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Center for Computational Systems Medicine
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Protein Summary

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AS Summary

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Protein Functional Features

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Gene Isoform Structures and Expression Levels

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Protein Structures

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pLDDT Score Distribution

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Ramachandran Plot of Protein Structures

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Potential Active Site Information

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Protein Structure and Feature Comparision

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Protein-Protein Interaction

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Related Drugs

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Related Diseases

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Clinically Important Variants

Protein:FOXP3

Protein Summary

check button Gene summary
Gene name: FOXP3
ASpdb.0 ID: 50943
Gene
Gene symbol

FOXP3

Gene ID

50943

Gene nameforkhead box P3
SynonymsAIID|DIETER|IPEX|JM2|PIDX|XPID
Cytomap

Xp11.23

Type of geneprotein-coding
Descriptionforkhead box protein P3FOXP3delta7immune dysregulation, polyendocrinopathy, enteropathy, X-linkedimmunodeficiency, polyendocrinopathy, enteropathy, X-linked
Modification date20240407
UniProtAcc

Q9BZS1


check button Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
GeneFOXP3

GO:0001228

DNA-binding transcription activator activity, RNA polymerase II-specific

19276356

GeneFOXP3

GO:0001818

negative regulation of cytokine production

11483607

GeneFOXP3

GO:0002725

negative regulation of T cell cytokine production

15466453

GeneFOXP3

GO:0003700

DNA-binding transcription factor activity

11483607|32644293

GeneFOXP3

GO:0005634

nucleus

32644293

GeneFOXP3

GO:0005634

nucleus

11483607|16873067|16920951|22678915|24012345

GeneFOXP3

GO:0005654

nucleoplasm

-

GeneFOXP3

GO:0005737

cytoplasm

22678915

GeneFOXP3

GO:0005829

cytosol

-

GeneFOXP3

GO:0008285

negative regulation of cell population proliferation

15652505

GeneFOXP3

GO:0032088

negative regulation of NF-kappaB transcription factor activity

16652169

GeneFOXP3

GO:0032689

negative regulation of type II interferon production

15466453

GeneFOXP3

GO:0032693

negative regulation of interleukin-10 production

15466453

GeneFOXP3

GO:0032703

negative regulation of interleukin-2 production

15466453|17360565|17377532

GeneFOXP3

GO:0032713

negative regulation of interleukin-4 production

15466453

GeneFOXP3

GO:0032792

negative regulation of CREB transcription factor activity

16652169

GeneFOXP3

GO:0042110

T cell activation

15466453

GeneFOXP3

GO:0042130

negative regulation of T cell proliferation

15466453

GeneFOXP3

GO:0042803

protein homodimerization activity

21458306

GeneFOXP3

GO:0043433

negative regulation of DNA-binding transcription factor activity

16873067

GeneFOXP3

GO:0043565

sequence-specific DNA binding

11483607|16873067|19276356

GeneFOXP3

GO:0045066

regulatory T cell differentiation

32644293

GeneFOXP3

GO:0045591

positive regulation of regulatory T cell differentiation

30513302

GeneFOXP3

GO:0045892

negative regulation of DNA-templated transcription

11483607|16920951|17360565|22678915

GeneFOXP3

GO:0045893

positive regulation of DNA-templated transcription

15466453

GeneFOXP3

GO:0050777

negative regulation of immune response

15652505

GeneFOXP3

GO:1990837

sequence-specific double-stranded DNA binding

28473536



AS Summary

check button Information of the canonical protein with experimentally identified structure from PDB (2023).
UniProt AccFile namePDB IDMethodResolutionChainStartEnd
Q9BZS1-1Q9BZS1-1_3qrf_F.pdb3QRFX-ray2.8F336417

check button ASpdb's canonical and alternatively spliced isoform information.
accession_idgene_namecanonical_idalternative_idcanonical_lengthalternative_lengthcanonical_startcanonical_endtypeoriginalSEQvariationSEQalternative_startalternative_end
Q9BZS1FOXP3Q9BZS1-1Q9BZS1-243139672106Deletionnonenone7171
Q9BZS1FOXP3Q9BZS1-1Q9BZS1-343145672106Deletionnonenone7171
Q9BZS1FOXP3Q9BZS1-1Q9BZS1-3431456382382SubstitutionKKVSSSEVAVTGMASSAIAAQSGQAWVWAHRHIGEERDVGCWWWLLASEVDAHLLPVPGLPQ347407
Q9BZS1FOXP3Q9BZS1-1Q9BZS1-4431404246272Deletionnonenone245245

