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FOXD4L1 Gene

protein-coding   GIFtS: 41
GCID: GC02P114256

Forkhead Box D4-Like 1

  Search for FOXD4L1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Forkhead Box D4-Like 11 2
FOXD4-Like 12 3
FOXD52
bA395L14.12
Forkhead Box D4 Like 12
Forkhead Box Protein D4-Like 12

External Ids:    HGNC: 185211   Entrez Gene: 2003502   Ensembl: ENSG000001844927   OMIM: 6110845   UniProtKB: Q9NU393   

Export aliases for FOXD4L1 gene to outside databases

Previous GC identifers: GC02P112177 GC02P114163 GC02P114351 GC02P113972


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for FOXD4L1 Gene:
This gene is a member of the forkhead/winged-helix (FOX) family of transcription factors with highly conserved FOX
DNA-binding domains. Members of the FOX family of transcription factors are regulators of embryogenesis and may
play a role in human cancer. This gene lies in a region of chromosome 2 that surrounds the site where two
ancestral chromosomes fused to form human chromosome 2. This region is duplicated elsewhere in the human genome,
primarily in subtelomeric and pericentromeric locations, thus mutiple copies of this gene have been found.
(provided by RefSeq, Jul 2008)

GeneCards Summary for FOXD4L1 Gene:
FOXD4L1 (forkhead box D4-like 1) is a protein-coding gene. GO annotations related to this gene include double-stranded DNA binding and sequence-specific DNA binding. An important paralog of this gene is FOXA2.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NC_018913.2  NT_005403.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the FOXD4L1 gene promoter:
         TBP   C/EBPbeta   p53   LCR-F1   GATA-1   GATA-2   Pax-3   CP2   FOXO4   STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFOXD4L1 promoter sequence
   Search Chromatin IP Primers for FOXD4L1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FOXD4L1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q13   Ensembl cytogenetic band:  2q13   HGNC cytogenetic band: 2q14.1

FOXD4L1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FOXD4L1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P114256:  view genomic region     (about GC identifiers)

Start:
114,256,661 bp from pter      End:
114,258,728 bp from pter
Size:
2,068 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: FX4L1_HUMAN, Q9NU39 (See protein sequence)
Recommended Name: Forkhead box protein D4-like 1  
Size: 408 amino acids; 43610 Da
Secondary accessions: B3KWN1 B9EGF3

Explore the universe of human proteins at neXtProt for FOXD4L1: NX_Q9NU39

Explore proteomics data for FOXD4L1 at MOPED


See FOXD4L1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_036316.1  
ENSEMBL proteins: 
 ENSP00000302756  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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3 InterPro protein domains:
 IPR011991 WHTH_DNA-bd_dom
 IPR018122 TF_fork_head_CS
 IPR001766 TF_fork_head

Graphical View of Domain Structure for InterPro Entry Q9NU39

ProtoNet protein and cluster: Q9NU39

UniProtKB/Swiss-Prot: FX4L1_HUMAN, Q9NU39
Similarity: Contains 1 fork-head DNA-binding domain


Find genes that share domains with FOXD4L1           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003690double-stranded DNA binding IBA--
GO:0003700sequence-specific DNA binding transcription factor activity ----
GO:0003705RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity IBA--
GO:0008134transcription factor binding IBA--
GO:0008301DNA binding, bending IBA--
     
Find genes that share ontologies with FOXD4L1           About GenesLikeMe


Animal Models:
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SwitchGear 3'UTR luciferase reporter plasmidFOXD4L1 3' UTR sequence
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
FX4L1_HUMAN, Q9NU39: Nucleus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus3
cytosol2

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--
GO:0005667transcription factor complex IBA--

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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for FOXD4L1
Interactions:

    Search GeneGlobe Interaction Network for FOXD4L1

STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

3 Interacting proteins for FOXD4L1 (ENSP000003027564) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
TIMM13ENSP000002155704STRING: ENSP00000215570
TIMM8AENSP000003619934STRING: ENSP00000361993
--ENSP000002803544STRING: ENSP00000280354
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Gene Ontology (GO): Selected biological process terms (see all 18):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000122negative regulation of transcription from RNA polymerase II promoter IBA--
GO:0001658branching involved in ureteric bud morphogenesis IBA--
GO:0001755neural crest cell migration IBA--
GO:0001822kidney development IBA--
GO:0006355regulation of transcription, DNA-templated ----

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for FOXD4L1 (FX4L1)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for FOXD4L1 gene: 
NM_012184.4  

Unigene Cluster for FOXD4L1:

Forkhead box D4-like 1
Hs.591554  [show with all ESTs]
Unigene Representative Sequence: AK125398
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000306507(uc002tjw.4)
miRNA
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2 qRT-PCR Assays for microRNAs that regulate FOXD4L1:
hsa-miR-19b hsa-miR-19a
SwitchGear 3'UTR luciferase reporter plasmidFOXD4L1 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat FOXD4L1
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  QuantiFast Probe-based Assays in human, mouse, rat FOXD4L1

Additional mRNA sequence: 

