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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

LYAR Gene

protein-coding   GIFtS: 50
GCID: GC04M004269

Ly1 antibody reactive

(Previous name: Ly1 antibody reactive homolog (mouse) )
 Explore 2 diseases affiliated with
LYAR via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for LYAR    

Aliases
for LYAR gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Ly1 Antibody Reactive1 2
ZC2HC21 2
ZLYAR1 2
Ly1 Antibody Reactive Homolog (Mouse)1
Cell Growth-Regulating Nucleolar Protein2
Ly1 Antibody Reactive Homolog2

External Ids:    HGNC: 260211   Entrez Gene: 556462   Ensembl: ENSG000001452207   UniProtKB: Q9NX583   

Export aliases for LYAR gene to outside databases

Previous GC identifers: GC04M004146 GC04M004262 GC04M004333 GC04M004387 GC04M004206


Summaries
for LYAR gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Gene Wiki entry for LYAR


Genomic Views
for LYAR gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.1  NT_006051.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the LYAR gene promoter:
         TBP   AML1a   Ik-2   MyoD   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: LYAR promoter sequence
   Search SABiosciences Chromatin IP Primers for LYAR

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LYAR


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4p16.3   Ensembl cytogenetic band:  4p16.3   HGNC cytogenetic band: 4p16.3

LYAR Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LYAR gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M004269:  view genomic region     (about GC identifiers)

Start:
 4,269,428 bp from pter      End:
 4,291,896 bp from pter
Size:
 22,469 bases      Orientation:
 minus strand

Proteins
for LYAR gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: LYAR_HUMAN, Q9NX58 (See protein sequence)
Recommended Name: Cell growth-regulating nucleolar protein  
Size: 379 amino acids; 43615 Da
Subcellular location: Nucleus, nucleolus
Secondary accessions: D3DVS4 Q6FI78 Q9NYS1

Explore the universe of human proteins at neXtProt for LYAR: NX_Q9NX58

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NX58

    • LYAR Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001139197.1  NP_060286.1  

    ENSEMBL proteins: 
     ENSP00000345917   ENSP00000420902   ENSP00000397367  

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    Uscn Proteins for LYAR

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005730nucleolus IDA--


    LYAR for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for LYAR

    Protein Domains /
    Families
    for LYAR gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    LYAR for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR014898 Znf_C2H2_LYAR

    Graphical View of Domain Structure for InterPro Entry Q9NX58

    ProtoNet protein and cluster: Q9NX58

    UniProtKB/Swiss-Prot: LYAR_HUMAN, Q9NX58
    Similarity: Contains 2 C2HC-type zinc fingers


    Function
    for LYAR gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    miRNA
    Products:            		 OriGene 3'-UTR Clone (see all 2): LYAR
    Browse MicroRNA Expression Plasmids
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    SwitchGear 3'UTR luciferase reporter plasmid: LYAR 3' UTR sequence
    Inhib. RNA
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    OriGene shRNA RFP: LYAR
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    Gene Editing
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    Clone
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    Search LifeMap BioReagents cell lines for LYAR

    In Situ Assay
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0046872metal ion binding IEA--


    LYAR for ontologies           About GeneDecksing



    Pathways & Interactions
    for LYAR gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for LYAR

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/174 Interacting proteins for LYAR (Q9NX582, 3 ENSP000003459174) via UniProtKB, MINT, STRING, and/or I2D (see all 174)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GNL3Q9BVP22, 3, ENSP000003957724MINT-6488590 I2D: score=1 STRING: ENSP00000395772
    RPL21P467782, 3, ENSP000003460274MINT-6488590 I2D: score=1 STRING: ENSP00000346027
    ZBTB16Q055162, 3MINT-65657 I2D: score=5 
    ZHX1Q9UKY12, 3MINT-65658 I2D: score=5 
    RPL18AQ025432, 3MINT-6488590 I2D: score=2 
    About this table

    Drugs & Compounds
    for LYAR gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for LYAR
    Search CenterWatch for drugs/clinical trials and news about LYAR 

    Transcripts
    for LYAR gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for LYAR gene (2 alternative transcripts): 
    NM_001145725.1  NM_017816.2  

    Unigene Cluster for LYAR:

    Ly1 antibody reactive
    Hs.425427  [show with all ESTs]
    Unigene Representative Sequence: AK000432
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000502917 ENST00000343470(uc011bvx.2 uc003ght.3) ENST00000513174
    ENST00000452476(uc011bvy.2)

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    SwitchGear 3'UTR luciferase reporter plasmid: LYAR 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for LYAR (see all 7)
    OriGene shRNA RFP: LYAR
    OriGene siRNA: LYAR
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat LYAR
    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 2): LYAR (NM_001145725)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LYAR 
    Primer
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    Additional cDNA sequence: 

    AF229835.1 AK000432.1 AK290750.1 AL136750.1 BC015796.2 CR533548.1 

    8 DOTS entries:

    DT.410315  DT.100776371  DT.102823585  DT.92434601  DT.92434604  DT.95165954  DT.100776370  DT.100035677 

    24/111 AceView cDNA sequences (see all 111):

