Human Gene IRX4 (ENST00000622814.4) from GENCODE V44
  Description: Homo sapiens iroquois homeobox 4 (IRX4), transcript variant 2, mRNA. (from RefSeq NM_001278633)
Gencode Transcript: ENST00000622814.4
Gencode Gene: ENSG00000113430.10
Transcript (Including UTRs)
   Position: hg38 chr5:1,877,427-1,887,179 Size: 9,753 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg38 chr5:1,877,969-1,882,647 Size: 4,679 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:1,877,427-1,887,179)mRNA (may differ from genome)Protein (545 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: IRX4_HUMAN
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.
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Predominantly expressed in cardiac ventricles.
SIMILARITY: Belongs to the TALE/IRO homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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

-  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
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -104.60218-0.480 Picture PostScript Text
3' UTR -206.00542-0.380 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:
PF05920 - Homeobox KN domain

ModBase Predicted Comparative 3D Structure on P78413
FrontTopSide
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  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.
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.
JD189481 - Sequence 170505 from Patent EP1572962.
JD189480 - Sequence 170504 from Patent EP1572962.
JD189479 - Sequence 170503 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, ENST00000622814.1, ENST00000622814.2, ENST00000622814.3, IRX4_HUMAN, IRXA3, NM_001278633, P78413, Q2NL64, Q9UHR2, uc031siq.1
UCSC ID: ENST00000622814.4
RefSeq Accession: NM_001278633
Protein: P78413 (aka IRX4_HUMAN)
CCDS: CCDS3867.1, CCDS75225.1

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