Pax1 (paired box 1) - Rat Genome Database

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Gene: Pax1 (paired box 1) Rattus norvegicus
Analyze
Symbol: Pax1
Name: paired box 1
RGD ID: 1588548
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in sclerotome development. Predicted to act upstream of or within several processes, including alpha-beta T cell differentiation; parathyroid gland development; and thymus development. Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in branchiootorenal syndrome. Orthologous to human PAX1 (paired box 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: paired box gene 1; paired box gene 1 (mapped); Paired box homeotic gene 1; paired box protein Pax-1; Pax-1; Pax1_mapped
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83155,244,961 - 155,254,836 (+)NCBIGRCr8
mRatBN7.23134,792,330 - 134,801,637 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3134,789,182 - 134,801,636 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3138,710,682 - 138,720,045 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03147,294,766 - 147,304,129 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03144,997,920 - 145,007,281 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03141,577,124 - 141,589,849 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3141,577,504 - 141,589,849 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03147,995,989 - 148,008,334 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43136,006,504 - 136,018,849 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3133,651,867 - 133,663,861 (+)NCBICelera
Cytogenetic Map3q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Cellular Component
nucleus  (IEA)

References

References - curated
# Reference Title Reference Citation
1. The molecular basis of the undulated/Pax-1 mutation. Chalepakis G, etal., Cell 1991 Sep 6;66(5):873-84.
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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7607069   PMID:7743923   PMID:10364424   PMID:11476574   PMID:11900462   PMID:12490554   PMID:15024065   PMID:16093716   PMID:34453169  


Genomics

Comparative Map Data
Pax1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83155,244,961 - 155,254,836 (+)NCBIGRCr8
mRatBN7.23134,792,330 - 134,801,637 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3134,789,182 - 134,801,636 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3138,710,682 - 138,720,045 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03147,294,766 - 147,304,129 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03144,997,920 - 145,007,281 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03141,577,124 - 141,589,849 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3141,577,504 - 141,589,849 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03147,995,989 - 148,008,334 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43136,006,504 - 136,018,849 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3133,651,867 - 133,663,861 (+)NCBICelera
Cytogenetic Map3q41NCBI
PAX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382021,705,664 - 21,718,481 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2021,705,659 - 21,718,481 (+)EnsemblGRCh38hg38GRCh38
GRCh372021,686,302 - 21,699,119 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362021,634,297 - 21,644,620 (+)NCBINCBI36Build 36hg18NCBI36
Build 342021,635,074 - 21,643,441NCBI
Celera2021,760,205 - 21,770,528 (+)NCBICelera
Cytogenetic Map20p11.22NCBI
HuRef2021,649,121 - 21,661,830 (+)NCBIHuRef
CHM1_12021,686,612 - 21,699,440 (+)NCBICHM1_1
T2T-CHM13v2.02021,762,357 - 21,775,174 (+)NCBIT2T-CHM13v2.0
Pax1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392147,203,850 - 147,216,972 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2147,203,845 - 147,235,215 (+)EnsemblGRCm39 Ensembl
GRCm382147,361,930 - 147,375,049 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2147,361,925 - 147,393,295 (+)EnsemblGRCm38mm10GRCm38
MGSCv372147,190,730 - 147,200,785 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362147,056,501 - 147,066,490 (+)NCBIMGSCv36mm8
Celera2148,637,978 - 148,647,942 (+)NCBICelera
Cytogenetic Map2G2NCBI
cM Map272.63NCBI
Pax1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541529,413,253 - 29,420,682 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541529,413,253 - 29,420,682 (+)NCBIChiLan1.0ChiLan1.0
PAX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22122,594,415 - 22,607,324 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12022,591,251 - 22,604,160 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02021,663,155 - 21,676,880 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12021,623,771 - 21,633,468 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2021,623,771 - 21,632,608 (+)Ensemblpanpan1.1panPan2
PAX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1241,742,570 - 1,752,593 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl241,743,940 - 1,753,185 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha241,769,451 - 1,778,164 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0242,148,503 - 2,157,210 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl242,147,192 - 2,157,210 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1241,746,038 - 1,754,735 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0241,848,749 - 1,857,442 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0242,124,459 - 2,134,423 (-)NCBIUU_Cfam_GSD_1.0
Pax1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640150,344,618 - 150,353,321 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366203,765,444 - 3,776,467 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366203,765,481 - 3,773,779 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PAX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1729,422,129 - 29,431,990 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11729,421,117 - 29,436,481 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21733,372,514 - 33,386,866 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PAX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1250,706,029 - 50,722,634 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660785,504,274 - 5,519,056 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pax1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474122,007,778 - 22,017,325 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474122,009,733 - 22,017,377 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pax1
68 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:114
Count of miRNA genes:90
Interacting mature miRNAs:101
Transcripts:ENSRNOT00000067983
Prediction methods: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
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3115638168135181505Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3112287552135181505Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat

