Human Gene FOXG1 (uc001wqe.4) Description and Page Index
  Description: Homo sapiens forkhead box G1 (FOXG1), mRNA.
RefSeq Summary (NM_005249): This locus encodes a member of the forked-head transcription factor family. The encoded protein, which functions as a repressor, may play a role in brain development. Mutations at this locus have been associated with Rett syndrome. [provided by RefSeq, Feb 2012]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript is intronless :: BC035020.2, ERR279867.2446.1 [ECO:0000345] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr14:29,236,278-29,239,483 Size: 3,206 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr14:29,236,486-29,237,955 Size: 1,470 Coding Exon Count: 1 

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 (chr14:29,236,278-29,239,483)mRNA (may differ from genome)Protein (489 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Forkhead box protein G1; AltName: Full=Brain factor 1; Short=BF-1; Short=BF1; AltName: Full=Brain factor 2; Short=BF-2; Short=BF2; Short=hBF-2; AltName: Full=Forkhead box protein G1A; AltName: Full=Forkhead box protein G1B; AltName: Full=Forkhead box protein G1C; AltName: Full=Forkhead-related protein FKHL1; Short=HFK1; AltName: Full=Forkhead-related protein FKHL2; Short=HFK2; AltName: Full=Forkhead-related protein FKHL3; Short=HFK3;
FUNCTION: Transcription repression factor which plays an important role in the establishment of the regional subdivision of the developing brain and in the development of the telencephalon.
SUBUNIT: Interacts with KDM5B.
TISSUE SPECIFICITY: Expression is restricted to the neurons of the developing telencephalon.
DISEASE: Defects in FOXG1 are the cause of congenital variant of Rett syndrome (RTTCV) [MIM:613454]. RTTCV is a severe neurodevelopmental disorder with features of classic Rett syndrome but earlier onset in the first months of life. Clinical features include progressive microcephaly, hypotonia, irresponsiveness and irritability in the neonatal period, mental retardation, psychomotor regression and stereotypical movements.
SIMILARITY: Contains 1 fork-head DNA-binding domain.
CAUTION: PubMed:7959731 claims that there are 3 different FOXG1 proteins, FOXG1A, FOXG1B, and FOXG1C. It was latter found that there is only one gene and the differences between these three may be sequencing errors since the protein is coded in a unique exon.
WEB RESOURCE: Name=Wikipedia; Note=FOXG1 entry; URL="";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): FOXG1
CDC HuGE Published Literature: FOXG1

-  MalaCards Disease Associations
  MalaCards Gene Search: FOXG1
Diseases sorted by gene-association score: rett syndrome, congenital variant* (1329), rett syndrome* (235), 14q12 microdeletion syndrome* (25), 14q11.2 microduplication syndrome* (25), foxg1 syndrome (18), classic rett syndrome (13), chromosome 14q11-q22 deletion syndrome (11), mental retardation, x-linked syndromic, christianson type (7), scleral staphyloma (7), primary thrombocytopenia (5), west syndrome (5), microcephaly (3)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.18 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 169.94 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 -76.51208-0.368 Picture PostScript Text
3' UTR -365.021528-0.239 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
IPR018122 - TF_fork_head_CS
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00250 - Forkhead domain

SCOP Domains:
46785 - "Winged helix" DNA-binding domain

ModBase Predicted Comparative 3D Structure on P55316
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene 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:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0002052 positive regulation of neuroblast proliferation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007346 regulation of mitotic cell cycle
GO:0007420 brain development
GO:0007568 aging
GO:0009653 anatomical structure morphogenesis
GO:0009953 dorsal/ventral pattern formation
GO:0010468 regulation of gene expression
GO:0016199 axon midline choice point recognition
GO:0021852 pyramidal neuron migration
GO:0021954 central nervous system neuron development
GO:0021987 cerebral cortex development
GO:0022008 neurogenesis
GO:0030154 cell differentiation
GO:0030900 forebrain development
GO:0042472 inner ear morphogenesis
GO:0045665 negative regulation of neuron differentiation
GO:0045666 positive regulation of neuron differentiation
GO:0045787 positive regulation of cell cycle
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048664 neuron fate determination
GO:0048667 cell morphogenesis involved in neuron differentiation
GO:0051726 regulation of cell cycle
GO:2000177 regulation of neural precursor cell proliferation

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  BC050072 - Homo sapiens forkhead box G1, mRNA (cDNA clone MGC:48322 IMAGE:5284335), complete cds.
X74142 - H.sapiens HBF-1 mRNA for transcription factor.
X74143 - H.sapiens HBF-2 mRNA for transcription factor.
BC035020 - Homo sapiens forkhead box G1, mRNA (cDNA clone IMAGE:4823883), with apparent retained intron.
JD416384 - Sequence 397408 from Patent EP1572962.
JD056696 - Sequence 37720 from Patent EP1572962.
KJ905195 - Synthetic construct Homo sapiens clone ccsbBroadEn_14642 FOXG1 gene, encodes complete protein.
JD364230 - Sequence 345254 from Patent EP1572962.
JD110950 - Sequence 91974 from Patent EP1572962.
JD458488 - Sequence 439512 from Patent EP1572962.
JD461122 - Sequence 442146 from Patent EP1572962.
JD187226 - Sequence 168250 from Patent EP1572962.
JD404652 - Sequence 385676 from Patent EP1572962.
JD187227 - Sequence 168251 from Patent EP1572962.
JD271278 - Sequence 252302 from Patent EP1572962.
BC040960 - Homo sapiens forkhead box G1A, mRNA (cDNA clone IMAGE:5248592), partial cds.
X74144 - H.sapiens HBF-3 mRNA.
JD163245 - Sequence 144269 from Patent EP1572962.
JD174760 - Sequence 155784 from Patent EP1572962.
JD112883 - Sequence 93907 from Patent EP1572962.
JD299470 - Sequence 280494 from Patent EP1572962.
JD231691 - Sequence 212715 from Patent EP1572962.
JD131206 - Sequence 112230 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NFY2, FKH2, FKHL1, FKHL2, FKHL3, FKHL4, FOXG1A, FOXG1B, FOXG1C, FOXG1_HUMAN, NM_005249, NP_005240, P55315, P55316, Q14488, Q86XT7, uc001wqe.3
UCSC ID: uc001wqe.4
RefSeq Accession: NM_005249
Protein: P55316 (aka FOXG1_HUMAN)
CCDS: CCDS9636.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_005249.4
exon count: 1CDS single in 3' UTR: no RNA size: 3216
ORF size: 1470CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2780.50frame shift in genome: no % Coverage: 99.69
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: 0# 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.