Pbx1 (PBX homeobox 1) - Rat Genome Database

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Gene: Pbx1 (PBX homeobox 1) Rattus norvegicus
Analyze
Symbol: Pbx1
Name: PBX homeobox 1
RGD ID: 1308213
Description: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and transcription corepressor binding activity. Predicted to contribute to RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including natural killer cell differentiation; nervous system development; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including hematopoietic or lymphoid organ development; positive regulation of G2/M transition of mitotic cell cycle; and regionalization. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of RNA polymerase II transcription regulator complex. Biomarker of brain infarction and glaucoma. Human ortholog(s) of this gene implicated in congenital anomalies of kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay. Orthologous to human PBX1 (PBX homeobox 1); INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC304947; pre-B-cell leukemia homeobox 1; pre-B-cell leukemia transcription factor 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21380,278,766 - 80,588,563 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1380,278,770 - 80,588,594 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1382,940,830 - 83,217,210 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01384,248,904 - 84,525,004 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01381,480,869 - 81,756,919 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01386,390,741 - 86,671,460 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1386,390,741 - 86,451,002 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01391,028,026 - 91,307,274 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41383,839,256 - 84,115,516 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11383,853,894 - 84,129,704 (-)NCBI
Celera1380,014,082 - 80,284,838 (-)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acetaldehyde  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (EXP,ISO)
antimonite  (ISO)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
atrazine  (EXP,ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
calciol  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chrysene  (ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (EXP,ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cyproconazole  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
flusilazole  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
glyphosate  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
mitoxantrone  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
niclosamide  (ISO)
paracetamol  (EXP,ISO)
PCB138  (ISO)
perfluorohexanesulfonic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (EXP)
pirinixic acid  (ISO)
piroxicam  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
tetraphene  (ISO)
thioacetamide  (EXP)
trimellitic anhydride  (ISO)
valproic acid  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Functional characterization of a novel PBX1 de novo missense variant identified in a patient with syndromic congenital heart disease. Alankarage D, etal., Hum Mol Genet. 2020 May 8;29(7):1068-1082. doi: 10.1093/hmg/ddz231.
2. Neuronal replacement from endogenous precursors in the adult brain after stroke. Arvidsson A, etal., Nat Med. 2002 Sep;8(9):963-70. doi: 10.1038/nm747. Epub 2002 Aug 5.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
11. De novo, deleterious sequence variants that alter the transcriptional activity of the homeoprotein PBX1 are associated with intellectual disability and pleiotropic developmental defects. Slavotinek A, etal., Hum Mol Genet. 2017 Dec 15;26(24):4849-4860. doi: 10.1093/hmg/ddx363.
12. Pbx/Meis deficiencies demonstrate multigenetic origins of congenital heart disease. Stankunas K, etal., Circ Res. 2008 Sep 26;103(7):702-9. doi: 10.1161/CIRCRESAHA.108.175489. Epub 2008 Aug 21.
13. Expression of transcription factors and precursor cell markers during regeneration of beta cells in pancreata of rats treated with streptozotocin. Tiemann K, etal., Virchows Arch. 2007 Mar;450(3):261-6. Epub 2007 Jan 18.
14. Integrated microarray analysis provided novel insights to the pathogenesis of glaucoma. Wang J, etal., Mol Med Rep. 2017 Dec;16(6):8735-8746. doi: 10.3892/mmr.2017.7711. Epub 2017 Oct 4.
Additional References at PubMed
PMID:9079637   PMID:9315626   PMID:9405651   PMID:10052460   PMID:10381567   PMID:10842069   PMID:11010815   PMID:11468159   PMID:11566859   PMID:11912494   PMID:12412021   PMID:12477932  
PMID:12591246   PMID:12724421   PMID:14595835   PMID:14764653   PMID:15087118   PMID:15581866   PMID:15634706   PMID:15684392   PMID:15944191   PMID:16672333   PMID:16847320   PMID:17049510  
PMID:18164701   PMID:18787068   PMID:18973687   PMID:19799567   PMID:22560297   PMID:28270404  


