Lyar MGI Mouse Gene Detail - MGI:107470 - Ly1 antibody reactive clone

Symbol

Lyar
Name

Ly1 antibody reactive clone

Feature Type

protein coding gene
IDs

MGI:107470
NCBI Gene: 17089
Alliance

gene page
Transcription Start Sites

10 TSS

Sequence Map

Chr5:38377815-38391650 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 5, 20.29 cM
Mapping Data

3 experiments

SNPs within 2kb

93 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_107470	protein coding gene	Chr5:38377814-38391650 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0029508	protein coding gene	Chr5:36627785-36641608 (+)
A/J	MGP_AJ_G0029474	protein coding gene	Chr5:35399510-35413344 (+)
AKR/J	MGP_AKRJ_G0029424	protein coding gene	Chr5:36734720-36748554 (+)
BALB/cJ	MGP_BALBcJ_G0029485	protein coding gene	Chr5:35896077-35909919 (+)
C3H/HeJ	MGP_C3HHeJ_G0029208	protein coding gene	Chr5:36726801-36740665 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0029939	protein coding gene	Chr5:38569998-38583821 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0027177	protein coding gene	Chr5:33076702-33090587 (+)
CAST/EiJ	MGP_CASTEiJ_G0028616	protein coding gene	Chr5:35890719-35906323 (+)
CBA/J	MGP_CBAJ_G0029175	protein coding gene	Chr5:39484256-39498092 (+)
DBA/2J	MGP_DBA2J_G0029322	protein coding gene	Chr5:35522034-35535857 (+)
FVB/NJ	MGP_FVBNJ_G0029281	protein coding gene	Chr5:35009216-35023039 (+)
LP/J	MGP_LPJ_G0029408	protein coding gene	Chr5:37076191-37090115 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0029311	protein coding gene	Chr5:40192969-40206792 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0029972	protein coding gene	Chr5:36223290-36237136 (+)
PWK/PhJ	MGP_PWKPhJ_G0028340	protein coding gene	Chr5:34691177-34705287 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0028174	protein coding gene	Chr5:35674408-35690222 (+)
WSB/EiJ	MGP_WSBEiJ_G0028697	protein coding gene	Chr5:36304102-36317943 (+)

Human Ortholog

LYAR, Ly1 antibody reactive

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LYAR, Ly1 antibody reactive
Synonyms

ZC2HC2, ZLYAR
Links

HGNC:26021

NCBI Gene ID: 55646

neXtProt AC: NX_Q9NX58

UniProt: Q9NX58
Chr Location

4p16.3; chr4:4267701-4290154 (-) GRCh38

MGI Vertebrate Homology

Lyar stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: LYAR
Gene Tree

Lyar

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References

1 with disease annotations

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Phenotype Summary

3 phenotypes from 2 alleles in 2 genetic backgrounds
6 phenotypes from multigenic genotypes
30 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

23
Chemically induced (ENU)

1
Chemically induced (other)

2
Endonuclease-mediated

3
Gene trapped

12
Radiation induced

2
Spontaneous

1
Targeted

2
Genomic Mutations

6 involving Lyar
Incidental Mutations

APF , CvDC
Find Mice (IMSR)

30 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit reduced proliferation of mouse embryonic fibroblasts and results in female prenatal lethality when presnt with a Trp53 null allele.

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All GO Annotations

34
GO References

9

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

859
Tissues

41
cDNA Data

92
Literature Summary

4

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase lyar

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All Sequences

89
RefSeq

30
UniProt

8
CCDS

CCDS19253.1

Ensembl

ENSMUSG00000067367 (Evidence)
NCBI Gene

17089

			Length	Strain/Species	Flank
genomic	17089	NCBI Gene Model \| MGI Sequence Detail	13836	C57BL/6J	± kb
transcript	NM_001424423	RefSeq \| MGI Sequence Detail	1750	C57BL/6
polypeptide	Q08288	UniProt \| EBI \| MGI Sequence Detail	388	Not Applicable

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UniProt

8 Sequences
Protein Ontology

PR:000009998 cell growth-regulating nucleolar protein

(term hierarchy)
PDB

1WJV
InterPro Domains

IPR041010 Acetyl-coA carboxylase zinc finger domain

IPR039999 Cell growth-regulating nucleolar protein

IPR014898 Zinc finger, C2H2, LYAR-type

IPR036236 Zinc finger C2H2 superfamily

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All nucleic 93

cDNA 92

Primer pair 1

Microarray probesets 3

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MGD-MRK-35942

Summaries

All 58

Developmental Gene Expression 4

Diseases 1

Gene Ontology 9

Phenotypes 30
Earliest

J:5021 Batchelor AL, et al., A comparison of the mutagenic effectiveness of chronic neutron- and gamma-irradiation of mouse spermatogonia. Mutat Res. 1966 Jun;3(3):218-29
Latest

J:252004 Guo F, et al., Lyar Is a New Ligand for Retinal Pigment Epithelial Phagocytosis. J Cell Biochem. 2015 Oct;116(10):2177-87

TSS for Lyar:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr46044	Chr5:38377304-38377314 (+)	-506 bp
Tssr46045	Chr5:38377825-38377904 (+)	50 bp
Tssr46046	Chr5:38377921-38377932 (+)	112 bp
Tssr46047	Chr5:38377936-38377947 (+)	127 bp
Tssr46048	Chr5:38377972-38377993 (+)	168 bp
Tssr46049	Chr5:38383230-38383243 (+)	5,422 bp
Tssr46050	Chr5:38385443-38385452 (+)	7,633 bp
Tssr46051	Chr5:38387897-38387926 (+)	10,097 bp
Tssr46052	Chr5:38387927-38387944 (+)	10,121 bp
Tssr46053	Chr5:38388005-38388022 (+)	10,199 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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