Rxra (retinoid X receptor alpha) - Rat Genome Database

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Gene: Rxra (retinoid X receptor alpha) Ictidomys tridecemlineatus
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Symbol: Rxra
Name: retinoid X receptor alpha
RGD ID: 12546750
Description: ENCODES a protein that exhibits chromatin DNA binding (ortholog); double-stranded DNA binding (ortholog); nuclear receptor activity (ortholog); INVOLVED IN axon regeneration (ortholog); camera-type eye development (ortholog); cardiac muscle cell proliferation (ortholog); PARTICIPATES IN retinoic acid signaling pathway; ASSOCIATED WITH alcoholic cardiomyopathy (ortholog); amyotrophic lateral sclerosis type 1 (ortholog); congenital heart disease (ortholog); FOUND IN axon (ortholog); chromatin (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: retinoic acid receptor RXR-alpha
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947200,612,017 - 200,639,947 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366692,738,448 - 2,763,070 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366692,735,111 - 2,763,060 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
axon regeneration  (ISO)
camera-type eye development  (ISO)
cardiac muscle cell proliferation  (ISO)
cellular response to insulin stimulus  (ISO)
embryo implantation  (ISO)
female pregnancy  (ISO)
gene expression  (ISO)
heart development  (ISO)
hormone-mediated signaling pathway  (IEA)
in utero embryonic development  (ISO)
liver development  (ISO)
maternal placenta development  (ISO)
midgut development  (ISO)
mRNA transcription by RNA polymerase II  (IEA)
negative regulation of cell population proliferation  (ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
nuclear receptor-mediated steroid hormone signaling pathway  (IEA)
peroxisome proliferator activated receptor signaling pathway  (IEA)
placenta development  (ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of DNA-templated transcription  (IEA,ISO)
positive regulation of thyroid hormone receptor signaling pathway  (IEA)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
positive regulation of translational initiation by iron  (ISO)
positive regulation of vitamin D receptor signaling pathway  (IEA)
regulation of branching involved in prostate gland morphogenesis  (ISO)
regulation of DNA-templated transcription  (IEA,ISO)
regulation of myelination  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
response to ethanol  (ISO)
response to glucocorticoid  (ISO)
response to nutrient  (ISO)
response to retinoic acid  (IEA,ISO)
response to selenium ion  (ISO)
response to vitamin A  (ISO)
response to vitamin D  (ISO)
retinoic acid receptor signaling pathway  (IEA,ISO)
secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development  (ISO)
ventricular cardiac muscle cell differentiation  (ISO)
ventricular cardiac muscle tissue morphogenesis  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Rxra
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947200,612,017 - 200,639,947 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366692,738,448 - 2,763,070 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366692,735,111 - 2,763,060 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RXRA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389134,326,455 - 134,440,585 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9134,317,098 - 134,440,585 (+)EnsemblGRCh38hg38GRCh38
GRCh379137,218,301 - 137,332,431 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369136,358,231 - 136,472,252 (+)NCBINCBI36Build 36hg18NCBI36
Build 349134,519,421 - 134,558,376NCBI
Celera9107,734,128 - 107,848,213 (+)NCBICelera
Cytogenetic Map9q34.2NCBI
HuRef9106,757,493 - 106,796,351 (+)NCBIHuRef
CHM1_19137,442,044 - 137,480,968 (+)NCBICHM1_1
T2T-CHM13v2.09146,541,633 - 146,657,063 (+)NCBIT2T-CHM13v2.0
Rxra
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39227,566,457 - 27,653,331 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl227,566,452 - 27,652,969 (+)EnsemblGRCm39 Ensembl
GRCm38227,676,445 - 27,763,319 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl227,676,440 - 27,762,957 (+)EnsemblGRCm38mm10GRCm38
MGSCv37227,532,721 - 27,618,839 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36227,499,210 - 27,585,328 (+)NCBIMGSCv36mm8
Celera227,439,778 - 27,465,824 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.38NCBI
Rxra
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8331,387,892 - 31,474,415 (+)NCBIGRCr8
