Irx3 (iroquois homeobox 3) - Rat Genome Database

Name: Irx3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Irx3 (iroquois homeobox 3) Ictidomys tridecemlineatus

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Symbol:

Irx3

Name:

iroquois homeobox 3

RGD ID:

12461773

Description:

ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription activator activity, RNA polymerase II-specific (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); INVOLVED IN mesoderm development (ortholog); negative regulation of neuron differentiation (ortholog); neuron differentiation (ortholog); ASSOCIATED WITH Chromosome 16q12 Duplication Syndrome (ortholog); Joubert syndrome 1 (ortholog); lung disease (ortholog); FOUND IN axon (inferred); cytoplasm (inferred); nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

iroquois-class homeodomain protein IRX-3

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	IRX3 (iroquois homeobox 3)	NCBI	Ortholog
Mus musculus (house mouse):	Irx3 (Iroquois related homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Irx3 (iroquois homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Irx3 (iroquois homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	IRX3 (iroquois homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	IRX3 (iroquois homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	IRX3 (iroquois homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	IRX3 (iroquois homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Irx3 (iroquois homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

NCBI Annotation Information:

Annotation category: partial on reference assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409349	52,775,883 - 52,778,397 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936475	6,810,666 - 6,813,192 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936475	6,810,678 - 6,813,186 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Chromosome 16q12 Duplication Syndrome (ISO)

Joubert syndrome 1 (ISO)

lung disease (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

atrioventricular bundle cell differentiation (IEA)

cell development (IEA)

energy homeostasis (IEA)

His-Purkinje system cell differentiation (IEA)

mesoderm development (IEA,ISO)

metanephros development (IEA)

negative regulation of neuron differentiation (IEA,ISO)

negative regulation of transcription by RNA polymerase II (IEA)

neuron differentiation (IEA,ISO)

positive regulation of gap junction assembly (IEA)

positive regulation of neuron differentiation (IEA,ISO)

positive regulation of transcription by RNA polymerase II (IEA)

proximal/distal pattern formation involved in nephron development (IEA)

Purkinje myocyte development (IEA)

regulation of cell communication by electrical coupling involved in cardiac conduction (IEA,ISO)

regulation of DNA-templated transcription (IEA)

regulation of transcription by RNA polymerase II (IEA)

specification of loop of Henle identity (IEA)

Cellular Component

axon (IEA)

cytoplasm (IEA)

nucleus (IEA)

Molecular Function

DNA binding (IEA)

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

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

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

protein binding (ISO)

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

sequence-specific double-stranded DNA binding (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Irx3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409349	52,775,883 - 52,778,397 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936475	6,810,666 - 6,813,192 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936475	6,810,678 - 6,813,186 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

IRX3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	16	54,283,304 - 54,286,787 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	16	54,283,304 - 54,286,787 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	16	54,317,216 - 54,320,699 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	16	52,874,713 - 52,877,879 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	16	52,874,712 - 52,877,879	NCBI
Celera	16	38,831,683 - 38,834,849 (-)	NCBI		Celera
Cytogenetic Map	16	q12.2	NCBI
HuRef	16	40,203,767 - 40,206,921 (-)	NCBI		HuRef
CHM1_1	16	55,724,203 - 55,727,369 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	16	60,081,297 - 60,084,780 (-)	NCBI		T2T-CHM13v2.0

Irx3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	92,525,139 - 92,528,282 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	8	92,525,153 - 92,528,695 (-)	Ensembl		GRCm39 Ensembl
GRCm38	8	91,798,511 - 91,801,654 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	91,798,525 - 91,802,067 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	8	94,322,424 - 94,325,273 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	8	94,687,653 - 94,690,502 (-)	NCBI		MGSCv36	mm8
Celera	8	96,103,077 - 96,105,918 (-)	NCBI		Celera
Cytogenetic Map	8	C5	NCBI
cM Map	8	44.55	NCBI

