Incidental Mutation 'R5154:Rxra'
ID 396553
Institutional Source Beutler Lab
Gene Symbol Rxra
Ensembl Gene ENSMUSG00000015846
Gene Name retinoid X receptor alpha
Synonyms RXRalpha1, 9530071D11Rik, RXR alpha 1
MMRRC Submission 042736-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5154 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 27566452-27652969 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to C at 27647880 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000133044 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000077257] [ENSMUST00000100251] [ENSMUST00000113934] [ENSMUST00000166775]
AlphaFold P28700
PDB Structure CRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAND-BINDING DOMAINS [X-RAY DIFFRACTION]
Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex with 9-cis Retinoic Acid and a Fragment of the TRAP220 Coactivator [X-RAY DIFFRACTION]
Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha heterodimer ligand binding domains [X-RAY DIFFRACTION]
Predicted Effect probably null
Transcript: ENSMUST00000077257
SMART Domains Protein: ENSMUSP00000076491
Gene: ENSMUSG00000015846

DomainStartEndE-ValueType
Pfam:Nuc_recep-AF1 18 132 4.2e-42 PFAM
ZnF_C4 137 208 1.76e-40 SMART
Blast:HOLI 233 265 1e-8 BLAST
HOLI 275 434 1.62e-53 SMART
Predicted Effect probably null
Transcript: ENSMUST00000100251
SMART Domains Protein: ENSMUSP00000097822
Gene: ENSMUSG00000015846

DomainStartEndE-ValueType
Pfam:Nuc_recep-AF1 1 104 1.8e-38 PFAM
ZnF_C4 109 180 1.76e-40 SMART
Blast:HOLI 205 237 1e-8 BLAST
HOLI 247 406 1.62e-53 SMART
Predicted Effect probably null
Transcript: ENSMUST00000113934
SMART Domains Protein: ENSMUSP00000109567
Gene: ENSMUSG00000015846

DomainStartEndE-ValueType
Pfam:Nuc_recep-AF1 1 104 1.8e-38 PFAM
ZnF_C4 109 180 1.76e-40 SMART
Blast:HOLI 205 237 1e-8 BLAST
HOLI 247 406 1.62e-53 SMART
Predicted Effect probably null
Transcript: ENSMUST00000166775
SMART Domains Protein: ENSMUSP00000133044
Gene: ENSMUSG00000015846

