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Aliases for LYPD6B Gene

Aliases for LYPD6B Gene

  • LY6/PLAUR Domain Containing 6B 2 3 5
  • Cancer/Testis Antigen 116 2 3
  • Ly6/PLAUR Domain-Containing Protein 6B 3
  • CT116 3
  • LYPD7 3

External Ids for LYPD6B Gene

Previous GeneCards Identifiers for LYPD6B Gene

  • GC02P149604
  • GC02P149895
  • GC02P141793

Summaries for LYPD6B Gene

GeneCards Summary for LYPD6B Gene

LYPD6B (LY6/PLAUR Domain Containing 6B) is a Protein Coding gene. Diseases associated with LYPD6B include Nicotine Dependence, Protection Against. Among its related pathways are Metabolism of proteins and Post-translational modification- synthesis of GPI-anchored proteins. An important paralog of this gene is LYPD6.

UniProtKB/Swiss-Prot for LYPD6B Gene

  • Believed to act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro acts on nAChRs in a subtype- and stoichiometry-dependent manner. Modulates specifally alpha-3(3):beta-4(2) nAChRs by enhancing the sensitivity to ACh, decreasing ACh-induced maximal current response and increasing the rate of desensitization to ACh; has no effect on alpha-7 homomeric nAChRs; modulates alpha-3(2):alpha-5:beta-4(2) nAChRs in the context of CHRNA5/alpha-5 variant Asn-398 but not its wild-type sequence.

Additional gene information for LYPD6B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LYPD6B Gene

Genomics for LYPD6B Gene

Regulatory Elements for LYPD6B Gene

Enhancers for LYPD6B 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
GH02H149068 1.6 FANTOM5 Ensembl ENCODE dbSUPER 23 +31.5 31482 2.1 MXI1 NFIB MAX SIN3A CEBPG BMI1 CTBP1 GATA3 FOS RCOR1 LYPD6B EPC2 KIF5C TXNP5 GC02M149098
GH02H149099 0.8 ENCODE dbSUPER 17.6 +62.4 62389 3 CTCF GATA3 FOXA2 POLR2A LYPD6B GC02M149098 TXNP5
GH02H149018 1.5 Ensembl ENCODE dbSUPER 9 -17.0 -17041 4.3 FOXA2 FOS ATF7 RUNX3 MCM3 KAT8 SREBF1 NFIL3 ATF4 GLIS1 LYPD6 LYPD6B LOC101928553
GH02H149064 1.1 ENCODE dbSUPER 10.9 +26.9 26941 1.1 PKNOX1 FEZF1 BCL11B CTBP1 GATA3 POLR2A ZNF366 GLI2 NFE2 NFE2L2 LYPD6B GC02M149069
GH02H149562 1.1 Ensembl ENCODE 10.9 +524.4 524412 0.5 FOXA2 INSM2 FEZF1 ZNF366 ZSCAN5C ZNF391 TSHZ1 ZEB2 ZNF843 ZFP69B LYPD6B LOC101929231 GC02P149515
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LYPD6B on UCSC Golden Path with GeneCards custom track

Promoters for LYPD6B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000124330 593 601 SMARCE1 CTCF MXI1 ZNF687 SIN3A SP2 CTBP2 KLF9 ZBTB26 ZFX

Genomic Locations for LYPD6B Gene

Genomic Locations for LYPD6B Gene
chr2:149,038,107-149,215,262
(GRCh38/hg38)
Size:
177,156 bases
Orientation:
Plus strand
chr2:149,894,621-150,071,776
(GRCh37/hg19)

Genomic View for LYPD6B Gene

Genes around LYPD6B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYPD6B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYPD6B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYPD6B Gene

Proteins for LYPD6B Gene

  • Protein details for LYPD6B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NI32-LPD6B_HUMAN
    Recommended name:
    Ly6/PLAUR domain-containing protein 6B
    Protein Accession:
    Q8NI32
    Secondary Accessions:
    • D3DP90
    • Q53TK0
    • Q7Z747
    • Q8IXK7

