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    CNTN5 contactin 5 [ Homo sapiens (human) ]

    Gene ID: 53942, updated on 28-Oct-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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    See CNTN5 in Genome Data Viewer
    Location:
    11q22.1
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (99020949..100358885)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (99027636..100368160)
    RS_2024_09 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 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. Characterization of the contactin 5 protein and its risk-associated polymorphic variant throughout the Alzheimer's disease spectrum. Dauar MT, et al. Alzheimers Dement, 2023 Jul. PMID 36583624
    4. 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
    5. 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

    See all (27) 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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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