Irx4 (iroquois homeobox 4) - Rat Genome Database

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Gene: Irx4 (iroquois homeobox 4) Rattus norvegicus
Analyze
Symbol: Irx4
Name: iroquois homeobox 4
RGD ID: 1309309
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in establishment of animal organ orientation and negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human IRX4 (iroquois homeobox 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,7-dihydropurine-6-thione.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Iroquois related homeobox 4; Iroquois related homeobox 4 (Drosophila) ; iroquois-class homeodomain protein IRX-4; LOC306655
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8131,859,101 - 31,868,089 (-)NCBIGRCr8
mRatBN7.2130,030,561 - 30,039,549 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl130,030,561 - 30,039,549 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx129,832,663 - 29,841,651 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0135,831,585 - 35,840,573 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0130,031,431 - 30,040,421 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0132,634,774 - 32,645,151 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl132,634,796 - 32,643,771 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0134,059,592 - 34,069,967 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.417106,225 - 116,183 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.117106,237 - 115,891 (-)NCBI
Celera128,670,547 - 28,679,535 (-)NCBICelera
Cytogenetic Map1p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA)

References

References - curated
# Reference Title Reference Citation
1. Cardiomyopathy in Irx4-deficient mice is preceded by abnormal ventricular gene expression. Bruneau BG, etal., Mol Cell Biol. 2001 Mar;21(5):1730-6.
2. Chamber formation and morphogenesis in the developing mammalian heart. Christoffels VM, etal., Dev Biol. 2000 Jul 15;223(2):266-78.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Interaction between transcription factors Iroquois proteins 4 and 5 controls cardiac potassium channel Kv4.2 gene transcription. He W, etal., Cardiovasc Res. 2009 Jan 1;81(1):64-71. doi: 10.1093/cvr/cvn259. Epub 2008 Sep 24.
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Irx4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8131,859,101 - 31,868,089 (-)NCBIGRCr8
mRatBN7.2130,030,561 - 30,039,549 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl130,030,561 - 30,039,549 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx129,832,663 - 29,841,651 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0135,831,585 - 35,840,573 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0130,031,431 - 30,040,421 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0132,634,774 - 32,645,151 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl132,634,796 - 32,643,771 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0134,059,592 - 34,069,967 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.417106,225 - 116,183 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.117106,237 - 115,891 (-)NCBI
Celera128,670,547 - 28,679,535 (-)NCBICelera
Cytogenetic Map1p11NCBI
IRX4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3851,877,413 - 1,887,179 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl51,877,413 - 1,887,236 (-)EnsemblGRCh38hg38GRCh38
GRCh3751,877,527 - 1,887,293 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3651,930,549 - 1,935,880 (-)NCBINCBI36Build 36hg18NCBI36
Build 3451,930,548 - 1,935,880NCBI
Celera51,914,716 - 1,920,055 (-)NCBICelera
Cytogenetic Map5p15.33NCBI
HuRef51,859,971 - 1,869,709 (-)NCBIHuRef
CHM1_151,877,411 - 1,887,153 (-)NCBICHM1_1
T2T-CHM13v2.051,794,071 - 1,803,829 (-)NCBIT2T-CHM13v2.0
Irx4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391373,407,708 - 73,417,741 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1373,408,598 - 73,417,727 (+)EnsemblGRCm39 Ensembl
GRCm381373,259,589 - 73,269,622 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1373,260,479 - 73,269,608 (+)EnsemblGRCm38mm10GRCm38
MGSCv371373,397,945 - 73,407,068 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361373,726,801 - 73,735,598 (+)NCBIMGSCv36mm8
Celera1375,588,186 - 75,597,409 (+)NCBICelera
Cytogenetic Map13C1NCBI
cM Map1339.64NCBI
Irx4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955504937,621 - 940,787 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955504937,152 - 940,842 (-)NCBIChiLan1.0ChiLan1.0
IRX4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v242,149,654 - 2,159,181 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15303,263 - 312,790 (-)NCBINHGRI_mPanPan1
PanPan1.1 Ensembl51,929,977 - 1,939,622 (-)Ensemblpanpan1.1panPan2
IRX4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13410,926,042 - 10,929,142 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3410,923,097 - 10,929,164 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3415,436,562 - 15,441,344 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03410,827,001 - 10,831,785 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3410,825,113 - 10,831,773 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13410,878,209 - 10,882,991 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03410,857,416 - 10,862,195 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03411,068,071 - 11,072,857 (+)NCBIUU_Cfam_GSD_1.0
Irx4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213243,929,469 - 243,932,853 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493681590,942 - 94,147 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493681590,707 - 94,138 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IRX4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1678,937,566 - 78,945,269 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11678,940,033 - 78,944,855 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21685,558,917 - 85,563,495 (+)NCBISscrofa10.2Sscrofa10.2susScr3
IRX4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.141,712,382 - 1,723,284 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl41,718,737 - 1,723,403 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606427,033,339 - 27,043,099 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Irx4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624751913,691 - 916,842 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624751913,127 - 916,583 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Irx4
39 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:280
Count of miRNA genes:176
Interacting mature miRNAs:200
Transcripts:ENSRNOT00000016975
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)11148148232355910Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11543162149361612Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11543162149361612Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11620621049268520Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)12076315844095856Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12234064749361612Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)12234064749361612Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat

