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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

FOXN4 Gene

protein-coding GIFtS: 45
GCID: GC12M109715

forkhead box N4

Explore 4 diseases affiliated with
FOXN4 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Forkhead Box N4¹ ²
Forkhead Box Protein N4²
Forkhead/Winged Helix Transcription Factor FOXN4²

External Ids:	HGNC: 21399¹	Entrez Gene: 121643²	Ensembl: ENSG00000139445⁷	OMIM: 609429⁵	UniProtKB: Q96NZ1³

Export aliases for FOXN4 gene to outside databases

Previous GC identifers: GC12M108775 GC12M109554 GC12M108180 GC12M108178 GC12M106733

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for FOXN4:

Members of the winged-helix/forkhead family of transcription factors, such as FOXN4, are characterized by a 110-amino

acid DNA-binding domain that can fold into a variant of the helix-turn-helix motif consisting of 3 alpha helices

flanked by 2 large loops or wings. These transcription factors are involved in a variety of biologic processes as key

regulators in development and metabolism (Li et al., 2004 (PubMed 15363391)).(supplied by OMIM, Mar 2008)

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000012.11 NC_018923.1 NT_009775.17

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the FOXN4 gene promoter:
AML1a FOXO4 FOXO1a Ik-3 FOXO1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: FOXN4 promoter sequence

Search SABiosciences Chromatin IP Primers for FOXN4

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FOXN4

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

Entrez Gene cytogenetic band: 12q24.11 Ensembl cytogenetic band: 12q24.11 HGNC cytogenetic band: 12q24.12

FOXN4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FOXN4 gene location

GeneLoc information about chromosome 12 GeneLoc Exon Structure

GeneLoc location for GC12M109715: view genomic region (about GC identifiers)

Start:	109,715,783 bp from pter	End:	109,747,025 bp from pter
Size:	31,243 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: FOXN4_HUMAN, Q96NZ1 (See protein sequence)

Recommended Name: Forkhead box protein N4

Size: 517 amino acids; 55215 Da

Subcellular location: Nucleus (Potential)

Sequence caution: Sequence=BAD18661.1; Type=Erroneous initiation;

Secondary accessions: Q6ZMR4 Q96NZ0

Alternative splicing: 2 isoforms: Q96NZ1-1 Q96NZ1-2 (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for FOXN4: NX_Q96NZ1

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q96NZ1

FOXN4 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_998761.2

ENSEMBL proteins:

ENSP00000347354 ENSP00000299162 ENSP00000408085

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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005667	transcription factor complex	IBA	--

FOXN4 for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

FOXN4 for domains About GeneDecksing

3 InterPro domains/families:

IPR011991 WHTH_trsnscrt_rep_DNA-bd_dom

IPR018122 TF_fork_head_CS

IPR001766 TF_fork_head

Graphical View of Domain Structure for InterPro Entry Q96NZ1

ProtoNet protein and cluster: Q96NZ1

UniProtKB/Swiss-Prot: FOXN4_HUMAN, Q96NZ1

Similarity: Contains 1 fork-head DNA-binding domain

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

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Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003690	double-stranded DNA binding	IBA	--
GO:0003705	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity	IBA	--
GO:0008134	transcription factor binding	IBA	--
GO:0008301	DNA binding, bending	IBA	--
GO:0043565	sequence-specific DNA binding	IEA	--

FOXN4 for ontologies About GeneDecksing

1 GenomeRNAi human phenotype for FOXN4:

Decreased viability with pacli

Animal Models:
Mouse knock-out Foxn4^tm1Xia for FOXN4
4 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Foxn4):

cellular

mortality/aging

nervous system

vision/eye

FOXN4 for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for FOXN4

Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007389	pattern specification process	IBA	--
GO:0008016	regulation of heart contraction	IBA	--
GO:0009790	embryo development	IBA	--
GO:0009888	tissue development	IBA	--
GO:0030154	cell differentiation	--	--

