Aliases for LYAR Gene

Aliases for LYAR Gene

  • Ly1 Antibody Reactive 2 3 5
  • Cell Growth-Regulating Nucleolar Protein 3 4
  • Ly1 Antibody Reactive Homolog (Mouse) 2
  • Ly1 Antibody Reactive Homolog 3
  • ZC2HC2 3
  • ZLYAR 3

External Ids for LYAR Gene

Previous GeneCards Identifiers for LYAR Gene

  • GC04M004146
  • GC04M004262
  • GC04M004333
  • GC04M004387
  • GC04M004206

Summaries for LYAR Gene

GeneCards Summary for LYAR Gene

LYAR (Ly1 Antibody Reactive) is a Protein Coding gene. Diseases associated with LYAR include Neuroblastoma.

UniProtKB/Swiss-Prot Summary for LYAR Gene

  • Plays a role in the maintenance of the appropriate processing of 47S/45S pre-rRNA to 32S/30S pre-rRNAs and their subsequent processing to produce 18S and 28S rRNAs (PubMed:24495227). Also acts at the level of transcription regulation. Along with PRMT5, binds the gamma-globin (HBG1/HBG2) promoter and represses its expression (PubMed:25092918). In neuroblastoma cells, may also repress the expression of oxidative stress genes, including CHAC1, HMOX1, SLC7A11, ULBP1 and SNORD41 that encodes a small nucleolar RNA (PubMed:28686580). Preferentially binds to a DNA motif containing 5'-GGTTAT-3' (PubMed:25092918). Negatively regulates the antiviral innate immune response by targeting IRF3 and impairing its DNA-binding activity (PubMed:31413131). In addition, inhibits NF-kappa-B-mediated expression of proinflammatory cytokines (PubMed:31413131). Stimulates phagocytosis of photoreceptor outer segments by retinal pigment epithelial cells (By similarity). Prevents nucleolin/NCL self-cleavage, maintaining a normal steady-state level of NCL protein in undifferentiated embryonic stem cells (ESCs), which in turn is essential for ESC self-renewal (By similarity).

Gene Wiki entry for LYAR Gene

Additional gene information for LYAR Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LYAR Gene

Genomics for LYAR Gene

GeneHancer (GH) Regulatory Elements for LYAR Gene

Promoters and enhancers for LYAR 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
GH04J004288 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 539.6 -0.1 -119 3 ZBTB40 SIN3A NRF1 MYC POLR2G USF1 SP1 ZFX REST POLR2A LYAR ZBTB49 piR-41306-197
GH04J004284 Enhancer 0.7 Ensembl ENCODE 39.8 +4.8 4768 1.2 MYC CTBP1 KLF9 NFIC MNT RARA KLF1 NFIA NR2F6 MAX LYAR NSG1 lnc-LYAR-2
GH04J004323 Enhancer 1 Ensembl ENCODE 28 -33.9 -33932 2.2 PHB2 MYC CTBP1 HDAC3 NCOR1 RELA NFIC MYNN TRIM24 ZNF592 LYAR TMEM128 ZBTB49 ENSG00000248516 hsa-miR-1273e-051
GH04J004264 Promoter/Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 16.5 +21.5 21470 7.5 CTCF CEBPB CEBPG FOS ZNF146 RAD21 ZBTB33 JUN MAX POLR2A lnc-LYAR-2 TMEM128 LYAR ZBTB49 piR-31534-498
GH04J003529 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 11 +758.6 758612 4.1 ZNF217 SIN3A NRF1 POLR2G PHF8 SIX5 ZFX EP300 REST POLR2A LRPAP1 FAM86EP LYAR lnc-NOP14-8
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LYAR on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LYAR

Top Transcription factor binding sites by QIAGEN in the LYAR gene promoter:
  • AML1a
  • Ik-2
  • Meis-1
  • MyoD
  • TBP

Genomic Locations for LYAR Gene

Genomic Locations for LYAR Gene
chr4:4,267,701-4,290,169
(GRCh38/hg38)
Size:
22,469 bases
Orientation:
Minus strand
chr4:4,269,428-4,291,896
(GRCh37/hg19)
Size:
22,469 bases
Orientation:
Minus strand

Genomic View for LYAR Gene

Genes around LYAR on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for LYAR Gene

Proteins for LYAR Gene

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

    Protein Symbol:
    Q9NX58-LYAR_HUMAN
    Recommended name:
    Cell growth-regulating nucleolar protein
    Protein Accession:
    Q9NX58
    Secondary Accessions:
    • D3DVS4
    • Q6FI78
    • Q9NYS1