check buttonMultiple sequence alignment of our canonical and alternatively spliced FOXP3

check button Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of FOXP3
UniProt-idENSGENSTENSP
Q9BZS1-1ENSG00000049768.18ENST00000376207.10ENSP00000365380.4
Q9BZS1-2ENSG00000049768.18ENST00000376199.7ENSP00000365372.2
Q9BZS1-3ENSG00000049768.18ENST00000557224.6ENSP00000451208.1
Q9BZS1-4ENSG00000049768.18ENST00000518685.6ENSP00000428952.2

UniProt-idNM IDNP ID
Q9BZS1-1NM_014009.3NP_054728.2
Q9BZS1-2NM_001114377.1NP_001107849.1

check buttonAmino acid sequences of our canonical and alternatively spliced FOXP3
accession_idProtein sequence
Q9BZS1-1MPNPRPGKPSAPSLALGPSPGASPSWRAAPKASDLLGARGPGGTFQGRDLRGGAHASSSSLNPMPPSQLQLPTLPLVMVAPSGARLGPLP
HLQALLQDRPHFMHQLSTVDAHARTPVLQVHPLESPAMISLTPPTTATGVFSLKARPGLPPGINVASLEWVSREPALLCTFPNPSAPRKD
STLSAVPQSSYPLLANGVCKWPGCEKVFEEPEDFLKHCQADHLLDEKGRAQCLLQREMVQSLEQQLVLEKEKLSAMQAHLAGKMALTKAS
SVASSDKGSCCIVAAGSQGPVVPAWSGPREAPDSLFAVRRHLWGSHGNSTFPEFLHNMDYFKFHNMRPPFTYATLIRWAILEAPEKQRTL
Q9BZS1-2MPNPRPGKPSAPSLALGPSPGASPSWRAAPKASDLLGARGPGGTFQGRDLRGGAHASSSSLNPMPPSQLQLSTVDAHARTPVLQVHPLES
PAMISLTPPTTATGVFSLKARPGLPPGINVASLEWVSREPALLCTFPNPSAPRKDSTLSAVPQSSYPLLANGVCKWPGCEKVFEEPEDFL
KHCQADHLLDEKGRAQCLLQREMVQSLEQQLVLEKEKLSAMQAHLAGKMALTKASSVASSDKGSCCIVAAGSQGPVVPAWSGPREAPDSL
FAVRRHLWGSHGNSTFPEFLHNMDYFKFHNMRPPFTYATLIRWAILEAPEKQRTLNEIYHWFTRMFAFFRNHPATWKNAIRHNLSLHKCF
Q9BZS1-3MPNPRPGKPSAPSLALGPSPGASPSWRAAPKASDLLGARGPGGTFQGRDLRGGAHASSSSLNPMPPSQLQLSTVDAHARTPVLQVHPLES
PAMISLTPPTTATGVFSLKARPGLPPGINVASLEWVSREPALLCTFPNPSAPRKDSTLSAVPQSSYPLLANGVCKWPGCEKVFEEPEDFL
KHCQADHLLDEKGRAQCLLQREMVQSLEQQLVLEKEKLSAMQAHLAGKMALTKASSVASSDKGSCCIVAAGSQGPVVPAWSGPREAPDSL
FAVRRHLWGSHGNSTFPEFLHNMDYFKFHNMRPPFTYATLIRWAILEAPEKQRTLNEIYHWFTRMFAFFRNHPATWKVSSSEVAVTGMAS
SAIAAQSGQAWVWAHRHIGEERDVGCWWWLLASEVDAHLLPVPGLPQNAIRHNLSLHKCFVRVESEKGAVWTVDELEFRKKRSQRPSRCS
Q9BZS1-4MPNPRPGKPSAPSLALGPSPGASPSWRAAPKASDLLGARGPGGTFQGRDLRGGAHASSSSLNPMPPSQLQLPTLPLVMVAPSGARLGPLP
HLQALLQDRPHFMHQLSTVDAHARTPVLQVHPLESPAMISLTPPTTATGVFSLKARPGLPPGINVASLEWVSREPALLCTFPNPSAPRKD
STLSAVPQSSYPLLANGVCKWPGCEKVFEEPEDFLKHCQADHLLDEKGRAQCLLQREMVQSLEQQASSDKGSCCIVAAGSQGPVVPAWSG
PREAPDSLFAVRRHLWGSHGNSTFPEFLHNMDYFKFHNMRPPFTYATLIRWAILEAPEKQRTLNEIYHWFTRMFAFFRNHPATWKNAIRH

