Irx5 (iroquois homeobox 5) - Rat Genome Database

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Gene: Irx5 (iroquois homeobox 5) Rattus norvegicus
Analyze
Symbol: Irx5
Name: iroquois homeobox 5
RGD ID: 1565518
Description: Enables DNA-binding transcription factor binding activity and protein self-association. Involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human IRX5 (iroquois homeobox 5); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: iroquois homeobox protein 5; iroquois-class homeodomain protein IRX-5; LOC498918
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
mRatBN7.21914,639,052 - 14,643,911 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1914,624,225 - 14,642,318 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1916,335,573 - 16,338,267 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01921,530,376 - 21,533,070 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01924,476,554 - 24,479,248 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01916,415,813 - 16,421,088 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1916,415,636 - 16,421,191 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01927,490,017 - 27,494,759 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41915,747,720 - 15,750,414 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1914,553,091 - 14,555,785 (-)NCBICelera
Cytogenetic Map19p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Aetiology-specific patterns in end-stage heart failure patients identified by functional annotation and classification of microarray data. Beisvag V, etal., Eur J Heart Fail. 2006 Jun;8(4):381-9. doi: 10.1016/j.ejheart.2006.05.004. Epub 2006 Jun 6.
2. 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.
3. 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.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16182275   PMID:16239150   PMID:16412459   PMID:18322081   PMID:22581230   PMID:27170637  


Genomics

Comparative Map Data
Irx5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21914,639,052 - 14,643,911 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1914,624,225 - 14,642,318 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1916,335,573 - 16,338,267 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01921,530,376 - 21,533,070 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01924,476,554 - 24,479,248 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01916,415,813 - 16,421,088 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1916,415,636 - 16,421,191 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01927,490,017 - 27,494,759 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41915,747,720 - 15,750,414 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1914,553,091 - 14,555,785 (-)NCBICelera
Cytogenetic Map19p11NCBI
IRX5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381654,930,865 - 54,934,485 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1654,930,865 - 54,934,485 (+)EnsemblGRCh38hg38GRCh38
GRCh371654,964,777 - 54,968,397 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361653,522,612 - 53,525,898 (+)NCBINCBI36Build 36hg18NCBI36
Build 341653,522,611 - 53,525,894NCBI
Celera1639,479,883 - 39,483,213 (+)NCBICelera
Cytogenetic Map16q12.2NCBI
HuRef1640,851,390 - 40,854,676 (+)NCBIHuRef
CHM1_11656,372,071 - 56,375,357 (+)NCBICHM1_1
T2T-CHM13v2.01660,728,978 - 60,732,598 (+)NCBIT2T-CHM13v2.0
Irx5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39893,084,424 - 93,088,084 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl893,084,253 - 93,102,914 (+)EnsemblGRCm39 Ensembl
GRCm38892,357,796 - 92,361,456 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl892,357,625 - 92,376,286 (+)EnsemblGRCm38mm10GRCm38
MGSCv37894,881,695 - 94,885,355 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36895,246,924 - 95,250,584 (+)NCBIMGSCv36mm8
Celera896,669,925 - 96,673,589 (+)NCBICelera
Cytogenetic Map8C5NCBI
cM Map844.93NCBI
Irx5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543312,519,338 - 12,522,118 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543312,518,786 - 12,522,744 (+)NCBIChiLan1.0ChiLan1.0
IRX5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11670,278,544 - 70,282,165 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01635,164,884 - 35,168,189 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11654,272,272 - 54,275,431 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1654,272,412 - 54,275,124 (+)Ensemblpanpan1.1panPan2
IRX5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1260,957,353 - 60,978,782 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl260,968,193 - 61,041,385 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha257,609,385 - 57,612,765 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0261,516,686 - 61,520,066 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl261,509,877 - 61,582,135 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1258,341,971 - 58,345,349 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0259,367,066 - 59,370,437 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0260,245,608 - 60,248,977 (-)NCBIUU_Cfam_GSD_1.0
Irx5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934952,231,182 - 52,234,905 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364757,354,642 - 7,358,553 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364757,354,273 - 7,358,328 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IRX5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl630,511,894 - 30,514,808 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1630,511,263 - 30,515,015 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
IRX5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1540,705,061 - 40,708,749 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604735,643,147 - 35,667,057 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Irx5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247571,947,032 - 1,966,352 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247571,962,574 - 1,966,330 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Irx5
10 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:18
Count of miRNA genes:17
Interacting mature miRNAs:18
Transcripts:ENSRNOT00000015272
Prediction methods: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
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
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)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032318023069265Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191392640130303727Rat

Markers in Region
Irx5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21914,639,221 - 14,639,272 (-)MAPPERmRatBN7.2
Rnor_6.01916,420,400 - 16,420,450NCBIRnor6.0
Rnor_5.01927,494,543 - 27,494,593UniSTSRnor5.0
RGSC_v3.41915,747,781 - 15,747,831UniSTSRGSC3.4
Celera1914,553,152 - 14,553,202UniSTS
Cytogenetic Map19p11UniSTS
Irx5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21914,640,477 - 14,641,678 (-)MAPPERmRatBN7.2
Rnor_6.01916,417,994 - 16,419,194NCBIRnor6.0
Rnor_5.01927,492,137 - 27,493,337UniSTSRnor5.0
Celera1914,554,408 - 14,555,608UniSTS
Cytogenetic Map19p11UniSTS


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 8 27 6 2
Low 35 12 6 1 6 6 9 30 31 26 9 6
Below cutoff 1 31 21 17 21 2 2 13 4 9 2

Sequence


RefSeq Acc Id: ENSRNOT00000015272   ⟹   ENSRNOP00000015272
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1914,624,225 - 14,642,318 (-)Ensembl
Rnor_6.0 Ensembl1916,417,817 - 16,420,511 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089975   ⟹   ENSRNOP00000072299
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1914,638,527 - 14,642,318 (-)Ensembl
Rnor_6.0 Ensembl1916,415,636 - 16,421,191 (+)Ensembl
RefSeq Acc Id: NM_001030044   ⟹   NP_001025215
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21914,639,161 - 14,641,855 (-)NCBI
Rnor_6.01916,417,817 - 16,420,511 (+)NCBI
Rnor_5.01927,490,017 - 27,494,759 (+)NCBI
RGSC_v3.41915,747,720 - 15,750,414 (-)RGD
Celera1914,553,091 - 14,555,785 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255197   ⟹   XP_006255259
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21914,639,052 - 14,643,911 (-)NCBI
Rnor_6.01916,415,813 - 16,421,088 (+)NCBI
Rnor_5.01927,490,017 - 27,494,759 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001025215 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255259 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAZ20811 (Get FASTA)   NCBI Sequence Viewer  
  EDL87565 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000015272.2
  ENSRNOP00000072299
  ENSRNOP00000072299.2
RefSeq Acc Id: NP_001025215   ⟸   NM_001030044
- UniProtKB: Q45V74 (UniProtKB/TrEMBL),   A0A0G2K2M1 (UniProtKB/TrEMBL),   A6KD61 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255259   ⟸   XM_006255197
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K2M1 (UniProtKB/TrEMBL),   A6KD61 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072299   ⟸   ENSRNOT00000089975
RefSeq Acc Id: ENSRNOP00000015272   ⟸   ENSRNOT00000015272
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V7I4-F1-model_v2 AlphaFold G3V7I4 1-484 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:1565518 AgrOrtholog
BioCyc Gene G2FUF-6384 BioCyc
Ensembl Genes ENSRNOG00000011180 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015272.3 UniProtKB/TrEMBL
  ENSRNOT00000089975 ENTREZGENE
  ENSRNOT00000089975.2 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:498918 UniProtKB/TrEMBL
NCBI Gene 498918 ENTREZGENE
PANTHER IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX UniProtKB/TrEMBL
  IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-5 UniProtKB/TrEMBL
Pfam Homeobox_KN UniProtKB/TrEMBL
PhenoGen Irx5 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011180 RatGTEx
SMART HOX UniProtKB/TrEMBL
  IRO UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A0A0G2K2M1 ENTREZGENE, UniProtKB/TrEMBL
  A6KD61 ENTREZGENE, UniProtKB/TrEMBL
  G3V7I4_RAT UniProtKB/TrEMBL
  Q45V74 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Irx5  iroquois homeobox 5  LOC498918  iroquois homeobox protein 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC498918  iroquois homeobox protein 5      Symbol and Name status set to provisional 70820 PROVISIONAL