Irx6 (iroquois homeobox 6) - Rat Genome Database

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Gene: Irx6 (iroquois homeobox 6) Rattus norvegicus
Analyze
Symbol: Irx6
Name: iroquois homeobox 6
RGD ID: 1564830
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in cell development; neuron differentiation; and regulation of DNA-templated transcription. Predicted to act upstream of or within detection of visible light; negative regulation of DNA-templated transcription; and retina morphogenesis in camera-type eye. Predicted to be active in nucleus. Orthologous to human IRX6 (iroquois homeobox 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Iroquois related homeobox 6; Iroquois related homeobox 6 (Drosophila); iroquois-class homeodomain protein IRX-6; LOC307715; RGD1564830; similar to iroquois homeobox protein 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81930,503,416 - 30,509,396 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1930,503,419 - 30,509,382 (-)EnsemblGRCr8
mRatBN7.21914,330,440 - 14,336,403 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1914,330,440 - 14,336,403 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1916,026,560 - 16,032,511 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01921,221,366 - 21,227,321 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01924,167,163 - 24,173,104 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01915,726,633 - 15,733,442 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1915,727,514 - 15,733,412 (-)Ensemblrn6Rnor6.0
Rnor_5.01926,812,637 - 26,819,392 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41915,433,142 - 15,439,105 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1914,246,025 - 14,251,980 (-)NCBICelera
Cytogenetic Map19p11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23172916  


Genomics

Comparative Map Data
Irx6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81930,503,416 - 30,509,396 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1930,503,419 - 30,509,382 (-)EnsemblGRCr8
mRatBN7.21914,330,440 - 14,336,403 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1914,330,440 - 14,336,403 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1916,026,560 - 16,032,511 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01921,221,366 - 21,227,321 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01924,167,163 - 24,173,104 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01915,726,633 - 15,733,442 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1915,727,514 - 15,733,412 (-)Ensemblrn6Rnor6.0
Rnor_5.01926,812,637 - 26,819,392 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41915,433,142 - 15,439,105 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1914,246,025 - 14,251,980 (-)NCBICelera
Cytogenetic Map19p11NCBI
IRX6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381655,324,203 - 55,330,756 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1655,323,974 - 55,330,757 (+)Ensemblhg38GRCh38
GRCh371655,358,115 - 55,364,668 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361653,915,972 - 53,922,173 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341653,915,971 - 53,922,172NCBI
Celera1639,872,722 - 39,878,927 (+)NCBICelera
Cytogenetic Map16q12.2NCBI
HuRef1641,244,432 - 41,250,656 (+)NCBIHuRef
CHM1_11656,765,742 - 56,771,956 (+)NCBICHM1_1
T2T-CHM13v2.01661,122,362 - 61,128,939 (+)NCBIT2T-CHM13v2.0
Irx6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39893,400,917 - 93,407,584 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl893,400,916 - 93,407,584 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38892,674,289 - 92,680,956 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl892,674,288 - 92,680,956 (+)Ensemblmm10GRCm38
MGSCv37895,198,301 - 95,203,979 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36895,563,530 - 95,569,208 (+)NCBIMGSCv36mm8
Celera897,001,163 - 97,006,835 (+)NCBICelera
Cytogenetic Map8C5NCBI
cM Map844.99NCBI
Irx6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543312,889,001 - 12,895,121 (+)Ensembl
ChiLan1.0NW_00495543312,889,025 - 12,895,090 (+)NCBIChiLan1.0ChiLan1.0
IRX6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21864,752,187 - 64,758,915 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11670,670,684 - 70,677,639 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01635,556,558 - 35,563,568 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11654,662,732 - 54,669,745 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1654,662,732 - 54,669,745 (+)EnsemblpanPan2panpan1.1
IRX6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1260,630,688 - 60,636,285 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl260,630,447 - 60,636,416 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha257,265,053 - 57,270,525 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0261,169,456 - 61,174,927 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl261,169,219 - 61,174,825 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1257,997,933 - 58,003,402 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0259,022,212 - 59,027,683 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0259,900,508 - 59,905,979 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Irx6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934951,916,943 - 51,924,125 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364757,665,841 - 7,670,582 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364757,665,100 - 7,672,132 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IRX6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl630,198,956 - 30,205,319 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1630,198,948 - 30,204,587 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2627,666,518 - 27,672,096 (-)NCBISscrofa10.2Sscrofa10.2susScr3
IRX6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1541,104,302 - 41,112,663 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl541,105,631 - 41,109,866 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604735,258,091 - 35,263,434 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Irx6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247571,619,023 - 1,622,800 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247571,617,674 - 1,623,928 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Irx6
37 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:176
Count of miRNA genes:129
Interacting mature miRNAs:139
Transcripts:ENSRNOT00000014831
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
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131969901Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19799775052997750Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19799775052997750Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)19574806450748064Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19799775052997750Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19799775052997750Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)193009938347207961Rat


