IRX4 (iroquois homeobox 4) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: IRX4 (iroquois homeobox 4) Canis lupus familiaris
Analyze
Symbol: IRX4
Name: iroquois homeobox 4
RGD ID: 12075833
Description: ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); RNA polymerase II cis-regulatory region sequence-specific DNA binding (inferred); INVOLVED IN establishment of animal organ orientation (ortholog); heart development (ortholog); negative regulation of transcription by RNA polymerase II (ortholog); ASSOCIATED WITH adenoid cystic carcinoma (ortholog); autosomal dominant dyskeratosis congenita 2 (ortholog); Cardiomegaly (ortholog); FOUND IN nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: iroquois homeobox protein 4; iroquois-class homeodomain protein IRX-4
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
65 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 5 6 8 5
Low
Below cutoff 4 13 1 2 1 6 6 5 6

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_022414202 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038445416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038445417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038462770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038462771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038520328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038520329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038583258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038583259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038647669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038647670 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCAFT00000016576   ⟹   ENSCAFP00000015338
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl3410,923,097 - 10,929,164 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845044026   ⟹   ENSCAFP00845034500
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl3410,825,113 - 10,831,773 (+)Ensembl
RefSeq Acc Id: XM_038445416   ⟹   XP_038301344
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.03410,827,001 - 10,831,785 (+)NCBI
RefSeq Acc Id: XM_038445417   ⟹   XP_038301345
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.03410,827,001 - 10,831,785 (+)NCBI
RefSeq Acc Id: XM_038462770   ⟹   XP_038318698
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha3415,436,562 - 15,441,344 (+)NCBI
RefSeq Acc Id: XM_038462771   ⟹   XP_038318699
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha3415,436,562 - 15,441,344 (+)NCBI
RefSeq Acc Id: XM_038520328   ⟹   XP_038376256
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.13410,878,209 - 10,882,991 (+)NCBI
RefSeq Acc Id: XM_038520329   ⟹   XP_038376257
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.13410,878,209 - 10,882,991 (+)NCBI
RefSeq Acc Id: XM_038583258   ⟹   XP_038439186
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.03411,068,071 - 11,072,857 (+)NCBI
RefSeq Acc Id: XM_038583259   ⟹   XP_038439187
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.03411,068,071 - 11,072,857 (+)NCBI
RefSeq Acc Id: XM_038647669   ⟹   XP_038503597
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.03410,857,416 - 10,862,195 (+)NCBI
RefSeq Acc Id: XM_038647670   ⟹   XP_038503598
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.03410,857,416 - 10,862,195 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSCAFP00000015338   ⟸   ENSCAFT00000016576
RefSeq Acc Id: XP_038376256   ⟸   XM_038520328
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038376257   ⟸   XM_038520329
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038503597   ⟸   XM_038647669
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038503598   ⟸   XM_038647670
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038301344   ⟸   XM_038445416
- Peptide Label: isoform X1
- UniProtKB: A0A8C0TS93 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038301345   ⟸   XM_038445417
- Peptide Label: isoform X2
- UniProtKB: A0A8C0TTW1 (UniProtKB/TrEMBL),   A0A8I3PPB3 (UniProtKB/TrEMBL),   A0A8C0TS93 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038318698   ⟸   XM_038462770
- Peptide Label: isoform X1
- UniProtKB: A0A8C0TS93 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038318699   ⟸   XM_038462771
- Peptide Label: isoform X2
- UniProtKB: A0A8C0LE77 (UniProtKB/TrEMBL),   A0A8P0SF96 (UniProtKB/TrEMBL),   A0A8C0TS93 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038439186   ⟸   XM_038583258
- Peptide Label: isoform X1
- UniProtKB: A0A8C0TS93 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038439187   ⟸   XM_038583259
- Peptide Label: isoform X2
- UniProtKB: A0A8C0TS93 (UniProtKB/TrEMBL),   A0A8C0TTW1 (UniProtKB/TrEMBL),   A0A8I3PPB3 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845034500   ⟸   ENSCAFT00845044026
Protein Domains
Homeobox

Promoters
RGD ID:13688867
Promoter ID:EPDNEW_C6935
Type:multiple initiation site
Name:IRX4_1
Description:iroquois homeobox 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.13410,926,033 - 10,926,093EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000010441 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030009907 UniProtKB/TrEMBL
  ENSCAFG00040024341 UniProtKB/TrEMBL
  ENSCAFG00845024941 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000016576.5 UniProtKB/TrEMBL
  ENSCAFT00030018317.1 UniProtKB/TrEMBL
  ENSCAFT00040045336.1 UniProtKB/TrEMBL
  ENSCAFT00040045346.1 UniProtKB/TrEMBL
  ENSCAFT00845044026 ENTREZGENE
  ENSCAFT00845044026.1 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 IRX4 ENTREZGENE
PANTHER IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX UniProtKB/TrEMBL
  IROQUOIS-CLASS HOMEODOMAIN PROTEIN IRX-4 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 A0A8C0LE77 ENTREZGENE
  A0A8C0TS93 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0TTW1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PPB3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0SF96 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:54102 ENTREZGENE