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CNTN5 contactin 5 [ Homo sapiens (human) ]

Gene ID: 53942, updated on 3-Apr-2024

Summary

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Official Symbol
CNTN5provided by HGNC
Official Full Name
contactin 5provided by HGNC
Primary source
HGNC:HGNC:2175
See related
Ensembl:ENSG00000149972 MIM:607219; AllianceGenome:HGNC:2175
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NB-2; HNB-2s
Summary
The protein encoded by this gene is a member of the immunoglobulin superfamily, and contactin family, which mediate cell surface interactions during nervous system development. This protein is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]
Expression
Biased expression in placenta (RPKM 1.0), thyroid (RPKM 1.0) and 5 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
11q22.1
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (99020949..100358885)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (99027636..100368160)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (98891679..100229616)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:98323806-98324306 Neighboring gene NANOG hESC enhancer GRCh37_chr11:98366426-98366927 Neighboring gene MPRA-validated peak1422 silencer Neighboring gene MPRA-validated peak1423 silencer Neighboring gene MPRA-validated peak1424 silencer Neighboring gene MPRA-validated peak1425 silencer Neighboring gene MPRA-validated peak1427 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:98472057-98472556 Neighboring gene zinc finger protein 614 pseudogene Neighboring gene MPRA-validated peak1429 silencer Neighboring gene MPRA-validated peak1430 silencer Neighboring gene MPRA-validated peak1431 silencer Neighboring gene MPRA-validated peak1433 silencer Neighboring gene MPRA-validated peak1434 silencer Neighboring gene MPRA-validated peak1435 silencer Neighboring gene MPRA-validated peak1437 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21952 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22004 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22054 Neighboring gene RN7SK pseudogene 53 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22152 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22162 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22201 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22214 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:99195590-99196789 Neighboring gene NANOG hESC enhancer GRCh37_chr11:99289721-99290406 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:99293814-99294789 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22279 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:99454493-99454616 Neighboring gene uncharacterized LOC107984431 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:99796493-99797261 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22387 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22407 Neighboring gene Sharpr-MPRA regulatory region 1581 Neighboring gene uncharacterized LOC105369456 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22479 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22485 Neighboring gene NANOG hESC enhancer GRCh37_chr11:99976083-99977077 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:100199299-100200498 Neighboring gene replication protein A2 pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:100421613-100422390 Neighboring gene Sharpr-MPRA regulatory region 9794 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:100534084-100535013 Neighboring gene RNA, 7SL, cytoplasmic 222, pseudogene Neighboring gene peptidylprolyl isomerase A pseudogene 43

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Association of rs1568885, rs1813443 and rs4411591 polymorphisms with anti-TNF medication response in Greek patients with Crohn's disease. Thomas D, et al. World J Gastroenterol, 2014 Apr 7. PMID 24707144, Free PMC Article
  2. Contactin-associated protein (Caspr) and contactin form a complex that is targeted to the paranodal junctions during myelination. Rios JC, et al. J Neurosci, 2000 Nov 15. PMID 11069942, Free PMC Article
  3. CNTN5(-)(/+)or EHMT2(-)(/+)human iPSC-derived neurons from individuals with autism develop hyperactive neuronal networks. Deneault E, et al. Elife, 2019 Feb 12. PMID 30747104, Free PMC Article
  4. Genome-wide association study revealed novel loci which aggravate asymptomatic hyperuricaemia into gout. Kawamura Y, et al. Ann Rheum Dis, 2019 Oct. PMID 31289104, Free PMC Article
  5. Framingham Heart Study 100K project: genome-wide associations for cardiovascular disease outcomes. Larson MG, et al. BMC Med Genet, 2007 Sep 19. PMID 17903304, Free PMC Article