AF452723.1 AK122950.1 AK125398.1 AY344639.1 BC136428.1 

4 DOTS entries:

DT.120985299  DT.101983633  DT.121174326  DT.436073 

11 AceView cDNA sequences:

NM_012184 AF452723 AK125398 BV196387 AY344639 BV196388 BV190165 BV196386 
AK122950 CB856755 AI860024 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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FOXD4L1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
FOXD4L1 Expression
About this image

FOXD4L1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

FOXD4L1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.591554
    Custom PCR Arrays for FOXD4L1
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FOXD4L1

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for FOXD4L1 gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
64(a)
1 → many
2(49994144-49994639)
tropical clawed frog
(Xenopus tropicalis)
Amphibia foxd4l1.11 forkhead box D4-like 1, gene 1 57.56(n)
59.79(a)
  549682  NM_001016928.1  NP_001016928.1 
zebrafish
(Danio rerio)
Actinopterygii foxd56
forkhead box D5
39(a)
many ↔ many
8(31300987-31302138) ENSDARG00000042485
fruit fly
(Drosophila melanogaster)
Insecta fd59A6
forkhead domain 59A
25(a)
1 → many
2R(18754044-18758229)
worm
(Caenorhabditis elegans)
Secernentea unc-1306
Protein UNC-130 (unc-130) mRNA, complete cds
30(a)
1 → many
II(11281986-11283954) WBGene00006853
        Species with no ortholog for FOXD4L1

ENSEMBL Gene Tree for FOXD4L1 (if available)
TreeFam Gene Tree for FOXD4L1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for FOXD4L1 gene
FOXA22  FOXC22  FOXI22  FOXB12  FOXE32  FOXC12  FOXD4L22  FOXD4L32  
FOXA32  FOXD4L52  FOXD12  FOXD32  FOXD4L42  FOXA12  FOXE12  FOXL12  
FOXB22  FOXI12  FOXD4L62  FOXS12  FOXD22  FOXL22  FOXD42  
9 SIMAP similar genes for FOXD4L1 using alignment to 1 protein entry:     FX4L1_HUMAN:
FOXD4L2    FOXD4L3    FOXD4L4    FOXD4L5    FOXD4L6    FOXD4
FOXD3    FOXE3    FOXC2

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(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for FOXD4L1 (see all 128)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs742673441,2
C--114255204(+) TGAAAA/GAATGA 1 -- us2k12Minor allele frequency- G:0.25NA 4
rs75948471,2
C,F--114255236(+) acgccG/Tgtaat 1 -- us2k13Minor allele frequency- T:0.33NA 6
rs2002302561,2
C--114255298(+) GACCAC/TCCTGG 1 -- us2k10--------
rs1923081041,2
--114255351(+) TTAGCC/TGGGCG 1 -- us2k10--------
rs748271701,2
C--114255358(+) GGCGTG/AGTGGC 1 -- us2k11Minor allele frequency- A:0.50NA 2
rs1832773191,2
--114255388(+) TACTCG/TGGAGG 1 -- us2k10--------
rs76069641,2
C,F--114255401(+) gaggcA/Gggaga 1 -- us2k13Minor allele frequency- G:0.17NA 6
rs794785621,2
F--114255444(+) GGTCCT/GAGATT 1 -- us2k12Minor allele frequency- G:0.25NA 4
rs29006791,2
F--114255486(+) cgacaC/Acgtct 1 -- us2k13Minor allele frequency- A:0.17NA 6
rs27579671,2
C--114255629(+) gcctgC/Tgcaac 1 -- us2k10--------

HapMap Linkage Disequilibrium report for FOXD4L1 (114256661 - 114258728 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for FOXD4L1:    About this table    
Variant IDTypeSubtypePubMed ID
esv2675836CNV Deletion23128226
esv28287CNV Gain19812545
nsv874903CNV Gain21882294
nsv874902CNV Gain21882294
nsv834334CNV Gain17160897
esv380CNV CNV17122850
essv901CNV CNV17122850

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 611084    OMIM disorders: --


Find genes that share disorders with FOXD4L1           About GenesLikeMe


Export disorders for FOXD4L1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for FOXD4L1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with FOXD4L1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Diverse fates of paralogs following segmental duplication of telomeric genes. (PubMed id 15233989)1, 2, 3 Wong A.... Ledbetter D.H. (Genomics 2004)
  2. Gene content and function of the ancestral chromosome fusion site in human chromosome 2q13-2q14.1 and paralogous regions. (PubMed id 12421752)1, 2, 3 Fan Y.... Trask B.J. (Genome Res. 2002)
  3. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W.... Wilson R.K. (Nature 2005)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  5. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
  6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  8. Cloning and characterization of seven human forkhead proteins: binding site specificity and DNA bending. (PubMed id 7957066)1 Pierrou S.... Carlsson P. (EMBO J. 1994)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 200350 HGNC: 18521 AceView: FOXD4L1 Ensembl:ENSG00000184492 euGenes: HUgn200350
ECgene: FOXD4L1 H-InvDB: FOXD4L1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for FOXD4L1 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for FOXD4L1 Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for FOXD4L1 gene:
Search GeneIP for patents involving FOXD4L1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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