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Aliases for MCCC1 Gene

Aliases for MCCC1 Gene

  • Methylcrotonoyl-CoA Carboxylase 1 2 3 5
  • 3-Methylcrotonyl-CoA Carboxylase Biotin-Containing Subunit 3 4
  • 3-Methylcrotonyl-CoA:Carbon Dioxide Ligase Subunit Alpha 3 4
  • Methylcrotonoyl-Coenzyme A Carboxylase 1 (Alpha) 2 3
  • Methylcrotonoyl-CoA Carboxylase Alpha 2 3
  • 3-Methylcrotonyl-CoA Carboxylase 1 3 4
  • MCCase Subunit Alpha 3 4
  • EC 4 58
  • MCCA 3 4
  • Methylcrotonoyl-CoA Carboxylase Subunit Alpha, Mitochondrial 3
  • Methylcrotonoyl-CoA Carboxylase 1 (Alpha) 3
  • EC 6.4.1 58
  • MCC-B 3

External Ids for MCCC1 Gene

Previous GeneCards Identifiers for MCCC1 Gene

  • GC03M179498
  • GC03M183588
  • GC03M184135
  • GC03M184053
  • GC03M184215
  • GC03M182733
  • GC03M180137

Summaries for MCCC1 Gene

Entrez Gene Summary for MCCC1 Gene

  • This gene encodes the large subunit of 3-methylcrotonyl-CoA carboxylase. This enzyme functions as a heterodimer and catalyzes the carboxylation of 3-methylcrotonyl-CoA to form 3-methylglutaconyl-CoA. Mutations in this gene are associated with 3-Methylcrotonylglycinuria, an autosomal recessive disorder of leucine catabolism. [provided by RefSeq, Jul 2008]

GeneCards Summary for MCCC1 Gene

MCCC1 (Methylcrotonoyl-CoA Carboxylase 1) is a Protein Coding gene. Diseases associated with MCCC1 include 3-Methylcrotonyl-Coa Carboxylase 1 Deficiency and 3-Methylcrotonyl-Coa Carboxylase Deficiency. Among its related pathways are Metabolism and HIV Life Cycle. GO annotations related to this gene include ligase activity and D-alanine-D-alanine ligase activity. An important paralog of this gene is PCCA.

UniProtKB/Swiss-Prot for MCCC1 Gene

  • Biotin-attachment subunit of the 3-methylcrotonyl-CoA carboxylase, an enzyme that catalyzes the conversion of 3-methylcrotonyl-CoA to 3-methylglutaconyl-CoA, a critical step for leucine and isovaleric acid catabolism.

Additional gene information for MCCC1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MCCC1 Gene

Genomics for MCCC1 Gene

Regulatory Elements for MCCC1 Gene

Enhancers for MCCC1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03H183178 1.1 Ensembl ENCODE 16.7 -63.5 -63457 1.9 BCOR HDAC1 CTCF SUZ12 HINFP BMI1 ZBTB40 ZFHX2 GLIS2 MTA3 MCCC1 RPS3P3 DVL3 MCF2L2 ATP11B EIF2B5 SNORD3P4 B3GNT5
GH03H183369 1.6 FANTOM5 Ensembl ENCODE 10.9 -254.8 -254818 3.7 HDAC1 HDGF PKNOX1 CHAMP1 TCF12 ZNF766 GATA2 RCOR1 ATF7 FOS B3GNT5 KLHL6 LAMP3 MCCC1 MCF2L2 KLHL24 GC03M183259 RNA5SP151
GH03H183098 1.1 ENCODE 15.8 +16.7 16651 2.4 HDGF FOXA2 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207 MCCC1 LAMP3 LOC105374247 MCCC1-AS1
GH03H183294 1.4 Ensembl ENCODE dbSUPER 10.3 -180.1 -180060 2.9 TBP PKNOX1 NFIB BMI1 ZBTB40 ZBTB7B RFX5 YY1 CBX5 ZNF366 RNA5SP151 B3GNT5 ENSG00000273261 MCCC1 GC03M183259 MCF2L2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around MCCC1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for MCCC1 Gene

