Pbx2 (PBX homeobox 2) - Rat Genome Database

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Gene: Pbx2 (PBX homeobox 2) Rattus norvegicus
Analyze
Symbol: Pbx2
Name: PBX homeobox 2
RGD ID: 1303084
Description: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Predicted to be involved in several processes, including embryonic organ development; eye development; and nervous system development. Predicted to act upstream of or within embryonic limb morphogenesis; positive regulation of transcription by RNA polymerase II; and proximal/distal pattern formation. Predicted to be located in nucleus. Predicted to be part of transcription regulator complex. Orthologous to human PBX2 (PBX homeobox 2); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: pre-B-cell leukemia homeobox 2; pre-B-cell leukemia transcription factor 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,156,107 - 4,161,503 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl204,156,107 - 4,161,827 (-)EnsemblGRCr8
mRatBN7.2204,151,500 - 4,156,425 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,151,500 - 4,156,425 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx204,858,099 - 4,863,027 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0204,219,851 - 4,224,779 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,750,751 - 4,755,674 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,357,805 - 4,362,730 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,357,733 - 4,362,682 (+)Ensemblrn6Rnor6.0
Rnor_5.0206,437,161 - 6,442,086 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4204,253,962 - 4,259,185 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera203,873,856 - 3,878,704 (+)NCBICelera
RGSC_v3.1204,254,236 - 4,259,412 (-)NCBI
Cytogenetic Map20p12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. 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.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. The TALE homeodomain protein Pbx2 is not essential for development and long-term survival. Selleri L, etal., Mol Cell Biol 2004 Jun;24(12):5324-31.
Additional References at PubMed
PMID:10381567   PMID:10842069   PMID:12054735   PMID:15087118   PMID:16672333   PMID:18973687   PMID:19356220  


Genomics

Comparative Map Data
Pbx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,156,107 - 4,161,503 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl204,156,107 - 4,161,827 (-)EnsemblGRCr8
mRatBN7.2204,151,500 - 4,156,425 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,151,500 - 4,156,425 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx204,858,099 - 4,863,027 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0204,219,851 - 4,224,779 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,750,751 - 4,755,674 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,357,805 - 4,362,730 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,357,733 - 4,362,682 (+)Ensemblrn6Rnor6.0
Rnor_5.0206,437,161 - 6,442,086 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4204,253,962 - 4,259,185 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera203,873,856 - 3,878,704 (+)NCBICelera
RGSC_v3.1204,254,236 - 4,259,412 (-)NCBI
Cytogenetic Map20p12NCBI
PBX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38632,184,733 - 32,190,202 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl632,184,733 - 32,190,202 (-)Ensemblhg38GRCh38
GRCh37632,152,510 - 32,157,979 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,260,488 - 32,265,941 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34632,260,495 - 32,265,941NCBI
Celera633,719,557 - 33,725,007 (-)NCBICelera
Cytogenetic Map6p21.32NCBI
HuRef631,906,708 - 31,912,158 (-)NCBIHuRef
CHM1_1632,154,994 - 32,160,447 (-)NCBICHM1_1
T2T-CHM13v2.0632,037,924 - 32,043,391 (-)NCBIT2T-CHM13v2.0
Pbx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,811,233 - 34,816,374 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1734,810,240 - 34,816,374 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381734,592,259 - 34,597,400 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,591,266 - 34,597,400 (+)Ensemblmm10GRCm38
MGSCv371734,729,416 - 34,734,286 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361734,200,527 - 34,205,397 (+)NCBIMGSCv36mm8
Celera1737,687,631 - 37,692,501 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.17NCBI
Pbx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955437646,906 - 654,008 (-)Ensembl
ChiLan1.0NW_004955437648,935 - 654,008 (-)NCBIChiLan1.0ChiLan1.0
PBX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2546,647,812 - 46,653,296 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1642,609,292 - 42,614,773 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0631,832,131 - 31,837,585 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1632,708,252 - 32,717,181 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,711,166 - 32,717,453 (-)EnsemblpanPan2panpan1.1
PBX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,577,639 - 1,582,609 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,578,707 - 1,584,688 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha121,711,340 - 1,716,366 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0121,715,867 - 1,720,898 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl121,715,861 - 1,720,883 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1121,578,901 - 1,583,922 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0121,644,490 - 1,649,520 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,710,814 - 1,715,841 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pbx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494636,143,042 - 36,148,303 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367271,412,632 - 1,419,438 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367271,413,063 - 1,418,304 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PBX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl724,221,565 - 24,226,940 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1724,221,565 - 24,226,940 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2728,042,407 - 28,047,793 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PBX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11739,841,798 - 39,847,244 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1739,842,064 - 39,845,618 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604432,084,507 - 32,089,966 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pbx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475424,132,886 - 24,137,699 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Pbx2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1187,275,352 - 7,280,481 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pbx2
16 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:595
Count of miRNA genes:256
Interacting mature miRNAs:320
Transcripts:ENSRNOT00000000509
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015332005306452Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2016693431Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362632310078622Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)2016693431Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036263239244918Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20114100378Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat

Markers in Region
RH133069  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,157,191 - 4,157,392 (-)MAPPERmRatBN7.2
Rnor_6.0204,356,838 - 4,357,038NCBIRnor6.0
Rnor_5.0206,436,194 - 6,436,394UniSTSRnor5.0
RGSC_v3.4204,259,952 - 4,260,152UniSTSRGSC3.4
Celera203,872,889 - 3,873,089UniSTS
RH 3.4 Map2052.92UniSTS
Cytogenetic Map20p12UniSTS
AI176804  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,151,744 - 4,151,845 (-)MAPPERmRatBN7.2
Rnor_6.0204,362,385 - 4,362,485NCBIRnor6.0
Rnor_5.0206,441,741 - 6,441,841UniSTSRnor5.0
RGSC_v3.4204,254,207 - 4,254,307UniSTSRGSC3.4
Celera203,878,359 - 3,878,459UniSTS
RH 3.4 Map2052.92UniSTS
Cytogenetic Map20p12UniSTS
MARC_5887-5888:991939775:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,154,572 - 4,155,304 (-)MAPPERmRatBN7.2
Rnor_6.0204,358,926 - 4,359,657NCBIRnor6.0
Rnor_5.0206,438,282 - 6,439,013UniSTSRnor5.0
RGSC_v3.4204,257,035 - 4,257,766UniSTSRGSC3.4
Celera203,874,900 - 3,875,631UniSTS
Cytogenetic Map20p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000000509   ⟹   ENSRNOP00000000509
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl204,156,107 - 4,161,827 (-)Ensembl
mRatBN7.2 Ensembl204,151,500 - 4,156,425 (-)Ensembl
Rnor_6.0 Ensembl204,357,733 - 4,362,682 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000082667
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,359,786 - 4,360,201 (+)Ensembl
RefSeq Acc Id: NM_001002828   ⟹   NP_001002828
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,156,107 - 4,161,032 (-)NCBI
mRatBN7.2204,151,500 - 4,156,425 (-)NCBI
Rnor_6.0204,357,805 - 4,362,730 (+)NCBI
Rnor_5.0206,437,161 - 6,442,086 (+)NCBI
RGSC_v3.4204,253,962 - 4,259,185 (-)RGD
Celera203,873,856 - 3,878,704 (+)RGD
Sequence:
RefSeq Acc Id: XM_063279348   ⟹   XP_063135418
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,156,107 - 4,161,503 (-)NCBI
RefSeq Acc Id: NP_001002828   ⟸   NM_001002828
- UniProtKB: Q6MG87 (UniProtKB/TrEMBL),   F1LNM5 (UniProtKB/TrEMBL),   A6KTF7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000000509   ⟸   ENSRNOT00000000509
RefSeq Acc Id: XP_063135418   ⟸   XM_063279348
- Peptide Label: isoform X1
Protein Domains
Homeobox   PBC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MG87-F1-model_v2 AlphaFold Q6MG87 1-430 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:1303084 AgrOrtholog
BioCyc Gene G2FUF-4583 BioCyc
Ensembl Genes ENSRNOG00000000440 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000509 ENTREZGENE
  ENSRNOT00000000509.8 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_KN_domain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  PBX UniProtKB/TrEMBL
  TALE_homeobox UniProtKB/TrEMBL
KEGG Report rno:406164 UniProtKB/TrEMBL
NCBI Gene 406164 ENTREZGENE
PANTHER HOMEOBOX PROTEIN TRANSCRIPTION FACTORS UniProtKB/TrEMBL
Pfam Homeobox_KN UniProtKB/TrEMBL
  PBC UniProtKB/TrEMBL
PhenoGen Pbx2 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
  PBC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000440 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A0ABZ3NN70_RAT UniProtKB/TrEMBL
  A6KTF6_RAT UniProtKB/TrEMBL
  A6KTF7 ENTREZGENE, UniProtKB/TrEMBL
  A6KTF8_RAT UniProtKB/TrEMBL
  A6KTF9_RAT UniProtKB/TrEMBL
  A6KTG0_RAT UniProtKB/TrEMBL
  A6KTG1_RAT UniProtKB/TrEMBL
  F1LNM5 ENTREZGENE
  Q6MG87 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1LNM5 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-26 Pbx2  PBX homeobox 2  Pbx2  pre-B-cell leukemia homeobox 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-30 Pbx2  pre-B-cell leukemia homeobox 2  Pbx2  pre-B-cell leukemia transcription factor 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-02-14 Pbx2  pre-B-cell leukemia transcription factor 2      Symbol and Name status set to provisional 70820 PROVISIONAL