Rora MGI Mouse Gene Detail - MGI:104661 - RAR-related orphan receptor alpha

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Rora Gene Detail

Symbol

Rora
Name

RAR-related orphan receptor alpha
Synonyms

9530021D13Rik, Nr1f1, tmgc26

Feature Type

protein coding gene
IDs

MGI:104661
NCBI Gene: 19883
Alliance

gene page
Transcription Start Sites

30 TSS

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Sequence Map

Chr9:68561068-69295528 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 9, 37.45 cM
Mapping Data

24 experiments

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SNPs within 2kb

19062 from dbSNP Build 142
Strain Annotations

18
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_104661	protein coding gene	Chr9:68560627-69295528 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0034990	protein coding gene	Chr9:68595201-69379315 (+)
A/J	MGP_AJ_G0034970	protein coding gene	Chr9:66249690-66995388 (+)
AKR/J	MGP_AKRJ_G0034900	protein coding gene	Chr9:67823909-68582738 (+)
BALB/cJ	MGP_BALBcJ_G0034963	protein coding gene	Chr9:65979406-66723424 (+)
C3H/HeJ	MGP_C3HHeJ_G0034672	protein coding gene	Chr9:68323731-69091180 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0035482	protein coding gene	Chr9:70459613-71234723 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032393	protein coding gene	Chr9:65831158-66564788 (+)
CAST/EiJ	MGP_CASTEiJ_G0033994	protein coding gene	Chr9:68571843-69340363 (+)
CBA/J	MGP_CBAJ_G0034644	protein coding gene	Chr9:72921221-73738132 (+)
DBA/2J	MGP_DBA2J_G0034803	protein coding gene	Chr9:66009842-66750277 (+)
FVB/NJ	MGP_FVBNJ_G0034745	protein coding gene	Chr9:65314946-66065714 (+)
LP/J	MGP_LPJ_G0034885	protein coding gene	Chr9:68869348-69643360 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0034787	protein coding gene	Chr9:74068467-74851367 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0035504	protein coding gene	Chr9:67953791-68721493 (+)
PWK/PhJ	MGP_PWKPhJ_G0033698	protein coding gene	Chr9:66204344-66962075 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0033531	protein coding gene	Chr9:68237637-69018505 (+)
WSB/EiJ	MGP_WSBEiJ_G0034106	protein coding gene	Chr9:67845286-68613330 (+)

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Human Ortholog

RORA, RAR related orphan receptor A

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

RORA, RAR related orphan receptor A
Synonyms

IDDECA, NR1F1, ROR1, ROR2, ROR3, RORa1, RORalpha, RZRA, RZR-ALPHA
Links

HGNC:10258

NCBI Gene ID: 6095

neXtProt AC: NX_P35398

UniProt: P35398
Chr Location

15q22.2; chr15:60488284-61229302 (-) GRCh38

MGI Vertebrate Homology

Rora stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: RORA
Gene Tree

Rora

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Phenotype Summary

107 phenotypes from 6 alleles in 9 genetic backgrounds
241 phenotype references

Phenotype Overview

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

28
Chemically induced (ENU)

2
Chemically induced (other)

1
Endonuclease-mediated

8
Gene trapped

3
Spontaneous

1
Targeted

12
Transgenic

1
Genomic Mutations

1 involving Rora
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

43 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygotes for null mutations exhibit ataxia, cerebellar dysgenesis, impaired Purkinje and granule cell development, olfactory defects, hypoalphalipoproteinemia, and death around 4 weeks. Heterozygotes show slow Purkinje cell dedritic atrophy and loss.

