Human Gene FOXQ1 (ENST00000296839.5_4) from GENCODE V45lift37 (2024)

Human Gene FOXQ1 (ENST00000296839.5_4) from GENCODE V45lift37

Description: hom*o sapiens forkhead box Q1 (FOXQ1), mRNA. (from RefSeq NM_033260)
RefSeq Summary (NM_033260): FOXQ1 is a member of the FOX gene family, which is characterized by a conserved 110-amino acid DNA-binding motif called the forkhead or winged helix domain. FOX genes are involved in embryonic development, cell cycle regulation, tissue-specific gene expression, cell signaling, and tumorigenesis (Bieller et al., 2001 [PubMed 11747606]).[supplied by OMIM, May 2009]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Gencode Transcript: ENST00000296839.5_4
Gencode Gene: ENSG00000164379.7_7
Transcript (Including UTRs)
Position:hg19 chr6:1,312,333-1,314,993Size:2,661Total Exon Count:1Strand:+
Coding Region
Position:hg19 chr6:1,312,940-1,314,151Size:1,212Coding Exon Count:1

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Other Names	Model Information	Methods

Data last updated at UCSC:2024-04-24 11:59:55

Sequence and Links to Tools and Databases

Genomic Sequence (chr6:1,312,333-1,314,993)			mRNA (may differ from genome)		Protein (403 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
GeneNetwork	HGNC	Malacards	MGI	OMIM	PubMed
UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: FOXQ1_HUMAN DESCRIPTION: RecName: Full=Forkhead box protein Q1; AltName: Full=HNF-3/forkhead-like protein 1; Short=HFH-1; AltName: Full=Hepatocyte nuclear factor 3 forkhead homolog 1; FUNCTION:* Plays a role in hair follicle differentiation (By similarity). SUBCELLULAR LOCATION: Nucleus (By similarity). TISSUE SPECIFICITY: Expressed predominantly in the stomach, trachea, bladder and salivary gland. 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

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: FOXQ1 Diseases sorted by gene-association score: ritscher-schinzel syndrome (2)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D013749Tetrachlorodibenzodioxin D000082Acetaminophen D001564Benzo(a)pyrene D002737Chloroprene D003993Dibutyl Phthalate C1111182',3,3',4',5-pentachloro-4-hydroxybiphenyl C5486512-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester D0151237,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide D000079Acetaldehyde D016604Aflatoxin B1 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: 39.51 RPKM in Bladder Total median expression: 176.09 RPKM View in GTEx track of Genome BrowserView at GTEx portalView GTEx Body Map

Highest median expression: 39.51 RPKM in Bladder
Total median expression: 176.09 RPKM

View in GTEx track of Genome BrowserView at GTEx portalView GTEx Body Map

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-257.00	607	-0.423	Picture	PostScript	Text
3' UTR	-212.70	842	-0.253	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 Q9C009


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding GO:0003677 DNA binding GO:0003700 transcription factor activity, sequence-specific DNA binding GO:0043565 sequence-specific DNA binding Biological Process: GO:0000122 negative regulation of transcription from RNA polymerase II promoter GO:0006351 transcription, DNA-templated GO:0006355 regulation of transcription, DNA-templated GO:0009653 anatomical structure morphogenesis GO:0030154 cell differentiation GO:0031069 hair follicle morphogenesis Cellular Component: GO:0005634 nucleus

Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0009653 anatomical structure morphogenesis
GO:0030154 cell differentiation
GO:0031069 hair follicle morphogenesis

Cellular Component:
GO:0005634 nucleus

Descriptions from all associated GenBank mRNAs


	BC053850 - hom*o sapiens forkhead box Q1, mRNA (cDNA clone MGC:61699 IMAGE:6010412), complete cds. JD477860 - Sequence 458884 from Patent EP1572962. JD320580 - Sequence 301604 from Patent EP1572962. JD380013 - Sequence 361037 from Patent EP1572962. JD132261 - Sequence 113285 from Patent EP1572962. JD507460 - Sequence 488484 from Patent EP1572962. JD417905 - Sequence 398929 from Patent EP1572962.

Other Names for This Gene


	Alternate Gene Symbols: ENST00000296839.1, ENST00000296839.2, ENST00000296839.3, ENST00000296839.4, FOXQ1_HUMAN, HFH1, NM_033260, Q9C009, Q9NS06, uc317lxc.1 UCSC ID: ENST00000296839.5_4 RefSeq Accession: NM_033260 Protein: Q9C009 (aka FOXQ1_HUMAN or FXQ1_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


	Click here for details on how this gene model was made and data restrictions if any.