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LYAR Ly1 antibody reactive [ Homo sapiens (human) ]

Gene ID: 55646, updated on 3-Apr-2024

Summary

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Official Symbol
LYARprovided by HGNC
Official Full Name
Ly1 antibody reactiveprovided by HGNC
Primary source
HGNC:HGNC:26021
See related
Ensembl:ENSG00000145220 MIM:617684; AllianceGenome:HGNC:26021
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
ZLYAR; ZC2HC2
Summary
Enables several functions, including DNA-binding transcription factor binding activity; identical protein binding activity; and transcription regulator inhibitor activity. Involved in several processes, including erythrocyte development; negative regulation of innate immune response; and regulation of transcription, DNA-templated. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 46.8), lymph node (RPKM 8.5) and 20 other tissues See more
Orthologs
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Genomic context

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See LYAR in Genome Data Viewer
Location:
4p16.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (4267701..4290154, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (4237159..4259618, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (4269428..4291881, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene otopetrin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4227786-4228406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4229028-4229648 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:4249292-4249918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21227 Neighboring gene transmembrane protein 128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4258767-4259267 Neighboring gene Sharpr-MPRA regulatory region 9855 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:4271128-4271305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4289830-4290368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4290369-4290906 Neighboring gene zinc finger and BTB domain containing 49 Neighboring gene uncharacterized LOC112268462

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. The rs368698783 (G>A) Polymorphism Affecting LYAR Binding to the Aγ-Globin Gene Is Associated with High Fetal Hemoglobin (HbF) in β-Thalassemia Erythroid Precursor Cells Treated with HbF Inducers. Zuccato C, et al. Int J Mol Sci, 2023 Jan 1. PMID 36614221, Free PMC Article
  2. LYAR promotes the proliferation of non-small cell lung cancer and is associated with poor prognosis. Lu XN, et al. Folia Histochem Cytobiol, 2021. PMID 34890041
  3. Analysis of the role of Ly-1 antibody reactive in different cancer types. Chen L, et al. Bioengineered, 2021 Dec. PMID 34696677, Free PMC Article
  4. Upregulation of LYAR induces neuroblastoma cell proliferation and survival. Sun Y, et al. Cell Death Differ, 2017 Sep. PMID 28686580, Free PMC Article
  5. LYAR Suppresses Beta Interferon Induction by Targeting Phosphorylated Interferon Regulatory Factor 3. Yang C, et al. J Virol, 2019 Nov 1. PMID 31413131, Free PMC Article

See all (148) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The rs368698783 (G>A) Polymorphism Affecting LYAR Binding to the Agamma-Globin Gene Is Associated with High Fetal Hemoglobin (HbF) in beta-Thalassemia Erythroid Precursor Cells Treated with HbF Inducers.
    Title: The rs368698783 (G>A) Polymorphism Affecting LYAR Binding to the Aγ-Globin Gene Is Associated with High Fetal Hemoglobin (HbF) in β-Thalassemia Erythroid Precursor Cells Treated with HbF Inducers.
  2. Analysis of the role of Ly-1 antibody reactive in different cancer types.
    Title: Analysis of the role of Ly-1 antibody reactive in different cancer types.
  3. LYAR promotes the proliferation of non-small cell lung cancer and is associated with poor prognosis.
    Title: LYAR promotes the proliferation of non-small cell lung cancer and is associated with poor prognosis.
  4. Ly1 antibody reactive cell growth-regulating nucleolar protein (LYAR) expression is induced by beta interferon (IFN-beta) during virus infection. LYAR interacts with phosphorylated IFN regulatory factor 3 (IRF3) to impede the DNA binding capacity of IRF3, thereby suppressing the transcription of IFN-beta and downstream IFN-stimulated genes (ISGs). LYAR is a repressor of host innate immune responses to promote virus rep...
    Title: LYAR Suppresses Beta Interferon Induction by Targeting Phosphorylated Interferon Regulatory Factor 3.
  5. These data suggest that LYAR promotes the association of the BRD2-KAT7 and BRD4-KAT7 complexes with transcription-competent rDNA loci but not to transcriptionally silent rDNA loci, thereby increasing rRNA synthesis by altering the local acetylation status of histone H3 and H4.
    Title: LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA.
  6. Data suggest that LYAR induces proliferation and promotes survival of neuroblastoma cells by repressing the expression of oxidative stress genes such as CHAC1 and suppressing oxidative stress, and identify LYAR as a novel co-factor in N-Myc oncogenesis.
    Title: Upregulation of LYAR induces neuroblastoma cell proliferation and survival.
  7. LYAR may promote tumor cell migration and invasion by upregulating galectin-1 gene expression in colorectal cancer.
    Title: LYAR promotes colorectal cancer cell mobility by activating galectin-1 expression.
  8. Results show that LYAR protein expression is testis-predominant but can also be found in cancer cells originated from tissues other than testis. Lyar seems to promote proliferation of NIH-3T3 cells.
    Title: Lyar, a cell growth-regulating zinc finger protein, was identified to be associated with cytoplasmic ribosomes in male germ and cancer cells.
  9. The data indicate that LYAR acts as a novel transcription factor that binds the gamma-globin gene, and is essential for silencing the gamma-globin gene.
    Title: Human fetal globin gene expression is regulated by LYAR.
  10. Over-expression of LYAR increases cell proliferation without affecting the expression of c-Myc or p53. Some rapidly growing cells enhance ribosome biogenesis by increasing the expression of LYAR.
    Title: Human cell growth regulator Ly-1 antibody reactive homologue accelerates processing of preribosomal RNA.
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

