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Rxra retinoid X receptor alpha [ Mus musculus (house mouse) ]

Gene ID: 20181, updated on 13-Aug-2019

Summary

Official Symbol
Rxraprovided by MGI
Official Full Name
retinoid X receptor alphaprovided by MGI
Primary source
MGI:MGI:98214
See related
Ensembl:ENSMUSG00000015846
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Nr2b1; RXRalpha1; 9530071D11Rik
Expression
Ubiquitous expression in liver adult (RPKM 80.9), mammary gland adult (RPKM 32.7) and 23 other tissues See more
Orthologs

Genomic context

See Rxra in Genome Data Viewer
Location:
2 A3; 2 19.38 cM
Exon count:
14
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (27676445..27763319)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (27532721..27618839)

Chromosome 2 - NC_000068.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105244102 Neighboring gene uncharacterized LOC115489444 Neighboring gene predicted gene, 39776 Neighboring gene predicted gene, 39777 Neighboring gene collagen, type V, alpha 1 Neighboring gene uncharacterized LOC115489445

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DBD domain binding ISO
Inferred from Sequence Orthology
more info
 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding IPI
Inferred from Physical Interaction
more info
PubMed 
DNA binding ISO
Inferred from Sequence Orthology
more info
 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity IGI
Inferred from Genetic Interaction
more info
PubMed 
DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
LBD domain binding ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
enzyme binding ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
nuclear receptor activity ISO
Inferred from Sequence Orthology
more info
 
nuclear receptor binding ISO
Inferred from Sequence Orthology
more info
 
peptide binding ISO
Inferred from Sequence Orthology
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding ISO
Inferred from Sequence Orthology
more info
 
protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
 
protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
 
retinoic acid binding ISO
Inferred from Sequence Orthology
more info
 
retinoic acid receptor binding ISO
Inferred from Sequence Orthology
more info
 
retinoic acid-responsive element binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retinoic acid-responsive element binding ISO
Inferred from Sequence Orthology
more info
 
sequence-specific DNA binding IGI
Inferred from Genetic Interaction
more info
PubMed 
sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to transcription regulatory region DNA binding ISO
Inferred from Sequence Orthology
more info
 
vitamin D receptor binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to vitamin D response element binding ISO
Inferred from Sequence Orthology
more info
 
zinc ion binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
angiogenesis involved in coronary vascular morphogenesis TAS
Traceable Author Statement
more info
PubMed 
camera-type eye development IGI
Inferred from Genetic Interaction
more info
PubMed 
cardiac muscle cell differentiation TAS
Traceable Author Statement
more info
PubMed 
cardiac muscle cell proliferation IGI
Inferred from Genetic Interaction
more info
PubMed 
cardiac muscle cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cardiac muscle cell proliferation TAS
Traceable Author Statement
more info
PubMed 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
embryo implantation IGI
Inferred from Genetic Interaction
more info
PubMed 
heart development IMP
Inferred from Mutant Phenotype
more info
PubMed 
heart development TAS
Traceable Author Statement
more info
PubMed 
heart morphogenesis TAS
Traceable Author Statement
more info
PubMed 
in utero embryonic development IGI
Inferred from Genetic Interaction
more info
PubMed 
maternal placenta development IGI
Inferred from Genetic Interaction
more info
PubMed 
mesenchyme development TAS
Traceable Author Statement
more info
PubMed 
modulation by virus of host morphology or physiology ISO
Inferred from Sequence Orthology
more info
 
negative regulation of cell proliferation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of gene expression TAS
Traceable Author Statement
more info
PubMed 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
peroxisome proliferator activated receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
placenta development IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of apoptotic process ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription, DNA-templated TAS
Traceable Author Statement
more info
PubMed 
positive regulation of translational initiation by iron IGI
Inferred from Genetic Interaction
more info
PubMed 
protein homotetramerization ISO
Inferred from Sequence Orthology
more info
 
regulation of branching involved in prostate gland morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of myelination ISO
Inferred from Sequence Orthology
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
response to glucocorticoid ISO
Inferred from Sequence Orthology
more info
 
response to retinoic acid IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to retinoic acid ISO
Inferred from Sequence Orthology
more info
 
retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retinoic acid receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
retinoic acid receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
retinoic acid receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
ventricular cardiac muscle cell differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
ventricular cardiac muscle cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
ventricular cardiac muscle tissue morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
visceral serous pericardium development TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II transcription factor complex ISO
Inferred from Sequence Orthology
more info
 
axon ISO
Inferred from Sequence Orthology
more info
 
nuclear chromatin ISO
Inferred from Sequence Orthology
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
protein-containing complex ISO
Inferred from Sequence Orthology
more info
 
receptor complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
retinoic acid receptor RXR-alpha
Names
RXR alpha 1
nuclear receptor subfamily 2 group B member 1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001290481.1NP_001277410.1  retinoic acid receptor RXR-alpha isoform 2

    See identical proteins and their annotated locations for NP_001277410.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon and it thus differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 3 encode isoform 2.
    Source sequence(s)
    AI647710, AK029121, BC138800
    Consensus CDS
    CCDS71011.1
    UniProtKB/TrEMBL
    A2AJP1, Q6LC96
    Related
    ENSMUSP00000097822.2, ENSMUST00000100251.8
    Conserved Domains (3) summary
    cd06943
    Location:206417
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:110186
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:1103
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
  2. NM_001290482.1NP_001277411.1  retinoic acid receptor RXR-alpha isoform 2

    See identical proteins and their annotated locations for NP_001277411.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon and it thus differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 3 encode isoform 2.
    Source sequence(s)
    AK029121, AL772166, BC138800
    Consensus CDS
    CCDS71011.1
    UniProtKB/TrEMBL
    A2AJP1, Q6LC96
    Related
    ENSMUSP00000109567.1, ENSMUST00000113934.1
    Conserved Domains (3) summary
    cd06943
    Location:206417
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:110186
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:1103
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
  3. NM_011305.3NP_035435.1  retinoic acid receptor RXR-alpha isoform 1

    See identical proteins and their annotated locations for NP_035435.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK029121, AK144675, X66223
    Consensus CDS
    CCDS15830.1
    UniProtKB/Swiss-Prot
    P28700
    UniProtKB/TrEMBL
    A2AJP1, Q3UMU4
    Related
    ENSMUSP00000076491.5, ENSMUST00000077257.11
    Conserved Domains (3) summary
    cd06943
    Location:234445
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:138214
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:18131
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 108 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm38.p6 C57BL/6J

Genomic

  1. NC_000068.7 Reference GRCm38.p6 C57BL/6J

    Range
    27676445..27763319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006497805.1XP_006497868.1  retinoic acid receptor RXR-alpha isoform X1

    See identical proteins and their annotated locations for XP_006497868.1

    UniProtKB/TrEMBL
    Q6LC96
    Conserved Domains (3) summary
    cd06943
    Location:206417
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:110186
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:1103
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
  2. XM_030248867.1XP_030104727.1  retinoic acid receptor RXR-alpha isoform X1

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