DomainStartEndE-ValueType
Pfam:Nuc_recep-AF1 17 132 6.5e-41 PFAM
ZnF_C4 137 208 1.76e-40 SMART
Blast:HOLI 233 265 1e-8 BLAST
HOLI 275 434 1.62e-53 SMART
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.2%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Retinoid X receptors (RXRs) and retinoic acid receptors (RARs) are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]
PHENOTYPE: Null embryos have multiple organ defects and die of cardiac failure by E14.5. Gene ablation in liver, prostate, fat or epidermis tissue-specifically affects development, function and/or neoplasia. Hypomorphic mutants develop alopecia, progressively severe dermal cysts and late corneal opacity. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700009N14Rik A C 4: 39,450,938 (GRCm39) H48P probably damaging Het
Angptl7 C T 4: 148,581,882 (GRCm39) R168H probably damaging Het
Ankrd11 A C 8: 123,619,878 (GRCm39) F1325V probably damaging Het
Ankrd13c A G 3: 157,694,297 (GRCm39) D266G possibly damaging Het
Apold1 A T 6: 134,960,636 (GRCm39) H30L possibly damaging Het
Arel1 A G 12: 84,978,547 (GRCm39) F362L probably benign Het
Arhgef4 T A 1: 34,771,455 (GRCm39) M1254K probably benign Het
Arid2 T A 15: 96,299,866 (GRCm39) V1793E probably damaging Het
Bcl7a T C 5: 123,507,422 (GRCm39) S156P probably damaging Het
Cbr3 A G 16: 93,482,027 (GRCm39) I128V probably benign Het
Cct6b G A 11: 82,630,521 (GRCm39) P299L probably damaging Het
Cd180 A T 13: 102,842,282 (GRCm39) N443Y probably damaging Het
Cd80 A G 16: 38,294,342 (GRCm39) K75R probably benign Het
Cdk1 A T 10: 69,176,298 (GRCm39) probably benign Het
Cep192 T A 18: 67,983,755 (GRCm39) F1565I probably damaging Het
Chtf18 T C 17: 25,942,694 (GRCm39) T412A probably damaging Het
Cit T C 5: 116,126,464 (GRCm39) L1590P probably damaging Het
Clcn2 T A 16: 20,522,053 (GRCm39) R845S probably benign Het
Cndp2 C T 18: 84,686,727 (GRCm39) V432I probably benign Het
Cnnm2 A T 19: 46,751,571 (GRCm39) R454W probably benign Het
Cpne8 T G 15: 90,384,121 (GRCm39) I480L probably benign Het
Cr2 A G 1: 194,841,754 (GRCm39) W400R probably damaging Het
Cul5 A G 9: 53,537,167 (GRCm39) L528P probably damaging Het
Dlgap5 C T 14: 47,651,177 (GRCm39) V119M probably damaging Het
Dnah12 T C 14: 26,571,320 (GRCm39) S190P probably benign Het
Dnah3 T A 7: 119,551,642 (GRCm39) K2881N probably damaging Het
Dnmt3a A T 12: 3,946,008 (GRCm39) I288F probably damaging Het
Dse T A 10: 34,029,657 (GRCm39) T478S possibly damaging Het
Edn1 C T 13: 42,458,499 (GRCm39) T104I probably benign Het
Eef2 GCCC GCCCC 10: 81,014,601 (GRCm39) probably null Het
Eprs1 A G 1: 185,145,662 (GRCm39) H1157R probably damaging Het
Fam168b G A 1: 34,857,180 (GRCm39) T179I possibly damaging Het
Fzd5 A G 1: 64,775,131 (GRCm39) V210A probably benign Het
Gm9742 T C 13: 8,085,081 (GRCm39) noncoding transcript Het
Gpc1 G A 1: 92,784,751 (GRCm39) G308D probably damaging Het
Gpr141 C T 13: 19,936,412 (GRCm39) R121K probably benign Het
Greb1l A G 18: 10,458,312 (GRCm39) T30A probably benign Het
Grk3 A T 5: 113,089,583 (GRCm39) I281N probably damaging Het
Hnrnpdl A T 5: 100,184,371 (GRCm39) Y289* probably null Het
Hsf2 T G 10: 57,380,808 (GRCm39) V214G probably benign Het
Igf2bp1 G A 11: 95,854,373 (GRCm39) Q563* probably null Het
Il31ra T A 13: 112,660,531 (GRCm39) D605V possibly damaging Het
Insm2 G A 12: 55,646,982 (GRCm39) C242Y probably damaging Het
Ints3 C T 3: 90,322,868 (GRCm39) V121I probably benign Het
Kcnt2 A T 1: 140,278,994 (GRCm39) L48F possibly damaging Het
Kit G A 5: 75,801,200 (GRCm39) V529M probably damaging Het
Mark2 G A 19: 7,260,439 (GRCm39) P13S probably damaging Het
Mthfsd A G 8: 121,825,479 (GRCm39) V364A probably damaging Het
Mtmr11 C G 3: 96,071,636 (GRCm39) S185R probably benign Het
Myot A G 18: 44,487,281 (GRCm39) I373V probably benign Het
N4bp3 A T 11: 51,536,139 (GRCm39) V231D probably benign Het
Or5t17 T C 2: 86,832,382 (GRCm39) V23A probably benign Het
Or8k39 A T 2: 86,563,121 (GRCm39) Y278* probably null Het
Pdcd6ip A G 9: 113,520,610 (GRCm39) F125L probably damaging Het
Prpf39 A T 12: 65,095,051 (GRCm39) Q124L probably benign Het
Reln A T 5: 22,193,763 (GRCm39) N1398K probably damaging Het
Rhod A T 19: 4,482,122 (GRCm39) D97E probably damaging Het
Slc1a3 T C 15: 8,672,433 (GRCm39) I349V probably benign Het
Slc37a2 A T 9: 37,142,939 (GRCm39) *502R probably null Het
Slc9b1 T C 3: 135,078,940 (GRCm39) I199T probably damaging Het
Spart C T 3: 55,024,750 (GRCm39) P115L probably damaging Het
Tnpo1 A T 13: 99,006,813 (GRCm39) C205S possibly damaging Het
Tubb1 T A 2: 174,298,657 (GRCm39) I113N probably benign Het
Tyrp1 G A 4: 80,768,954 (GRCm39) V483I probably benign Het
Vwde T C 6: 13,215,757 (GRCm39) S100G probably benign Het
Zfhx3 A T 8: 109,527,207 (GRCm39) I1035F probably damaging Het
Zfp618 G T 4: 63,051,446 (GRCm39) K742N probably damaging Het
Zfp873 T C 10: 81,896,025 (GRCm39) V252A possibly damaging Het
Other mutations in Rxra
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01941:Rxra APN 2 27,644,253 (GRCm39) missense probably damaging 1.00
IGL03006:Rxra APN 2 27,649,657 (GRCm39) missense probably damaging 1.00
pinkie UTSW 2 27,642,346 (GRCm39) missense probably damaging 0.98
R0265:Rxra UTSW 2 27,642,442 (GRCm39) missense probably damaging 1.00
R0578:Rxra UTSW 2 27,649,582 (GRCm39) missense probably damaging 1.00
R1555:Rxra UTSW 2 27,638,690 (GRCm39) missense probably benign 0.00
R1775:Rxra UTSW 2 27,646,256 (GRCm39) missense probably damaging 1.00
R3725:Rxra UTSW 2 27,644,289 (GRCm39) missense probably damaging 1.00
R3756:Rxra UTSW 2 27,631,923 (GRCm39) missense probably damaging 1.00
R3804:Rxra UTSW 2 27,646,272 (GRCm39) missense probably damaging 1.00
R3965:Rxra UTSW 2 27,642,318 (GRCm39) splice site probably benign
R4490:Rxra UTSW 2 27,631,207 (GRCm39) missense probably damaging 0.99
R4898:Rxra UTSW 2 27,631,195 (GRCm39) missense probably damaging 1.00
R5651:Rxra UTSW 2 27,627,353 (GRCm39) missense probably benign 0.25
R6880:Rxra UTSW 2 27,638,668 (GRCm39) missense possibly damaging 0.64
R6913:Rxra UTSW 2 27,631,186 (GRCm39) missense probably damaging 1.00
R7404:Rxra UTSW 2 27,631,866 (GRCm39) missense probably damaging 0.99
R8324:Rxra UTSW 2 27,631,195 (GRCm39) missense probably damaging 1.00
R9098:Rxra UTSW 2 27,638,756 (GRCm39) missense possibly damaging 0.50
R9200:Rxra UTSW 2 27,627,496 (GRCm39) missense possibly damaging 0.64
R9356:Rxra UTSW 2 27,649,675 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CTCTGCTATGCTTGCATGTG -3'
(R):5'- ATAGCAAGGACCTACTGTGCAC -3'

Sequencing Primer
(F):5'- CTTGCATGTGGATAGGAGATAGTC -3'
(R):5'- AAGTGGGTAGTCCTCAGAGCTC -3'
Posted On 2016-06-21