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Lyar Ly1 antibody reactive clone [ Mus musculus (house mouse) ]

Gene ID: 17089, updated on 2-Nov-2024

Summary

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Official Symbol
Lyarprovided by MGI
Official Full Name
Ly1 antibody reactive cloneprovided by MGI
Primary source
MGI:MGI:107470
See related
Ensembl:ENSMUSG00000067367 AllianceGenome:MGI:107470
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
MLZ-264
Summary
Predicted to enable several functions, including DNA-binding transcription factor binding activity; identical protein binding activity; and transcription regulator inhibitor activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of phagocytosis. Located in nucleolus and photoreceptor outer segment. Is expressed in several structures, including gonad; hemolymphoid system; jaw; liver; and metanephros. Orthologous to human LYAR (Ly1 antibody reactive). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in testis adult (RPKM 89.4), liver E14 (RPKM 24.9) and 8 other tissues See more
Orthologs
human all
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Genomic context

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See Lyar in Genome Data Viewer
Location:
5 B3; 5 20.29 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (38377815..38391650)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (38220471..38234306)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene syntaxin 18 Neighboring gene neuron specific gene family member 1 Neighboring gene zinc finger and BTB domain containing 49 Neighboring gene STARR-positive B cell enhancer mm9_chr5:38602912-38603212 Neighboring gene transmembrane protein 128 Neighboring gene otopetrin 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Expression and function of the testis-predominant protein LYAR in mice. Lee B, et al. Mol Cells, 2013 Jan. PMID 23212345, Free PMC Article
  2. Lyar, a cell growth-regulating zinc finger protein, was identified to be associated with cytoplasmic ribosomes in male germ and cancer cells. Yonezawa K, et al. Mol Cell Biochem, 2014 Oct. PMID 24990247
  3. Mutations in Lyar and p53 are synergistically lethal in female mice. Wang G, et al. Birth Defects Res A Clin Mol Teratol, 2012 Sep. PMID 22815056
  4. Lyar Is a New Ligand for Retinal Pigment Epithelial Phagocytosis. Guo F, et al. J Cell Biochem, 2015 Oct. PMID 25735755, Free PMC Article
  5. Human fetal globin gene expression is regulated by LYAR. Ju J, et al. Nucleic Acids Res, 2014 Sep. PMID 25092918, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. These results suggest that Lyar is a genuine RPE phagocytosis ligand, which in turn supports the validity of OPD/PFC as the only available approach for unbiased identification of phagocytosis ligands with broad applicability to various phagocytes
    Title: Lyar Is a New Ligand for Retinal Pigment Epithelial Phagocytosis.
  2. 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.
  3. Lyar is a novel candidate gene for a role in human neural tube defects.
    Title: Mutations in Lyar and p53 are synergistically lethal in female mice.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3) 
  • Gene trapped (1) 
  • Targeted (1) 

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

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

General protein information

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Preferred Names
cell growth-regulating nucleolar protein
Names
ly1 antibody-reactive protein
protein expressed in male leptotene and zygotene spermatocytes 264

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_001424421.1 → NP_001411350.1  cell growth-regulating nucleolar protein isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC115931
    UniProtKB/Swiss-Prot
    Q08288, Q9D9X2

  2. NM_001424422.1 → NP_001411351.1  cell growth-regulating nucleolar protein isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC115931
    UniProtKB/Swiss-Prot
    Q08288, Q9D9X2

  3. NM_001424423.1 → NP_001411352.1  cell growth-regulating nucleolar protein isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC115931
    UniProtKB/Swiss-Prot
    Q08288, Q9D9X2

  4. NM_001424424.1 → NP_001411353.1  cell growth-regulating nucleolar protein isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC115931
    UniProtKB/Swiss-Prot
    Q08288, Q9D9X2

  5. NM_001424425.1 → NP_001411354.1  cell growth-regulating nucleolar protein isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC115931
    UniProtKB/Swiss-Prot
    Q08288, Q9D9X2

  6. NM_001424426.1 → NP_001411355.1  cell growth-regulating nucleolar protein isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC115931

  7. NM_001424427.1 → NP_001411356.1  cell growth-regulating nucleolar protein isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC115931

  8. NM_001424428.1 → NP_001411357.1  cell growth-regulating nucleolar protein isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC115931

  9. NM_001424429.1 → NP_001411358.1  cell growth-regulating nucleolar protein isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC115931

  10. NM_001424430.1 → NP_001411359.1  cell growth-regulating nucleolar protein isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC115931

  11. NM_001424431.1 → NP_001411360.1  cell growth-regulating nucleolar protein isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC115931

  12. NM_025281.4 → NP_079557.2  cell growth-regulating nucleolar protein isoform 1

    See identical proteins and their annotated locations for NP_079557.2

    Status: VALIDATED

    Source sequence(s)
    AC115931
    Consensus CDS
    CCDS19253.1
    UniProtKB/Swiss-Prot
    Q08288, Q9D9X2
    Related
    ENSMUSP00000084791.3, ENSMUST00000087514.9
    Conserved Domains (3) summary
    pfam08790
    Location:31 → 58
    zf-LYAR; LYAR-type C2HC zinc finger
    pfam17848
    Location:3 → 28
    zf-ACC; Acetyl-coA carboxylase zinc finger domain
    cl30717
    Location:122 → 300
    InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    38377815..38391650
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006503766.2 → XP_006503829.1  cell growth-regulating nucleolar protein isoform X2

    See identical proteins and their annotated locations for XP_006503829.1

    Conserved Domains (1) summary
    cl30717
    Location:48 → 227
    InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]

  2. XM_030254182.1 → XP_030110042.1  cell growth-regulating nucleolar protein isoform X2

    Conserved Domains (1) summary
    cl30717
    Location:48 → 227
    InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]

  3. XM_006503764.3 → XP_006503827.1  cell growth-regulating nucleolar protein isoform X1

    See identical proteins and their annotated locations for XP_006503827.1

    UniProtKB/Swiss-Prot
    Q08288, Q9D9X2
    Related
    ENSMUSP00000109741.2, ENSMUST00000114106.8
    Conserved Domains (3) summary
    pfam08790
    Location:31 → 58
    zf-LYAR; LYAR-type C2HC zinc finger
    pfam17848
    Location:3 → 28
    zf-ACC; Acetyl-coA carboxylase zinc finger domain
    cl30717
    Location:122 → 300
    InfB; Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q08288.2 GenPept UniProtKB/Swiss-Prot:Q08288

Gene LinkOut

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