Irx3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	19	31,384,803 - 31,388,241 (+)	NCBI		GRCr8
mRatBN7.2	19	15,211,882 - 15,215,317 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	19	15,211,878 - 15,215,317 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	19	16,902,097 - 16,905,213 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	19	22,096,906 - 22,100,022 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	19	25,042,791 - 25,045,908 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	19	15,838,714 - 15,842,135 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	19	15,838,714 - 15,840,990 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	19	26,917,882 - 26,921,326 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	19	16,345,179 - 16,347,455 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	19	16,349,206 - 16,352,281 (+)	NCBI
Celera	19	15,124,412 - 15,126,688 (+)	NCBI		Celera
Cytogenetic Map	19	p11	NCBI

Irx3
(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_004955433	11,944,890 - 11,948,369 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955433	11,944,890 - 11,948,372 (-)	NCBI	ChiLan1.0	ChiLan1.0

IRX3
(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	18	63,708,015 - 63,712,146 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	16	69,626,818 - 69,630,821 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	16	34,514,107 - 34,517,576 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	16	53,622,028 - 53,627,033 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	16	53,622,409 - 53,624,653 (-)	Ensembl	panpan1.1		panPan2

IRX3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	2	61,555,608 - 61,559,185 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	2	61,555,492 - 61,558,958 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	2	58,190,062 - 58,192,778 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	2	62,094,083 - 62,096,798 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	2	62,094,083 - 62,096,571 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	2	58,923,158 - 58,925,876 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	2	59,949,850 - 59,952,564 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	2	60,825,325 - 60,828,040 (+)	NCBI		UU_Cfam_GSD_1.0

IRX3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	31,046,146 - 31,049,054 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	31,044,919 - 31,049,067 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	28,167,076 - 28,171,233 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

IRX3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	5	40,064,471 - 40,069,630 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	5	40,066,008 - 40,068,505 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666047	36,306,655 - 36,310,144 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Irx3
(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_female_1.0 Ensembl	NW_004624757	2,543,992 - 2,547,464 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624757	2,543,968 - 2,547,452 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

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_013365647	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010004409	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000021638 ⟹ ENSSTOP00000014884

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936475	6,810,666 - 6,813,192 (-)	Ensembl

RefSeq Acc Id:

XM_013365647 ⟹ XP_013221101

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024409349	52,775,883 - 52,778,397 (+)	NCBI
SpeTri2.0	NW_004936475	6,810,678 - 6,813,186 (-)	NCBI

Sequence:

