Human Gene FOXP1 (uc003doj.3) Description and Page Index
  Description: Homo sapiens forkhead box P1 (FOXP1), transcript variant 8, mRNA.
RefSeq Summary (NM_001244815): This gene belongs to subfamily P of the forkhead box (FOX) transcription factor family. Forkhead box transcription factors play important roles in the regulation of tissue- and cell type-specific gene transcription during both development and adulthood. Forkhead box P1 protein contains both DNA-binding- and protein-protein binding-domains. This gene may act as a tumor suppressor as it is lost in several tumor types and maps to a chromosomal region (3p14.1) reported to contain a tumor suppressor gene(s). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. 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 exon combination :: SRR3476690.881274.1, SRR1803614.265714.1 [ECO:0000332] ##Evidence-Data-END##
Transcript (Including UTRs)
   Position: hg19 chr3:71,003,865-71,180,092 Size: 176,228 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr3:71,008,398-71,179,834 Size: 171,437 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:71,003,865-71,180,092)mRNA (may differ from genome)Protein (679 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIOMIMPubMed
Stanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: E9PFD3_HUMAN
DESCRIPTION: SubName: Full=Forkhead box protein P1;
SIMILARITY: Contains 1 fork-head DNA-binding domain.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): FOXP1
CDC HuGE Published Literature: FOXP1
Positive Disease Associations: ADHD | attention-deficit hyperactivity disorder , Attention Deficit Disorder with Hyperactivity , Behcet Syndrome , Eosinophils , Tunica Media
Related Studies:
  1. ADHD | attention-deficit hyperactivity disorder
    Lasky-Su ,et al. 2008, Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations, American journal of medical genetics. Part B, Neuropsychiatric genetics 2008 147B- 8 : 1345-54. [PubMed 18821565]
  2. Attention Deficit Disorder with Hyperactivity
    Jessica Lasky-Su et al. American journal of medical genetics. Part B, Neuropsychiatric genetics 2008, Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations., American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetic. [PubMed 18821565]
  3. Behcet Syndrome
    Elaine F Remmers et al. Nature genetics 2010, , Nature genetics. [PubMed 20622878]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: FOXP1
Diseases sorted by gene-association score: mental retardation with language impairment and with or without autistic features* (1550), lymphoma, malt, somatic* (183), mental retardation with language impairment and autistic features* (131), leukemia, acute lymphoblastic 3* (90), relapsed/refractory diffuse large b-cell lymphoma (18), b-cell lymphomas (10), speech disorder (10), testicular lymphoma (9), diffuse large b-cell lymphoma (8), central nervous system lymphoma (8), blepharophimosis (7), speech and communication disorders (2)
* = 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: 12.51 RPKM in Esophagus - Muscularis
Total median expression: 227.13 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 -82.20258-0.319 Picture PostScript Text
3' UTR -1220.294533-0.269 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
IPR015880 - Znf_C2H2-like

Pfam Domains:
PF00250 - Forkhead domain
PF16159 - FOXP coiled-coil domain

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

ModBase Predicted Comparative 3D Structure on E9PFD3
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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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AF250920 - Homo sapiens 12CC4 mRNA, complete cds.
BC131720 - Homo sapiens forkhead box P1, mRNA (cDNA clone IMAGE:40123493), partial cds.
BC054505 - Homo sapiens forkhead box P1, mRNA (cDNA clone IMAGE:5503553), with apparent retained intron.
BC068481 - Homo sapiens cDNA clone IMAGE:4813876, containing frame-shift errors.
AK122710 - Homo sapiens cDNA FLJ16198 fis, clone CTONG1000220, highly similar to Forkhead box protein P1.
AF146696 - Homo sapiens clone pAB195 FOXP1 (FOXP1) mRNA, complete cds.
AK092383 - Homo sapiens cDNA FLJ35064 fis, clone PEBLM1000147, moderately similar to Glutamine (Q)-rich factor 1, QRF-1.
AX747510 - Sequence 1035 from Patent EP1308459.
DQ845346 - Homo sapiens PAX5/FOXP1 fusion protein (PAX5/FOXP1 fusion) mRNA, complete cds.
AK297649 - Homo sapiens cDNA FLJ58267 complete cds, highly similar to Forkhead box protein P1.
AF146698 - Homo sapiens FOXP1 (FOXP1) mRNA, complete cds.
AF146697 - Homo sapiens clone pAB196 FOXP1 (FOXP1) mRNA, partial cds.
AK027264 - Homo sapiens cDNA FLJ14358 fis, clone HEMBA1000158, weakly similar to HEPATOCYTE NUCLEAR FACTOR 3-GAMMA.
AB052767 - Homo sapiens hFKHLB mRNA for fork head-related protein like B, complete cds.
AF275309 - Homo sapiens transcription factor FOXP1 (FOXP1) mRNA, partial cds.
AK074321 - Homo sapiens cDNA FLJ23741 fis, clone HEP15377.
AK074569 - Homo sapiens cDNA FLJ90088 fis, clone HEMBA1005246.
BC152752 - Synthetic construct Homo sapiens clone IMAGE:100015965, MGC:184148 forkhead box P1 (FOXP1) mRNA, encodes complete protein.
AB527726 - Synthetic construct DNA, clone: pF1KB6240, Homo sapiens FOXP1 gene for forkhead box P1, without stop codon, in Flexi system.
BX647682 - Homo sapiens mRNA; cDNA DKFZp686K12112 (from clone DKFZp686K12112).
AK026898 - Homo sapiens cDNA: FLJ23245 fis, clone COL02931.
JD507587 - Sequence 488611 from Patent EP1572962.
JD109706 - Sequence 90730 from Patent EP1572962.
JD511079 - Sequence 492103 from Patent EP1572962.
JD096993 - Sequence 78017 from Patent EP1572962.
JD315463 - Sequence 296487 from Patent EP1572962.
JD062041 - Sequence 43065 from Patent EP1572962.
JD328397 - Sequence 309421 from Patent EP1572962.
JD132167 - Sequence 113191 from Patent EP1572962.
JD054841 - Sequence 35865 from Patent EP1572962.
JD182896 - Sequence 163920 from Patent EP1572962.
JD036464 - Sequence 17488 from Patent EP1572962.
JD403204 - Sequence 384228 from Patent EP1572962.
JD195535 - Sequence 176559 from Patent EP1572962.
JD237707 - Sequence 218731 from Patent EP1572962.
JD100344 - Sequence 81368 from Patent EP1572962.
JD458180 - Sequence 439204 from Patent EP1572962.
JD255083 - Sequence 236107 from Patent EP1572962.
JD236177 - Sequence 217201 from Patent EP1572962.
JD290560 - Sequence 271584 from Patent EP1572962.
JD239666 - Sequence 220690 from Patent EP1572962.
JD146664 - Sequence 127688 from Patent EP1572962.
JD229403 - Sequence 210427 from Patent EP1572962.
JD306681 - Sequence 287705 from Patent EP1572962.
AF151049 - Homo sapiens HSPC215 mRNA, complete cds.
CR457164 - Homo sapiens full open reading frame cDNA clone RZPDo834B098D for gene FOXP1, forkhead box P1; complete cds, incl. stopcodon.
JD370757 - Sequence 351781 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: E9PFD3, E9PFD3_HUMAN, NM_001244815, NP_001231742
UCSC ID: uc003doj.3
RefSeq Accession: NM_001244815
Protein: E9PFD3 CCDS: CCDS58837.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001244815.1
exon count: 16CDS single in 3' UTR: no RNA size: 6840
ORF size: 2040CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4247.00frame shift in genome: no % Coverage: 99.87
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.