Markers in Region
PMC310936P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2130,034,375 - 30,034,480 (+)MAPPERmRatBN7.2
Rnor_6.0132,638,598 - 32,638,702NCBIRnor6.0
Rnor_5.0134,063,510 - 34,063,614UniSTSRnor5.0
RGSC_v3.417111,010 - 111,114UniSTSRGSC3.4
Celera128,674,365 - 28,674,469UniSTS
Cytogenetic Map17p14UniSTS
BE101276  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2130,034,593 - 30,034,768 (+)MAPPERmRatBN7.2
Rnor_6.0132,638,816 - 32,638,990NCBIRnor6.0
Rnor_5.0134,063,728 - 34,063,902UniSTSRnor5.0
RGSC_v3.417111,228 - 111,402UniSTSRGSC3.4
Celera128,674,583 - 28,674,757UniSTS
RH 3.4 Map1358.82UniSTS
Cytogenetic Map17p14UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 33
Low 10 8 2 6 2 25 4
Below cutoff 3 27 24 9 24 3 4 25 22 22 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016975   ⟹   ENSRNOP00000016975
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl130,030,561 - 30,039,549 (-)Ensembl
Rnor_6.0 Ensembl132,634,796 - 32,643,771 (-)Ensembl
RefSeq Acc Id: NM_001107330   ⟹   NP_001100800
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8131,859,101 - 31,868,089 (-)NCBI
mRatBN7.2130,030,561 - 30,039,549 (-)NCBI
Rnor_6.0132,634,796 - 32,643,771 (-)NCBI
Rnor_5.0134,059,592 - 34,069,967 (-)NCBI
RGSC_v3.417106,225 - 116,183 (-)RGD
Celera128,670,547 - 28,679,535 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100800 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87645 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016975
  ENSRNOP00000016975.4
Reference Protein Sequences
RefSeq Acc Id: NP_001100800   ⟸   NM_001107330
- UniProtKB: D3ZRI4 (UniProtKB/TrEMBL),   A6JUY4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016975   ⟸   ENSRNOT00000016975
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRI4-F1-model_v2 AlphaFold D3ZRI4 1-515 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309309 AgrOrtholog
BioCyc Gene G2FUF-61913 BioCyc
Ensembl Genes ENSRNOG00000012720 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016975 ENTREZGENE
  ENSRNOT00000016975.5 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_KN_domain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Iroquois_homeo UniProtKB/TrEMBL
KEGG Report rno:306655 UniProtKB/TrEMBL
NCBI Gene 306655 ENTREZGENE
PANTHER IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX UniProtKB/TrEMBL
  IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-4 UniProtKB/TrEMBL
Pfam Homeobox_KN UniProtKB/TrEMBL
PhenoGen Irx4 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012720 RatGTEx
SMART HOX UniProtKB/TrEMBL
  IRO UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6JUY4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZRI4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-26 Irx4  iroquois homeobox 4  Irx4  Iroquois related homeobox 4 (Drosophila)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Irx4  Iroquois related homeobox 4 (Drosophila)   Irx4_predicted  Iroquois related homeobox 4 (Drosophila) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Irx4_predicted  Iroquois related homeobox 4 (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED