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

Summary

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

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_000071.7 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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)

NM_001424421.1 → NP_001411350.1 cell growth-regulating nucleolar protein isoform 1

Status: VALIDATED

Source sequence(s)

AC115931

UniProtKB/Swiss-Prot

Q08288, Q9D9X2
NM_001424422.1 → NP_001411351.1 cell growth-regulating nucleolar protein isoform 1

Status: VALIDATED

Source sequence(s)

AC115931

UniProtKB/Swiss-Prot

Q08288, Q9D9X2
NM_001424423.1 → NP_001411352.1 cell growth-regulating nucleolar protein isoform 1

Status: VALIDATED

Source sequence(s)

AC115931

UniProtKB/Swiss-Prot

Q08288, Q9D9X2
NM_001424424.1 → NP_001411353.1 cell growth-regulating nucleolar protein isoform 1

Status: VALIDATED

Source sequence(s)

AC115931

UniProtKB/Swiss-Prot

Q08288, Q9D9X2
NM_001424425.1 → NP_001411354.1 cell growth-regulating nucleolar protein isoform 1

Status: VALIDATED

Source sequence(s)

AC115931

UniProtKB/Swiss-Prot

Q08288, Q9D9X2
NM_001424426.1 → NP_001411355.1 cell growth-regulating nucleolar protein isoform 2

Status: VALIDATED

Source sequence(s)

AC115931
NM_001424427.1 → NP_001411356.1 cell growth-regulating nucleolar protein isoform 3

Status: VALIDATED

Source sequence(s)

AC115931
NM_001424428.1 → NP_001411357.1 cell growth-regulating nucleolar protein isoform 4

Status: VALIDATED

Source sequence(s)

AC115931
NM_001424429.1 → NP_001411358.1 cell growth-regulating nucleolar protein isoform 4

Status: VALIDATED

Source sequence(s)

AC115931
NM_001424430.1 → NP_001411359.1 cell growth-regulating nucleolar protein isoform 4

Status: VALIDATED

Source sequence(s)

AC115931
NM_001424431.1 → NP_001411360.1 cell growth-regulating nucleolar protein isoform 5

Status: VALIDATED

Source sequence(s)

AC115931
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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

38377815..38391650

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
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]
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]