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Aliases for LY6G5C Gene

Aliases for LY6G5C Gene

  • Lymphocyte Antigen 6 Family Member G5C 2 3 5
  • Lymphocyte Antigen 6 Complex, Locus G5C 2 3
  • C6orf20 3 4
  • NG33 3 4
  • G5C 3 4
  • Lymphocyte Antigen 6 Complex Locus Protein G5c 3
  • Chromosome 6 Open Reading Frame 20 2
  • Lymphocyte Antigen-6 G5C 3
  • LY6G5CA 3
  • LY6G5CB 3

External Ids for LY6G5C Gene

Previous HGNC Symbols for LY6G5C Gene

  • C6orf20

Previous GeneCards Identifiers for LY6G5C Gene

  • GC06M031707
  • GC06M031416
  • GC06M031748
  • GC06M031753
  • GC06M031644
  • GC06M031432

Summaries for LY6G5C Gene

Entrez Gene Summary for LY6G5C Gene

  • LY6G5C belongs to a cluster of leukocyte antigen-6 (LY6) genes located in the major histocompatibility complex (MHC) class III region on chromosome 6. Members of the LY6 superfamily typically contain 70 to 80 amino acids, including 8 to 10 cysteines. Most LY6 proteins are attached to the cell surface by a glycosylphosphatidylinositol (GPI) anchor that is directly involved in signal transduction (Mallya et al., 2002 [PubMed 12079290]).[supplied by OMIM, Mar 2008]

GeneCards Summary for LY6G5C Gene

LY6G5C (Lymphocyte Antigen 6 Family Member G5C) is a Protein Coding gene.

UniProtKB/Swiss-Prot for LY6G5C Gene

  • May have a role in hematopoietic cell differentiation.

Additional gene information for LY6G5C Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LY6G5C Gene

Genomics for LY6G5C Gene

GeneHancer (GH) Regulatory Elements for LY6G5C Gene

Promoters and enhancers for LY6G5C Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I031682 Enhancer 0.9 Ensembl ENCODE 596.9 +0.5 490 1.5 MXI1 SAP130 MAX ARID4B SIN3A ZNF384 BMI1 RARA TEAD3 NR2F6 LY6G5C LOC105375019 STK19B BAG6
GH06I031658 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 46.3 +23.9 23902 3.9 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 SLC30A9 POLR2B E2F8 BAG6 C6orf47 C6orf47-AS1 LY6G5C C4A LY6G5B MICB STK19B VWA7 CYP21A1P
GH06I031733 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 33.8 -53.4 -53415 8.5 CLOCK MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 MSH5 CLIC1 DDX39B LY6G5B ATF6B LSM2 CSNK2B SKIV2L GPANK1 BAG6
GH06I031680 Promoter/Enhancer 1.4 Ensembl ENCODE 46.8 +2.9 2934 1.8 HDGF ATF1 ARNT ARID4B SIN3A YY1 ARID2 ZNF143 ATF7 RXRA LOC105375019 LY6G5C STK19B LY6G5B
GH06I031662 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 27.2 +19.0 18994 5 MLX ZFP64 YBX1 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF263 SP3 CSNK2B GPANK1 ENSG00000201207 GC06P032042 ENSG00000263020 DDX39B LY6G5B ATF6B MDC1 GTF2H4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LY6G5C on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LY6G5C gene promoter:

Genomic Locations for LY6G5C Gene

Genomic Locations for LY6G5C Gene
chr6:31,676,684-31,684,040
(GRCh38/hg38)
Size:
7,357 bases
Orientation:
Minus strand
chr6:31,644,461-31,651,817
(GRCh37/hg19)

Genomic View for LY6G5C Gene

Genes around LY6G5C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LY6G5C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LY6G5C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for LY6G5C Gene

  • Protein details for LY6G5C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5SRR4-LY65C_HUMAN
    Recommended name:
    Lymphocyte antigen 6 complex locus protein G5c
    Protein Accession:
    Q5SRR4
    Secondary Accessions:
    • A6NCW4
    • B0UXB3
    • B0UXB4
    • B0UZ69
    • B0UZQ0
    • B1B0L9
    • O95871
    • Q5SQ59
    • Q8NDY0
    • Q8NDY1

    Protein attributes for LY6G5C Gene

    Size:
    150 amino acids
    Molecular mass:
    16650 Da
    Quaternary structure:
    • Forms oligomers.
    SequenceCaution:
    • Sequence=CAI18529.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAM45830.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAQ06577.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAQ07007.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAQ10884.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for LY6G5C Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LY6G5C Gene

Post-translational modifications for LY6G5C Gene

Other Protein References for LY6G5C Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LY6G5C Gene

Domains & Families for LY6G5C Gene

Gene Families for LY6G5C Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for LY6G5C Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LY6G5C: view

No data available for UniProtKB/Swiss-Prot for LY6G5C Gene

Function for LY6G5C Gene

Molecular function for LY6G5C Gene

UniProtKB/Swiss-Prot Function:
May have a role in hematopoietic cell differentiation.