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Characterization of the contactin 5 protein and its risk-associated polymorphic variant throughout the Alzheimer's disease spectrum.
    Title: Characterization of the contactin 5 protein and its risk-associated polymorphic variant throughout the Alzheimer's disease spectrum.
  2. The present study revealed three gout specific loci, CNTN5, MIR302F, ZNF724, to be clearly associated with mechanisms of gout development, which distinctly differ from the known gout risk loci that basically elevate serum uric acid level. This meta-analysis is the first to reveal the loci associated with crystal-induced inflammation, the last step in gout development that aggravates asymptomatic hyperuricaemia into gout.
    Title: Genome-wide association study revealed novel loci which aggravate asymptomatic hyperuricaemia into gout.
  3. The most compelling new results revealed a consistent spontaneous network hyperactivity in neurons deficient for CNTN5 or EHMT2.
    Title: CNTN5(-)(/+)or EHMT2(-)(/+)human iPSC-derived neurons from individuals with autism develop hyperactive neuronal networks.
  4. rs1568885 and rs1813443, but not rs4411591 polymorphisms are associated with clinical and biochemical response to infliximab in Greek patients with Crohn's disease
    Title: Association of rs1568885, rs1813443 and rs4411591 polymorphisms with anti-TNF medication response in Greek patients with Crohn's disease.
  5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  6. This study shown that established and candidate AD genes have a role in 6 neuroimaging traits linked to AD. 2 promising genes from Alzheimer disease GWASs, CNTN5 and BIN1, are associated with these neuroimaging measures.
    Title: Genetic variation and neuroimaging measures in Alzheimer disease.
  7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
  9. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Genetic variation and neuroimaging measures in Alzheimer disease.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
EBI GWAS Catalog
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
EBI GWAS Catalog
Framingham Heart Study 100K project: genome-wide associations for cardiovascular disease outcomes.
EBI GWAS Catalog
Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study.
EBI GWAS Catalog
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC163491

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cell-cell adhesion mediator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in presynapse assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in sensory perception of sound IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in axon IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in presynaptic membrane IEA
Inferred from Electronic Annotation
more info
  
located_in side of membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
contactin-5
Names
neural adhesion molecule
neural recognition molecule NB-2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_047156.1 RefSeqGene

    Range
    4974..1342910
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243270.2 → NP_001230199.1  contactin-5 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001230199.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' non-coding region, thus has a shorter 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AB013802, AK308788, AP001892, AP002428, BC130619, BM697855, BU737133, BX090703, R26700
    Consensus CDS
    CCDS53696.1
    UniProtKB/Swiss-Prot
    A1L4P0, B7ZM07, E9PKE8, O94779, O94780, Q49AF3
    UniProtKB/TrEMBL
    B7ZM08
    Related
    ENSP00000436185.1, ENST00000528682.5
    Conserved Domains (6) summary
    cd04969
    Location:496 → 568
    Ig5_Contactin_like; Fifth Ig domain of contactin
    cd05848
    Location:98 → 191
    Ig1_Contactin-5; First Ig domain of contactin-5
    smart00410
    Location:205 → 278
    IG_like; Immunoglobulin like
    cd00063
    Location:671 → 768
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:489 → 568
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:300 → 387
    Ig; Immunoglobulin domain

  2. NM_001243271.2 → NP_001230200.1  contactin-5 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs at the 3' end compared to variant 1. This results in a frame-shift, and a shorter isoform (3) with a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AK308788, AP002428, BC039255
    Consensus CDS
    CCDS58168.1
    UniProtKB/TrEMBL
    B7ZM08
    Related
    ENSP00000433575.1, ENST00000527185.5
    Conserved Domains (5) summary
    cd05848
    Location:98 → 191
    Ig1_Contactin-5; First Ig domain of contactin-5
    smart00410
    Location:205 → 278
    IG_like; Immunoglobulin like
    cd00063
    Location:671 → 768
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:489 → 568
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:300 → 387
    Ig; Immunoglobulin domain

  3. NM_014361.4 → NP_055176.1  contactin-5 isoform 1 precursor

    See identical proteins and their annotated locations for NP_055176.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript, and encodes the longest isoform (1, also known as long isoform). Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AB013802, AK308788, AP001892, AP002428, BC130619, BM697855, BU737133, BX090703, R26700
    Consensus CDS
    CCDS53696.1
    UniProtKB/Swiss-Prot
    A1L4P0, B7ZM07, E9PKE8, O94779, O94780, Q49AF3
    UniProtKB/TrEMBL
    B7ZM08
    Related
    ENSP00000435637.1, ENST00000524871.6
    Conserved Domains (6) summary
    cd04969
    Location:496 → 568
    Ig5_Contactin_like; Fifth Ig domain of contactin
    cd05848
    Location:98 → 191
    Ig1_Contactin-5; First Ig domain of contactin-5
    smart00410
    Location:205 → 278
    IG_like; Immunoglobulin like
    cd00063
    Location:671 → 768
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:489 → 568
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:300 → 387
    Ig; Immunoglobulin domain

  4. NM_175566.2 → NP_780775.1  contactin-5 isoform 2 precursor

    See identical proteins and their annotated locations for NP_780775.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame coding exon compared to variant 1. This results in a shorter isoform (2, also known as short isoform) missing an internal protein segment compared to isoform 1.
    Source sequence(s)
    AB013803, AP001892, BM697855, BU737133, BX090703, R26700
    Consensus CDS
    CCDS53697.1
    UniProtKB/TrEMBL
    B7ZM08
    Related
    ENSP00000393229.2, ENST00000418526.6
    Conserved Domains (6) summary
    cd04969
    Location:422 → 494
    Ig5_Contactin_like; Fifth Ig domain of contactin
    cd05848
    Location:24 → 117
    Ig1_Contactin-5; First Ig domain of contactin-5
    smart00410
    Location:131 → 204
    IG_like; Immunoglobulin like
    cd00063
    Location:597 → 694
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:415 → 494
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:226 → 313
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    99020949..100358885
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017017926.2 → XP_016873415.1  contactin-5 isoform X1

    UniProtKB/Swiss-Prot
    A1L4P0, B7ZM07, E9PKE8, O94779, O94780, Q49AF3
    UniProtKB/TrEMBL
    B7ZM08
    Conserved Domains (6) summary
    cd04969
    Location:496 → 568
    Ig5_Contactin_like; Fifth Ig domain of contactin
    cd05848
    Location:98 → 191
    Ig1_Contactin-5; First Ig domain of contactin-5
    smart00410
    Location:205 → 278
    IG_like; Immunoglobulin like
    cd00063
    Location:671 → 768
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:489 → 568
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:300 → 387
    Ig; Immunoglobulin domain

  2. XM_011542871.2 → XP_011541173.1  contactin-5 isoform X2

    See identical proteins and their annotated locations for XP_011541173.1

    UniProtKB/TrEMBL
    B7ZM08
    Conserved Domains (6) summary
    cd04969
    Location:422 → 494
    Ig5_Contactin_like; Fifth Ig domain of contactin
    cd05848
    Location:24 → 117
    Ig1_Contactin-5; First Ig domain of contactin-5
    smart00410
    Location:131 → 204
    IG_like; Immunoglobulin like
    cd00063
    Location:597 → 694
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam07679
    Location:415 → 494
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:226 → 313
    Ig; Immunoglobulin domain

  3. XM_047427130.1 → XP_047283086.1  contactin-5 isoform X2

  4. XM_047427131.1 → XP_047283087.1  contactin-5 isoform X4

  5. XM_017017927.2 → XP_016873416.1  contactin-5 isoform X3

    Conserved Domains (5) summary
    cd04969
    Location:496 → 568
    Ig5_Contactin_like; Fifth Ig domain of contactin
    cd05848
    Location:98 → 191
    Ig1_Contactin-5; First Ig domain of contactin-5
    smart00410
    Location:205 → 278
    IG_like; Immunoglobulin like
    pfam07679
    Location:489 → 568
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:300 → 387
    Ig; Immunoglobulin domain

  6. XM_011542873.2 → XP_011541175.1  contactin-5 isoform X3

    Conserved Domains (5) summary
    cd04969
    Location:496 → 568
    Ig5_Contactin_like; Fifth Ig domain of contactin
    cd05848
    Location:98 → 191
    Ig1_Contactin-5; First Ig domain of contactin-5
    smart00410
    Location:205 → 278
    IG_like; Immunoglobulin like
    pfam07679
    Location:489 → 568
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:300 → 387
    Ig; Immunoglobulin domain

  7. XM_017017929.2 → XP_016873418.1  contactin-5 isoform X5

  8. XM_017017928.2 → XP_016873417.1  contactin-5 isoform X3

    Conserved Domains (5) summary
    cd04969
    Location:496 → 568
    Ig5_Contactin_like; Fifth Ig domain of contactin
    cd05848
    Location:98 → 191
    Ig1_Contactin-5; First Ig domain of contactin-5
    smart00410
    Location:205 → 278
    IG_like; Immunoglobulin like
    pfam07679
    Location:489 → 568
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:300 → 387
    Ig; Immunoglobulin domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    99027636..100368160
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369144.1 → XP_054225119.1  contactin-5 isoform X1

  2. XM_054369145.1 → XP_054225120.1  contactin-5 isoform X2

  3. XM_054369146.1 → XP_054225121.1  contactin-5 isoform X2

  4. XM_054369150.1 → XP_054225125.1  contactin-5 isoform X4

  5. XM_054369148.1 → XP_054225123.1  contactin-5 isoform X3

  6. XM_054369147.1 → XP_054225122.1  contactin-5 isoform X3

  7. XM_054369151.1 → XP_054225126.1  contactin-5 isoform X5

  8. XM_054369149.1 → XP_054225124.1  contactin-5 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O94779.2 GenPept UniProtKB/Swiss-Prot:O94779

Gene LinkOut

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