Genomics

Comparative Map Data
Pbx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21380,278,766 - 80,588,563 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1380,278,770 - 80,588,594 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1382,940,830 - 83,217,210 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01384,248,904 - 84,525,004 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01381,480,869 - 81,756,919 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01386,390,741 - 86,671,460 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1386,390,741 - 86,451,002 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01391,028,026 - 91,307,274 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41383,839,256 - 84,115,516 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11383,853,894 - 84,129,704 (-)NCBI
Celera1380,014,082 - 80,284,838 (-)NCBICelera
Cytogenetic Map13q24NCBI
PBX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381164,559,184 - 164,886,047 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1164,555,584 - 164,899,296 (+)EnsemblGRCh38hg38GRCh38
GRCh371164,528,421 - 164,855,284 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361162,795,561 - 163,082,934 (+)NCBINCBI36Build 36hg18NCBI36
Build 341161,260,594 - 161,547,967NCBI
Celera1137,634,090 - 137,926,324 (+)NCBICelera
Cytogenetic Map1q23.3NCBI
HuRef1135,774,690 - 136,068,016 (+)NCBIHuRef
CHM1_11165,951,428 - 166,243,870 (+)NCBICHM1_1
T2T-CHM13v2.01163,905,317 - 164,232,389 (+)NCBIT2T-CHM13v2.0
Pbx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391167,946,933 - 168,259,898 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1167,946,933 - 168,259,839 (-)EnsemblGRCm39 Ensembl
GRCm381168,119,364 - 168,432,365 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1168,119,364 - 168,432,270 (-)EnsemblGRCm38mm10GRCm38
MGSCv371170,049,495 - 170,362,389 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361169,956,674 - 170,268,631 (-)NCBIMGSCv36mm8
MGSCv361169,328,392 - 169,641,347 (-)NCBIMGSCv36mm8
Celera1170,542,293 - 170,864,365 (-)NCBICelera
Cytogenetic Map1H2.3NCBI
cM Map175.95NCBI
Pbx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546211,812,649 - 12,082,316 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495546211,777,168 - 12,083,068 (-)NCBIChiLan1.0ChiLan1.0
PBX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1184,554,490 - 84,880,947 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01139,985,392 - 140,311,845 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11143,778,426 - 144,104,493 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1143,778,701 - 144,104,797 (+)Ensemblpanpan1.1panPan2
PBX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13818,378,997 - 18,703,694 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3818,418,093 - 18,703,497 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3818,435,288 - 18,759,350 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03818,460,019 - 18,784,434 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3818,458,914 - 18,783,979 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13818,431,748 - 18,755,044 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03818,781,894 - 19,105,974 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03819,078,211 - 19,402,654 (-)NCBIUU_Cfam_GSD_1.0
Pbx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344102,354,727 - 102,593,874 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648120,203,405 - 20,440,629 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648120,200,236 - 20,440,623 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PBX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl485,824,666 - 86,170,191 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1485,824,590 - 86,170,328 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2493,531,066 - 93,876,673 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PBX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12563,990,553 - 64,317,901 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2563,989,612 - 64,084,673 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605565,810,334 - 66,103,813 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pbx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248262,945,004 - 3,215,110 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248262,944,272 - 3,250,957 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pbx1
1066 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:188
Count of miRNA genes:139
Interacting mature miRNAs:150
Transcripts:ENSRNOT00000027996, ENSRNOT00000043004
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
4889861Pur29Proteinuria QTL 2913.80.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat
11530006Niddm72Non-insulin dependent diabetes mellitus QTL 720.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)137402391880753406Rat
8655959Pur32Proteinuria QTL 328.4urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)137486211785581182Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat

Markers in Region
RH142689  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21380,570,212 - 80,570,438 (+)MAPPERmRatBN7.2
Rnor_6.01386,653,901 - 86,654,126NCBIRnor6.0
Rnor_5.01391,289,715 - 91,289,940UniSTSRnor5.0
RGSC_v3.41384,097,528 - 84,097,753UniSTSRGSC3.4
Celera1380,266,859 - 80,267,084UniSTS
RH 3.4 Map13527.2UniSTS
Cytogenetic Map13q24UniSTS
BE097482  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21380,575,939 - 80,576,098 (+)MAPPERmRatBN7.2
Rnor_6.01386,659,232 - 86,659,390NCBIRnor6.0
Rnor_5.01391,295,046 - 91,295,204UniSTSRnor5.0
RGSC_v3.41384,103,255 - 84,103,413UniSTSRGSC3.4
Celera1380,272,579 - 80,272,737UniSTS
RH 3.4 Map13535.9UniSTS
Cytogenetic Map13q24UniSTS
BI281745  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21380,576,077 - 80,576,241 (+)MAPPERmRatBN7.2
Rnor_6.01386,659,370 - 86,659,533NCBIRnor6.0
Rnor_5.01391,295,184 - 91,295,347UniSTSRnor5.0
RGSC_v3.41384,103,393 - 84,103,556UniSTSRGSC3.4
Celera1380,272,717 - 80,272,880UniSTS
RH 3.4 Map13526.3UniSTS
Cytogenetic Map13q24UniSTS
AW535487  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21380,587,363 - 80,587,516 (+)MAPPERmRatBN7.2
Rnor_6.01386,670,656 - 86,670,808NCBIRnor6.0
Rnor_5.01391,306,470 - 91,306,622UniSTSRnor5.0
RGSC_v3.41384,114,679 - 84,114,831UniSTSRGSC3.4
Celera1380,284,006 - 80,284,158UniSTS
RH 3.4 Map13524.6UniSTS
Cytogenetic Map13q24UniSTS
AL033591  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21380,509,545 - 80,509,629 (+)MAPPERmRatBN7.2
Rnor_6.01386,592,140 - 86,592,223NCBIRnor6.0
Rnor_5.01391,228,297 - 91,228,380UniSTSRnor5.0
RGSC_v3.41384,036,334 - 84,036,417UniSTSRGSC3.4
Celera1380,206,226 - 80,206,309UniSTS
Cytogenetic Map13q24UniSTS