Phenotypes From GWAS Catalog for LY6G5C Gene

Gene Ontology (GO) - Molecular Function for LY6G5C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042802 identical protein binding IDA,IEA 17008713
genes like me logo Genes that share ontologies with LY6G5C: view

Phenotypes for LY6G5C Gene

genes like me logo Genes that share phenotypes with LY6G5C: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LY6G5C Gene

Localization for LY6G5C Gene

Subcellular locations from UniProtKB/Swiss-Prot for LY6G5C Gene

Secreted.

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 LY6G5C gene
Compartment Confidence
extracellular 4
plasma membrane 2
nucleus 2
peroxisome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LY6G5C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0009897 colocalizes_with external side of plasma membrane IDA,IEA 17008713
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0043234 protein complex IDA,IEA 17008713
genes like me logo Genes that share ontologies with LY6G5C: view

Pathways & Interactions for LY6G5C Gene

SuperPathways for LY6G5C Gene

No Data Available

Interacting Proteins for LY6G5C Gene

Selected Interacting proteins: Q5SRR4-LY65C_HUMAN for LY6G5C Gene via IID

Gene Ontology (GO) - Biological Process for LY6G5C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0051260 protein homooligomerization IDA,IEA 17008713
genes like me logo Genes that share ontologies with LY6G5C: view

No data available for Pathways by source and SIGNOR curated interactions for LY6G5C Gene

Drugs & Compounds for LY6G5C Gene

No Compound Related Data Available

Transcripts for LY6G5C Gene

Unigene Clusters for LY6G5C Gene

Lymphocyte antigen 6 complex, locus G5C:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for LY6G5C Gene

No ASD Table

Relevant External Links for LY6G5C Gene

GeneLoc Exon Structure for
LY6G5C
ECgene alternative splicing isoforms for
LY6G5C

Expression for LY6G5C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LY6G5C Gene

NURSA nuclear receptor signaling pathways regulating expression of LY6G5C Gene:

LY6G5C

SOURCE GeneReport for Unigene cluster for LY6G5C Gene:

Hs.25738

mRNA Expression by UniProt/SwissProt for LY6G5C Gene:

Q5SRR4-LY65C_HUMAN
Tissue specificity: Detected in T-cell lines and fetal and adult lung.
genes like me logo Genes that share expression patterns with LY6G5C: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LY6G5C Gene

Orthologs for LY6G5C Gene

This gene was present in the common ancestor of mammals.

Orthologs for LY6G5C Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LY6G5C 33 34
  • 98.89 (n)
dog
(Canis familiaris)
Mammalia LY6G5C 33 34
  • 87.33 (n)
cow
(Bos Taurus)
Mammalia LY6G5C 33 34
  • 78.57 (n)
mouse
(Mus musculus)
Mammalia Ly6g5c 33 16 34
  • 75 (n)
rat
(Rattus norvegicus)
Mammalia Ly6g5c 33
  • 74.18 (n)
Species where no ortholog for LY6G5C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LY6G5C Gene

ENSEMBL:
Gene Tree for LY6G5C (if available)
TreeFam:
Gene Tree for LY6G5C (if available)

Paralogs for LY6G5C Gene

No data available for Paralogs for LY6G5C Gene

Variants for LY6G5C Gene

Sequence variations from dbSNP and Humsavar for LY6G5C Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000181067 -- 31,679,491(-) C/G intron_variant
rs1000256018 -- 31,676,640(-) A/G downstream_transcript_variant
rs1000608145 -- 31,676,371(-) CCC/CC downstream_transcript_variant
rs1000637702 -- 31,679,211(-) A/G coding_sequence_variant, missense_variant
rs1001912133 -- 31,682,048(-) T/TT upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LY6G5C Gene

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv1161370 CNV deletion 26073780
nsv830627 CNV loss 17160897

Variation tolerance for LY6G5C Gene

Residual Variation Intolerance Score: 69.1% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LY6G5C Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LY6G5C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LY6G5C Gene

Disorders for LY6G5C Gene

Additional Disease Information for LY6G5C

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for LY6G5C Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LY6G5C Gene

Publications for LY6G5C Gene

  1. Transcriptional analysis of a novel cluster of LY-6 family members in the human and mouse major histocompatibility complex: five genes with many splice forms. (PMID: 12079290) Mallya M … Aguado B (Genomics 2002) 2 3 4 58
  2. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 44 58
  3. Fine mapping of the MHC Class III region demonstrates association of AIF1 and rheumatoid arthritis. (PMID: 18835879) Harney SM … Brown MA (Rheumatology (Oxford, England) 2008) 3 44 58
  4. Characterization of the five novel Ly-6 superfamily members encoded in the MHC, and detection of cells expressing their potential ligands. (PMID: 17008713) Mallya M … Aguado B (Protein science : a publication of the Protein Society 2006) 3 4 58
  5. Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins. (PMID: 17192395) Macaulay IC … Ouwehand WH (Blood 2007) 3 58

Products for LY6G5C Gene

Sources for LY6G5C Gene

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