mRatBN7.2310,989,832 - 11,076,366 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,989,832 - 11,073,712 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx314,057,333 - 14,141,119 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0322,642,768 - 22,726,554 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,896,722 - 20,980,500 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.036,272,560 - 6,295,354 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl36,211,789 - 6,295,908 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0311,631,209 - 11,653,959 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.436,605,782 - 6,689,224 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.136,606,054 - 6,690,078 (+)NCBI
Celera35,843,675 - 5,866,536 (+)NCBICelera
Cytogenetic Map3p12NCBI
Rxra
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555133,335,897 - 3,386,994 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555133,313,544 - 3,386,544 (+)NCBIChiLan1.0ChiLan1.0
RXRA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2114,937,570 - 5,052,654 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan194,939,903 - 5,054,985 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09105,424,046 - 105,539,241 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19134,082,865 - 134,144,704 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9134,082,865 - 134,144,704 (+)Ensemblpanpan1.1panPan2
RXRA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1950,525,195 - 50,575,720 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl950,484,567 - 50,573,119 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha949,766,609 - 49,860,130 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0951,360,100 - 51,453,773 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl951,359,634 - 51,453,363 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1950,120,766 - 50,214,385 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0950,464,001 - 50,557,538 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0950,541,613 - 50,635,257 (+)NCBIUU_Cfam_GSD_1.0
RXRA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1273,705,505 - 273,797,620 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11273,698,842 - 273,797,622 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RXRA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1123,704,129 - 3,814,707 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl123,699,923 - 3,814,678 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660581,284,770 - 1,401,711 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rxra
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247602,380,708 - 2,456,928 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247602,379,809 - 2,455,749 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSSTOT00000026913   ⟹   ENSSTOP00000016521
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049366692,738,448 - 2,763,070 (-)Ensembl
RefSeq Acc Id: XM_005336950   ⟹   XP_005337007
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024404947200,612,017 - 200,639,947 (+)NCBI
SpeTri2.0NW_0049366692,735,111 - 2,763,060 (-)NCBI
Sequence:
RefSeq Acc Id: XM_040286593   ⟹   XP_040142527
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024404947200,616,483 - 200,639,947 (+)NCBI
Protein Sequences
Protein RefSeqs XP_005337007 (Get FASTA)   NCBI Sequence Viewer  
  XP_040142527 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000016521.2
GenBank Protein KAG3288308 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_005337007   ⟸   XM_005336950
- Peptide Label: isoform X1
- UniProtKB: I3MWM6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_040142527   ⟸   XM_040286593
- Peptide Label: isoform X2
Ensembl Acc Id: ENSSTOP00000016521   ⟸   ENSSTOT00000026913
Protein Domains
NR LBD   Nuclear receptor


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000028427 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000026913.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/TrEMBL
InterPro NHR-like_dom_sf UniProtKB/TrEMBL
  Nuc_recep-AF1 UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/TrEMBL
  Nuclear_hormone_rcpt_NR2 UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/TrEMBL
  Retinoid-X_rcpt/HNF4 UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/TrEMBL
NCBI Gene Rxra ENTREZGENE
PANTHER NUCLEAR HORMONE RECEPTOR UniProtKB/TrEMBL
  RETINOIC ACID RECEPTOR RXR-ALPHA UniProtKB/TrEMBL
Pfam Hormone_recep UniProtKB/TrEMBL
  Nuc_recep-AF1 UniProtKB/TrEMBL
  zf-C4 UniProtKB/TrEMBL
PRINTS RETINOIDXR UniProtKB/TrEMBL
  STRDHORMONER UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/TrEMBL
SMART HOLI UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
  SSF48508 UniProtKB/TrEMBL
UniProt I3MWM6 ENTREZGENE, UniProtKB/TrEMBL