Protein Functional Features

check buttonMain function of this protein. (from UniProt)
FOXP3 (go to UniProt):Q9BZS1

check buttonRetention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.
- Retained protein feature among the 13 regional features.
Accession_idSubsectionStartEndFuncitonal featureSplicing information
Q9BZS1DNA binding337423Note=Fork-head;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00089Type=Substitution;Start=382;End=382
Q9BZS1Region106198Note=Interaction with ZFP90;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23543754;Dbxref=PMID:23543754Type=Deletion;Start=72;End=106
Q9BZS1Region106198Note=Interaction with ZFP90;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23543754;Dbxref=PMID:23543754Type=Deletion;Start=72;End=106
Q9BZS1Region106190Note=Essential for transcriptional repressor activity and for interaction with KAT5 and HDAC7;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17360565;Dbxref=PMID:17360565Type=Deletion;Start=72;End=106
Q9BZS1Region106190Note=Essential for transcriptional repressor activity and for interaction with KAT5 and HDAC7;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17360565;Dbxref=PMID:17360565Type=Deletion;Start=72;End=106
Q9BZS1Region239260Note=Leucine-zipperType=Deletion;Start=246;End=272
Q9BZS1Motif6876Note=Nuclear export signal;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22678915;Dbxref=PMID:22678915Type=Deletion;Start=72;End=106
Q9BZS1Motif6876Note=Nuclear export signal;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22678915;Dbxref=PMID:22678915Type=Deletion;Start=72;End=106
Q9BZS1Motif9296Note=LXXLL motif;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18354202;Dbxref=PMID:18354202Type=Deletion;Start=72;End=106
Q9BZS1Motif9296Note=LXXLL motif;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18354202;Dbxref=PMID:18354202Type=Deletion;Start=72;End=106
Q9BZS1Motif239248Note=Nuclear export signal;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:22678915;Dbxref=PMID:22678915Type=Deletion;Start=246;End=272


Gene Isoform Structures and Expression Levels for FOXP3

check buttonGene structures of our canonical and alternative spliced genes of FOXP3
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
gene isoform structure of FOXP3

check button Expression levels of gene isoforms across GTEx.
gtex expression

check button Expression levels of gene isoforms across TCGA.
tcga expression


Protein Structures

check button PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
3D view using mol* of Q9BZS1-1
3D view using mol* of Q9BZS1-2
3D view using mol* of Q9BZS1-3
3D view using mol* of Q9BZS1-4


pLDDT Score Distribution

check button pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
pLDDT distribution across the protein length of Q9BZS1-1
all structure
pLDDT distribution across the protein length of Q9BZS1-2
all structure
pLDDT distribution across the protein length of Q9BZS1-3
all structure
pLDDT distribution across the protein length of Q9BZS1-4
all structure


Ramachandran Plot of Protein Structures


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.
Ramachandran plot of Q9BZS1-1
all structure
Ramachandran plot of Q9BZS1-2
all structure
Ramachandran plot of Q9BZS1-3
all structure
Ramachandran plot of Q9BZS1-4
all structure