    Protein attributes for LYAR Gene

    Size:
    379 amino acids
    Molecular mass:
    43615 Da
    Quaternary structure:
    • Interacts with PRMT5; this interaction is direct (PubMed:25092918). Interacts with GNL2 and RPL23A (PubMed:26203195). Interacts with nucleolin/NCL; this interaction is direct (By similarity). Interacts with phosphorylated IRF3; this interaction impairs IRF3 DNA-binding activity (PubMed:31413131).

neXtProt entry for LYAR Gene

Post-translational modifications for LYAR Gene

  • Ubiquitination at Lys80
  • Modification sites at PhosphoSitePlus

Other Protein References for LYAR Gene

No data available for DME Specific Peptides for LYAR Gene

Domains & Families for LYAR Gene

Gene Families for LYAR Gene

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

Protein Domains for LYAR Gene

Suggested Antigen Peptide Sequences for LYAR Gene

GenScript: Design optimal peptide antigens:
  • Cell growth-regulating nucleolar protein (LYAR_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NX58

UniProtKB/Swiss-Prot:

LYAR_HUMAN :
  • The N-terminal zinc-finger domains are required for the appropriate production of 28S rRNA and the formation of pre-60S particles.
Domain:
  • The N-terminal zinc-finger domains are required for the appropriate production of 28S rRNA and the formation of pre-60S particles.
genes like me logo Genes that share domains with LYAR: view

Function for LYAR Gene

Molecular function for LYAR Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the maintenance of the appropriate processing of 47S/45S pre-rRNA to 32S/30S pre-rRNAs and their subsequent processing to produce 18S and 28S rRNAs (PubMed:24495227). Also acts at the level of transcription regulation. Along with PRMT5, binds the gamma-globin (HBG1/HBG2) promoter and represses its expression (PubMed:25092918). In neuroblastoma cells, may also repress the expression of oxidative stress genes, including CHAC1, HMOX1, SLC7A11, ULBP1 and SNORD41 that encodes a small nucleolar RNA (PubMed:28686580). Preferentially binds to a DNA motif containing 5'-GGTTAT-3' (PubMed:25092918). Negatively regulates the antiviral innate immune response by targeting IRF3 and impairing its DNA-binding activity (PubMed:31413131). In addition, inhibits NF-kappa-B-mediated expression of proinflammatory cytokines (PubMed:31413131). Stimulates phagocytosis of photoreceptor outer segments by retinal pigment epithelial cells (By similarity). Prevents nucleolin/NCL self-cleavage, maintaining a normal steady-state level of NCL protein in undifferentiated embryonic stem cells (ESCs), which in turn is essential for ESC self-renewal (By similarity).
UniProtKB/Swiss-Prot Induction:
Induced by MYCN (PubMed:28686580). Induced by interferon-beta (PubMed:31413131).

Phenotypes From GWAS Catalog for LYAR Gene

Gene Ontology (GO) - Molecular Function for LYAR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA,IDA 25092918
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 21516116
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LYAR: view
genes like me logo Genes that share phenotypes with LYAR: view

Animal Model Products

CRISPR Products

miRNA for LYAR Gene

miRTarBase miRNAs that target LYAR

Clone Products

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

Localization for LYAR Gene

Subcellular locations from UniProtKB/Swiss-Prot for LYAR Gene

Nucleus. Nucleus, nucleolus. Cytoplasm. Cell projection, cilium, photoreceptor outer segment. Note=Component of pre-ribosomal particles, including pre-40S, pre-60S and pre-90S (PubMed:24495227). Associated with cytoplasmic ribosomes, but not polysomes, as a component of the 60S subunit (PubMed:24990247). In the retina, predominantly expressed in photoreceptor outer segments (By similarity). In the nucleolus, colocalizes with nucleolin/NCL, therefore may reside in the dense fibrillar component (DFC) (By similarity). {ECO:0000250 UniProtKB:Q08288, ECO:0000269 PubMed:24495227, ECO:0000269 PubMed:24990247}.