Genomic Locations for MCCC1 Gene
100,858 bases
Minus strand

Genomic View for MCCC1 Gene

Genes around MCCC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MCCC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MCCC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MCCC1 Gene

Proteins for MCCC1 Gene

  • Protein details for MCCC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • Q59ES4
    • Q9H959
    • Q9NS97

    Protein attributes for MCCC1 Gene

    725 amino acids
    Molecular mass:
    80473 Da
    Name=biotin; Xref=ChEBI:CHEBI:57586;
    Quaternary structure:
    • Probably a dodecamer composed of six biotin-containing alpha subunits (MCCC1) and six beta (MCCC2) subunits.
    • Sequence=BAD92974.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for MCCC1 Gene

neXtProt entry for MCCC1 Gene

Selected DME Specific Peptides for MCCC1 Gene


Post-translational modifications for MCCC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for MCCC1 Gene

Gene Families for MCCC1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for MCCC1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with MCCC1: view

No data available for UniProtKB/Swiss-Prot for MCCC1 Gene

Function for MCCC1 Gene

Molecular function for MCCC1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + 3-methylcrotonoyl-CoA + HCO(3)(-) = ADP + phosphate + 3-methylglutaconyl-CoA.
UniProtKB/Swiss-Prot Function:
Biotin-attachment subunit of the 3-methylcrotonyl-CoA carboxylase, an enzyme that catalyzes the conversion of 3-methylcrotonyl-CoA to 3-methylglutaconyl-CoA, a critical step for leucine and isovaleric acid catabolism.

Enzyme Numbers (IUBMB) for MCCC1 Gene

Phenotypes From GWAS Catalog for MCCC1 Gene

Gene Ontology (GO) - Molecular Function for MCCC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004075 biotin carboxylase activity NAS,IEA 22869039
GO:0004485 contributes_to methylcrotonoyl-CoA carboxylase activity NAS,IEA 11170888
GO:0005515 protein binding IPI 17360195
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with MCCC1: view
genes like me logo Genes that share phenotypes with MCCC1: view

Human Phenotype Ontology for MCCC1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for MCCC1 Gene

miRTarBase miRNAs that target MCCC1

Inhibitory RNA Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for MCCC1 Gene

Localization for MCCC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MCCC1 Gene

Mitochondrion matrix.

Subcellular locations from

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 MCCC1 gene
Compartment Confidence
mitochondrion 5
cytosol 5
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for MCCC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002169 3-methylcrotonyl-CoA carboxylase complex, mitochondrial TAS 22869039
GO:0005739 mitochondrion IDA --
GO:0005743 mitochondrial inner membrane IEA --
GO:0005759 mitochondrial matrix TAS,IDA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with MCCC1: view

Pathways & Interactions for MCCC1 Gene

genes like me logo Genes that share pathways with MCCC1: view

UniProtKB/Swiss-Prot Q96RQ3-MCCA_HUMAN

  • Pathway: Amino-acid degradation; L-leucine degradation; (S)-3-hydroxy-3-methylglutaryl-CoA from 3-isovaleryl-CoA: step 2/3.

Gene Ontology (GO) - Biological Process for MCCC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006552 leucine catabolic process ISS,NAS 11170888
GO:0006768 biotin metabolic process NAS,TAS --
GO:0009083 branched-chain amino acid catabolic process TAS --
GO:0051291 protein heterooligomerization NAS 11170888
genes like me logo Genes that share ontologies with MCCC1: view

No data available for SIGNOR curated interactions for MCCC1 Gene

Drugs & Compounds for MCCC1 Gene

(3) Drugs for MCCC1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Biotin Approved Nutra Target 49
Phosphoric acid Approved Pharma 0
ATP Nutra Agonist 0

(7) Additional Compounds for MCCC1 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 3-Methylbut-2-enoyl-CoA
  • 3-Methylbut-2-enoyl-Coenzyme A
  • 3-Methylcrotonoyl-CoA
  • 3-Methylcrotonoyl-Coenzyme A
  • 3-Methylcrotonyl-CoA
(E)-2-Methylglutaconic acid
  • (E)-2-methyl-2-Pentenedioate
  • (E)-2-methyl-2-Pentenedioic acid
  • (E)-2-Methylglutaconate
  • trans-2-Methylglutaconate
  • trans-2-Methylglutaconic acid
  • 3-Methylglutaconyl-CoA
  • 3-Methylglutaconyl-Coenzyme A
  • trans-3-Methylglutaconyl-CoA
  • trans-3-Methylglutaconyl-Coenzyme A
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
Carbonic acid
  • Acid of air
  • Aerial acid
  • Bisodium carbonate
  • Calcined
  • Carbonic acid sodium salt
genes like me logo Genes that share compounds with MCCC1: view