FOXN4 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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About This Section

REFSEQ mRNAs for FOXN4 gene:

NM_213596.2

Unigene Cluster for FOXN4:

Forkhead box N4

Hs.528316 [show with all ESTs]

Unigene Representative Sequence: BC146825

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000468516 ENST00000355216(uc001tof.4) ENST00000299162(uc009zvg.3 uc001toe.4)

ENST00000423960

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Additional cDNA sequence:

AF425596.1 AF425597.1 AK093286.1 AK131519.1 BC113073.1 BC146825.1

2 DOTS entries:

DT.99974511 DT.95259358

14 AceView cDNA sequences:

AI805494 AK093286 AF425597 BU156681 AF425596 AA421371 AK131519 NM_213596

AI221704 AI243313 AI187920 AW117425 AA421288 BX096551

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for FOXN4 About this scheme

ExUns:	1	^	2	^	3a	·	3b	^	4	^	5a	·	5b	^	6	^	7a	·	7b	^	8a	·	8b	^	9	^	10	^	11
SP1:													-
SP2:													-		-
SP3:
SP4:																							-		-		-

ECgene alternative splicing isoforms for FOXN4

(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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

FOXN4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: ACCCCTGATA

About this image

FOXN4 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

3 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Eye

Neuroblastic Layer

Early Amacrine Horizontal Precursor Cells

Selective marker (cell-identifying gene)

Amacrine, Horizontal, Retina

Eye

Neuroblastic Layer

Late Amacrine Horizontal Precursor Cells

Amacrine, Retina

Eye

Retina

Eye

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

Dorsal forebrain-like neurons (Generation of midbra...)

Brain

See FOXN4 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for FOXN4

SOURCE GeneReport for Unigene cluster: Hs.528316

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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)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for FOXN4 gene from 4/16 species (see all 16) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	FOXN4¹	forkhead box N4	71.36(n) 70.24(a)		416898 NM_001083359.1 NP_001076828.1
lizard (Anolis carolinensis)	Reptilia	FOXN4⁶	--	62(a)	1 ↔ 1	AAWZ02041607(466-5471)
zebrafish (Danio rerio)	Actinopterygii	foxn4²	forkhead box N4	75.58(n)		30315 AF198446.2
fruit fly (Drosophila melanogaster)	Insecta	Crg-1⁶ jumu⁶ (see all 3)	jumeau (see all 3)	18(a) 13(a) (see all 3)	possible ortholog 1 ↔ many (see all 3)	X(3688900-3691372) 3R(6175906-6187343)

ENSEMBL Gene Tree for FOXN4 (if available)
TreeFam Gene Tree for FOXN4 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for FOXN4 gene

FOXJ1² FOXN3² FOXK1² FOXN1² FOXK2² FOXP4² FOXG1² FOXJ3²

FOXJ2² FOXP2² FOXN2² FOXP3² FOXP1²

1 SIMAP similar gene for FOXN4 using alignment to 3 protein entries: FOXN4_HUMAN (see all proteins):

FOXN1

FOXN4 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 12 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs143148001^1,2	C,	--	109715321(+)	`CTGTT-/AATGAG`	1	--	int¹		0	--	--	--	--
rs34290629^1,2	C,F	--	109715441(+)	`CCTGAG/TCTGTG`	1	--	int¹		3		NA	10
rs181115971^1,2		--	109715801(+)	`TTATTA/GATAGA`	1	--	ut3¹		0	--	--	--	--
rs146853631^1,2	C,	--	109715868(+)	`TGTGAA/GTAACA`	1	--	ut3¹		0	--	--	--	--
rs59226497^1,2	C,	--	109715932(+)	`TCAGAC/AGGGTA`	1	--	ut3¹		1		WA	2
rs150331860^1,2		--	109716104(+)	`CTCCCA/GGACAC`	1	--	ut3¹		0	--	--	--	--
rs77663197^1,2	C,	--	109716292(+)	`GAGAGA/GAAAAG`	1	--	ut3¹		3		CSA WA EA	240
rs11066073^1,2	C,F,A,H,	--	109716331(+)	`GAGGTG/AAGGAA`	1	--	ut3¹ ese³		8		NA WA EA	370
rs137893073^1,2		--	109716390(+)	`GGTTCA/GAGCTT`	1	--	ut3¹		0	--	--	--	--
rs60689998^1,2	C,	--	109716455(+)	`AAGCA-/CCCCCC`	1	--	ut3¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for FOXN4 (109715783 - 109747025 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for FOXN4: --

