WDR4 Gene (Protein Coding)

WD Repeat Domain 4

GC21M042843
GIFtS:
38
This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal tran... See more...

Aliases for WDR4 Gene

Aliases for WDR4 Gene

  • WD Repeat Domain 4 2 3 5
  • TRNA (Guanine-N(7)-)-Methyltransferase Non-Catalytic Subunit WDR4 3 4
  • WD Repeat-Containing Protein 4 3 4
  • Protein Wuho Homolog 3 4
  • TRMT82 2 3
  • TRM82 2 3
  • HWH 3 4
  • TRM82 TRNA Methyltransferase 82 Homolog (S. Cerevisiae) 2
  • TRNA (Guanine-N(7)-)-Methyltransferase Subunit WDR4 3
  • TRM82 TRNA Methyltransferase 82 Homolog 3
  • GAMOS6 3
  • MIGSB 3
  • WDR4 5

External Ids for WDR4 Gene

Previous GeneCards Identifiers for WDR4 Gene

  • GC21M040810
  • GC21M043157
  • GC21M043136
  • GC21M044263
  • GC21M029678

Summaries for WDR4 Gene

Entrez Gene Summary for WDR4 Gene

  • This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This gene is excluded as a candidate for a form of nonsyndromic deafness (DFNB10), but is still a candidate for other disorders mapped to 21q22.3 as well as for the development of Down syndrome phenotypes. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, May 2012]

GeneCards Summary for WDR4 Gene

WDR4 (WD Repeat Domain 4) is a Protein Coding gene. Diseases associated with WDR4 include Galloway-Mowat Syndrome 6 and Microcephaly, Growth Deficiency, Seizures, And Brain Malformations. Among its related pathways are Gene Expression and tRNA processing. Gene Ontology (GO) annotations related to this gene include tRNA (guanine-N7-)-methyltransferase activity.

UniProtKB/Swiss-Prot Summary for WDR4 Gene

  • Non-catalytic component of a methyltransferase complex required for the formation of N(7)-methylguanine in a subset of RNA species, such as tRNAs, mRNAs and microRNAs (miRNAs) (PubMed:12403464, PubMed:31031084, PubMed:31031083). In the methyltransferase complex, it is required to stabilize and induce conformational changes of the catalytic subunit (PubMed:12403464). Required for the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA (PubMed:12403464, PubMed:31031084). Also required for the formation of N(7)-methylguanine at internal sites in a subset of mRNAs (PubMed:31031084). Also required for methylation of a specific subset of miRNAs, such as let-7 (PubMed:31031083). Independently of METTL1, also plays a role in genome stability: localizes at the DNA replication site and regulates endonucleolytic activities of FEN1 (PubMed:26751069).

Gene Wiki entry for WDR4 Gene

Additional gene information for WDR4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for WDR4 Gene

Genomics for WDR4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for WDR4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around WDR4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for WDR4

Top Transcription factor binding sites by QIAGEN in the WDR4 gene promoter:
  • ATF-2
  • c-Ets-1
  • c-Jun
  • E2F
  • E2F-1
  • E47
  • Hand1
  • HEN1
  • ZIC2
  • Zic3

Genomic Locations for WDR4 Gene

Genomic Locations for WDR4 Gene
chr21:42,843,075-42,891,695
(GRCh38/hg38)
Size:
48,621 bases
Orientation:
Minus strand
chr21:44,263,204-44,299,678
(GRCh37/hg19)
Size:
36,475 bases
Orientation:
Minus strand

Genomic View for WDR4 Gene

Genes around WDR4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WDR4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for WDR4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for WDR4 Gene

Proteins for WDR4 Gene

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  • Protein details for WDR4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P57081-WDR4_HUMAN
    Recommended name:
    tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
    Protein Accession:
    P57081
    Secondary Accessions:
    • A8KA58
    • B2RCA3
    • B4DNQ7
    • D3DSK3
    • Q9BVM5
    • Q9HCR3

    Protein attributes for WDR4 Gene

    Size:
    412 amino acids
    Molecular mass:
    45490 Da
    Quaternary structure:
    • Forms a heterodimer with the catalytic subunit METTL1 (PubMed:12403464, PubMed:26751069). Interacts with FEN1; the interaction is direct (PubMed:26751069).

    Alternative splice isoforms for WDR4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for WDR4 Gene

Protein Expression for WDR4 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for WDR4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for WDR4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for WDR4 Gene

Domains & Families for WDR4 Gene

Gene Families for WDR4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for WDR4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for WDR4 Gene

GenScript: Design optimal peptide antigens:
  • WD repeat-containing protein 4 (WDR4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P57081

UniProtKB/Swiss-Prot:

WDR4_HUMAN :
  • Belongs to the WD repeat TRM82 family.
Family:
  • Belongs to the WD repeat TRM82 family.
genes like me logo Genes that share domains with WDR4: view

Function for WDR4 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for WDR4 Gene

UniProtKB/Swiss-Prot Function:
Non-catalytic component of a methyltransferase complex required for the formation of N(7)-methylguanine in a subset of RNA species, such as tRNAs, mRNAs and microRNAs (miRNAs) (PubMed:12403464, PubMed:31031084, PubMed:31031083). In the methyltransferase complex, it is required to stabilize and induce conformational changes of the catalytic subunit (PubMed:12403464). Required for the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA (PubMed:12403464, PubMed:31031084). Also required for the formation of N(7)-methylguanine at internal sites in a subset of mRNAs (PubMed:31031084). Also required for methylation of a specific subset of miRNAs, such as let-7 (PubMed:31031083). Independently of METTL1, also plays a role in genome stability: localizes at the DNA replication site and regulates endonucleolytic activities of FEN1 (PubMed:26751069).

Phenotypes From GWAS Catalog for WDR4 Gene

Gene Ontology (GO) - Molecular Function for WDR4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15861136
GO:0008176 contributes_to tRNA (guanine-N7-)-methyltransferase activity IBA,IDA 12403464
genes like me logo Genes that share ontologies with WDR4: view
genes like me logo Genes that share phenotypes with WDR4: view

Human Phenotype Ontology for WDR4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for WDR4 Gene

MGI Knock Outs for WDR4:
  • Wdr4 Wdr4<tm1.1Hsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for WDR4

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for WDR4 Gene

Localization for WDR4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WDR4 Gene

Nucleus. Chromosome. Note=Localizes at the site of nascent DNA synthesis. {ECO:0000269 PubMed:26751069}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for WDR4 gene
Compartment Confidence
nucleus 5
cytosol 4
extracellular 2
mitochondrion 2
cytoskeleton 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for WDR4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 15861136
GO:0005654 nucleoplasm HDA,IDA --
GO:0005694 chromosome IEA --
GO:0005829 cytosol IBA,IDA --
GO:0043527 tRNA methyltransferase complex IBA,IDA 12403464
genes like me logo Genes that share ontologies with WDR4: view

Pathways & Interactions for WDR4 Gene

PathCards logo

SuperPathways for WDR4 Gene

genes like me logo Genes that share pathways with WDR4: view

Pathways by source for WDR4 Gene

UniProtKB/Swiss-Prot P57081-WDR4_HUMAN

  • Pathway: tRNA modification; N(7)-methylguanine-tRNA biosynthesis.

Gene Ontology (GO) - Biological Process for WDR4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006400 tRNA modification IDA 15861136
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0008033 tRNA processing IEA --
GO:0030488 tRNA methylation IEA --
GO:0036265 RNA (guanine-N7)-methylation IEA --
genes like me logo Genes that share ontologies with WDR4: view

No data available for SIGNOR curated interactions for WDR4 Gene

Drugs & Compounds for WDR4 Gene

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  1. Drug
No Compound Related Data Available

Transcripts for WDR4 Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for WDR4 Gene

6 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for WDR4

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for WDR4 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14
SP1: - - - -
SP2: - - - - -
SP3: - - -
SP4: - -
SP5:
SP6: -

Relevant External Links for WDR4 Gene

GeneLoc Exon Structure for
WDR4

Expression for WDR4 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for WDR4 Gene

mRNA expression in normal human tissues for WDR4 Gene
mRNA expression by GTEx for WDR4 GenemRNA expression by BioGPS for WDR4 Gene

Protein differential expression in normal tissues from HIPED for WDR4 Gene

This gene is overexpressed in Lung (56.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for WDR4 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for WDR4

SOURCE GeneReport for Unigene cluster for WDR4 Gene:

Hs.248815

Evidence on tissue expression from TISSUES for WDR4 Gene

  • Lung(4.2)
  • Nervous system(2.9)
genes like me logo Genes that share expression patterns with WDR4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for WDR4 Gene

Orthologs for WDR4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for WDR4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia WDR4 30 31
  • 98.86 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia WDR4 30 31
  • 83 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia WDR4 30 31
  • 81.46 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Wdr4 30 17 31
  • 79.92 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Wdr4 30
  • 79.87 (n)
Oppossum
(Monodelphis domestica)
 Mammalia WDR4 31
  • 69 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia WDR4 31
  • 67 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves WDR4 30 31
  • 62.43 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia WDR4 31
  • 52 (a)
 OneToOne
African clawed frog
(Xenopus laevis)
 Amphibia wdr4-prov 30
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia Str.4956 30
Zebrafish
(Danio rerio)
 Actinopterygii LOC100536637 30
  • 53.14 (n)
wdr4 31
  • 43 (a)
 OneToMany
FP017279.3 31
  • 43 (a)
 OneToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta wuho 31
  • 24 (a)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea Y102E9.2 31
  • 21 (a)
 OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes TRM82 31 33
  • 20 (a)
 OneToOne
Species where no ortholog for WDR4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for WDR4 Gene