    AI382479 AK000432 CB135957 BM974170 AA424566 AI183462 AL136750 CR605760 
    AI708352 AI688625 NM_017816 BQ439081 BM823927 BF197522 BP354367 CR609495 
    BQ220279 AW294480 CR616708 AF229835 AA355932 BI837521 BC015796 AI377696 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for LYAR    About this scheme

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


    ECgene alternative splicing isoforms for LYAR

    Expression
    for LYAR gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    LYAR expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CAGAAATCTC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    LYAR expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    3 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    EyeOuter Nuclear LayerMature Rod CellsPhotoreceptors, Retina
    OvaryAntral FollicleSecondary OocyteFemale Gametocytes, Germ Cells
    LiverLiver LobuleLiver
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See LYAR Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for LYAR

    SOURCE GeneReport for Unigene cluster: Hs.425427
        SABiosciences Custom PCR Arrays for LYAR
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat LYAR
    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LYAR

    Orthologs
    for LYAR gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of eukaryotes.

    Orthologs for LYAR gene from 9/27 species (see all 27)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Lyar1 , 5 Ly1 antibody reactive clone1, 5 77.87(n)1
    75.2(a)1    		   5 (20.29 cM)5
    170891  NM_025281.31  NP_079557.21 
     382204705 
    chicken
    (Gallus gallus)    		 Aves LYAR1 Ly1 antibody reactive homolog (mouse) 67.04(n)
    60.28(a)    		   422846  XM_420792.3  XP_420792.2 
    lizard
    (Anolis carolinensis)    		 Reptilia LYAR6
    		 --
    		 85(a)
    		 1 ↔ 1
    		 GL343236.1(653554-660176)
    African clawed frog
    (Xenopus laevis)    		 Amphibia BU901561.12   -- 78.68(n)    BU901561.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii AF332588.12   -- 73.8(n)   393652  AF332588.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG129091 CG12909 48.83(n)
    40.33(a)    		   36087  NM_136729.3  NP_610573.1 
    worm
    (Caenorhabditis elegans)    		 Secernentea CELE_C16C10.81 Protein C16C10.8 48.86(n)
    40.64(a)    		   175531  NM_065428.3  NP_497829.1 
    thale cress
    (Arabidopsis thaliana)    		 eudicotyledons AT2G193851 zinc ion binding protein 45.93(n)
    37.33(a)    		   816457  NM_127496.2  NP_565451.1 
    rice
    (Oryza sativa)    		 Liliopsida Os01g05832001 hypothetical protein 42.25(n)
    28.09(a)    		   4324202  NM_001049951.1  NP_001043416.2 


    ENSEMBL Gene Tree for LYAR (if available)
    TreeFam Gene Tree for LYAR (if available) 

    Paralogs
    for LYAR gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for LYAR gene

    LYAR for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for LYAR
    PGOHUM00000240114


    Genomic Variants
    for LYAR gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for LYAR
         2 CNVs: 31156 3477
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing LYAR
    DNA2.0 Custom Variant and Variant Library Synthesis for LYAR

    Disorders / Diseases
    for LYAR gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    LYAR for disorders           About GeneDecksing

    2 diseases for LYAR:    About MalaCards
    treacher collins syndrome    metastasis efficiency


    Export disorders for LYAR gene to outside databases

    Publications
    for LYAR gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for LYAR gene, integrated from 9 sources (see all 30):
    (articles sorted by number of sources associating them with LYAR)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2, 3 Wiemann S.... Poustka A. (2001)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Functional proteomic analysis of human nucleolus. (PubMed id 12429849)1, 2 Scherl A.... Diaz J.-J. (2002)
    5. LYAR, a novel nucleolar protein with zinc finger DNA-binding motifs, is involved in cell growth regulation. (PubMed id 8491376)1, 3 Su L....Weissman I.L. (1993)
    6. Targeted ubiquitination and degradation of G-protein-c oupled receptor kinase 5 by the DDB1-CUL4 ubiquitin ligase complex. (PubMed id 22952844)1 Wu Z....Ma L. (2012)
    7. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (2012)
    8. Mapping a dynamic innate immunity protein interaction network regulating type I interferon production. (PubMed id 21903422)1 Li S....Dorf M.E. (2011)
    9. Interactome study suggests multiple cellular functions of hepatoma-derived growth factor (HDGF). (PubMed id 21907836)1 Zhao J....Yang P. (2011)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)

    External Searches for LYAR gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing LYAR gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 55646 HGNC: 26021 AceView: LYAR Ensembl:ENSG00000145220 euGenes: HUgn55646
    ECgene: LYAR H-InvDB: LYAR

    Other Databases showing LYAR gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing LYAR gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for LYAR Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for LYAR gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for LYAR gene:
    Search GeneIP for patents involving LYAR

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for LYAR gene

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    In Situ Hybridization Assays from
    Advanced Cell Diagnostics
    About This Section

     
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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