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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.)
About This Section

FOXN4 for disorders           About GeneDecksing

OMIM gene information: 609429    OMIM disorders: --

4 diseases for FOXN4:    About MalaCards

hallervorden-spatz syndrome hermaphroditism retinitis neuronitis

1 disease from the University of Copenhagen DISEASES database for FOXN4:

Hallervorden-Spatz syndrome

Export disorders for FOXN4 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)
About This Section

PubMed articles for FOXN4 gene integrated from 9 sources:
(articles sorted by number of sources associating them with FOXN4)

Utopia: connect your pdf to the dynamic
world of online information

The finished DNA sequence of human chromosome 12. (PubMed id 16541075)^{1, 2} Scherer S.E.... Gibbs R.A. (2006)
Expression of the winged helix/forkhead gene, foxn4, during zebrafish development. (PubMed id 15464224)^{1, 2} Danilova N.... Steiner L.A. (2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{1, 2} Ota T.... Sugano S. (2004)
Characterization of human FOXN4 gene in silico. (PubMed id 15492871)¹ Katoh M. and Katoh M. (2004)
Foxn4 controls the genesis of amacrine and horizontal cells by retinal progenitors. (PubMed id 15363391)¹ Li S....Xiang M. (2004)
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. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
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)
About This Section

Entrez Gene: 121643	HGNC: 21399	AceView: FOXN4	Ensembl:ENSG00000139445	euGenes: HUgn121643
ECgene: FOXN4	H-InvDB: FOXN4

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for FOXN4	Pharmacogenomics, SNPs, Pathways

Intellectual Property for FOXN4 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for FOXN4 gene:
Search GeneIP for patents involving FOXN4

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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About This Section


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	OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for FOXN4		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for FOXN4
	Browse OriGene Protein Over-expression Lysates		Browse OriGene Fluorogenic Cell Assay Kits
	OriGene siRNA for FOXN4		OriGene 3'-UTR Clone for FOXN4
	OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for FOXN4		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for FOXN4
	Browse OriGene GFP tagged cDNA clones in CMV expression vector		Browse OriGene MicroRNA Expression Plasmids
	Browse OriGene basic RS shRNAs		Browse OriGene validated miRNA SYBR primer pairs
	Browse OriGene full length recombinant human proteins expressed in human HEK293 cells		OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
	OriGene Custom Antibody Services for FOXN4		OriGene Custom Protein Services for FOXN4
	OriGene Custom Immunoassay Development

	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat FOXN4
	QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing FOXN4
	QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FOXN4
	QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat FOXN4
	QIAGEN QuantiFast Probe-based Assays in human, mouse, rat FOXN4
	QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat FOXN4

	GenScript Custom Purified and Recombinant Proteins Services for FOXN4		GenScript cDNA clones with any tag delivered in your preferred vector for FOXN4
	GenScript Custom Assay Services for FOXN4		GenScript Custom Superior Antibodies Services for FOXN4
	GenScript Custom overexpressing Cell Line Services for FOXN4		CloneReady with Over 120,000 Genes
	Gene Synthesis: Any Gene in Any Vector		Vector-based siRNA and miRNA, Ready for Transfection
	Gene Mutant Library, Variants up to 10^11		Plasmid Preparation
	Custom Peptide Services

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Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FOXN4

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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FOXN4

GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes Disease genes FOXN4 gene at Home site.

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