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    LYPD6B LY6/PLAUR domain containing 6B [ Homo sapiens (human) ]

    Gene ID: 130576, updated on 27-Nov-2024

    Summary

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    Official Symbol
    LYPD6Bprovided by HGNC
    Official Full Name
    LY6/PLAUR domain containing 6Bprovided by HGNC
    Primary source
    HGNC:HGNC:27018
    See related
    Ensembl:ENSG00000150556 AllianceGenome:HGNC:27018
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CT116; LYPD7
    Summary
    Enables acetylcholine receptor regulator activity. Predicted to be located in extracellular region and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in gall bladder (RPKM 13.0), skin (RPKM 12.7) and 8 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LYPD6B in Genome Data Viewer
    Location:
    2q23.2
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (149038699..149215262)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (149489053..149665643)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (149895213..150071776)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12001 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149633462-149634040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149634041-149634620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:149645774-149646369 Neighboring gene KIF5C antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 1843 Neighboring gene uncharacterized LOC101928553 Neighboring gene kinesin family member 5C Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149683568-149684192 Neighboring gene Sharpr-MPRA regulatory region 9639 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:149830455-149831291 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149855785-149856718 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149856719-149857650 Neighboring gene NANOG hESC enhancer GRCh37_chr2:149883850-149884499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16625 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:149937379-149937971 Neighboring gene thioredoxin pseudogene 5 Neighboring gene uncharacterized LOC105373677 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_53218 Neighboring gene NANOG hESC enhancer GRCh37_chr2:150080194-150080695 Neighboring gene uncharacterized LOC105373679 Neighboring gene family with sequence similarity 8 member A3, pseudogene

    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. Cloning and characterization of a human LYPD7, a new member of the Ly-6 superfamily. Ni J, et al. Mol Biol Rep, 2009 Apr. PMID 18360792
    2. The prototoxin LYPD6B modulates heteromeric α3β4-containing nicotinic acetylcholine receptors, but not α7 homomers. Ochoa V, et al. FASEB J, 2016 Mar. PMID 26586467, Free PMC Article
    3. Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors. Paramonov AS, et al. Int J Mol Sci, 2020 Oct 1. PMID 33019770, Free PMC Article
    4. A novel LZAP-binding protein, NLBP, inhibits cell invasion. Kwon J, et al. J Biol Chem, 2010 Apr 16. PMID 20164180, Free PMC Article
    5. Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis. Cross-Disorder Group of the Psychiatric Genomics Consortium. Lancet, 2013 Apr 20. PMID 23453885, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors.
      Title: Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors.
    2. 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.
    3. LYPD7 was especially highly expressed in testis, lung, stomach, and prostate.
      Title: Cloning and characterization of a human LYPD7, a new member of the Ly-6 superfamily.
    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
    Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables acetylcholine receptor regulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables acetylcholine receptor regulator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ly6/PLAUR domain-containing protein 6B
    Names
    cancer/testis antigen 116

    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.

    mRNA and Protein(s)

    1. NM_001317002.2 → NP_001303931.1  ly6/PLAUR domain-containing protein 6B isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC009230, BC040176, DB042901, DB461489
      Consensus CDS
      CCDS46423.1
      UniProtKB/TrEMBL
      H7BXI7
      Conserved Domains (1) summary
      pfam16975
      Location:77 → 195
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    2. NM_001317003.2 → NP_001303932.1  ly6/PLAUR domain-containing protein 6B isoform b precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 3, 4, and 5 all encode the same isoform (b).
      Source sequence(s)
      AC009230, AC073271
      Consensus CDS
      CCDS82519.1
      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32
      UniProtKB/TrEMBL
      H7BXI7
      Related
      ENSP00000386479.1, ENST00000409876.5
      Conserved Domains (1) summary
      pfam16975
      Location:53 → 171
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    3. NM_001317004.1 → NP_001303933.1  ly6/PLAUR domain-containing protein 6B isoform b precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 3, 4, and 5 all encode the same isoform (b).
      Source sequence(s)
      AC009230, AC073271, AF435957, BC040176
      Consensus CDS
      CCDS82519.1
      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32
      UniProtKB/TrEMBL
      H7BXI7
      Related
      ENSP00000386650.1, ENST00000409029.5
      Conserved Domains (1) summary
      pfam16975
      Location:53 → 171
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    4. NM_001317005.2 → NP_001303934.1  ly6/PLAUR domain-containing protein 6B isoform b precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 3, 4, and 5 all encode the same isoform (b).
      Source sequence(s)
      AC009230, AC073271
      Consensus CDS
      CCDS82519.1
      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32
      UniProtKB/TrEMBL
      H7BXI7
      Conserved Domains (1) summary
      pfam16975
      Location:53 → 171
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    5. NM_001317006.2 → NP_001303935.1  ly6/PLAUR domain-containing protein 6B isoform c precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks two alternate exons compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AC009230, AC073271
      UniProtKB/TrEMBL
      H7BXI7
      Related
      ENSP00000280115.8, ENST00000280115.8
      Conserved Domains (1) summary
      pfam16975
      Location:40 → 144
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    6. NM_177964.5 → NP_808879.2  ly6/PLAUR domain-containing protein 6B isoform a

      See identical proteins and their annotated locations for NP_808879.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC009230, AC073271
      Consensus CDS
      CCDS46423.1
      UniProtKB/TrEMBL
      H7BXI7
      Related
      ENSP00000387077.3, ENST00000409642.8
      Conserved Domains (1) summary
      pfam16975
      Location:77 → 195
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      149038699..149215262
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047443412.1 → XP_047299368.1  ly6/PLAUR domain-containing protein 6B isoform X6

    2. XM_017003366.2 → XP_016858855.1  ly6/PLAUR domain-containing protein 6B isoform X9

      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32
      UniProtKB/TrEMBL
      H7BXI7
      Conserved Domains (1) summary
      pfam16975
      Location:53 → 171
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    3. XM_047443404.1 → XP_047299360.1  ly6/PLAUR domain-containing protein 6B isoform X1

    4. XM_047443411.1 → XP_047299367.1  ly6/PLAUR domain-containing protein 6B isoform X6

    5. XM_011510623.3 → XP_011508925.1  ly6/PLAUR domain-containing protein 6B isoform X9

      See identical proteins and their annotated locations for XP_011508925.1

      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32
      UniProtKB/TrEMBL
      H7BXI7
      Conserved Domains (1) summary
      pfam16975
      Location:53 → 171
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    6. XM_047443405.1 → XP_047299361.1  ly6/PLAUR domain-containing protein 6B isoform X1

    7. XM_047443407.1 → XP_047299363.1  ly6/PLAUR domain-containing protein 6B isoform X3

    8. XM_017003364.2 → XP_016858853.1  ly6/PLAUR domain-containing protein 6B isoform X6

      UniProtKB/TrEMBL
      H7BXI7
      Conserved Domains (1) summary
      pfam16975
      Location:77 → 195
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    9. XM_017003365.2 → XP_016858854.1  ly6/PLAUR domain-containing protein 6B isoform X9

      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32
      UniProtKB/TrEMBL
      H7BXI7
      Conserved Domains (1) summary
      pfam16975
      Location:53 → 171
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    10. XM_047443402.1 → XP_047299358.1  ly6/PLAUR domain-containing protein 6B isoform X1

    11. XM_047443410.1 → XP_047299366.1  ly6/PLAUR domain-containing protein 6B isoform X6

    12. XM_047443403.1 → XP_047299359.1  ly6/PLAUR domain-containing protein 6B isoform X1

    13. XM_047443401.1 → XP_047299357.1  ly6/PLAUR domain-containing protein 6B isoform X1

    14. XM_047443408.1 → XP_047299364.1  ly6/PLAUR domain-containing protein 6B isoform X4

    15. XM_047443406.1 → XP_047299362.1  ly6/PLAUR domain-containing protein 6B isoform X2

    16. XM_047443416.1 → XP_047299372.1  ly6/PLAUR domain-containing protein 6B isoform X7

    17. XM_047443414.1 → XP_047299370.1  ly6/PLAUR domain-containing protein 6B isoform X7

    18. XM_047443409.1 → XP_047299365.1  ly6/PLAUR domain-containing protein 6B isoform X5

    19. XM_011510620.3 → XP_011508922.1  ly6/PLAUR domain-containing protein 6B isoform X3

      See identical proteins and their annotated locations for XP_011508922.1

      UniProtKB/TrEMBL
      H7BXI7
      Conserved Domains (1) summary
      pfam16975
      Location:88 → 206
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    20. XM_005246306.5 → XP_005246363.1  ly6/PLAUR domain-containing protein 6B isoform X7

