Human Gene IRX4 (uc003jcz.2) Description and Page Index
  Description: Homo sapiens iroquois homeobox 4 (IRX4), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:1,877,541-1,882,880 Size: 5,340 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr5:1,878,083-1,882,761 Size: 4,679 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr5:1,877,541-1,882,880)mRNA (may differ from genome)Protein (519 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Iroquois-class homeodomain protein IRX-4; AltName: Full=Homeodomain protein IRXA3; AltName: Full=Iroquois homeobox protein 4;
FUNCTION: Likely to be an important mediator of ventricular differentiation during cardiac development.
TISSUE SPECIFICITY: Predominantly expressed in cardiac ventricles.
SIMILARITY: Belongs to the TALE/IRO homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): IRX4
CDC HuGE Published Literature: IRX4
Positive Disease Associations: Alzheimer Disease , Blood Pressure , Cardiovascular Diseases , Iron , monocyte chemoattractant protein 1 (66-77) , Monocytes , Pancreatic Neoplasms , Prostatic Neoplasms
Related Studies:
  1. Alzheimer Disease
    , , . [PubMed 0]
  2. Blood Pressure
    , , . [PubMed 0]
  3. Cardiovascular Diseases
    Markus Schurks et al. PloS one 2011, Genetic determinants of cardiovascular events among women with migraine: a genome-wide association study., PloS one. [PubMed 21779381]
    Our results provide some suggestion for an association of five SNPs with CVD events among women with migraine; none of the results was genome-wide significant. Four associations appeared among migraineurs with aura, two of those with ischemic stroke. Although our population is among the largest with migraine and incident CVD information, these results must be treated with caution, given the limited number of CVD events among women with migraine and the low minor allele frequencies for three of the SNPs. Our results await independent replication and should be considered hypothesis generating for future research.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: IRX4
Diseases sorted by gene-association score: familial atrial fibrillation (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.25 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 55.64 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -47.30119-0.397 Picture PostScript Text
3' UTR -208.60542-0.385 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017970 - Homeobox_CS
IPR008422 - Homeobox_KN_domain
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR003893 - Iroquois_homeo

Pfam Domains:
PF00046 - Homeobox domain
PF05920 - Homeobox KN domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P78413
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007507 heart development
GO:0048561 establishment of animal organ orientation

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  AB690780 - Homo sapiens IRX4 mRNA for iroquois-class homeodomain protein IRX-4 variant 3, complete cds.
AB690781 - Homo sapiens IRX4 mRNA for iroquois-class homeodomain protein IRX-4 variant 4, complete cds.
AB690778 - Homo sapiens IRX4 mRNA for iroquois-class homeodomain protein IRX-4 variant 1, complete cds.
AB690779 - Homo sapiens IRX4 mRNA for iroquois-class homeodomain protein IRX-4 variant 2, complete cds.
AF124733 - Homo sapiens iroquois homeobox protein 4 (IRX4) mRNA, complete cds.
JD467960 - Sequence 448984 from Patent EP1572962.
BC110912 - Homo sapiens iroquois homeobox 4, mRNA (cDNA clone MGC:131996 IMAGE:3450161), complete cds.
JD244250 - Sequence 225274 from Patent EP1572962.
JD398194 - Sequence 379218 from Patent EP1572962.
JD278321 - Sequence 259345 from Patent EP1572962.
JD056253 - Sequence 37277 from Patent EP1572962.
JD100516 - Sequence 81540 from Patent EP1572962.
JD269487 - Sequence 250511 from Patent EP1572962.
JD435798 - Sequence 416822 from Patent EP1572962.
BC144204 - Homo sapiens cDNA clone IMAGE:9052724, with apparent retained intron.
BC136505 - Homo sapiens iroquois homeobox 4, mRNA (cDNA clone MGC:168117 IMAGE:9020494), complete cds.
BC136506 - Homo sapiens iroquois homeobox 4, mRNA (cDNA clone MGC:168118 IMAGE:9020495), complete cds.
JD485738 - Sequence 466762 from Patent EP1572962.
KJ898787 - Synthetic construct Homo sapiens clone ccsbBroadEn_08181 IRX4 gene, encodes complete protein.
AB527533 - Synthetic construct DNA, clone: pF1KB5973, Homo sapiens IRX4 gene for iroquois homeobox protein 4, without stop codon, in Flexi system.
JD458512 - Sequence 439536 from Patent EP1572962.
JD458511 - Sequence 439535 from Patent EP1572962.
U90306 - Human iroquois-class homeodomain protein IRX-4 mRNA, partial cds.
JD128855 - Sequence 109879 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RMW5, D3DTC5, IRX4_HUMAN, IRXA3, NM_016358, NP_057442, P78413, Q2NL64, Q9UHR2
UCSC ID: uc003jcz.2
RefSeq Accession: NM_016358
Protein: P78413 (aka IRX4_HUMAN)
CCDS: CCDS3867.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_016358.2
exon count: 5CDS single in 3' UTR: no RNA size: 2229
ORF size: 1560CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3308.00frame shift in genome: no % Coverage: 99.64
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 19# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.