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 LYAR gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (4)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LYAR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001750 photoreceptor outer segment ISS --
GO:0005634 nucleus IDA,IEA 22720776
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IDA,IBA 24495227
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with LYAR: view

Pathways & Interactions for LYAR Gene

PathCards logo

SuperPathways for LYAR Gene

No Data Available

Gene Ontology (GO) - Biological Process for LYAR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IMP 25092918
GO:0006364 rRNA processing IMP,IBA 24495227
GO:0048821 erythrocyte development IMP 25092918
GO:0050766 positive regulation of phagocytosis ISS --
genes like me logo Genes that share ontologies with LYAR: view

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

Drugs & Compounds for LYAR Gene

(1) Drugs for LYAR Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Copper Approved, Investigational Pharma Target 236
genes like me logo Genes that share compounds with LYAR: view

Transcripts for LYAR Gene

mRNA/cDNA for LYAR Gene

2 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
SP1: -
SP2:
SP3:

Relevant External Links for LYAR Gene

GeneLoc Exon Structure for
LYAR

Expression for LYAR Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Testis (x6.0).

Protein differential expression in normal tissues from HIPED for LYAR Gene

This gene is overexpressed in Platelet (35.4) and Lung (15.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LYAR Gene



Protein tissue co-expression partners for LYAR Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LYAR

SOURCE GeneReport for Unigene cluster for LYAR Gene:

Hs.425427

mRNA Expression by UniProt/SwissProt for LYAR Gene:

Q9NX58-LYAR_HUMAN
Tissue specificity: Predominantly expressed in testis.
genes like me logo Genes that share expression patterns with LYAR: view

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LYAR Gene

Orthologs for LYAR Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for LYAR Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LYAR 31 30
  • 98.5 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LYAR 31 30
  • 84.72 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LYAR 31 30
  • 83.89 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lyar 30
  • 79.95 (n)
mouse
(Mus musculus)
Mammalia Lyar 17 31 30
  • 77.78 (n)
oppossum
(Monodelphis domestica)
Mammalia LYAR 31
  • 64 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LYAR 31
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves LYAR 31 30
  • 66.01 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 85 (a)
OneToMany
-- 31
  • 39 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia lyar 30
  • 62.73 (n)
zebrafish
(Danio rerio)
Actinopterygii lyar 30
  • 60.4 (n)
LYAR 31
  • 41 (a)
OneToOne
-- 30
fruit fly
(Drosophila melanogaster)
Insecta CG12909 31
  • 34 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea C16C10.8 31
  • 35 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 46 (a)
OneToOne
Species where no ortholog for LYAR 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)
  • 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)
  • 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 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)

Evolution for LYAR Gene

ENSEMBL:
Gene Tree for LYAR (if available)
TreeFam:
Gene Tree for LYAR (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LYAR: view image

Paralogs for LYAR Gene

Pseudogenes.org Pseudogenes for LYAR Gene

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

No data available for Paralogs for LYAR Gene

Variants for LYAR Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LYAR Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs2272739 - p.Asp151Tyr
rs7376390 - p.His265Arg

Additional dbSNP identifiers (rs#s) for LYAR Gene

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

Variant ID Type Subtype PubMed ID
esv2759219 CNV gain 17122850
esv34196 OTHER inversion 12058347
nsv1001885 CNV gain 25217958
nsv10437 CNV gain 18304495

Variation tolerance for LYAR Gene

Residual Variation Intolerance Score: 86.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.26; 40.62% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LYAR Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for LYAR Gene

MalaCards: The human disease database

(1) MalaCards diseases for LYAR Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
neuroblastoma
  • nb
- elite association - COSMIC cancer census association via MalaCards
Search LYAR in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LYAR

genes like me logo Genes that share disorders with LYAR: view

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

Publications for LYAR Gene

  1. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 2 3 4 54
  2. Upregulation of LYAR induces neuroblastoma cell proliferation and survival. (PMID: 28686580) Sun Y … Liu T (Cell death and differentiation 2017) 3 4 54
  3. Nucleolar GTP-binding Protein-1 (NGP-1) Promotes G1 to S Phase Transition by Activating Cyclin-dependent Kinase Inhibitor p21 Cip1/Waf1. (PMID: 26203195) Datta D … Mahalingam S (The Journal of biological chemistry 2015) 3 4 54
  4. Lyar, a cell growth-regulating zinc finger protein, was identified to be associated with cytoplasmic ribosomes in male germ and cancer cells. (PMID: 24990247) Yonezawa K … Nadano D (Molecular and cellular biochemistry 2014) 3 4 54
  5. Human cell growth regulator Ly-1 antibody reactive homologue accelerates processing of preribosomal RNA. (PMID: 24495227) Miyazawa N … Takahashi N (Genes to cells : devoted to molecular & cellular mechanisms 2014) 3 4 54

Products for LYAR Gene

Sources for LYAR Gene