Transcripts for MCCC1 Gene

Unigene Clusters for MCCC1 Gene

Methylcrotonoyl-CoA carboxylase 1 (alpha):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for MCCC1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19
SP1: -
SP2: - -
SP3: - - -
SP4: -
SP5: -

Relevant External Links for MCCC1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MCCC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MCCC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for MCCC1 Gene

This gene is overexpressed in Heart (9.2) and Nasal epithelium (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for MCCC1 Gene

Protein tissue co-expression partners for MCCC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of MCCC1 Gene:


SOURCE GeneReport for Unigene cluster for MCCC1 Gene:


Evidence on tissue expression from TISSUES for MCCC1 Gene

  • Liver(4.5)
  • Kidney(4.4)
  • Muscle(4.3)
  • Nervous system(3.1)
  • Adrenal gland(2.9)

Phenotype-based relationships between genes and organs from Gene ORGANizer for MCCC1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • urinary
Head and neck:
  • brain
  • ear
  • head
  • esophagus
  • heart
  • adrenal gland
  • kidney
  • liver
  • stomach
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
  • sweat gland
genes like me logo Genes that share expression patterns with MCCC1: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for MCCC1 Gene

Orthologs for MCCC1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for MCCC1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia MCCC1 33 34
  • 99.45 (n)
(Bos Taurus)
Mammalia MCCC1 33 34
  • 88.92 (n)
(Canis familiaris)
Mammalia MCCC1 33 34
  • 88.47 (n)
(Mus musculus)
Mammalia Mccc1 33 16 34
  • 83.89 (n)
(Rattus norvegicus)
Mammalia Mccc1 33
  • 83.64 (n)
(Ornithorhynchus anatinus)
Mammalia MCCC1 34
  • 83 (a)
(Monodelphis domestica)
Mammalia MCCC1 34
  • 60 (a)
(Gallus gallus)
Aves MCCC1 33 34
  • 73.85 (n)
(Anolis carolinensis)
Reptilia MCCC1 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia mccc1 33
  • 71.7 (n)
(Danio rerio)
Actinopterygii mccc1 33 34
  • 68.66 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010228 33
  • 56.93 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG2118 35 33 34
  • 56.82 (n)
(Caenorhabditis elegans)
Secernentea F32B6.2 35 33
  • 56.23 (n)
mccc-1 34
  • 52 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DUR1,2 34 36
  • 12 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons MCCA 33
  • 54.78 (n)
(Glycine max)
eudicotyledons Gma.6752 33
(Oryza sativa)
Liliopsida Os12g0605800 33
  • 53.23 (n)
Os.19628 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU00591 33
  • 52.48 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1502 33
Species where no ortholog for MCCC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for MCCC1 Gene

Gene Tree for MCCC1 (if available)
Gene Tree for MCCC1 (if available)

Paralogs for MCCC1 Gene

Paralogs for MCCC1 Gene

genes like me logo Genes that share paralogs with MCCC1: view

Variants for MCCC1 Gene

Sequence variations from dbSNP and Humsavar for MCCC1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs119103212 Pathogenic, 3-methylcrotonoyl-CoA carboxylase 1 deficiency (MCC1D) [MIM:210200] 183,045,522(-) TATTA(G/T)GGACT nc-transcript-variant, reference, missense
rs119103214 Pathogenic, 3-methylcrotonoyl-CoA carboxylase 1 deficiency (MCC1D) [MIM:210200] 183,037,218(-) CACAT(C/G)GTATG intron-variant, nc-transcript-variant, reference, missense
rs119103216 Pathogenic, 3-methylcrotonoyl-CoA carboxylase 1 deficiency (MCC1D) [MIM:210200] 183,034,068(-) ATTCT(C/T)TCCAT nc-transcript-variant, reference, missense
rs119103218 Pathogenic, 3-methylcrotonoyl-CoA carboxylase 1 deficiency (MCC1D) [MIM:210200] 183,037,432(-) TAGAT(G/T)GTTGG intron-variant, nc-transcript-variant, reference, missense
rs186209189 3-methylcrotonoyl-CoA carboxylase 1 deficiency (MCC1D) [MIM:210200] 183,071,223(+) CTCCA(A/C/T)CCCGG nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for MCCC1 Gene

