Prrx2 (paired related homeobox 2) - Rat Genome Database

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Gene: Prrx2 (paired related homeobox 2) Rattus norvegicus
Analyze
Symbol: Prrx2
Name: paired related homeobox 2
RGD ID: 1311471
Description: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; HMG box domain binding activity; and RNA polymerase II general transcription initiation factor activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including embryonic morphogenesis; positive regulation of cell population proliferation; and positive regulation of smoothened signaling pathway. Predicted to be active in nucleus. Orthologous to human PRRX2 (paired related homeobox 2); INTERACTS WITH 17alpha-ethynylestradiol; 3,3',4,4',5-pentachlorobiphenyl; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: paired mesoderm homeobox protein 2; Prx2
RGD Orthologs
Human
Mouse
Bonobo
Dog
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
GRCr8334,530,331 - 34,566,284 (+)NCBIGRCr8
mRatBN7.2314,132,574 - 14,168,533 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl314,094,004 - 14,168,535 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx317,204,856 - 17,240,853 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0325,789,846 - 25,825,841 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0324,037,214 - 24,073,226 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.039,681,871 - 9,718,051 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl39,681,871 - 9,718,051 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0315,040,931 - 15,077,369 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.439,899,066 - 9,936,837 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.139,794,587 - 9,832,199 (+)NCBI
Celera38,892,836 - 8,928,706 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9729491   PMID:9876178   PMID:9882503   PMID:10664157   PMID:11532916   PMID:12713735   PMID:16582099   PMID:22577874   PMID:23644741   PMID:24881871   PMID:25795141  


Genomics

Comparative Map Data
Prrx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8334,530,331 - 34,566,284 (+)NCBIGRCr8
mRatBN7.2314,132,574 - 14,168,533 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl314,094,004 - 14,168,535 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx317,204,856 - 17,240,853 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0325,789,846 - 25,825,841 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0324,037,214 - 24,073,226 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.039,681,871 - 9,718,051 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl39,681,871 - 9,718,051 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0315,040,931 - 15,077,369 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.439,899,066 - 9,936,837 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.139,794,587 - 9,832,199 (+)NCBI
Celera38,892,836 - 8,928,706 (+)NCBICelera
Cytogenetic Map3p12NCBI
PRRX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389129,665,647 - 129,722,674 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9129,665,647 - 129,722,674 (+)EnsemblGRCh38hg38GRCh38
GRCh379132,427,926 - 132,484,953 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369131,467,741 - 131,524,774 (+)NCBINCBI36Build 36hg18NCBI36
Build 349129,507,473 - 129,564,503NCBI
Celera9103,078,740 - 103,135,771 (+)NCBICelera
Cytogenetic Map9q34.11NCBI
HuRef9102,027,059 - 102,084,049 (+)NCBIHuRef
CHM1_19132,576,580 - 132,633,630 (+)NCBICHM1_1
T2T-CHM13v2.09141,870,240 - 141,927,272 (+)NCBIT2T-CHM13v2.0
Prrx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39230,735,076 - 30,771,263 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl230,724,984 - 30,771,263 (+)EnsemblGRCm39 Ensembl
GRCm38230,845,064 - 30,881,251 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl230,834,972 - 30,881,251 (+)EnsemblGRCm38mm10GRCm38
MGSCv37230,700,887 - 30,736,767 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36230,667,290 - 30,703,262 (+)NCBIMGSCv36mm8
Celera230,550,237 - 30,586,613 (+)NCBICelera
Cytogenetic Map2BNCBI
cM Map221.74NCBI
PRRX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2119,626,787 - 9,684,403 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan199,629,131 - 9,686,753 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09100,792,324 - 100,849,923 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19129,478,374 - 129,506,866 (+)NCBIpanpan1.1PanPan1.1panPan2
PRRX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1954,089,046 - 54,112,595 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl954,093,163 - 54,096,348 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha953,285,306 - 53,346,966 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0954,984,314 - 55,035,503 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl954,988,556 - 55,035,116 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1953,767,114 - 53,825,066 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0954,083,947 - 54,145,111 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0954,176,396 - 54,229,502 (-)NCBIUU_Cfam_GSD_1.0
PRRX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1269,853,200 - 269,903,469 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11269,853,134 - 269,902,808 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21303,710,625 - 303,770,644 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRRX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1128,424,415 - 8,447,959 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl128,424,737 - 8,480,393 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660796,958,220 - 7,015,963 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prrx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247605,656,521 - 5,692,934 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247605,656,456 - 5,684,383 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Prrx2
272 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:216
Count of miRNA genes:153
Interacting mature miRNAs:163
Transcripts:ENSRNOT00000008270
Prediction methods:Microtar, Miranda, Rnahybrid
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
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat

Markers in Region
D3Rat231  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2314,158,705 - 14,158,916 (+)MAPPERmRatBN7.2
Rnor_6.039,708,213 - 9,708,423NCBIRnor6.0
Rnor_5.0315,067,140 - 15,067,350UniSTSRnor5.0
RGSC_v3.439,925,540 - 9,925,751RGDRGSC3.4
RGSC_v3.439,925,541 - 9,925,751UniSTSRGSC3.4
RGSC_v3.139,820,908 - 9,821,119RGD
Celera38,918,780 - 8,918,990UniSTS
SHRSP x BN Map33.5699RGD
SHRSP x BN Map33.5699UniSTS
Cytogenetic Map3p12UniSTS
RH128429  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2314,168,188 - 14,168,404 (+)MAPPERmRatBN7.2
Rnor_6.039,717,705 - 9,717,920NCBIRnor6.0
Rnor_5.0315,077,023 - 15,077,238UniSTSRnor5.0
RGSC_v3.439,936,491 - 9,936,706UniSTSRGSC3.4
Celera38,928,360 - 8,928,575UniSTS
RH 3.4 Map348.5UniSTS
Cytogenetic Map3p12UniSTS
UniSTS:234365  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2314,168,292 - 14,168,416 (+)MAPPERmRatBN7.2
Rnor_6.039,717,809 - 9,717,932NCBIRnor6.0
Rnor_5.0315,077,127 - 15,077,250UniSTSRnor5.0
RGSC_v3.439,936,595 - 9,936,718UniSTSRGSC3.4
Celera38,928,464 - 8,928,587UniSTS
Cytogenetic Map3p12UniSTS


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 16 4 4 4 6 2 29
Low 1 25 11 2 11 2 6 9 58 22 8 11 6
Below cutoff 2 2 19 12 8 12 2 2 8 11 4 2

Sequence


RefSeq Acc Id: ENSRNOT00000083251   ⟹   ENSRNOP00000070422
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl314,132,315 - 14,168,535 (+)Ensembl
Rnor_6.0 Ensembl39,681,871 - 9,718,051 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098429   ⟹   ENSRNOP00000096583
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl314,122,414 - 14,168,535 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105946   ⟹   ENSRNOP00000095627
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl314,133,139 - 14,168,533 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114142   ⟹   ENSRNOP00000085942
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl314,094,004 - 14,168,492 (+)Ensembl
RefSeq Acc Id: NM_001415156   ⟹   NP_001402085
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8334,530,331 - 34,566,284 (+)NCBI
mRatBN7.2314,132,574 - 14,168,533 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001402085 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93289 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000070422
  ENSRNOP00000070422.2
  ENSRNOP00000085942.1
  ENSRNOP00000095627.1
  ENSRNOP00000096583.1
RefSeq Acc Id: ENSRNOP00000070422   ⟸   ENSRNOT00000083251
RefSeq Acc Id: ENSRNOP00000096583   ⟸   ENSRNOT00000098429
RefSeq Acc Id: ENSRNOP00000095627   ⟸   ENSRNOT00000105946
RefSeq Acc Id: ENSRNOP00000085942   ⟸   ENSRNOT00000114142
RefSeq Acc Id: NP_001402085   ⟸   NM_001415156
- UniProtKB: A0A0G2JXV9 (UniProtKB/TrEMBL)
Protein Domains
Homeobox   OAR

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JXV9-F1-model_v2 AlphaFold A0A0G2JXV9 1-247 view protein structure

Transcriptome

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

Promoters
RGD ID:13691967
Promoter ID:EPDNEW_R2492
Type:initiation region
Name:Prrx2_1
Description:paired related homeobox 2
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_6.039,681,934 - 9,681,994EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311471 AgrOrtholog
BioCyc Gene G2FUF-50193 BioCyc
Ensembl Genes ENSRNOG00000058329 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000083251 ENTREZGENE
  ENSRNOT00000083251.2 UniProtKB/TrEMBL
  ENSRNOT00000098429.1 UniProtKB/TrEMBL
  ENSRNOT00000105946.1 UniProtKB/TrEMBL
  ENSRNOT00000114142.1 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeo_OAR UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  PRRX1/2 UniProtKB/TrEMBL
NCBI Gene 113931 ENTREZGENE
PANTHER PAIRED MESODERM HOMEOBOX PROTEIN 2 UniProtKB/TrEMBL
  PTHR46385 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
  OAR UniProtKB/TrEMBL
PhenoGen Prrx2 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
  OAR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000058329 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A0A0G2JXV9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A4E1_RAT UniProtKB/TrEMBL
  A0A8I6AK36_RAT UniProtKB/TrEMBL
  A0A8I6ASS2_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Prrx2  paired related homeobox 2   Prrx2_predicted  paired related homeobox 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Prrx2_predicted  paired related homeobox 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED