide Label: isoform X5

Transcriptome

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

Promoters
RGD ID:13698540
Promoter ID:EPDNEW_R9059
Type:initiation region
Name:Cux1_1
Description:cut-like homeobox 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_6.01223,151,157 - 23,151,217EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/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)
ACI/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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
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 25466588 25466589 C T snv NIG-III/Hok (KyushuU), KFRS3B/Kyo (KyushuU), LEC/Tj (KyushuU), HWY/Slc (KyushuU), FHL/EurMcwi (MCW), RCS/Kyo (KyushuU), LE/Stm (KyushuU)
12 25466613 25466614 G A snv IS/Kyo (KyushuU), SDLEF7/Barth (UDEL), DOB/Oda (KyushuU), IS-Tlk/Kyo (KyushuU)
12 25468181 25468182 G A snv HTX/Kyo (KyushuU), F344/DuCrlCrlj (KyushuU), BN/SsNSlc (KyushuU), BUF/MNa (KyushuU), RCS/Kyo (KyushuU), KFRS3B/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), Crl:SD (UDEL), LEC/Tj (KyushuU), LE/OrlBarth (UDEL), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), ZF (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU), F344/NSlc (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 23350307 23350308 A T snv WN/N (MCW)
12 23350366 23350367 T C snv Buf/N (MCW), M520/N (MCW), F344/NRrrc (MCW), WN/N (MCW), ACI/N (MCW), WKY/N (MCW)
12 23466238 23466239 C T snv FHL/EurMcwi (MCW), MHS/Gib (RGD), LE/Stm (RGD)
12 23466263 23466264 G A snv WKY/N (MCW), MR/N (MCW), SBN/Ygl (MCW), WKY/NCrl (RGD), WKY/Gcrc (RGD), SHR/NHsd (RGD), SBN/Ygl (RGD), MNS/Gib (RGD), BBDP/Wor (RGD)
12 23467831 23467832 G A snv COP/CrCrl (MCW & UW), MHS/Gib (RGD), WN/N (MCW), LE/Stm (RGD), SHRSP/Gcrc (RGD), ACI/EurMcwi (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 21421467 21421468 A G snv FHH/EurMcwi (MCW), HCR/1Mco (UMich), GH/OmrMcwi (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW)
12 21421472 21421473 A T snv GH/OmrMcwi (MCW), WN/N (KNAW)
12 21421531 21421532 T C snv WN/N (KNAW), ACI/EurMcwi (MCW), LCR/2Mco (UMich), ACI/N (KNAW), M520/N (KNAW), WKY/N (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW)
12 21456538 21456539 A G snv BN/NHsdMcwi (KNAW), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW), LE/Stm (KNAW), SR/JrHsd (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620618 AgrOrtholog
Ensembl Genes ENSRNOG00000001424 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000056243 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000059486 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.260.40 UniProtKB/Swiss-Prot
InterPro CUT_dom UniProtKB/Swiss-Prot
  Homeobox-like_sf UniProtKB/Swiss-Prot
  Homeobox_CS UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot
  Lambda_DNA-bd_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:116639 UniProtKB/Swiss-Prot
NCBI Gene 116639 ENTREZGENE
Pfam CUT UniProtKB/Swiss-Prot
  Homeodomain UniProtKB/Swiss-Prot
PhenoGen Cux1 PhenoGen
PROSITE CUT UniProtKB/Swiss-Prot
  HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot
SMART CUT UniProtKB/Swiss-Prot
  HOX UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot
  SSF47413 UniProtKB/Swiss-Prot
UniProt CUX1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary F1LRC5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-31 Cux1  cut-like homeobox 1  Cutl1  cut-like 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Cutl1  cut-like 1 (Drosophila)    cut (Drosophila)-like 1  Name updated 1299863 APPROVED
2002-08-07 Cutl1  cut (Drosophila)-like 1      Symbol and Name status set to provisional 70820 PROVISIONAL