Variant ID Type Subtype PubMed ID
nsv592654 CNV loss 21841781
nsv508968 CNV insertion 20534489
nsv482968 CNV gain 15286789
nsv461031 CNV loss 19166990
nsv1151591 CNV insertion 26484159
esv3575642 CNV gain 25503493
esv3302751 CNV tandem duplication 20981092
esv32850 CNV loss 17666407
esv28631 CNV gain 19812545
esv1601884 CNV insertion 17803354

Variation tolerance for MCCC1 Gene

Residual Variation Intolerance Score: 74.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.30; 95.32% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for MCCC1 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MCCC1 Gene

Disorders for MCCC1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for MCCC1 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
3-methylcrotonyl-coa carboxylase 1 deficiency
  • 3 methylcrotonyl-coa carboxylase 1 deficiency
3-methylcrotonyl-coa carboxylase deficiency
  • 3-methylcrotonylglycinuria
mccc1-related 3-methylcrotonyl-coa carboxylase deficiency
ketothiolase deficiency
  • beta-ketothiolase deficiency
multiple carboxylase deficiency
  • mcd
- elite association - COSMIC cancer census association via MalaCards
Search MCCC1 in MalaCards View complete list of genes associated with diseases


  • 3-methylcrotonoyl-CoA carboxylase 1 deficiency (MCC1D) [MIM:210200]: An autosomal recessive disorder of leucine catabolism. The phenotype is variable, ranging from neonatal onset with severe neurological involvement to asymptomatic adults. There is a characteristic organic aciduria with massive excretion of 3-hydroxyisovaleric acid and 3-methylcrotonylglycine, usually in combination with a severe secondary carnitine deficiency. {ECO:0000269 PubMed:11170888, ECO:0000269 PubMed:11181649, ECO:0000269 PubMed:11406611, ECO:0000269 PubMed:16010683, ECO:0000269 PubMed:17968484, ECO:0000269 PubMed:21071250, ECO:0000269 PubMed:22150417, ECO:0000269 PubMed:22264772, ECO:0000269 PubMed:22642865, ECO:0000269 PubMed:25382614, ECO:0000269 PubMed:27601257, ECO:0000269 Ref.6}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for MCCC1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with MCCC1: view

No data available for Genatlas for MCCC1 Gene

Publications for MCCC1 Gene

  1. The molecular basis of 3-methylcrotonylglycinuria, a disorder of leucine catabolism. (PMID: 11170888) Gallardo ME … Peñalva MA (American journal of human genetics 2001) 2 3 4 22 60
  2. Novel mutations in five Japanese patients with 3-methylcrotonyl-CoA carboxylase deficiency. (PMID: 17968484) Uematsu M … Ohura T (Journal of human genetics 2007) 3 4 22 60
  3. The molecular basis of human 3-methylcrotonyl-CoA carboxylase deficiency. (PMID: 11181649) Baumgartner MR … Valle D (The Journal of clinical investigation 2001) 3 4 22 60
  4. Human biotin-containing subunit of 3-methylcrotonyl-CoA carboxylase gene (MCCA): cDNA sequence, genomic organization, localization to chromosomal band 3q27, and expression. (PMID: 11401427) Obata K … Kondo I (Genomics 2001) 3 4 22 60
  5. Cloning of the human MCCA and MCCB genes and mutations therein reveal the molecular cause of 3-methylcrotonyl-CoA: carboxylase deficiency. (PMID: 11406611) Holzinger A … Roscher AA (Human molecular genetics 2001) 3 4 22 60

Products for MCCC1 Gene

Sources for MCCC1 Gene

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