    Protein attributes for LYPD6B Gene

    Size:
    183 amino acids
    Molecular mass:
    20656 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH18203.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH18203.1; Type=Frameshift; Positions=150; Evidence={ECO:0000305};

    Alternative splice isoforms for LYPD6B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LYPD6B Gene

Post-translational modifications for LYPD6B Gene

No Post-translational modifications

No data available for DME Specific Peptides for LYPD6B Gene

Domains & Families for LYPD6B Gene

Gene Families for LYPD6B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted secreted proteins
  • Transporters

Protein Domains for LYPD6B Gene

Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for LYPD6B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LYPD6B: view

No data available for UniProtKB/Swiss-Prot for LYPD6B Gene

Function for LYPD6B Gene

Molecular function for LYPD6B Gene

UniProtKB/Swiss-Prot Function:
Believed to act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro acts on nAChRs in a subtype- and stoichiometry-dependent manner. Modulates specifally alpha-3(3):beta-4(2) nAChRs by enhancing the sensitivity to ACh, decreasing ACh-induced maximal current response and increasing the rate of desensitization to ACh; has no effect on alpha-7 homomeric nAChRs; modulates alpha-3(2):alpha-5:beta-4(2) nAChRs in the context of CHRNA5/alpha-5 variant Asn-398 but not its wild-type sequence.

Gene Ontology (GO) - Molecular Function for LYPD6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030548 acetylcholine receptor regulator activity IDA 26586467
genes like me logo Genes that share ontologies with LYPD6B: view
genes like me logo Genes that share phenotypes with LYPD6B: view

Animal Models for LYPD6B Gene

MGI Knock Outs for LYPD6B:

Animal Model Products

CRISPR Products

miRNA for LYPD6B Gene

miRTarBase miRNAs that target LYPD6B

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LYPD6B Gene

Localization for LYPD6B Gene

Subcellular locations from UniProtKB/Swiss-Prot for LYPD6B Gene

Cell membrane; Lipid-anchor, GPI-anchor.

Subcellular locations from

COMPARTMENTS
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 LYPD6B gene
Compartment Confidence
plasma membrane 5
extracellular 5

Gene Ontology (GO) - Cellular Components for LYPD6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with LYPD6B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LYPD6B Gene

Pathways & Interactions for LYPD6B Gene

genes like me logo Genes that share pathways with LYPD6B: view

Interacting Proteins for LYPD6B Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000387077%0d%0a9606.ENSP00000344683%0d%0a
Selected Interacting proteins: Q8NI32-LPD6B_HUMAN ENSP00000387077 for LYPD6B Gene via IID STRING

Gene Ontology (GO) - Biological Process for LYPD6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006501 C-terminal protein lipidation TAS --
GO:0099601 regulation of neurotransmitter receptor activity IEA --
genes like me logo Genes that share ontologies with LYPD6B: view

No data available for SIGNOR curated interactions for LYPD6B Gene

Drugs & Compounds for LYPD6B Gene

No Compound Related Data Available

Transcripts for LYPD6B Gene

Unigene Clusters for LYPD6B Gene

LY6/PLAUR domain containing 6B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LYPD6B Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15a · 15b ^ 16a · 16b · 16c ·
SP1: - - - - - - - - - - - - -
SP2: - - - - - - - - - - - -
SP3: - - - - - - - - - - - - - -
SP4: - - -
SP5: -
SP6: - - - - - - - - - - - - - - -
SP7: -
SP8: - - - - - -
SP9:
SP10:
SP11:

ExUns: 16d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for LYPD6B Gene

GeneLoc Exon Structure for
LYPD6B
ECgene alternative splicing isoforms for
LYPD6B

Expression for LYPD6B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LYPD6B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LYPD6B Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x12.2), Skin - Sun Exposed (Lower leg) (x11.6), Stomach (x5.8), and Testis (x4.7).

NURSA nuclear receptor signaling pathways regulating expression of LYPD6B Gene:

LYPD6B

SOURCE GeneReport for Unigene cluster for LYPD6B Gene:

Hs.357567

Evidence on tissue expression from TISSUES for LYPD6B Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with LYPD6B: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LYPD6B Gene

Orthologs for LYPD6B Gene

This gene was present in the common ancestor of chordates.