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

Clone Names

  • FLJ20425

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables RNA binding HDA PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription regulator inhibitor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in erythrocyte development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of innate immune response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of phagocytosis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of transcription by RNA polymerase I IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in rRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in rRNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in photoreceptor outer segment ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
cell growth-regulating nucleolar protein
Names
Ly1 antibody reactive homolog

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_001145725.2 → NP_001139197.1  cell growth-regulating nucleolar protein

    See identical proteins and their annotated locations for NP_001139197.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL136750, BQ775341
    Consensus CDS
    CCDS3374.1
    UniProtKB/Swiss-Prot
    D3DVS4, Q6FI78, Q9NX58, Q9NYS1
    UniProtKB/TrEMBL
    A8K3Y5
    Related
    ENSP00000397367.1, ENST00000452476.5
    Conserved Domains (1) summary
    pfam08790
    Location:31 → 58
    zf-LYAR; LYAR-type C2HC zinc finger

  2. NM_017816.3 → NP_060286.1  cell growth-regulating nucleolar protein

    See identical proteins and their annotated locations for NP_060286.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AI418609, AK000432, BQ775341
    Consensus CDS
    CCDS3374.1
    UniProtKB/Swiss-Prot
    D3DVS4, Q6FI78, Q9NX58, Q9NYS1
    UniProtKB/TrEMBL
    A8K3Y5
    Related
    ENSP00000345917.4, ENST00000343470.9
    Conserved Domains (1) summary
    pfam08790
    Location:31 → 58
    zf-LYAR; LYAR-type C2HC zinc finger

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    4267701..4290154 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513506.4 → XP_011511808.1  cell growth-regulating nucleolar protein isoform X1

    See identical proteins and their annotated locations for XP_011511808.1

    UniProtKB/Swiss-Prot
    D3DVS4, Q6FI78, Q9NX58, Q9NYS1
    UniProtKB/TrEMBL
    A8K3Y5
    Conserved Domains (1) summary
    pfam08790
    Location:31 → 58
    zf-LYAR; LYAR-type C2HC zinc finger

  2. XM_011513505.2 → XP_011511807.1  cell growth-regulating nucleolar protein isoform X1

    See identical proteins and their annotated locations for XP_011511807.1

    UniProtKB/Swiss-Prot
    D3DVS4, Q6FI78, Q9NX58, Q9NYS1
    UniProtKB/TrEMBL
    A8K3Y5
    Conserved Domains (1) summary
    pfam08790
    Location:31 → 58
    zf-LYAR; LYAR-type C2HC zinc finger

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    4237159..4259618 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350461.1 → XP_054206436.1  cell growth-regulating nucleolar protein isoform X1

    UniProtKB/Swiss-Prot
    D3DVS4, Q6FI78, Q9NX58, Q9NYS1

  2. XM_054350460.1 → XP_054206435.1  cell growth-regulating nucleolar protein isoform X1

    UniProtKB/Swiss-Prot
    D3DVS4, Q6FI78, Q9NX58, Q9NYS1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NX58.3 GenPept UniProtKB/Swiss-Prot:Q9NX58

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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