show sequence

GCTGCCGCCGCCGCCGCCGCCCAAGGCTACGGCGCCTTCCTGCCCTACGCCGCGGAGCTGCCCA
TCTTCCCGCAGCTGGGCGCTCAGTATGAGCTGAAGGACAGCCCTGGGGTGCAGCATCCGGCCGC
GGCCGCAGCGTTTCCGCACCCGCACCCCGCTTTCTACCCGTATGGCCAGTACCAGTTTGGGGAC
CCGTCCCGTCCCAAGAACGCCACCCGAGAGAGCACCAGCACGCTCAAGGCCTGGCTCAACGAGC
ACCGCAAGAACCCCTACCCCACCAAGGGCGAGAAGATCATGCTGGCCATCATCACCAAGATGAC
CCTCACCCAGGTGTCCACCTGGTTCGCCAATGCACGCCGGCGTCTCAAGAAGGAGAACAAGATG
ACTTGGGCGCCCCGCAGTCGCACGGATGAAGAGGGCAACGCTTACGGGAGCGAGAGGGAGGAGG
AAGACGAGGAGGAGGACGAGGAAGATGGCAAGCGCGAGCTGGAGCTGGAGGAGGAGGAGCTCGT
GGGGGAGGAGGAGGACACGGGGGGCGAGGGCCTGGCAGACGACGACGAAGACGAGGAGATCGAT
TTGGAGAACTTAGACGGCACGGCTGCCGGGCCTGAGCTGGCCTTGACGGGGACAGCGCGCAGGG
ACGGTGACCTAGGCCTGGGACCCATTTCGGACTCCAAAAATAGCGACTCGGAAGACAGCACCGA
GGGCTTGGAGGAGCGGCCGCTGCCAGTCCTGAGTCTGGCCCCAGCGCCACCGCCAGTGACCGGG
ACTCCGCCCTCTCCGCCCTCGCCTCCCACCGGCCTAGACCCCTGCGCACCAGCACCCGCTCCCT
CCTCGGCCCTGCAGAAGCCCAAAATCTGGTCCCTGGCCGAGACGGCCACGAGCCCGGACAACCC
ACGCCGCTCGCCCCCTGGCACAGGATGTTCTCCTCCTGGGGCAGCGGTCGCACCCCCGGCTCTA
CAGCTTTCTCCCGCAGCAGCCGCCGCCGCCGCCGCCGCGGCTCACAGACTGGTCTCGGCGCCAC
TGGGCAAATTCCCGGCTTGGACCAACCGGCCGTTCCCAGGCCCGCCGCCCGGCCCTCGCCCGCA
CCCTCTCTCCCTGCTCGGTTCGGCCCCTCAGCACCTGCTGGGACTTCCCGGAGCCGCTGGTCAC
CCGGCTGCCGCCACCGCCTACGCTAGACCCACGGAGCCCGAGGGCGGAACAGATCGCTGTAGTG
CCTTGGAAGTGGAGAAAAAGTTACTCAAGACAGCTTTCCAGCCCGTGCCCAGGCGGCCCCAGAA
CCACCTGGATGCGGCTCTGGTCTTATCGGCTCTCTCCTCATCCTAGTTTTTTTCTTTTTTTTTT
TTTAAATACTTTTTAAATCGTTGTAATAATTGTAAAAACAACAACAACAACAAATCGCTCTGTA
TAGTTACAACTTGTAAGCATGTCCGTGTATGAATACCTAAAAAGAAAACTAAACAAAAAAAAAA
GAAAGAAAAAGAAATAAAATCAGTCCCCCTCATCCCTCCCCAAGTCGATTCTGTGCCACCCCAC
ATTAACTGCCATTGTCAGGTTGGTTTGTTCGATTGATTTGGGGAGGGGGGTGGAGTTTCAGTGA
GAATAAGCGTGTCTGACTGTTTTGTATATACAGAAAAATGTACATATGTGTGAACCAAATTGTA
CAAGAAAGTATCTATTTTTGGCTAAATAAATGAGCTGTTGCCACTTTGACTATA

hide sequence

Protein Sequences


Protein RefSeqs	XP_013221101	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000014884.2
GenBank Protein	KAG3257277	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_013221101 ⟸ XM_013365647

- UniProtKB:

I3MRY9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MLAIITKMTLTQVSTWFANARRRLKKENKMTWAPRSRTDEEGNAYGSEREEEDEEEDEEDGKRE
LELEEEELVGEEEDTGGEGLADDDEDEEIDLENLDGTAAGPELALTGTARRDGDLGLGPISDSK
NSDSEDSTEGLEERPLPVLSLAPAPPPVTGTPPSPPSPPTGLDPCAPAPAPSSALQKPKIWSLA
ETATSPDNPRRSPPGTGCSPPGAAVAPPALQLSPAAAAAAAAAAHRLVSAPLGKFPAWTNRPFP
GPPPGPRPHPLSLLGSAPQHLLGLPGAAGHPAAATAYARPTEPEGGTDRCSALEVEKKLLKTAF
QPVPRRPQNHLDAALVLSALSSS

hide sequence

Ensembl Acc Id:

ENSSTOP00000014884 ⟸ ENSSTOT00000021638

Protein Domains

Homeobox

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000019902	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000021638.2	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
	Homeobox_KN_domain	UniProtKB/TrEMBL
	Iroquois_homeo	UniProtKB/TrEMBL
NCBI Gene	Irx3	ENTREZGENE
PANTHER	IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX	UniProtKB/TrEMBL
	IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-3	UniProtKB/TrEMBL
Pfam	Homeobox_KN	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
	IRO	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	I3MRY9	ENTREZGENE, 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)

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