Human Gene EMX2 (ENST00000553456.5) from GENCODE V44
  Description: Homo sapiens empty spiracles homeobox 2 (EMX2), transcript variant 1, mRNA. (from RefSeq NM_004098)
RefSeq Summary (NM_004098): This gene encodes a homeobox-containing transcription factor that is the homolog to the 'empty spiracles' gene in Drosophila. Research on this gene in humans has focused on its expression in three tissues: dorsal telencephalon, olfactory neuroepithelium, and urogenetial system. It is expressed in the dorsal telencephalon during development in a low rostral-lateral to high caudal-medial gradient and is proposed to pattern the neocortex into defined functional areas. It is also expressed in embryonic and adult olfactory neuroepithelia where it complexes with eukaryotic translation initiation factor 4E (eIF4E) and possibly regulates mRNA transport or translation. In the developing urogenital system, it is expressed in epithelial tissues and is negatively regulated by HOXA10. Alternative splicing results in multiple transcript variants encoding distinct proteins.[provided by RefSeq, Sep 2009].
Gencode Transcript: ENST00000553456.5
Gencode Gene: ENSG00000170370.12
Transcript (Including UTRs)
   Position: hg38 chr10:117,542,746-117,549,546 Size: 6,801 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg38 chr10:117,543,268-117,548,232 Size: 4,965 Coding Exon Count: 3 

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 (chr10:117,542,746-117,549,546)mRNA (may differ from genome)Protein (252 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Homeobox protein EMX2; AltName: Full=Empty spiracles homolog 2; AltName: Full=Empty spiracles-like protein 2;
FUNCTION: Transcription factor, which in cooperation with EMX2, acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.
INTERACTION: P06730:EIF4E; NbExp=4; IntAct=EBI-399831, EBI-73440;
TISSUE SPECIFICITY: Cerebral cortex.
DISEASE: Defects in EMX2 are the cause of schizencephaly (SCHZC) [MIM:269160]. Schizencephaly is an extremely rare human congenital disorder characterized by a full-thickness cleft within the cerebral hemispheres. These clefts are lined with gray matter and most commonly involve the parasylvian regions. Large portions of the cerebral hemispheres may be absent and replaced by cerebro- spinal fluid.
SIMILARITY: Belongs to the EMX homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
WEB RESOURCE: Name=GeneReviews; URL="";

-  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: EMX2
Diseases sorted by gene-association score: schizencephaly* (557), familial schizencephaly, shh-related* (283), familial schizencephaly, emx2-related* (100), neuronal migration disorders (6), heterotopia, periventricular (5), kallmann syndrome (2)
* = Manually curated disease association

-  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: 53.99 RPKM in Uterus
Total median expression: 279.04 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 -133.90522-0.257 Picture PostScript Text
3' UTR -328.101314-0.250 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
IPR020479 - Homeobox_metazoa
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR000047 - HTH_motif

Pfam Domains:
PF00046 - Homeobox domain

ModBase Predicted Comparative 3D Structure on Q04743
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 BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  

-  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:0005515 protein 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:0007275 multicellular organism development
GO:0007420 brain development
GO:0009952 anterior/posterior pattern specification
GO:0010468 regulation of gene expression
GO:0021542 dentate gyrus development
GO:0021796 cerebral cortex regionalization
GO:0021846 cell proliferation in forebrain
GO:0021885 forebrain cell migration
GO:0021987 cerebral cortex development
GO:0030182 neuron differentiation
GO:0030900 forebrain development
GO:0042493 response to drug
GO:0072001 renal system development

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  LF212800 - JP 2014500723-A/20303: Polycomb-Associated Non-Coding RNAs.
MA448377 - JP 2018138019-A/20303: Polycomb-Associated Non-Coding RNAs.
LF211383 - JP 2014500723-A/18886: Polycomb-Associated Non-Coding RNAs.
MA446960 - JP 2018138019-A/18886: Polycomb-Associated Non-Coding RNAs.
AF301598 - Homo sapiens empty spiracles-like protein (EMX2) mRNA, complete cds.
AL161811 - Homo sapiens mRNA; cDNA DKFZp761M1614 (from clone DKFZp761M1614).
JD409998 - Sequence 391022 from Patent EP1572962.
AK055041 - Homo sapiens cDNA FLJ30479 fis, clone BRAWH1000168, highly similar to Homeotic protein emx2.
JD187462 - Sequence 168486 from Patent EP1572962.
BC152825 - Synthetic construct Homo sapiens clone IMAGE:100016047, MGC:184159 empty spiracles homeobox 2 (EMX2) mRNA, encodes complete protein.
AB463605 - Synthetic construct DNA, clone: pF1KB9694, Homo sapiens EMX2 gene for empty spiracles homeobox 2, without stop codon, in Flexi system.
X68880 - H.sapiens EMX2 mRNA.
AK311352 - Homo sapiens cDNA, FLJ18394.
LF346022 - JP 2014500723-A/153525: Polycomb-Associated Non-Coding RNAs.
MA581599 - JP 2018138019-A/153525: Polycomb-Associated Non-Coding RNAs.
BC010043 - Homo sapiens empty spiracles homolog 2 (Drosophila), mRNA (cDNA clone IMAGE:3632752), partial cds.
JD355175 - Sequence 336199 from Patent EP1572962.
JD176620 - Sequence 157644 from Patent EP1572962.
LF346023 - JP 2014500723-A/153526: Polycomb-Associated Non-Coding RNAs.
MA581600 - JP 2018138019-A/153526: Polycomb-Associated Non-Coding RNAs.
JD167862 - Sequence 148886 from Patent EP1572962.
JD045360 - Sequence 26384 from Patent EP1572962.
JD075882 - Sequence 56906 from Patent EP1572962.
JD188745 - Sequence 169769 from Patent EP1572962.
LF346024 - JP 2014500723-A/153527: Polycomb-Associated Non-Coding RNAs.
MA581601 - JP 2018138019-A/153527: Polycomb-Associated Non-Coding RNAs.
JD187616 - Sequence 168640 from Patent EP1572962.
JD371766 - Sequence 352790 from Patent EP1572962.
JD442067 - Sequence 423091 from Patent EP1572962.
JD103694 - Sequence 84718 from Patent EP1572962.
JD267845 - Sequence 248869 from Patent EP1572962.
JD085794 - Sequence 66818 from Patent EP1572962.
JD315878 - Sequence 296902 from Patent EP1572962.
JD246202 - Sequence 227226 from Patent EP1572962.
JD095073 - Sequence 76097 from Patent EP1572962.
JD286938 - Sequence 267962 from Patent EP1572962.
JD164226 - Sequence 145250 from Patent EP1572962.
JD498992 - Sequence 480016 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: EMX2_HUMAN, ENST00000553456.1, ENST00000553456.2, ENST00000553456.3, ENST00000553456.4, NM_004098, Q04743, Q96NN8, Q9BQF4, uc001ldh.1, uc001ldh.2, uc001ldh.3, uc001ldh.4, uc001ldh.5, uc001ldh.6
UCSC ID: ENST00000553456.5
RefSeq Accession: NM_004098
Protein: Q04743 (aka EMX2_HUMAN)
CCDS: CCDS7601.1

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