Potential Active Site Information


check button The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.
UniProt-idSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
Q9BZS1-11.0391291.107417.7740.6260.6570.8770.9820.6961.4120.75292,94,95,96,98,99,100,102,103,201,202,203,204,221,
222,223,224,225,226,227,228,230,231,232,233,234,23
5,237,238,328,329,332,333
Q9BZS1-20.9921360.979320.3620.5790.6860.9390.5691.1410.4980.495275,278,279,280,281,282,283,286,302,303,304,305,30
6,307,308,309,310,312,313,339,357,358,359,375,377,
378,379,381,382,383,384,385
Q9BZS1-31.051971.124365.9810.5910.6710.9581.1490.6271.8331.217343,346,347,348,385,388,389,391,392,395,399,400,40
1,402,403,404,405,407,411
Q9BZS1-41.0991231.154332.710.4770.7591.0241.6980.742.2950.899227,230,231,233,234,235,237,238,278,279,281,282,28
5,286,297,299,300,301,302,303,304,309,312,313

Protein Structure and Feature Comparision


check button Protein Structure Comparision Using Template Modeling Scores (TM-score).
all structure

check button Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)
3D view using mol* of Q9BZS1-1_Q9BZS1-1_3qrf_F.pdb

check button Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)
3D view using mol* of Q9BZS1-1_3qrf_F_Q9BZS1-2.pdb
3D view using mol* of Q9BZS1-1_3qrf_F_Q9BZS1-3.pdb
3D view using mol* of Q9BZS1-1_3qrf_F_Q9BZS1-4.pdb

check button Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)
3D view using mol* of Q9BZS1-1_Q9BZS1-2.pdb
3D view using mol* of Q9BZS1-1_Q9BZS1-3.pdb
3D view using mol* of Q9BZS1-1_Q9BZS1-4.pdb

check button Protein Feature Comparison of the protein sequendary structures among the protiens.
./stats/secondary_structure/figure/Q9BZS1-1_vs_Q9BZS1-2.png
all structure<
./stats/secondary_structure/figure/Q9BZS1-1_vs_Q9BZS1-3.png
all structure<
./stats/secondary_structure/figure/Q9BZS1-1_vs_Q9BZS1-4.png
all structure<

check button Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.
./stats/relative_asa/Q9BZS1-1_vs_Q9BZS1-2.png
all structure<
./stats/relative_asa/Q9BZS1-1_vs_Q9BZS1-3.png
all structure<
./stats/relative_asa/Q9BZS1-1_vs_Q9BZS1-4.png
all structure<


Protein-Protein Interaction


check button Interactors from UniProt.
Accession_idSubsectionStartEndFuncitonal featureSplicing information
Q9BZS1Region106198Note=Interaction with ZFP90;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23543754;Dbxref=PMID:23543754Type=Deletion;Start=72;End=106
Q9BZS1Region106198Note=Interaction with ZFP90;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23543754;Dbxref=PMID:23543754Type=Deletion;Start=72;End=106
Q9BZS1Region106190Note=Essential for transcriptional repressor activity and for interaction with KAT5 and HDAC7;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17360565;Dbxref=PMID:17360565Type=Deletion;Start=72;End=106
Q9BZS1Region106190Note=Essential for transcriptional repressor activity and for interaction with KAT5 and HDAC7;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17360565;Dbxref=PMID:17360565Type=Deletion;Start=72;End=106


check button Interactors from STRING.
Gene nameInteractors


Related Drugs to FOXP3


check button Drugs targeting this gene/protein.
(DrugBank)
UniProt accessionGene nameDrugBank IDDrug nameDrug groupActions

