Human Gene FOXR2 (ENST00000339140.5) from GENCODE V44
  Description: Homo sapiens forkhead box R2 (FOXR2), mRNA. (from RefSeq NM_198451)
Gencode Transcript: ENST00000339140.5
Gencode Gene: ENSG00000189299.7
Transcript (Including UTRs)
   Position: hg38 chrX:55,623,400-55,626,192 Size: 2,793 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg38 chrX:55,623,712-55,624,647 Size: 936 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:55,623,400-55,626,192)mRNA (may differ from genome)Protein (311 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FOXR2_HUMAN
DESCRIPTION: RecName: Full=Forkhead box protein R2; AltName: Full=Forkhead box protein N6;
SUBCELLULAR LOCATION: Nucleus (Potential).
TISSUE SPECIFICITY: Expressed in breast cancer cell lines and primary cancer.
SIMILARITY: Contains 1 fork-head 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


-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.17 RPKM in Testis
Total median expression: 1.17 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 -65.00312-0.208 Picture PostScript Text
3' UTR -350.201545-0.227 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
IPR001766 - TF_fork_head
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00250 - Forkhead domain

ModBase Predicted Comparative 3D Structure on Q6PJQ5
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:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0009653 anatomical structure morphogenesis
GO:0030154 cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  BC012934 - Homo sapiens forkhead box R2, mRNA (cDNA clone MGC:21658 IMAGE:4707447), complete cds.
JD113002 - Sequence 94026 from Patent EP1572962.
JD516733 - Sequence 497757 from Patent EP1572962.
AB464534 - Synthetic construct DNA, clone: pF1KB9820, Homo sapiens FOXR2 gene for forkhead box R2, without stop codon, in Flexi system.
EU446884 - Synthetic construct Homo sapiens clone IMAGE:100070212; IMAGE:100012093; FLH258178.01L forkhead box R2 (FOXR2) gene, encodes complete protein.
CU680452 - Synthetic construct Homo sapiens gateway clone IMAGE:100021104 5' read FOXR2 mRNA.
KJ895537 - Synthetic construct Homo sapiens clone ccsbBroadEn_04931 FOXR2 gene, encodes complete protein.
JD404211 - Sequence 385235 from Patent EP1572962.
JD048188 - Sequence 29212 from Patent EP1572962.
JD215567 - Sequence 196591 from Patent EP1572962.
JD045772 - Sequence 26796 from Patent EP1572962.
JD359339 - Sequence 340363 from Patent EP1572962.
JD359300 - Sequence 340324 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000339140.1, ENST00000339140.2, ENST00000339140.3, ENST00000339140.4, FOXN6, FOXR2_HUMAN, NM_198451, Q6PJQ5, uc004duo.1, uc004duo.2, uc004duo.3, uc004duo.4, uc004duo.5
UCSC ID: ENST00000339140.5
RefSeq Accession: NM_198451
Protein: Q6PJQ5 (aka FOXR2_HUMAN)
CCDS: CCDS35308.1

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