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FOXD4L3 Gene

protein-coding   GIFtS: 36
GCID: GC09P070917

Forkhead Box D4-Like 3

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(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 31 2     Forkhead Box D4 Like 32
FOXD4-Like 32 3     Forkhead Box Protein D4-Like 22
FOXD4L22     Forkhead Box Protein D4-Like 32
FOXD62     FOXD4-Like 22

External Ids:    HGNC: 185231   Entrez Gene: 2863802   Ensembl: ENSG000001875597   OMIM: 6110865   UniProtKB: Q6VB843   

Export aliases for FOXD4L3 gene to outside databases

Previous GC identifers: GC09U900383 GC09P066375 GC09M067936 GC09P068148 GC09P070107


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for FOXD4L3 Gene:
FOXD4L3 (forkhead box D4-like 3) 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_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the FOXD4L3 gene promoter:
         TBP   C/EBPbeta   p53   RREB-1   FOXD1   MyoD   GATA-1   GATA-2   STAT3   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFOXD4L3 promoter sequence
   Search Chromatin IP Primers for FOXD4L3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FOXD4L3


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

Entrez Gene cytogenetic band: 9q21.11   Ensembl cytogenetic band:  9q21.11   HGNC cytogenetic band: 9q13

FOXD4L3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FOXD4L3 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P070917:  view genomic region     (about GC identifiers)

Start:
70,917,276 bp from pter      End:
70,920,000 bp from pter
Size:
2,725 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: FX4L3_HUMAN, Q6VB84 (See protein sequence)
Recommended Name: Forkhead box protein D4-like 3  
Size: 417 amino acids; 45820 Da
Miscellaneous: 5 FOXD4-like proteins (FOXD4L2, FOXD4L3, FOXD4L4, FOXD4L5 and FOXD4L6) are encoded by a strongly
repeated region of the 9q12 chromosome region. They are very similar and it is therefore difficult to provide a
clear and unambiguous protein sequence. Our sequences are in agreement with HGNC nomenclature
Secondary accessions: Q5JTX9

Explore the universe of human proteins at neXtProt for FOXD4L3: NX_Q6VB84

Explore proteomics data for FOXD4L3 at MOPED


See FOXD4L3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_954586.4  
ENSEMBL proteins: 
 ENSP00000341961  

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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 Q6VB84

ProtoNet protein and cluster: Q6VB84

UniProtKB/Swiss-Prot: FX4L3_HUMAN, Q6VB84
Similarity: Contains 1 fork-head DNA-binding domain


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(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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 FOXD4L3           About GenesLikeMe


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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
FX4L3_HUMAN, Q6VB84: Nucleus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus4
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 FOXD4L3
Interactions:

    Search GeneGlobe Interaction Network for FOXD4L3

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

3 Interacting proteins for FOXD4L3 (ENSP000003419614) 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 Tocris compounds for FOXD4L3 (FX4L3)



(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 FOXD4L3 gene: 
NM_199135.4  

Unigene Cluster for FOXD4L3:

Forkhead box D4-like 3
Hs.449471
Unigene Representative Sequence: AY344642
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000342833(uc004agm.1)
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  QuantiFast Probe-based Assays in human, mouse, rat FOXD4L3

Additional mRNA sequence: 

AY344641.1 AY344642.1 

1 DOTS entry:

DT.101983633 

8 AceView cDNA sequences:

AA577100 AF343006 BV206348 NM_199358 AY344642 NM_199135 AY344641 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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FOXD4L3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
FOXD4L3 Expression
About this image