      See identical proteins and their annotated locations for XP_005246363.1

      UniProtKB/TrEMBL
      H7BXI7
      Conserved Domains (1) summary
      pfam16975
      Location:70 → 188
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    21. XM_047443417.1 → XP_047299373.1  ly6/PLAUR domain-containing protein 6B isoform X8

    22. XM_006712281.5 → XP_006712344.1  ly6/PLAUR domain-containing protein 6B isoform X9

      See identical proteins and their annotated locations for XP_006712344.1

      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32
      UniProtKB/TrEMBL
      H7BXI7
      Conserved Domains (1) summary
      pfam16975
      Location:53 → 171
      UPAR_LY6_2; Ly6/PLAUR domain-containing protein 6, Lypd6

    23. XM_047443413.1 → XP_047299369.1  ly6/PLAUR domain-containing protein 6B isoform X6

    24. XM_047443418.1 → XP_047299374.1  ly6/PLAUR domain-containing protein 6B isoform X10

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      149489053..149665643
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340554.1 → XP_054196529.1  ly6/PLAUR domain-containing protein 6B isoform X1

    2. XM_054340561.1 → XP_054196536.1  ly6/PLAUR domain-containing protein 6B isoform X6

    3. XM_054340570.1 → XP_054196545.1  ly6/PLAUR domain-containing protein 6B isoform X9

      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32

    4. XM_054340553.1 → XP_054196528.1  ly6/PLAUR domain-containing protein 6B isoform X1

    5. XM_054340559.1 → XP_054196534.1  ly6/PLAUR domain-containing protein 6B isoform X6

    6. XM_054340568.1 → XP_054196543.1  ly6/PLAUR domain-containing protein 6B isoform X9

      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32

    7. XM_054340555.1 → XP_054196530.1  ly6/PLAUR domain-containing protein 6B isoform X1

    8. XM_054340560.1 → XP_054196535.1  ly6/PLAUR domain-containing protein 6B isoform X6

    9. XM_054340569.1 → XP_054196544.1  ly6/PLAUR domain-containing protein 6B isoform X9

      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32

    10. XM_054340551.1 → XP_054196526.1  ly6/PLAUR domain-containing protein 6B isoform X1

    11. XM_054340558.1 → XP_054196533.1  ly6/PLAUR domain-containing protein 6B isoform X6

    12. XM_054340552.1 → XP_054196527.1  ly6/PLAUR domain-containing protein 6B isoform X1

    13. XM_054340550.1 → XP_054196525.1  ly6/PLAUR domain-containing protein 6B isoform X1

    14. XM_054340556.1 → XP_054196531.1  ly6/PLAUR domain-containing protein 6B isoform X4

    15. XM_054340564.1 → XP_054196539.1  ly6/PLAUR domain-containing protein 6B isoform X7

    16. XM_054340565.1 → XP_054196540.1  ly6/PLAUR domain-containing protein 6B isoform X7

    17. XM_054340557.1 → XP_054196532.1  ly6/PLAUR domain-containing protein 6B isoform X5

    18. XM_054340563.1 → XP_054196538.1  ly6/PLAUR domain-containing protein 6B isoform X7

    19. XM_054340566.1 → XP_054196541.1  ly6/PLAUR domain-containing protein 6B isoform X8

    20. XM_054340567.1 → XP_054196542.1  ly6/PLAUR domain-containing protein 6B isoform X9

      UniProtKB/Swiss-Prot
      D3DP90, Q53TK0, Q7Z747, Q8IXK7, Q8NI32

    21. XM_054340562.1 → XP_054196537.1  ly6/PLAUR domain-containing protein 6B isoform X6

    22. XM_054340571.1 → XP_054196546.1  ly6/PLAUR domain-containing protein 6B isoform X10

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NI32.1 GenPept UniProtKB/Swiss-Prot:Q8NI32

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