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    FOXP4 forkhead box P4 [ Homo sapiens (human) ]

    Gene ID: 116113, updated on 7-Apr-2024

    Summary

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    Official Symbol
    FOXP4provided by HGNC
    Official Full Name
    forkhead box P4provided by HGNC
    Primary source
    HGNC:HGNC:20842
    See related
    Ensembl:ENSG00000137166 MIM:608924; AllianceGenome:HGNC:20842
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    hFKHLA
    Summary
    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. Many members of the forkhead box gene family, including members of subfamily P, have roles in mammalian oncogenesis. This gene may play a role in the development of tumors of the kidney and larynx. Alternative splicing of this gene produces multiple transcript variants, some encoding different isoforms. [provided by RefSeq, Jul 2008]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
    Expression
    Ubiquitous expression in stomach (RPKM 7.0), testis (RPKM 4.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    6p21.1
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (41546381..41602384)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (41375416..41431427)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (41514119..41570122)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986538 Neighboring gene VISTA enhancer hs2104 Neighboring gene uncharacterized LOC112267957 Neighboring gene Sharpr-MPRA regulatory region 8968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41424325-41425112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41438012-41438663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41459644-41460288 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:41461668-41461828 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41470387-41471134 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41471135-41471882 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41473163-41473662 Neighboring gene long intergenic non-protein coding RNA 1276 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr6:41499390-41499960 and GRCh37_chr6:41499961-41500529 Neighboring gene FOXP4 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 11601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24511 Neighboring gene Sharpr-MPRA regulatory region 4049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17186 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17185 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:41522869-41523869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41527759-41528701 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41529644-41530586 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41530587-41531527 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41536528-41537428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41537429-41538327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41546115-41546738 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:41546739-41547361 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41549275-41549776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41551423-41552002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41552003-41552582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41552583-41553162 Neighboring gene VISTA enhancer hs1100 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41565978-41566562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41566563-41567146 Neighboring gene Sharpr-MPRA regulatory region 5412 Neighboring gene microRNA 4641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41601984-41602484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41602485-41602985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41608279-41608859 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:41612529-41613514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41614501-41615485 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41625153-41625767 Neighboring gene MyoD family inhibitor Neighboring gene nucleophosmin 1 pseudogene 51

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Recurrent FOXP4 nonsense variant in two unrelated patients: Association with neurodevelopmental disease and congenital diaphragmatic hernia. Del Viso F, et al. Am J Med Genet A, 2023 Jan. PMID 36301021
    2. FOXP4 promotes proliferation of human spermatogonial stem cells. Luo SW, et al. Asian J Androl, 2023 May-Jun. PMID 36018067, Free PMC Article
    3. FOXP4 inhibits squamous differentiation of atypical cells in cervical intraepithelial neoplasia via an ELF3-dependent pathway. Matsumoto T, et al. Cancer Sci, 2022 Oct. PMID 35838233, Free PMC Article
    4. FOXP4 promotes laryngeal squamous cell carcinoma progression through directly targeting LEF‑1. Shi J, et al. Mol Med Rep, 2021 Dec. PMID 34590150, Free PMC Article
    5. Heterozygous variants that disturb the transcriptional repressor activity of FOXP4 cause a developmental disorder with speech/language delays and multiple congenital abnormalities. Snijders Blok L, et al. Genet Med, 2021 Mar. PMID 33110267, Free PMC Article

