Irx1 (iroquois homeobox 1) - Rat Genome Database

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Gene: Irx1 (iroquois homeobox 1) Rattus norvegicus
Analyze
Symbol: Irx1
Name: iroquois homeobox 1
RGD ID: 1309060
Description: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of gene expression. Predicted to be active in nucleus. Used to study congestive heart failure. Human ortholog(s) of this gene implicated in congenital heart disease. Orthologous to human IRX1 (iroquois homeobox 1); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Iroquois related homeobox 1; Iroquois related homeobox 1 (Drosophila); iroquois-class homeodomain protein IRX-1; LOC306659
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8133,123,122 - 33,128,951 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl133,123,122 - 33,128,951 (+)EnsemblGRCr8
mRatBN7.2131,294,615 - 31,300,444 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl131,294,615 - 31,300,444 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx131,103,832 - 31,109,675 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0137,102,756 - 37,108,597 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0131,302,605 - 31,308,446 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0133,910,912 - 33,916,741 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl133,910,912 - 33,916,741 (+)Ensemblrn6Rnor6.0
Rnor_5.0135,319,895 - 35,325,724 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4171,390,894 - 1,396,724 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera129,929,767 - 29,935,596 (+)NCBICelera
RGSC_v3.1171,391,104 - 1,396,424 (+)NCBI
Cytogenetic Map1p11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cellular_component  (ND)
nucleus  (IBA,IEA)

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Exome sequencing reveals novel IRXI mutation in congenital heart disease. Guo C, etal., Mol Med Rep. 2017 May;15(5):3193-3197. doi: 10.3892/mmr.2017.6410. Epub 2017 Mar 30.
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
6. IRX1 hypermethylation promotes heart failure by inhibiting CXCL14 expression. Zeng L, etal., Cell Cycle. 2019 Dec;18(23):3251-3262. doi: 10.1080/15384101.2019.1673099. Epub 2019 Oct 22.
Additional References at PubMed
PMID:17875669   PMID:20440264   PMID:28473536  


Genomics

Comparative Map Data
Irx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8133,123,122 - 33,128,951 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl133,123,122 - 33,128,951 (+)EnsemblGRCr8
mRatBN7.2131,294,615 - 31,300,444 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl131,294,615 - 31,300,444 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx131,103,832 - 31,109,675 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0137,102,756 - 37,108,597 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0131,302,605 - 31,308,446 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0133,910,912 - 33,916,741 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl133,910,912 - 33,916,741 (+)Ensemblrn6Rnor6.0
Rnor_5.0135,319,895 - 35,325,724 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4171,390,894 - 1,396,724 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera129,929,767 - 29,935,596 (+)NCBICelera
RGSC_v3.1171,391,104 - 1,396,424 (+)NCBI
Cytogenetic Map1p11NCBI
IRX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3853,595,832 - 3,601,403 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl53,595,832 - 3,601,403 (+)Ensemblhg38GRCh38
GRCh3753,595,946 - 3,601,517 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3653,649,168 - 3,654,517 (+)NCBIBuild 36Build 36hg18NCBI36
Build 3453,649,167 - 3,654,517NCBI
Celera53,626,588 - 3,631,937 (+)NCBICelera
Cytogenetic Map5p15.33NCBI
HuRef53,569,035 - 3,575,436 (+)NCBIHuRef
CHM1_153,596,269 - 3,601,617 (+)NCBICHM1_1
T2T-CHM13v2.053,514,530 - 3,520,100 (+)NCBIT2T-CHM13v2.0
Irx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391372,106,351 - 72,111,842 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1372,106,040 - 72,111,842 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381371,958,232 - 71,963,723 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1371,957,921 - 71,963,723 (-)Ensemblmm10GRCm38
MGSCv371372,095,680 - 72,101,171 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361372,424,607 - 72,429,479 (-)NCBIMGSCv36mm8
Celera1374,285,058 - 74,290,917 (-)NCBICelera
Cytogenetic Map13C1NCBI
cM Map1338.43NCBI
Irx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555042,072,540 - 2,099,781 (+)NCBIChiLan1.0ChiLan1.0
IRX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v243,848,593 - 3,854,175 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan152,002,201 - 2,007,783 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v053,922,252 - 3,927,836 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.153,610,229 - 3,615,279 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl53,610,225 - 3,615,279 (+)EnsemblpanPan2panpan1.1
IRX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1349,537,231 - 9,544,029 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl349,538,479 - 9,544,029 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3414,053,493 - 14,058,919 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0349,440,824 - 9,446,274 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl349,440,808 - 9,446,627 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1349,488,276 - 9,493,698 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0349,467,500 - 9,472,927 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0349,682,784 - 9,688,233 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Irx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213242,538,955 - 242,544,555 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366343,130,167 - 3,135,537 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366343,130,197 - 3,135,273 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IRX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1677,695,071 - 77,701,236 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11677,695,704 - 77,701,089 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
IRX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.143,365,880 - 3,371,520 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl43,366,384 - 3,371,670 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606425,439,633 - 25,445,218 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Irx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247512,010,004 - 2,014,721 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247512,005,849 - 2,014,775 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Irx1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12203,281,747 - 203,287,298 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Irx1
6 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:320
Count of miRNA genes:195
Interacting mature miRNAs:237
Transcripts:ENSRNOT00000044690
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1529322934184556Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1774611852746118Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1774612152746121Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12940927974409279Rat
70179Xhs2X-ray hypersensitivity QTL 23.2intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)1143965634Rat
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)11037949255379492Rat
731169Bp153Blood pressure QTL 1530.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)13287937235320571Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1694102251941022Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1529322934184556Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)1690935351909353Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11731537851816258Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)1690935351909353Rat
5684999Bss102Bone structure and strength QTL 1025.57e-07tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)1690935351909353Rat
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)11282049457820494Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)1134184556Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12065642065656420Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12050832665508326Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11168446456684464Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13070837587558729Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1529322934184556Rat