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 2 39 24 14 4 14 2 2 74 35 34 11 2
Low 1 4 33 27 15 27 6 9 7 6
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000027996   ⟹   ENSRNOP00000027996
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1380,278,770 - 80,588,594 (-)Ensembl
Rnor_6.0 Ensembl1386,391,517 - 86,451,002 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000043004   ⟹   ENSRNOP00000039416
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1386,390,741 - 86,451,002 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103202   ⟹   ENSRNOP00000080916
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1380,312,058 - 80,588,594 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106300   ⟹   ENSRNOP00000096551
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1380,312,064 - 80,588,594 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107293   ⟹   ENSRNOP00000093157
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1380,312,058 - 80,588,594 (-)Ensembl
RefSeq Acc Id: NM_001100681   ⟹   NP_001094151
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21380,312,054 - 80,588,166 (-)NCBI
Rnor_6.01386,391,516 - 86,671,323 (-)NCBI
Rnor_5.01391,028,026 - 91,307,274 (-)NCBI
RGSC_v3.41383,839,256 - 84,115,516 (-)RGD
Celera1380,014,857 - 80,284,668 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001134862   ⟹   NP_001128334
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21380,312,054 - 80,588,166 (-)NCBI
Rnor_6.01386,390,741 - 86,671,460 (-)NCBI
Rnor_5.01391,028,026 - 91,307,274 (-)NCBI
RGSC_v3.41383,839,256 - 84,115,516 (-)RGD
Celera1380,014,082 - 80,284,838 (-)RGD
Sequence:
RefSeq Acc Id: XM_039090792   ⟹   XP_038946720
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21380,278,766 - 80,588,563 (-)NCBI
RefSeq Acc Id: XM_039090794   ⟹   XP_038946722
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21380,278,766 - 80,588,560 (-)NCBI
RefSeq Acc Id: NP_001128334   ⟸   NM_001134862
- Peptide Label: isoform a
- UniProtKB: A0A8I5ZR45 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001094151   ⟸   NM_001100681
- Peptide Label: isoform b
- UniProtKB: B1WC30 (UniProtKB/TrEMBL),   A0A8I6AM04 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039416   ⟸   ENSRNOT00000043004
RefSeq Acc Id: ENSRNOP00000027996   ⟸   ENSRNOT00000027996
RefSeq Acc Id: XP_038946720   ⟸   XM_039090792
- Peptide Label: isoform X1
- UniProtKB: F7EV88 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038946722   ⟸   XM_039090794
- Peptide Label: isoform X2
- UniProtKB: B1WC30 (UniProtKB/TrEMBL),   A0A8I6AM04 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000093157   ⟸   ENSRNOT00000107293
RefSeq Acc Id: ENSRNOP00000080916   ⟸   ENSRNOT00000103202
RefSeq Acc Id: ENSRNOP00000096551   ⟸   ENSRNOT00000106300
Protein Domains
Homeobox   PBC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZJI6-F1-model_v2 AlphaFold D3ZJI6 1-342 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308213 AgrOrtholog
BioCyc Gene G2FUF-17500 BioCyc
Ensembl Genes ENSRNOG00000004693 Ensembl
  ENSRNOG00000070119 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027996 ENTREZGENE
  ENSRNOT00000027996.5 UniProtKB/TrEMBL
  ENSRNOT00000103202 ENTREZGENE
  ENSRNOT00000103202.1 UniProtKB/TrEMBL
  ENSRNOT00000106300 ENTREZGENE
  ENSRNOT00000106300.1 UniProtKB/TrEMBL
  ENSRNOT00000107293.1 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9030389 IMAGE-MGC_LOAD
InterPro Homeobox_CS UniProtKB/TrEMBL
  Homeobox_KN_domain UniProtKB/TrEMBL
  Homeodomain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  PBX UniProtKB/TrEMBL
KEGG Report rno:304947 UniProtKB/TrEMBL
MGC_CLONE MGC:187800 IMAGE-MGC_LOAD
NCBI Gene 304947 ENTREZGENE
PANTHER HOMEOBOX PROTEIN EXTRADENTICLE UniProtKB/TrEMBL
  HOMEOBOX PROTEIN TRANSCRIPTION FACTORS UniProtKB/TrEMBL
  PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR 1 UniProtKB/TrEMBL
Pfam Homeobox_KN UniProtKB/TrEMBL
  PBC UniProtKB/TrEMBL
PhenoGen Pbx1 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
  PBC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004693 RatGTEx
  ENSRNOG00000070119 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A0A8I5ZR45 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AJF6_RAT UniProtKB/TrEMBL
  A0A8I6AM04 ENTREZGENE, UniProtKB/TrEMBL
  B1WC30 ENTREZGENE, UniProtKB/TrEMBL
  F7EV88 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-26 Pbx1  PBX homeobox 1  Pbx1  pre-B-cell leukemia homeobox 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-30 Pbx1  pre-B-cell leukemia homeobox 1  Pbx1  pre-B-cell leukemia transcription factor 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Pbx1  pre-B-cell leukemia transcription factor 1   Pbx1_predicted  pre-B-cell leukemia transcription factor 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pbx1_predicted  pre-B-cell leukemia transcription factor 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED