LYAR Ly1 antibody reactive [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 4p16.3

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (4267701..4290154, complement)
RS_2023_03	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_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-67674 (e-PCR)
- UniSTS:4487

D4S1359 (e-PCR)
- UniSTS:9889

LYAR (e-PCR)
- UniSTS:503515

G34214 (e-PCR)
- UniSTS:7399

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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 more info	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	PubMed
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	PubMed
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	PubMed
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)

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

Q9NX58, Q9NYS1

Related

ENSP00000397367.1, ENST00000452476.5

Conserved Domains (1) summary

pfam08790
Location:31 → 58

zf-LYAR; LYAR-type C2HC zinc finger
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

Q9NX58, Q9NYS1

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_03

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

4267701..4290154 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Q9NX58, Q9NYS1

Conserved Domains (1) summary

pfam08790
Location:31 → 58

zf-LYAR; LYAR-type C2HC zinc finger
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

Q9NX58, Q9NYS1

Conserved Domains (1) summary

pfam08790
Location:31 → 58

zf-LYAR; LYAR-type C2HC zinc finger

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

4237159..4259618 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q9NYS1
XM_054350460.1 → XP_054206435.1 cell growth-regulating nucleolar protein isoform X1

UniProtKB/Swiss-Prot

Q9NYS1