    See all (66) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Polymorphisms of IFN signaling genes and FOXP4 influence the severity of COVID-19.
      Title: Polymorphisms of IFN signaling genes and FOXP4 influence the severity of COVID-19.
    2. FOXP4 promotes proliferation of human spermatogonial stem cells.
      Title: FOXP4 promotes proliferation of human spermatogonial stem cells.
    3. Recurrent FOXP4 nonsense variant in two unrelated patients: Association with neurodevelopmental disease and congenital diaphragmatic hernia.
      Title: Recurrent FOXP4 nonsense variant in two unrelated patients: Association with neurodevelopmental disease and congenital diaphragmatic hernia.
    4. FOXP4 inhibits squamous differentiation of atypical cells in cervical intraepithelial neoplasia via an ELF3-dependent pathway.
      Title: FOXP4 inhibits squamous differentiation of atypical cells in cervical intraepithelial neoplasia via an ELF3-dependent pathway.
    5. Downregulation of microRNA4235p suppresses TGFbeta1induced EMT by targeting FOXP4 in airway fibrosis.
      Title: Downregulation of microRNA‑423‑5p suppresses TGF‑β1‑induced EMT by targeting FOXP4 in airway fibrosis.
    6. The forkhead box transcription factor FoxP4 regulates thermogenic programs in adipocytes.
      Title: The forkhead box transcription factor FoxP4 regulates thermogenic programs in adipocytes.
    7. FOXP4 promotes laryngeal squamous cell carcinoma progression through directly targeting LEF1.
      Title: FOXP4 promotes laryngeal squamous cell carcinoma progression through directly targeting LEF‑1.
    8. Heterozygous variants that disturb the transcriptional repressor activity of FOXP4 cause a developmental disorder with speech/language delays and multiple congenital abnormalities.
      Title: Heterozygous variants that disturb the transcriptional repressor activity of FOXP4 cause a developmental disorder with speech/language delays and multiple congenital abnormalities.
    9. circ0000212 promotes cell proliferation of colorectal cancer by sponging miR491 and modulating FOXP4 expression.
      Title: circ‑0000212 promotes cell proliferation of colorectal cancer by sponging miR‑491 and modulating FOXP4 expression.
    10. Long noncoding RNA LINC00858 promotes the proliferation, migration and invasion of gastric cancer cells via the miR-363-3p/FOXP4 axis.
      Title: Long noncoding RNA LINC00858 promotes the proliferation, migration and invasion of gastric cancer cells via the miR-363-3p/FOXP4 axis.
    Submit: New GeneRIF Correction See all GeneRIFs (28)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat specifically associates with FOXP4 promoter to upregulate FOXP4 expression in T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ40908, FLJ44184

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    forkhead box protein P4
    Names
    fork head-related protein like A
    winged-helix repressor FOXP4

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001012426.2 → NP_001012426.1  forkhead box protein P4 isoform 1

      See identical proteins and their annotated locations for NP_001012426.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB080747, AL139331, AW450805, BC040962
      Consensus CDS
      CCDS34447.1
      UniProtKB/Swiss-Prot
      Q5W098, Q7Z7F8, Q8IVH2, Q8IW55, Q96E19
      Related
      ENSP00000309823.4, ENST00000307972.10
      Conserved Domains (2) summary
      pfam00250
      Location:467 → 546
      Forkhead; Forkhead domain
      pfam16159
      Location:303 → 370
      FOXP-CC; FOXP coiled-coil domain

    2. NM_001012427.2 → NP_001012427.1  forkhead box protein P4 isoform 3

      See identical proteins and their annotated locations for NP_001012427.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the coding region, compared to variant 1, resulting in a shorter protein (isoform 3).
      Source sequence(s)
      AL139331, AW450805, BC040962, BC052803
      Consensus CDS
      CCDS34448.1
      UniProtKB/Swiss-Prot
      Q8IVH2
      Related
      ENSP00000362148.3, ENST00000373057.7
      Conserved Domains (2) summary
      smart00339
      Location:465 → 537
      FH; FORKHEAD
      pfam16159
      Location:301 → 368
      FOXP-CC; FOXP coiled-coil domain

    3. NM_001405824.1 → NP_001392753.1  forkhead box protein P4 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL139331
      Consensus CDS
      CCDS93916.1
      UniProtKB/TrEMBL
      B7ZBM3
      Related
      ENSP00000386958.1, ENST00000409208.5

    4. NM_001405825.1 → NP_001392754.1  forkhead box protein P4 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL139331

    5. NM_001405826.1 → NP_001392755.1  forkhead box protein P4 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL139331

    6. NM_138457.3 → NP_612466.1  forkhead box protein P4 isoform 2

      See identical proteins and their annotated locations for NP_612466.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses several alternate in-frame splice sites in the coding region, compared to variant 1, resulting in a shorter protein (isoform 2).
      Source sequence(s)
      AL139331, AW450805, BC040962
      Consensus CDS
      CCDS4856.1
      UniProtKB/Swiss-Prot
      Q8IVH2
      Related
      ENSP00000362154.3, ENST00000373063.7
      Conserved Domains (2) summary
      pfam00250
      Location:454 → 533
      Forkhead; Forkhead domain
      pfam16159
      Location:302 → 369
      FOXP-CC; FOXP coiled-coil domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      41546381..41602384
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011514289.3 → XP_011512591.1  forkhead box protein P4 isoform X1

      Conserved Domains (2) summary
      pfam00250
      Location:474 → 553
      Forkhead; Forkhead domain
      pfam16159
      Location:310 → 377
      FOXP-CC; FOXP coiled-coil domain

    2. XM_011514291.4 → XP_011512593.1  forkhead box protein P4 isoform X4

      Conserved Domains (2) summary
      pfam00250
      Location:462 → 541
      Forkhead; Forkhead domain
      pfam16159
      Location:310 → 377
      FOXP-CC; FOXP coiled-coil domain

    3. XM_006714991.4 → XP_006715054.1  forkhead box protein P4 isoform X3

      Conserved Domains (2) summary
      pfam00250
      Location:466 → 545
      Forkhead; Forkhead domain
      pfam16159
      Location:302 → 369
      FOXP-CC; FOXP coiled-coil domain

    4. XM_011514290.3 → XP_011512592.1  forkhead box protein P4 isoform X2

      Conserved Domains (2) summary
      pfam00250
      Location:472 → 551
      Forkhead; Forkhead domain
      pfam16159
      Location:308 → 375
      FOXP-CC; FOXP coiled-coil domain

    5. XM_047418160.1 → XP_047274116.1  forkhead box protein P4 isoform X5

    6. XM_011514292.4 → XP_011512594.1  forkhead box protein P4 isoform X6

      Conserved Domains (2) summary
      pfam00250
      Location:442 → 521
      Forkhead; Forkhead domain
      pfam16159
      Location:278 → 345
      FOXP-CC; FOXP coiled-coil domain

    7. XM_017010233.2 → XP_016865722.1  forkhead box protein P4 isoform X1

      Conserved Domains (2) summary
      pfam00250
      Location:474 → 553
      Forkhead; Forkhead domain
      pfam16159
      Location:310 → 377
      FOXP-CC; FOXP coiled-coil domain

    8. XM_011514293.4 → XP_011512595.1  forkhead box protein P4 isoform X7

      Conserved Domains (2) summary
      pfam00250
      Location:368 → 447
      Forkhead; Forkhead domain
      pfam16159
      Location:204 → 271
      FOXP-CC; FOXP coiled-coil domain

    RNA

    1. XR_926052.4 RNA Sequence

    2. XR_926053.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      41375416..41431427
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354179.1 → XP_054210154.1  forkhead box protein P4 isoform X1

    2. XM_054354183.1 → XP_054210158.1  forkhead box protein P4 isoform X4

    3. XM_054354182.1 → XP_054210157.1  forkhead box protein P4 isoform X3

    4. XM_054354181.1 → XP_054210156.1  forkhead box protein P4 isoform X2

    5. XM_054354184.1 → XP_054210159.1  forkhead box protein P4 isoform X5

    6. XM_054354185.1 → XP_054210160.1  forkhead box protein P4 isoform X6

    7. XM_054354180.1 → XP_054210155.1  forkhead box protein P4 isoform X1

    8. XM_054354186.1 → XP_054210161.1  forkhead box protein P4 isoform X7

    9. XM_054354187.1 → XP_054210162.1  forkhead box protein P4 isoform X8

    RNA

    1. XR_008487250.1 RNA Sequence

    2. XR_008487251.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IVH2.1 GenPept UniProtKB/Swiss-Prot:Q8IVH2

    Gene LinkOut

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