Related Diseases to FOXP3


check button Previous studies relating to the alternative splicing of FOXP3 and disease information from the MeSH term (PubMed)
GenePMIDTitleAbstractMeSH IDMeSH term
FOXP318413770The regulatory T cell-associated transcription factor FoxP3 is expressed by tumor cells.FoxP3 is a member of the forkhead family of transcription factors critically involved in the development and function of CD25(+) regulatory T cells (Treg). Until recently, FoxP3 expression was thought to be restricted to the T-cell lineage. However, using immunohistochemistry and flow cytometric analysis of human melanoma tissue, we detected FoxP3 expression not only in the tumor infiltrating Treg but also in the melanoma cells themselves. FoxP3 is also widely expressed by established human melanoma cell lines (as determined by flow cytometry, PCR, and Western blot), as well as cell lines derived from other solid tumors. Normal B cells do not express FoxP3; however, expression could be induced after transformation with EBV in vitro and in vivo, suggesting that malignant transformation of healthy cells can induce FoxP3. In addition, a FOXP3 mRNA variant lacking exons 3 and 4 was identified in tumor cell lines but was absent from Treg. Interestingly, this alternative splicing event introduces a translation frame-shift that is predicted to encode a novel protein. Together, our results show that FoxP3, a key regulator of immune suppression, is not only expressed by Treg but also by melanoma cells, EBV-transformed B cells, and a wide variety of tumor cell lines.D005910Glioma
FOXP318413770The regulatory T cell-associated transcription factor FoxP3 is expressed by tumor cells.FoxP3 is a member of the forkhead family of transcription factors critically involved in the development and function of CD25(+) regulatory T cells (Treg). Until recently, FoxP3 expression was thought to be restricted to the T-cell lineage. However, using immunohistochemistry and flow cytometric analysis of human melanoma tissue, we detected FoxP3 expression not only in the tumor infiltrating Treg but also in the melanoma cells themselves. FoxP3 is also widely expressed by established human melanoma cell lines (as determined by flow cytometry, PCR, and Western blot), as well as cell lines derived from other solid tumors. Normal B cells do not express FoxP3; however, expression could be induced after transformation with EBV in vitro and in vivo, suggesting that malignant transformation of healthy cells can induce FoxP3. In addition, a FOXP3 mRNA variant lacking exons 3 and 4 was identified in tumor cell lines but was absent from Treg. Interestingly, this alternative splicing event introduces a translation frame-shift that is predicted to encode a novel protein. Together, our results show that FoxP3, a key regulator of immune suppression, is not only expressed by Treg but also by melanoma cells, EBV-transformed B cells, and a wide variety of tumor cell lines.D008545Melanoma
FOXP318413770The regulatory T cell-associated transcription factor FoxP3 is expressed by tumor cells.FoxP3 is a member of the forkhead family of transcription factors critically involved in the development and function of CD25(+) regulatory T cells (Treg). Until recently, FoxP3 expression was thought to be restricted to the T-cell lineage. However, using immunohistochemistry and flow cytometric analysis of human melanoma tissue, we detected FoxP3 expression not only in the tumor infiltrating Treg but also in the melanoma cells themselves. FoxP3 is also widely expressed by established human melanoma cell lines (as determined by flow cytometry, PCR, and Western blot), as well as cell lines derived from other solid tumors. Normal B cells do not express FoxP3; however, expression could be induced after transformation with EBV in vitro and in vivo, suggesting that malignant transformation of healthy cells can induce FoxP3. In addition, a FOXP3 mRNA variant lacking exons 3 and 4 was identified in tumor cell lines but was absent from Treg. Interestingly, this alternative splicing event introduces a translation frame-shift that is predicted to encode a novel protein. Together, our results show that FoxP3, a key regulator of immune suppression, is not only expressed by Treg but also by melanoma cells, EBV-transformed B cells, and a wide variety of tumor cell lines.D011471Prostatic Neoplasms
FOXP326441347IL-1β promotes Th17 differentiation by inducing alternative splicing of FOXP3.CD4(+)FOXP3(+) regulatory T (Treg) cells are essential for maintaining immunological self-tolerance. Treg cell development and function depend on the transcription factor FOXP3, which is present in several distinct isoforms due to alternative splicing. Despite the importance of FOXP3 in the proper maintenance of Treg cells, the regulation and functional consequences of FOXP3 isoform expression remains poorly understood. Here, we show that in human Treg cells IL-1β promotes excision of FOXP3 exon 7. FOXP3 is not only expressed by Treg cells but is also transiently expressed when naïve T cells differentiate into Th17 cells. Forced splicing of FOXP3 into FOXP3Δ2Δ7 strongly favored Th17 differentiation in vitro. We also found that patients with Crohn's disease express increased levels of FOXP3 transcripts lacking exon 7, which correlate with disease severity and IL-17 production. Our results demonstrate that alternative splicing of FOXP3 modulates T cell differentiation. These results highlight the importance of characterizing FOXP3 expression on an isoform basis and suggest that immune responses may be manipulated by modulating the expression of FOXP3 isoforms, which has broad implications for the treatment of autoimmune diseases.D003424Crohn Disease


Clinically important variants in FOXP3


check button (ClinVar, 04/20/2024)
accession_iduniprot_idgene_nameTypeVariantClinical_significance