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
10 1 22 128 26 23 8 9 8 6 105 52 9 108 35 38 15 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000014831   ⟹   ENSRNOP00000014831
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1930,503,419 - 30,509,382 (-)Ensembl
mRatBN7.2 Ensembl1914,330,440 - 14,336,403 (-)Ensembl
Rnor_6.0 Ensembl1915,727,514 - 15,733,412 (-)Ensembl
RefSeq Acc Id: NM_001102413   ⟹   NP_001095883
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81930,503,419 - 30,509,382 (-)NCBI
mRatBN7.21914,330,440 - 14,336,403 (-)NCBI
Rnor_6.01915,727,514 - 15,733,412 (-)NCBI
Rnor_5.01926,812,637 - 26,819,392 (-)NCBI
RGSC_v3.41915,433,142 - 15,439,105 (-)RGD
Celera1914,246,025 - 14,251,980 (-)RGD
Sequence:
RefSeq Acc Id: XM_063278002   ⟹   XP_063134072
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81930,504,557 - 30,509,385 (-)NCBI
RefSeq Acc Id: XM_063278003   ⟹   XP_063134073
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81930,503,416 - 30,509,396 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001095883 (Get FASTA)   NCBI Sequence Viewer  
  NP_001421359 (Get FASTA)   NCBI Sequence Viewer  
  XP_063134072 (Get FASTA)   NCBI Sequence Viewer  
  XP_063134073 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87567 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000014831
  ENSRNOP00000014831.4
RefSeq Acc Id: NP_001095883   ⟸   NM_001102413
- UniProtKB: D4A7R4 (UniProtKB/TrEMBL),   A6KD59 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000014831   ⟸   ENSRNOT00000014831
RefSeq Acc Id: XP_063134073   ⟸   XM_063278003
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063134072   ⟸   XM_063278002
- Peptide Label: isoform X1
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A7R4-F1-model_v2 AlphaFold D4A7R4 1-443 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:1564830 AgrOrtholog
BioCyc Gene G2FUF-6387 BioCyc
Ensembl Genes ENSRNOG00000011037 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014831 ENTREZGENE
  ENSRNOT00000014831.6 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:307715 UniProtKB/TrEMBL
NCBI Gene 307715 ENTREZGENE
PANTHER IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX UniProtKB/TrEMBL
  IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-6 UniProtKB/TrEMBL
Pfam Homeobox_KN UniProtKB/TrEMBL
PhenoGen Irx6 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011037 RatGTEx
SMART HOX UniProtKB/TrEMBL
  IRO UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6KD59 ENTREZGENE, UniProtKB/TrEMBL
  D4A7R4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-26 Irx6  iroquois homeobox 6  Irx6  Iroquois related homeobox 6 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Irx6  Iroquois related homeobox 6 (Drosophila)  RGD1564830_predicted  similar to iroquois homeobox protein 6 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564830_predicted  similar to iroquois homeobox protein 6 (predicted)  LOC307715  similar to iroquois homeobox protein 6  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC307715  similar to iroquois homeobox protein 6      Symbol and Name status set to provisional 70820 PROVISIONAL