FOXD4L3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

FOXD4L3 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.449471
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In Situ
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(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 FOXD4L3 gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
platypus
(Ornithorhynchus anatinus)
Mammalia --
Uncharacterized protein
50(a)
1 → many
Contig530(367747-368893)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
65(a)
1 → many
2(49994144-49994639)
zebrafish
(Danio rerio)
Actinopterygii foxd56
forkhead box D5
38(a)
many ↔ many
8(31300987-31302138) ENSDARG00000042485
fruit fly
(Drosophila melanogaster)
Insecta fd59A6
forkhead domain 59A
26(a)
1 → many
2R(18754044-18758229)
worm
(Caenorhabditis elegans)
Secernentea unc-1306
Protein UNC-130 (unc-130) mRNA, complete cds
31(a)
1 → many
II(11281986-11283954) WBGene00006853


ENSEMBL Gene Tree for FOXD4L3 (if available)
TreeFam Gene Tree for FOXD4L3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for FOXD4L3 gene
FOXD4L61 2  FOXA22  FOXD4L12  FOXC22  FOXI22  FOXB12  FOXE32  FOXC12  
FOXD4L22  FOXA32  FOXD4L52  FOXD12  FOXD32  FOXD4L42  FOXA12  FOXE12  
FOXL12  FOXB22  FOXI12  FOXS12  FOXD22  FOXL22  FOXD42  
13 SIMAP similar genes for FOXD4L3 using alignment to 1 protein entry:     FX4L3_HUMAN:
FOXD4L6    FOXD4L2    FOXD4L4    FOXD4L5    FOXD4L1    FOXD4
FOXE1    FOXS1    FOXD2    FOXE3    FOXL1    FOXD3
FOXD1

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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 FOXD4L3 (see all 90)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs94107661,2
--70826486(+) TGGAGC/GGAGTG 1 -- us2k10--------
rs1837516141,2
C--70826693(-) CCTCCC/TAAAGT 1 -- us2k10--------
rs1912516671,2
--70828233(-) TGGCGA/GCCGAT 1 -- ut510--------
rs24822801,2
C--70916065(-) TAGAAA/GTAACA 1 -- us2k10--------
rs2005112631,2
F--70917838(+) GCCACA/GTCCCC 1 -- ut511Minor allele frequency- G:0.00EU 1315
rs2018874921,2
C,F--70917883(+) CAAGAG/ACTGAG 2 /T /A mis11Minor allele frequency- A:0.01EU 1297
rs2019198491,2
F--70918563(+) CCCCGC/TCCAGG 2 R syn11Minor allele frequency- T:0.01EU 1061
rs1998565981,2
F--70918607(+) AGTCCC/AGGGGG 2 /Q /P mis11Minor allele frequency- A:0.01EU 663
rs2012191601,2
F--70918627(+) ACACCG/CCCCCC 2 /P /A mis11Minor allele frequency- C:0.01EU 427
rs2018516811,2
F--70918632(+) GCCCCC/GGGGAG 2 P syn11Minor allele frequency- G:0.01EU 455

HapMap Linkage Disequilibrium report for FOXD4L3 (70917276 - 70920000 bp)

Structural Variations
     Database of Genomic Variants (DGV) 9 variations for FOXD4L3:    About this table    
Variant IDTypeSubtypePubMed ID
nsv428218CNV Loss18775914
nsv831609CNV Gain17160897
dgv8238n71CNV Gain21882294
nsv893404CNV Gain21882294
dgv8240n71CNV Gain21882294
essv2899CNV CNV17122850
dgv2384e1CNV Complex17122850
dgv2383e1CNV Complex17122850
dgv2385e1CNV Complex17122850

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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: 611086    OMIM disorders: --


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Export disorders for FOXD4L3 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 FOXD4L3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with FOXD4L3)
    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 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, 3 Fan Y.... Trask B.J. (Genome Res. 2002)
  3. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
  4. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 2004)
  5. 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)

(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: 286380 HGNC: 18523 AceView: FOXD4L2 Ensembl:ENSG00000187559 euGenes: HUgn286380
ECgene: FOXD4L3 H-InvDB: FOXD4L3

(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 FOXD4L3 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for FOXD4L3 gene:
Search GeneIP for patents involving FOXD4L3

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, eBioscience, antibodies-online, 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 genOway)
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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