Gene: Rarb (retinoic acid receptor beta) Ictidomys tridecemlineatus

Analyze

Symbol:

Rarb

Name:

retinoic acid receptor beta

RGD ID:

12547687

Description:

ENCODES a protein that exhibits heterocyclic compound binding (ortholog); nuclear retinoid X receptor binding (ortholog); protein-containing complex binding (ortholog); INVOLVED IN bone development (ortholog); embryonic eye morphogenesis (ortholog); embryonic hindlimb morphogenesis (ortholog); PARTICIPATES IN retinoic acid signaling pathway; ASSOCIATED WITH acute myeloid leukemia (ortholog); adenocarcinoma (ortholog); Anophthalmia (ortholog); FOUND IN cytoplasm (ortholog)

Type:

protein-coding

RefSeq Status:

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

mIctTri1.hap1 - mIctTri1.hap1 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mIctTri1.hap1	2	34,586,407 - 35,293,857 (-)	NCBI		mIctTri1.hap1
HiC_Itri_2	NW_024405118	183,488,653 - 184,007,944 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936473	16,983,600 - 17,148,885 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936473	16,983,829 - 17,146,517 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

acute myeloid leukemia (ISO)

adenocarcinoma (ISO)

Anophthalmia (ISO)

asbestos-related lung carcinoma (ISO)

autism spectrum disorder (ISO)

autistic disorder (ISO)

autosomal dominant intellectual developmental disorder 48 (ISO)

Breast Cancer, Familial (ISO)

Breast Neoplasms (ISO)

cervical cancer (ISO)

coloboma (ISO)

diaphragmatic eventration (ISO)

dystonia (ISO)

endometriosis (ISO)

esophageal cancer (ISO)

genetic disease (ISO)

Head and Neck Neoplasms (ISO)

hypoglycemia (ISO)

lung adenocarcinoma (ISO)

Lung Neoplasms (ISO)

lung non-small cell carcinoma (ISO)

lung small cell carcinoma (ISO)

microphthalmia (ISO)

Muscle Spasticity (ISO)

ovarian serous cystadenocarcinoma (ISO)

Pulmonary Arterial Hypertension (ISO)

sarcoma (ISO)

sciatic neuropathy (ISO)

squamous cell carcinoma (ISO)

Stomach Neoplasms (ISO)

syndromic microphthalmia 12 (ISO)

Uterine Cervical Neoplasms (ISO)

uterine corpus endometrial carcinoma (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

bone development (ISO)

camera-type eye development (IEA)

cellular response to corticotropin-releasing hormone stimulus (IEA)

DNA-templated transcription (IEA)

embryonic digestive tract development (IEA)

embryonic eye morphogenesis (ISO)

embryonic hindlimb morphogenesis (ISO)

glandular epithelial cell development (IEA,ISO)

growth plate cartilage development (IEA,ISO)

multicellular organism growth (IEA,ISO)

negative regulation of apoptotic process (IEA,ISO)

negative regulation of cartilage development (IEA,ISO)

negative regulation of cell population proliferation (ISO)

negative regulation of chondrocyte differentiation (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

neural precursor cell proliferation (ISO)

neurogenesis (ISO)

outflow tract septum morphogenesis (IEA,ISO)

positive regulation of apoptotic process (ISO)

positive regulation of cell population proliferation (ISO)

positive regulation of programmed cell death (ISO)

positive regulation of transcription by RNA polymerase II (IEA,ISO)

regulation of DNA-templated transcription (IEA)

regulation of myelination (ISO)

regulation of transcription by RNA polymerase II (IEA)

retina development in camera-type eye (ISO)

retinal pigment epithelium development (ISO)

retinoic acid receptor signaling pathway (IEA)

striatum development (ISO)

ureteric bud development (IEA,ISO)

ventricular cardiac muscle cell differentiation (IEA,ISO)

Cellular Component

cytoplasm (ISO)

nucleoplasm (IEA)

nucleus (IEA)

transcription regulator complex (IEA)

Molecular Function

DNA binding (IEA)

DNA-binding transcription factor activity (IEA)

DNA-binding transcription factor activity, RNA polymerase II-specific (IEA)

heterocyclic compound binding (ISO)

nuclear glucocorticoid receptor binding (IEA)

nuclear receptor activity (IEA)

nuclear retinoid X receptor binding (ISO)

protein binding (ISO)

protein-containing complex binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IEA)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (ISO)

sequence-specific DNA binding (IEA)

sequence-specific double-stranded DNA binding (IEA)

zinc ion binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

retinoic acid signaling pathway (ISO)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Rarb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mIctTri1.hap1	2	34,586,407 - 35,293,857 (-)	NCBI		mIctTri1.hap1
HiC_Itri_2	NW_024405118	183,488,653 - 184,007,944 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936473	16,983,600 - 17,148,885 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936473	16,983,829 - 17,146,517 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RARB
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	24,829,321 - 25,597,932 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	24,687,887 - 25,597,932 (+)	Ensembl		GRCh38.p14 Ensembl	hg38	GRCh38
GRCh37	3	24,870,812 - 25,639,423 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	25,444,758 - 25,614,424 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	3	25,444,757 - 25,614,424	NCBI
Celera	3	25,406,007 - 25,576,301 (+)	NCBI		Celera
Cytogenetic Map	3	p24.2	NCBI
HuRef	3	25,415,219 - 25,584,899 (+)	NCBI		HuRef
CHM1_1	3	25,419,771 - 25,589,413 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	3	24,833,434 - 25,600,779 (+)	NCBI		T2T-CHM13v2.0

Rarb
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	14	5,387,365 - 6,038,924 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	14	5,650,540 - 6,041,094 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	14	16,430,839 - 17,082,331 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	14	16,430,839 - 16,819,156 (-)	Ensembl		GRCm38.p6 Ensembl	mm10	GRCm38
MGSCv37	14	17,263,353 - 17,407,724 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	14	15,224,106 - 15,368,477 (-)	NCBI		MGSCv36	mm8
Celera	14	12,125,158 - 12,276,529 (-)	NCBI		Celera
Cytogenetic Map	14	A1	NCBI
cM Map	14	7.08	NCBI

Rarb
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	15	10,837,252 - 11,482,037 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	15	11,131,358 - 11,482,040 (+)	Ensembl				GRCr8
mRatBN7.2	15	8,700,533 - 9,051,288 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	8,406,492 - 9,051,288 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	15	11,048,162 - 11,193,786 (+)	NCBI	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	15	11,960,913 - 12,106,574 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	15	10,261,418 - 10,407,054 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd	15	10,325,422 - 10,471,060 (+)	NCBI
Lyon_Normotensive	15	10,245,339 - 10,391,418 (+)	NCBI
Lyon_Hypertensive	15	10,328,001 - 10,474,079 (+)	NCBI
F344_StmMcwi	15	10,935,294 - 11,080,937 (+)	NCBI
Rnor_6.0	15	9,915,223 - 10,262,599 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	10,120,206 - 10,262,599 (+)	Ensembl		Rnor_6.0 Ensembl	rn6	Rnor6.0
Rnor_5.0	15	13,963,567 - 14,307,996 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
Celera	15	8,949,068 - 9,094,754 (+)	NCBI		Celera
Cytogenetic Map	15	p16	NCBI

Rarb
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955430	17,295,174 - 17,460,045 (+)	Ensembl		ChiLan1.0 Ensembl
ChiLan1.0	NW_004955430	17,067,536 - 17,457,558 (+)	NCBI	ChiLan1.0	ChiLan1.0

RARB
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	2	24,788,545 - 25,558,542 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	3	24,793,311 - 25,563,309 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	3	24,729,220 - 25,499,187 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	3	25,660,850 - 25,830,372 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	3	25,660,922 - 25,833,297 (+)	Ensembl		PanPan1.1 Ensembl	panPan2	panpan1.1

RARB
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	23	18,207,253 - 18,931,128 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	23	18,207,760 - 18,482,652 (-)	Ensembl		CanFam3.1 Ensembl	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	23	18,204,235 - 18,714,201 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	23	18,509,719 - 19,020,664 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	23	18,509,722 - 18,682,067 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	23	18,328,357 - 18,839,472 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	23	18,431,214 - 18,948,405 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	23	18,545,126 - 19,056,015 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

RARB
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	12,336,972 - 12,507,680 (+)	Ensembl		Sscrofa11.1 Ensembl	susScr11	Sscrofa11.1
Sscrofa11.1	13	12,336,387 - 12,507,688 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	13,948,616 - 14,119,377 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RARB
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mChlSab1.0.hap1	15	70,218,508 - 70,987,958 (+)	NCBI		mChlSab1.0.hap1
Vero_WHO_p1.0	NW_023666041	42,594,825 - 43,404,888 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0
ChlSab1.1	15	69,851,447 - 70,266,215 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	15	70,096,117 - 70,264,905 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM

Rarb
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624788	2,738,341 - 3,493,140 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2
HetGla_female_1.0 Ensembl	NW_004624788	3,257,697 - 3,493,132 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
Naked mole-rat maternal Ensembl	9	33,876,604 - 34,284,764 (+)	Ensembl

Rarb
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	12	85,777,108 - 86,110,751 (-)	NCBI	Rrattus_CSIRO_v1	Rrattus_CSIRO_v1

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005317270	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040289866	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040289868	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_078038286	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000177	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JBPVTT010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000007989 ⟹ ENSSTOP00000007150

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936473	16,983,600 - 17,148,885 (+)	Ensembl

RefSeq Acc Id:

XM_078038286 ⟹ XP_077894412

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
mIctTri1.hap1	2	34,586,407 - 35,293,857 (-)	NCBI

Protein Sequences


Protein RefSeqs	XP_077894412	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000007150.3
GenBank Protein	KAG3279503	(Get FASTA)	NCBI Sequence Viewer

Ensembl Acc Id:

ENSSTOP00000007150 ⟸ ENSSTOT00000007989

RefSeq Acc Id:

XP_077894412 ⟸ XM_078038286

Protein Domains

NR LBD Nuclear receptor

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000007994	Ensembl, UniProtKB/TrEMBL
	ENSSTOG00015007672	ENTREZGENE
Ensembl Transcript	ENSSTOT00000007989.3	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
KEGG Report	iti:101973763	UniProtKB/TrEMBL
NCBI Gene	Rarb	ENTREZGENE
PANTHER	NUCLEAR HORMONE RECEPTOR	UniProtKB/TrEMBL
	RETINOIC ACID RECEPTOR BETA	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	I3MAT4_ICTTR	UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations