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: Enables protein-macromolecule adaptor activity. Involved in retrograde transport, vesicle recycling within Golgi. Located in 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
Previously 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 ...
Related Pseudogenes: Cux1-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21220,107,062 - 20,425,868 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1220,107,311 - 20,425,866 (+)Ensembl
Rnor_6.01223,150,886 - 23,470,095 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1223,151,180 - 23,445,074 (+)EnsemblRnor6.0rn6Rnor6.0
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)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-tribromophenol  (ISO)
2-butoxyethanol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (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,ISO)
bisphenol F  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
decabromodiphenyl ether  (ISO)
dichloromethane  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
gentamycin  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
hydrogen peroxide  (ISO)
L-methionine  (ISO)
lidocaine  (EXP)
methamphetamine  (EXP)
methapyrilene  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP,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)
thioacetamide  (EXP)
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

References - curated
# Reference Title Reference Citation
1. The transcriptional repressor CDP (Cutl1) is essential for epithelial cell differentiation of the lung and the hair follicle. Ellis T, etal., Genes Dev 2001 Sep 1;15(17):2307-19.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. CUX1: a modulator of tumour aggressiveness in pancreatic neuroendocrine neoplasms. Krug S, etal., Endocr Relat Cancer. 2014;21(6):879-90. doi: 10.1530/ERC-14-0152. Epub 2014 Sep 23.
4. Transcription factor CUTL1 is a negative regulator of drug resistance in gastric cancer. Li T, etal., J Biol Chem. 2013 Feb 8;288(6):4135-47. doi: 10.1074/jbc.M112.345942. Epub 2012 Dec 19.
5. Golgin tethers define subpopulations of COPI vesicles. Malsam J, etal., Science. 2005 Feb 18;307(5712):1095-8.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. CUTL1 induces epithelial-mesenchymal transition in non-small cell lung cancer. Wang J, etal., Oncol Rep. 2017 May;37(5):3068-3074. doi: 10.3892/or.2017.5571. Epub 2017 Apr 11.
12. Isolation of two E-box binding factors that interact with the rat tyrosine hydroxylase enhancer. Yoon SO and Chikaraishi DM, J Biol Chem 1994 Jul 15;269(28):18453-62.
13. 5-Hydroxytryptamine Receptor 1D Aggravates Hepatocellular Carcinoma Progression Through FoxO6 in AKT-Dependent and Independent Manners. Zuo X, etal., Hepatology. 2019 May;69(5):2031-2047. doi: 10.1002/hep.30430. Epub 2019 Mar 10.
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 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1220,107,311 - 20,425,866 (+)Ensembl
Rnor_6.01223,150,886 - 23,470,095 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1223,151,180 - 23,445,074 (+)EnsemblRnor6.0rn6Rnor6.0
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
GRCh387101,816,007 - 102,283,958 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl7101,815,904 - 102,283,958 (+)EnsemblGRCh38hg38GRCh38
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
T2T-CHM13v2.07103,136,249 - 103,601,363 (+)NCBI
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
ROS_Cfam_1.0 Ensembl67,640,269 - 8,004,638 (-)Ensembl
UMICH_Zoey_3.167,624,228 - 7,961,118 (-)NCBI
UNSW_CanFamBas_1.067,599,495 - 7,936,098 (-)NCBI
UNSW_CanFamBas_1.067,572,159 - 7,599,430 (-)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 Ensembl39,317,140 - 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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12810,901,529 - 11,370,834 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2810,937,512 - 11,370,702 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660705,031,645 - 5,502,364 (+)NCBIVero_WHO_p1.0
Cux1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474015,287,421 - 15,664,077 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462474015,289,616 - 15,664,090 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D12Got43  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21220,217,854 - 20,218,013 (+)MAPPERmRatBN7.2
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
mRatBN7.21220,117,962 - 20,118,168 (+)MAPPERmRatBN7.2
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
mRatBN7.21220,409,720 - 20,409,902 (+)MAPPERmRatBN7.2
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
mRatBN7.21220,408,156 - 20,408,325 (+)MAPPERmRatBN7.2
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
mRatBN7.21220,337,058 - 20,337,284 (+)MAPPERmRatBN7.2
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
mRatBN7.21220,288,564 - 20,288,658 (+)MAPPERmRatBN7.2
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
mRatBN7.21220,315,016 - 20,315,182 (+)MAPPERmRatBN7.2
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
mRatBN7.21220,425,376 - 20,425,583 (+)MAPPERmRatBN7.2
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
mRatBN7.21220,175,950 - 20,176,158 (+)MAPPERmRatBN7.2
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
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)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)12931821632103380Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121107382524234895Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382528064557Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121363552330827399Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121363552335682913Rat
61443Btemp2Thermal response to stress QTL 23.30.000094body temperature trait (VT:0005535)core body temperature (CMO:0001036)121502518320794014Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121555082638478808Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121587265332974238Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)121961087024139202Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
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)121961087046669029Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961088935682913Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121983578938193007Rat
631521Pia12Pristane induced arthritis QTL 128.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122025941723672083Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat

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: ENSRNOT00000044841   ⟹   ENSRNOP00000040645
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1220,108,512 - 20,425,866 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000059486   ⟹   ENSRNOP00000056243
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1220,107,311 - 20,409,127 (+)Ensembl
Rnor_6.0 Ensembl1223,151,180 - 23,445,074 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000097976   ⟹   ENSRNOP00000089950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1220,107,311 - 20,409,127 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112152   ⟹   ENSRNOP00000080302
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1220,107,311 - 20,409,127 (+)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_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_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_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_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_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_006249268   ⟸   XM_006249206
- Peptide Label: isoform X10
- 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_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
- UniProtKB: F1LRC5 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_038944951   ⟸   XM_039089023
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000080302   ⟸   ENSRNOT00000112152
RefSeq Acc Id: ENSRNOP00000040645   ⟸   ENSRNOT00000044841
RefSeq Acc Id: ENSRNOP00000089950   ⟸   ENSRNOT00000097976
Protein Domains
CASP_C   CUT   Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M8J7-F1-model_v2 AlphaFold F1M8J7 1-192 view protein structure
AF-P53565-F1-model_v2 AlphaFold P53565 1-1504 view protein structure

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 (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)
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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)
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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)
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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)
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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)
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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
Damaging Variants


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 ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), WKY/N (MCW), WN/N (MCW)
12 23466238 23466239 C T snv LEXF10A/StmMcwi (2020), LEXF2B/Stm (2019), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), FHH/EurMcwi (2019), MHS/Gib (RGD), FHL/EurMcwi (MCW), LE/Stm (RGD)
12 23466263 23466264 G A snv WAG/RijCrl (2020), WKY/NCrl (2019), SHR/OlalpcvMcwi (2019), MR/N (2020), LEW/Crl (2019), HXB4/IpcvMcwi (2020), SBN/Ygl (MCW), MR/N (MCW), WKY/N (MCW), BBDP/Wor (RGD), MNS/Gib (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), BXH2/CubMcwi (2020)
12 23467831 23467832 G A snv COP/CrCrl (MCW & UW), WN/N (MCW), ACI/EurMcwi (RGD), LE/Stm (RGD), MHS/Gib (RGD), SHRSP/Gcrc (RGD)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 25466588 25466589 C T snv HWY/Slc (KyushuU), LEC/Tj (KyushuU), KFRS3B/Kyo (KyushuU), LE/Stm (KyushuU), NIG-III/Hok (KyushuU), RCS/Kyo (KyushuU), FHL/EurMcwi (MCW)
12 25466613 25466614 G A snv SDLEF7/Barth (UDEL), IS-Tlk/Kyo (KyushuU), DOB/Oda (KyushuU), IS/Kyo (KyushuU)
12 25468181 25468182 G A snv HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), F344/Stm (KyushuU), RCS/Kyo (KyushuU), BN/SsNSlc (KyushuU), F344/NSlc (KyushuU), HTX/Kyo (KyushuU), LE/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), ZFDM (KyushuU), BUF/MNa (KyushuU), Crl:SD (UDEL), LE/OrlBarth (UDEL), NIG-III/Hok (KyushuU)


Assembly: RGSC_v3.4

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620618 AgrOrtholog
BioCyc Gene G2FUF-19659 BioCyc
Ensembl Genes ENSRNOG00000001424 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040645 ENTREZGENE
  ENSRNOP00000040645.6 UniProtKB/TrEMBL
  ENSRNOP00000056243 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000080302 ENTREZGENE
  ENSRNOP00000080302.1 UniProtKB/TrEMBL
  ENSRNOP00000089950.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044841 ENTREZGENE
  ENSRNOT00000044841.7 UniProtKB/TrEMBL
  ENSRNOT00000059486 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000097976.1 UniProtKB/TrEMBL
  ENSRNOT00000112152 ENTREZGENE
  ENSRNOT00000112152.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.260.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CASP_C UniProtKB/TrEMBL
  CUT_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lambda_DNA-bd_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 116639 ENTREZGENE
Pfam CASP_C UniProtKB/TrEMBL
  CUT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cux1 PhenoGen
PROSITE CUT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CUT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF47413 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AM13_RAT UniProtKB/TrEMBL
  A0A8I6G4D0_RAT UniProtKB/TrEMBL
  CUX1_RAT UniProtKB/Swiss-Prot
  F1LRC5 ENTREZGENE
  F1M8J7_RAT UniProtKB/TrEMBL
  P53565 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