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FOXP4 forkhead box P4 [ Homo sapiens (human) ]

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

Summary

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
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Genomic context

See FOXP4 in Genome Data Viewer
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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

HIV-1 interactions

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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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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_001012426.2NP_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:467546
    Forkhead; Forkhead domain
    pfam16159
    Location:303370
    FOXP-CC; FOXP coiled-coil domain
  2. NM_001012427.2NP_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:465537
    FH; FORKHEAD
    pfam16159
    Location:301368
    FOXP-CC; FOXP coiled-coil domain
  3. NM_001405824.1NP_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_001405825.1NP_001392754.1  forkhead box protein P4 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL139331
  5. NM_001405826.1NP_001392755.1  forkhead box protein P4 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL139331
  6. NM_138457.3NP_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:454533
    Forkhead; Forkhead domain
    pfam16159
    Location:302369
    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_011514289.3XP_011512591.1  forkhead box protein P4 isoform X1

    Conserved Domains (2) summary
    pfam00250
    Location:474553
    Forkhead; Forkhead domain
    pfam16159
    Location:310377
    FOXP-CC; FOXP coiled-coil domain
  2. XM_011514291.4XP_011512593.1  forkhead box protein P4 isoform X4

    Conserved Domains (2) summary
    pfam00250
    Location:462541
    Forkhead; Forkhead domain
    pfam16159
    Location:310377
    FOXP-CC; FOXP coiled-coil domain
  3. XM_006714991.4XP_006715054.1  forkhead box protein P4 isoform X3

    Conserved Domains (2) summary
    pfam00250
    Location:466545
    Forkhead; Forkhead domain
    pfam16159
    Location:302369
    FOXP-CC; FOXP coiled-coil domain
  4. XM_011514290.3XP_011512592.1  forkhead box protein P4 isoform X2

    Conserved Domains (2) summary
    pfam00250
    Location:472551
    Forkhead; Forkhead domain
    pfam16159
    Location:308375
    FOXP-CC; FOXP coiled-coil domain
  5. XM_047418160.1XP_047274116.1  forkhead box protein P4 isoform X5

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

    Conserved Domains (2) summary
    pfam00250
    Location:442521
    Forkhead; Forkhead domain
    pfam16159
    Location:278345
    FOXP-CC; FOXP coiled-coil domain
  7. XM_017010233.2XP_016865722.1  forkhead box protein P4 isoform X1

    Conserved Domains (2) summary
    pfam00250
    Location:474553
    Forkhead; Forkhead domain
    pfam16159
    Location:310377
    FOXP-CC; FOXP coiled-coil domain
  8. XM_011514293.4XP_011512595.1  forkhead box protein P4 isoform X7

    Conserved Domains (2) summary
    pfam00250
    Location:368447
    Forkhead; Forkhead domain
    pfam16159
    Location:204271
    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_054354179.1XP_054210154.1  forkhead box protein P4 isoform X1

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

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

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

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

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

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

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

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

RNA

  1. XR_008487250.1 RNA Sequence

  2. XR_008487251.1 RNA Sequence