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All GO Annotations

84
GO References

28

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

1561
Tissues

409
cDNA Data

29
Literature Summary

78

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase rora

ZFIN roraa, rorab

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All Sequences

81
RefSeq

27
UniProt

5
CCDS

CCDS23314.1, CCDS72268.1

Ensembl

ENSMUSG00000032238 (Evidence)
NCBI Gene

19883

Representative Sequences				Length	Strain/Species	Flank
	genomic	ENSMUSG00000032238	Ensembl Gene Model \| MGI Sequence Detail	734461	C57BL/6J	± kb
	transcript	ENSMUST00000034766	Ensembl \| MGI Sequence Detail	10878	Not Applicable
	polypeptide	ENSMUSP00000034766	Ensembl \| MGI Sequence Detail	523	Not Applicable

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UniProt

5 Sequences
Protein Ontology

PR:000014163 nuclear receptor ROR-alpha

(term hierarchy)
InterPro Domains

IPR001723 Nuclear hormone receptor

IPR000536 Nuclear hormone receptor, ligand-binding domain

IPR035500 Nuclear hormone receptor-like domain superfamily

IPR003079 Nuclear receptor ROR

IPR044101 Retinoid-related orphan receptors, DNA-binding domain

IPR013088 Zinc finger, NHR/GATA-type

IPR001628 Zinc finger, nuclear hormone receptor-type

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All nucleic 59

Genomic 11

cDNA 30

Primer pair 9

Other 9

Microarray probesets 11

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MGD-MRK-14383, MGD-MRK-26101, MGI:2442931, MGI:2670426, MGI:3054678

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Summaries

All 392

Developmental Gene Expression 78

Gene Ontology 28

Phenotypes 241
Earliest

J:13140 SIDMAN RL, et al., Staggerer, a new mutation in the mouse affecting the cerebellum. Science. 1962 Aug 24;137:610-2
Latest

J:358465 Kabil A, et al., Microbial intestinal dysbiosis drives long-term allergic susceptibility by sculpting an ILC2-B1 cell-innate IgE axis. J Allergy Clin Immunol. 2024 Nov;154(5):1260-1276.e9

TSS for Rora:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr85820	Chr9:68560908-68560921 (+)	-153 bp
Tssr85821	Chr9:68560997-68561013 (+)	-63 bp
Tssr85822	Chr9:68561024-68561039 (+)	-36 bp
Tssr85823	Chr9:68561043-68561067 (+)	-13 bp
Tssr85824	Chr9:68625018-68625023 (+)	63,953 bp
Tssr85825	Chr9:68635550-68635551 (+)	74,483 bp
Tssr85826	Chr9:68644303-68644308 (+)	83,238 bp
Tssr85828	Chr9:68732059-68732074 (+)	170,999 bp
Tssr85829	Chr9:68790130-68790131 (+)	229,063 bp
Tssr85831	Chr9:68873998-68874025 (+)	312,944 bp
Tssr85832	Chr9:68876410-68876423 (+)	315,349 bp
Tssr85833	Chr9:68876425-68876442 (+)	315,366 bp
Tssr85834	Chr9:68877665-68877685 (+)	316,607 bp
Tssr85835	Chr9:69001860-69001865 (+)	440,795 bp
Tssr85836	Chr9:69072972-69072992 (+)	511,914 bp
Tssr85837	Chr9:69134138-69134142 (+)	573,072 bp
Tssr85838	Chr9:69146405-69146408 (+)	585,339 bp
Tssr85839	Chr9:69195661-69195686 (+)	634,606 bp
Tssr85840	Chr9:69197123-69197131 (+)	636,059 bp
Tssr85841	Chr9:69197147-69197177 (+)	636,094 bp
Tssr85842	Chr9:69197184-69197189 (+)	636,119 bp
Tssr85843	Chr9:69197191-69197219 (+)	636,137 bp
Tssr85844	Chr9:69201947-69201960 (+)	640,886 bp
Tssr85845	Chr9:69207813-69207822 (+)	646,750 bp
Tssr85846	Chr9:69221407-69221411 (+)	660,341 bp
Tssr85847	Chr9:69222063-69222088 (+)	661,008 bp
Tssr85848	Chr9:69247507-69247517 (+)	686,444 bp
Tssr85849	Chr9:69248064-69248084 (+)	687,006 bp
Tssr85850	Chr9:69271135-69271149 (+)	710,074 bp
Tssr85851	Chr9:69271651-69271675 (+)	710,595 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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