Orthologs for LYPD6B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LYPD6B 33 34
  • 99.19 (n)
cow
(Bos Taurus)
Mammalia LYPD6B 34
  • 90 (a)
OneToOne
LOC616612 33
  • 88.17 (n)
mouse
(Mus musculus)
Mammalia Lypd6b 33 16 34
  • 81.98 (n)
rat
(Rattus norvegicus)
Mammalia Lypd6b 33
  • 80.85 (n)
oppossum
(Monodelphis domestica)
Mammalia LYPD6B 34
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LYPD6B 34
  • 67 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LYPD6B 34
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves LYPD6B 33 34
  • 72.39 (n)
lizard
(Anolis carolinensis)
Reptilia LYPD6B 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lypd6b 33
  • 65.58 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2791 33
zebrafish
(Danio rerio)
Actinopterygii LOC554606 33
  • 61.18 (n)
lypd6b 34
  • 45 (a)
OneToOne
Species where no ortholog for LYPD6B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LYPD6B Gene

ENSEMBL:
Gene Tree for LYPD6B (if available)
TreeFam:
Gene Tree for LYPD6B (if available)

Paralogs for LYPD6B Gene

Paralogs for LYPD6B Gene

(1) SIMAP similar genes for LYPD6B Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with LYPD6B: view

Variants for LYPD6B Gene

Sequence variations from dbSNP and Humsavar for LYPD6B Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000000215 -- 149,118,843(+) TCTAC(C/T)GCCTC intron-variant
rs1000004078 -- 149,160,470(+) GGAGG(G/T)ATGTG intron-variant, upstream-variant-2KB
rs1000018741 -- 149,062,153(+) AGGCT(A/G)ATTTT intron-variant
rs1000030037 -- 149,062,327(+) ACATG(C/T)AAAAT intron-variant
rs1000048572 -- 149,118,352(+) TGATA(A/T)ATACT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LYPD6B Gene

Variant ID Type Subtype PubMed ID
nsv834408 CNV gain 17160897
nsv834407 CNV loss 17160897
nsv583291 CNV gain 21841781
nsv515662 CNV loss 19592680
nsv459718 CNV gain 19166990
esv3592859 CNV loss 21293372
esv3592858 CNV loss 21293372
esv3592856 CNV loss 21293372
esv3592855 CNV loss 21293372
esv3592854 CNV loss 21293372
esv33982 CNV gain 17666407
esv3387934 CNV insertion 20981092
esv33162 CNV loss 17666407
esv2751831 CNV gain 17911159
esv2674737 CNV deletion 23128226
dgv230n21 CNV loss 19592680

Variation tolerance for LYPD6B Gene

Residual Variation Intolerance Score: 66.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.46; 43.29% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LYPD6B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LYPD6B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYPD6B Gene

Disorders for LYPD6B Gene

MalaCards: The human disease database

(1) MalaCards diseases for LYPD6B Gene - From: DISEASES

Disorder Aliases PubMed IDs
nicotine dependence, protection against
  • nicotine dependence
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for LYPD6B

Genetic Association Database (GAD)
LYPD6B
Human Genome Epidemiology (HuGE) Navigator
LYPD6B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LYPD6B
genes like me logo Genes that share disorders with LYPD6B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LYPD6B Gene

Publications for LYPD6B Gene

  1. The prototoxin LYPD6B modulates heteromeric α3β4-containing nicotinic acetylcholine receptors, but not α7 homomers. (PMID: 26586467) Ochoa V … Whiteaker P (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2016) 3 4 60
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  3. Cloning and characterization of a human LYPD7, a new member of the Ly-6 superfamily. (PMID: 18360792) Ni J … Yu L (Molecular biology reports 2009) 2 3 60
  4. Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis. (PMID: 23453885) Cross-Disorder Group of the Psychiatric Genomics Consortium (Lancet (London, England) 2013) 3 60
  5. A novel LZAP-binding protein, NLBP, inhibits cell invasion. (PMID: 20164180) Kwon J … Kim H (The Journal of biological chemistry 2010) 3 60

Products for LYPD6B Gene

Sources for LYPD6B Gene

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