ENSEMBL:
Gene Tree for WDR4 (if available)
TreeFam:
Gene Tree for WDR4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for WDR4: view image

Paralogs for WDR4 Gene

Pseudogenes.org Pseudogenes for WDR4 Gene

genes like me logo Genes that share paralogs with WDR4: view

No data available for Paralogs for WDR4 Gene

Variants for WDR4 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for WDR4 Gene

SNP ID Clinical significance and condition Chr 21 pos Variation AA Info Type
710985 Benign: not provided 42,852,333(-) G/A INTRON_VARIANT
726110 Likely Benign: not provided 42,852,264(-) T/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
773615 Benign: not provided 42,879,463(-) C/T SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT
777624 Benign: not provided 42,863,593(-) G/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
rs1292041526 Pathogenic: MICROCEPHALY, GROWTH DEFICIENCY, SEIZURES, AND BRAIN MALFORMATIONS. Pathogenic: GALLOWAY-MOWAT SYNDROME 6. Galloway-Mowat syndrome 6 (GAMOS6) [MIM:618347] 42,862,339(-) C/AC/Tp.Arg170Gln MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for WDR4 Gene

Structural Variations from Database of Genomic Variants (DGV) for WDR4 Gene

Variant ID Type Subtype PubMed ID
esv2666871 CNV deletion 23128226
esv2723576 CNV deletion 23290073
esv2723577 CNV deletion 23290073
esv2723578 CNV deletion 23290073
esv2723579 CNV deletion 23290073
esv3568210 CNV loss 25503493
esv3584478 CNV gain 24956385
esv3647094 CNV loss 21293372
esv3647095 CNV loss 21293372
nsv1135908 CNV deletion 24896259
nsv587657 CNV gain 21841781
nsv587659 CNV loss 21841781
nsv834105 CNV loss 17160897

Variation tolerance for WDR4 Gene

Residual Variation Intolerance Score: 60.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.03; 90.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for WDR4 Gene

Human Gene Mutation Database (HGMD)
WDR4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
WDR4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for WDR4 Gene

Disorders for WDR4 Gene

MalaCards: The human disease database

(9) MalaCards diseases for WDR4 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search WDR4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

WDR4_HUMAN
  • Galloway-Mowat syndrome 6 (GAMOS6) [MIM:618347]: A form of Galloway-Mowat syndrome, a severe renal-neurological disease characterized by early-onset nephrotic syndrome associated with microcephaly, central nervous system abnormalities, developmental delays, and a propensity for seizures. Brain anomalies include gyration defects ranging from lissencephaly to pachygyria and polymicrogyria, and cerebellar hypoplasia. Most patients show facial dysmorphism characterized by a small, narrow forehead, large/floppy ears, deep-set eyes, hypertelorism and micrognathia. Additional variable features are visual impairment and arachnodactyly. Most patients die in early childhood. GAMOS6 is an autosomal recessive form with onset in infancy or early childhood. Affected individuals manifest microcephaly, global developmental delay, variable degrees of intellectual disability, and growth deficiency. Renal impairment may be age-dependent or may not be present. {ECO:0000269 PubMed:28617965, ECO:0000269 PubMed:29597095, ECO:0000269 PubMed:30079490}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Microcephaly, growth deficiency, seizures, and brain malformations (MIGSB) [MIM:618346]: An autosomal recessive disorder characterized by intrauterine growth retardation, postnatal growth deficiency, microcephaly, facial dysmorphism, early-onset seizures, brain malformations such as partial agenesis of the corpus callosum and simplified gyration, and poor or absent psychomotor development. {ECO:0000269 PubMed:26416026}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for WDR4

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with WDR4: view

No data available for Genatlas for WDR4 Gene

Publications for WDR4 Gene

  1. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. (PMID: 12403464) Alexandrov A … Phizicky EM (RNA (New York, N.Y.) 2002) 2 3 4 23
  2. Isolation and characterization of a human chromosome 21q22.3 gene (WDR4) and its mouse homologue that code for a WD-repeat protein. (PMID: 10950928) Michaud J … Scott HS (Genomics 2000) 3 4 23
  3. Further delineation of the phenotype caused by biallelic variants in the WDR4 gene. (PMID: 28617965) Trimouille A … Lacombe D (Clinical genetics 2018) 3 4
  4. Mutations in WDR4 as a new cause of Galloway-Mowat syndrome. (PMID: 30079490) Braun DA … Hildebrandt F (American journal of medical genetics. Part A 2018) 3 4
  5. Wuho Is a New Member in Maintaining Genome Stability through its Interaction with Flap Endonuclease 1. (PMID: 26751069) Cheng IC … Hsieh TS (PLoS biology 2016) 3 4

ExternalLinks

View latest publications for WDR4 gene in Mastermind

Products for WDR4 Gene

  • Signalway Proteins for WDR4

Sources for WDR4 Gene