Rara (retinoic acid receptor alpha) - Rat Genome Database

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Gene: Rara (retinoic acid receptor alpha) Ictidomys tridecemlineatus
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Symbol: Rara
Name: retinoic acid receptor alpha
RGD ID: 12732369
Description: ENCODES a protein that exhibits heterocyclic compound binding (ortholog); histone deacetylase binding (ortholog); mRNA 5'-UTR binding (ortholog); INVOLVED IN bone development (ortholog); chondroblast differentiation (ortholog); embryonic camera-type eye development (ortholog); PARTICIPATES IN retinoic acid signaling pathway; ASSOCIATED WITH acute promyelocytic leukemia (ortholog); amyotrophic lateral sclerosis (ortholog); Breast Neoplasms (ortholog); FOUND IN chromatin (ortholog); dendrite (ortholog); perinuclear region of cytoplasm (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: retinoic acid receptor alpha, transcript variant X1; retinoic acid receptor alpha, transcript variant X2; retinoic acid receptor alpha, transcript variant X3; retinoic acid receptor alpha, transcript variant X4
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_02440560221,654,499 - 21,698,923 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649015,376,205 - 15,421,611 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649015,376,217 - 15,420,638 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
apoptotic cell clearance  (IEA)
bone development  (IEA,ISO)
cellular response to corticotropin-releasing hormone stimulus  (IEA)
cellular response to estrogen stimulus  (IEA)
cellular response to lipopolysaccharide  (IEA)
cellular response to retinoic acid  (IEA)
chondroblast differentiation  (IEA,ISO)
embryonic camera-type eye development  (IEA,ISO)
face development  (IEA,ISO)
female pregnancy  (ISO)
germ cell development  (IEA)
glandular epithelial cell development  (IEA,ISO)
growth plate cartilage development  (IEA,ISO)
hippocampus development  (ISO)
limb development  (IEA,ISO)
liver development  (ISO)
male gonad development  (ISO)
mRNA transcription by RNA polymerase II  (IEA)
multicellular organism growth  (IEA,ISO)
negative regulation of apoptotic process  (IEA)
negative regulation of cartilage development  (IEA,ISO)
negative regulation of cell differentiation  (IEA,ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of DNA-templated transcription  (IEA,ISO)
negative regulation of gene expression  (IEA,ISO)
negative regulation of granulocyte differentiation  (IEA)
negative regulation of miRNA transcription  (IEA)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of translation  (ISO)
negative regulation of tumor necrosis factor production  (IEA)
negative regulation of type II interferon production  (IEA)
neural tube closure  (IEA,ISO)
outflow tract septum morphogenesis  (IEA)
positive regulation of cell cycle  (IEA)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of DNA-templated transcription  (IEA)
positive regulation of gene expression  (IEA)
positive regulation of interleukin-13 production  (IEA)
positive regulation of interleukin-4 production  (IEA)
positive regulation of interleukin-5 production  (IEA)
positive regulation of neuron differentiation  (ISO)
positive regulation of T-helper 2 cell differentiation  (IEA)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
prostate gland development  (ISO)
protein phosphorylation  (ISO)
regulation of apoptotic process  (ISO)
regulation of DNA-templated transcription  (IEA,ISO)
regulation of granulocyte differentiation  (IEA,ISO)
regulation of hematopoietic progenitor cell differentiation  (IEA,ISO)
regulation of myelination  (ISO)
regulation of synaptic plasticity  (ISO)
regulation of transcription by RNA polymerase II  (IEA)
response to cytokine  (ISO)
response to estradiol  (ISO)
response to ethanol  (ISO)
response to retinoic acid  (IEA,ISO)
response to vitamin A  (ISO)
retinoic acid receptor signaling pathway  (IEA)
Sertoli cell fate commitment  (IEA)
spermatogenesis  (IEA)
trachea cartilage development  (IEA,ISO)
ureteric bud development  (IEA,ISO)
ventricular cardiac muscle cell differentiation  (IEA,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
Rara
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560221,654,499 - 21,698,923 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649015,376,205 - 15,421,611 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649015,376,217 - 15,420,638 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RARA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381740,309,180 - 40,357,643 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1740,309,180 - 40,357,643 (+)EnsemblGRCh38hg38GRCh38
GRCh371738,465,432 - 38,513,895 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361735,718,972 - 35,767,420 (+)NCBINCBI36Build 36hg18NCBI36
Build 341735,740,895 - 35,767,420NCBI
Celera1735,125,565 - 35,174,038 (+)NCBICelera
Cytogenetic Map17q21.2NCBI
HuRef1734,258,584 - 34,307,018 (+)NCBIHuRef
CHM1_11738,700,731 - 38,749,203 (+)NCBICHM1_1
T2T-CHM13v2.01741,172,682 - 41,221,155 (+)NCBIT2T-CHM13v2.0
Rara
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391198,818,626 - 98,865,768 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1198,818,644 - 98,865,768 (+)EnsemblGRCm39 Ensembl
GRCm381198,927,800 - 98,974,942 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1198,927,818 - 98,974,942 (+)EnsemblGRCm38mm10GRCm38
MGSCv371198,799,010 - 98,836,256 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361198,753,943 - 98,788,760 (+)NCBIMGSCv36mm8
Celera11108,602,792 - 108,640,796 (+)NCBICelera
Cytogenetic Map11DNCBI
cM Map1162.76NCBI
Rara
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81084,379,780 - 84,424,371 (+)NCBIGRCr8
mRatBN7.21083,883,490 - 83,928,932 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1083,893,384 - 83,928,142 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1088,859,187 - 88,872,075 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01088,357,291 - 88,370,179 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01083,749,813 - 83,762,723 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01086,838,819 - 86,884,224 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1086,860,685 - 86,884,210 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01086,663,856 - 86,681,847 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41087,740,479 - 87,753,265 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11087,754,841 - 87,767,635 (+)NCBI
Celera1082,656,708 - 82,669,574 (+)NCBICelera
Cytogenetic Map10q31NCBI
Rara
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545114,897,726 - 14,917,134 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545114,876,663 - 14,917,134 (+)NCBIChiLan1.0ChiLan1.0
RARA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21924,598,318 - 24,646,791 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11726,493,204 - 26,541,701 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01716,932,485 - 16,980,958 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11717,156,923 - 17,205,451 (-)NCBIpanpan1.1PanPan1.1panPan2
RARA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1922,254,803 - 22,298,614 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl922,254,806 - 22,289,459 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha921,727,250 - 21,761,701 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0923,046,731 - 23,091,126 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl923,046,740 - 23,081,981 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1921,821,642 - 21,856,078 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0922,080,340 - 22,114,785 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0922,205,221 - 22,239,665 (-)NCBIUU_Cfam_GSD_1.0
RARA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1222,047,443 - 22,085,673 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11222,047,449 - 22,085,759 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21222,356,038 - 22,403,796 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RARA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11665,817,849 - 65,866,862 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1665,817,757 - 65,866,878 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607736,718,924 - 36,759,030 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rara
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247952,934,731 - 2,967,232 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247952,935,432 - 2,975,226 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSSTOT00000004777   ⟹   ENSSTOP00000004290
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_00493649015,376,205 - 15,421,611 (+)Ensembl
Ensembl Acc Id: ENSSTOT00000034121   ⟹   ENSSTOP00000024128
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_00493649015,406,265 - 15,421,611 (+)Ensembl
Ensembl Acc Id: ENSSTOT00000041384   ⟹   ENSSTOP00000025927
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_00493649015,385,523 - 15,421,611 (+)Ensembl
RefSeq Acc Id: XM_005321817   ⟹   XP_005321874
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560221,654,499 - 21,689,595 (-)NCBI
SpeTri2.0NW_00493649015,385,523 - 15,420,638 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005321819   ⟹   XP_005321876
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560221,654,501 - 21,668,709 (-)NCBI
SpeTri2.0NW_00493649015,406,339 - 15,420,638 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021724202   ⟹   XP_021579877
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560221,654,499 - 21,698,923 (-)NCBI
SpeTri2.0NW_00493649015,376,217 - 15,420,638 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021724203   ⟹   XP_021579878
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560221,654,499 - 21,677,725 (-)NCBI
SpeTri2.0NW_00493649015,397,452 - 15,420,638 (+)NCBI
Sequence:
RefSeq Acc Id: XM_040268807   ⟹   XP_040124741
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560221,654,501 - 21,669,494 (-)NCBI
RefSeq Acc Id: XM_040268808   ⟹   XP_040124742
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560221,654,501 - 21,668,769 (-)NCBI
RefSeq Acc Id: XP_005321874   ⟸   XM_005321817
- Peptide Label: isoform X1
- UniProtKB: I3M4V2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005321876   ⟸   XM_005321819
- Peptide Label: isoform X2
- UniProtKB: A0A287CS79 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_021579877   ⟸   XM_021724202
- Peptide Label: isoform X1
- UniProtKB: I3M4V2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_021579878   ⟸   XM_021724203
- Peptide Label: isoform X1
- UniProtKB: I3M4V2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_040124741   ⟸   XM_040268807
- Peptide Label: isoform X3
RefSeq Acc Id: XP_040124742   ⟸   XM_040268808
- Peptide Label: isoform X4
Ensembl Acc Id: ENSSTOP00000025927   ⟸   ENSSTOT00000041384
Ensembl Acc Id: ENSSTOP00000024128   ⟸   ENSSTOT00000034121
Ensembl Acc Id: ENSSTOP00000004290   ⟸   ENSSTOT00000004777
Protein Domains
NR LBD   Nuclear receptor


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000004746 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000004777.3 UniProtKB/TrEMBL
  ENSSTOT00000034121.1 UniProtKB/TrEMBL
  ENSSTOT00000041384.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/TrEMBL
InterPro NHR-like_dom_sf UniProtKB/TrEMBL
  NR_DBD_RAR UniProtKB/TrEMBL
  NR_LBD_RAR UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/TrEMBL
  Retinoic_acid_rcpt UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/TrEMBL
NCBI Gene Rara ENTREZGENE
PANTHER NUCLEAR HORMONE RECEPTOR UniProtKB/TrEMBL
  RETINOIC ACID RECEPTOR ALPHA UniProtKB/TrEMBL
Pfam Hormone_recep UniProtKB/TrEMBL
  zf-C4 UniProtKB/TrEMBL
PRINTS RETNOICACIDR 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 A0A287CS79 ENTREZGENE, UniProtKB/TrEMBL
  I3M4V2 ENTREZGENE, UniProtKB/TrEMBL