Markers in Region
PMC21138P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23134,793,064 - 134,793,622 (+)MAPPERmRatBN7.2
Rnor_6.03141,581,278 - 141,581,835NCBIRnor6.0
Rnor_5.03147,999,763 - 148,000,320UniSTSRnor5.0
RGSC_v3.43136,010,278 - 136,010,835UniSTSRGSC3.4
Celera3133,655,290 - 133,655,847UniSTS
Cytogenetic Map3q41UniSTS


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
nervous system
renal system
reproductive system
respiratory system
1 2 4 15 23 25 6 20 6 6 55 29 6 17 32 19

Sequence


Ensembl Acc Id: ENSRNOT00000067983   ⟹   ENSRNOP00000062281
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3134,789,291 - 134,801,636 (+)Ensembl
Rnor_6.0 Ensembl3141,577,504 - 141,589,849 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000103021   ⟹   ENSRNOP00000096757
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3134,789,182 - 134,801,636 (+)Ensembl
RefSeq Acc Id: NM_001401899   ⟹   NP_001388828
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83155,245,529 - 155,254,836 (+)NCBI
mRatBN7.23134,792,330 - 134,801,637 (+)NCBI
RefSeq Acc Id: XM_063283810   ⟹   XP_063139880
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83155,244,961 - 155,254,830 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001388828 (Get FASTA)   NCBI Sequence Viewer  
  XP_063139880 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL95112 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000062281.2
  ENSRNOP00000096757.1
Ensembl Acc Id: ENSRNOP00000062281   ⟸   ENSRNOT00000067983
Ensembl Acc Id: ENSRNOP00000096757   ⟸   ENSRNOT00000103021
RefSeq Acc Id: NP_001388828   ⟸   NM_001401899
RefSeq Acc Id: XP_063139880   ⟸   XM_063283810
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GM82 (UniProtKB/TrEMBL)
Protein Domains
Paired

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LT82-F1-model_v2 AlphaFold F1LT82 1-191 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:1588548 AgrOrtholog
BioCyc Gene G2FUF-47544 BioCyc
Ensembl Genes ENSRNOG00000024882 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067983.2 UniProtKB/TrEMBL
  ENSRNOT00000103021.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  PAIRED_DNA-bd_dom UniProtKB/TrEMBL
  Paired_dom UniProtKB/TrEMBL
  PAX_fam UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene 311505 ENTREZGENE
PANTHER PTHR45636 UniProtKB/TrEMBL
  PTHR45636:SF15 UniProtKB/TrEMBL
Pfam PAX UniProtKB/TrEMBL
PhenoGen Pax1 PhenoGen
PRINTS PAIREDBOX UniProtKB/TrEMBL
PROSITE PAIRED_1 UniProtKB/TrEMBL
  PAIRED_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000024882 RatGTEx
SMART PAX UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt A0A8I6GM82 ENTREZGENE, UniProtKB/TrEMBL
  A6K7A7_RAT UniProtKB/TrEMBL
  F1LT82_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-30 Pax1  paired box 1  Pax1  paired box gene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-13   paired box gene 1  Pax1  paired box gene 1 (mapped)  Name updated 737654 APPROVED
2007-04-11 Pax1  paired box gene 1 (mapped)  Pax1_mapped  paired box gene 1 (mapped)  Data merged from RGD:3257 737654 APPROVED
2006-11-19 Pax1  paired box gene 1 (mapped)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 Pax1_mapped  paired box gene 1 (mapped)      Symbol and Name updated 1556543 APPROVED
2002-06-10 Pax1  Paired box homeotic gene 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_homology mouse homolog exhibits transcriptional activity; mutation causes undulating malformations in the vertebral column 1302229