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

Gene ID: 130576, updated on 3-Apr-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, Apr 2022]
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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Location:
2q23.2
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (149038699..149215262)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (149489053..149665643)
105.20220307 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)

Genotypes

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_2023_10

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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