Markers in Region
AI426466  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2131,299,868 - 31,300,108 (+)MAPPERmRatBN7.2
Rnor_6.0133,916,166 - 33,916,405NCBIRnor6.0
Rnor_5.0135,325,149 - 35,325,388UniSTSRnor5.0
RGSC_v3.4171,396,149 - 1,396,388UniSTSRGSC3.4
Celera129,935,021 - 29,935,260UniSTS
Cytogenetic Map17p14UniSTS
RH136785  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2131,299,866 - 31,299,952 (+)MAPPERmRatBN7.2
Rnor_6.0133,916,164 - 33,916,249NCBIRnor6.0
Rnor_5.0135,325,147 - 35,325,232UniSTSRnor5.0
RGSC_v3.4171,396,147 - 1,396,232UniSTSRGSC3.4
Celera129,935,019 - 29,935,104UniSTS
Cytogenetic Map17p14UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
8 4 64 137 88 87 59 13 59 6 255 103 10 109 81 57 28 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000044690   ⟹   ENSRNOP00000040590
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl133,123,122 - 33,128,951 (+)Ensembl
mRatBN7.2 Ensembl131,294,615 - 31,300,444 (+)Ensembl
Rnor_6.0 Ensembl133,910,912 - 33,916,741 (+)Ensembl
RefSeq Acc Id: NM_001107331   ⟹   NP_001100801
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8133,123,122 - 33,128,951 (+)NCBI
mRatBN7.2131,294,615 - 31,300,444 (+)NCBI
Rnor_6.0133,910,912 - 33,916,741 (+)NCBI
Rnor_5.0135,319,895 - 35,325,724 (+)NCBI
RGSC_v3.4171,390,894 - 1,396,724 (+)RGD
Celera129,929,767 - 29,935,596 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039110061   ⟹   XP_038965989
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8133,123,945 - 33,128,651 (+)NCBI
mRatBN7.2131,295,409 - 31,300,147 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100801 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965989 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87639 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000040590
  ENSRNOP00000040590.3
RefSeq Acc Id: NP_001100801   ⟸   NM_001107331
- UniProtKB: D4A9L1 (UniProtKB/TrEMBL),   A6JUZ0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000040590   ⟸   ENSRNOT00000044690
RefSeq Acc Id: XP_038965989   ⟸   XM_039110061
- Peptide Label: isoform X1
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A9L1-F1-model_v2 AlphaFold D4A9L1 1-480 view protein structure

Transcriptome

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

Promoters
RGD ID:13689572
Promoter ID:EPDNEW_R96
Type:initiation region
Name:Irx1_1
Description:iroquois homeobox 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0133,910,891 - 33,910,951EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309060 AgrOrtholog
BioCyc Gene G2FUF-61901 BioCyc
Ensembl Genes ENSRNOG00000033609 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044690 ENTREZGENE
  ENSRNOT00000044690.6 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:306659 UniProtKB/TrEMBL
NCBI Gene 306659 ENTREZGENE
PANTHER IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX UniProtKB/TrEMBL
  IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-1 UniProtKB/TrEMBL
Pfam Homeobox_KN UniProtKB/TrEMBL
PhenoGen Irx1 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000033609 RatGTEx
SMART HOX UniProtKB/TrEMBL
  IRO UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6JUZ0 ENTREZGENE, UniProtKB/TrEMBL
  D4A9L1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Irx1  iroquois homeobox 1  LOC501463  similar to Iroquois-class homeodomain protein IRX-1 (Iroquois homeobox protein 1) (Homeodomain protein IRXA1)  Data merged from RGD:1587224 1643240 APPROVED
2008-09-26 Irx1  iroquois homeobox 1  Irx1  Iroquois related homeobox 1 (Drosophila)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Irx1  Iroquois related homeobox 1 (Drosophila)   Irx1_predicted  Iroquois related homeobox 1 (Drosophila) (predicted)  'predicted' is removed 2292626 APPROVED
2006-11-19 LOC501463  similar to Iroquois-class homeodomain protein IRX-1 (Iroquois homeobox protein 1) (Homeodomain protein IRXA1)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Irx1_predicted  Iroquois related homeobox 1 (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED