Lsm4 MGI Mouse Gene Detail - MGI:1354692 - LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated

Symbol

Lsm4
Name

LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated

Feature Type

protein coding gene
IDs

MGI:1354692
NCBI Gene: 50783
Alliance

gene page
Transcription Start Sites

5 TSS

Sequence Map

Chr8:71125898-71131402 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 8, 34.15 cM
Mapping Data

2 experiments

SNPs within 2kb

175 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1354692	protein coding gene	Chr8:71124663-71131402 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0033718	protein coding gene	Chr8:70959722-70965610 (+)
A/J	MGP_AJ_G0033701	protein coding gene	Chr8:68075472-68081073 (+)
AKR/J	MGP_AKRJ_G0033626	protein coding gene	Chr8:70022292-70027797 (+)
BALB/cJ	MGP_BALBcJ_G0033697	protein coding gene	Chr8:68311471-68316959 (+)
C3H/HeJ	MGP_C3HHeJ_G0033407	protein coding gene	Chr8:70659763-70667075 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0034214	protein coding gene	Chr8:73632051-73638198 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0031158	protein coding gene	Chr8:62891856-62897657 (+)
CAST/EiJ	MGP_CASTEiJ_G0032732	protein coding gene	Chr8:70146906-70152393 (+)
CBA/J	MGP_CBAJ_G0033385	protein coding gene	Chr8:76296092-76301955 (+)
DBA/2J	MGP_DBA2J_G0033539	protein coding gene	Chr8:67791082-67796390 (+)
FVB/NJ	MGP_FVBNJ_G0033480	protein coding gene	Chr8:66917744-66924171 (+)
LP/J	MGP_LPJ_G0033626	protein coding gene	Chr8:70983394-70988919 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0033523	protein coding gene	Chr8:78941083-78946408 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0034232	protein coding gene	Chr8:70198782-70204100 (+)
PWK/PhJ	MGP_PWKPhJ_G0032440	protein coding gene	Chr8:67091183-67096875 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0032276	protein coding gene	Chr8:69168165-69174924 (+)
WSB/EiJ	MGP_WSBEiJ_G0032847	protein coding gene	Chr8:70559867-70565378 (+)

Human Ortholog

LSM4, LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LSM4, LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated
Synonyms

GRP, YER112W
Links

HGNC:17259

NCBI Gene ID: 25804

neXtProt AC: NX_Q9Y4Z0

UniProt: Q9Y4Z0
Chr Location

19p13.11; chr19:18306236-18323112 (-) GRCh38

MGI Vertebrate Homology

Lsm4 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: LSM4
Gene Tree

Lsm4

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Phenotype Summary

1 phenotype from 1 allele in 1 genetic background
11 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

156
Chemically induced (other)

1
Endonuclease-mediated

2
Gene trapped

151
Targeted

2
Genomic Mutations

1 involving Lsm4
Find Mice (IMSR)

77 strains or lines available

Embryos homozygous for a gene trap mutation in this gene die in the peri-implantation stage.

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All GO Annotations

24
GO References

7

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	membraneless 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

751
Tissues

45
cDNA Data

123
Literature Summary

3

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase lsm4

ZFIN lsm4

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All Sequences

53
RefSeq

6
UniProt

6
CCDS

CCDS40374.1

Ensembl

ENSMUSG00000031848 (Evidence)
NCBI Gene

50783

			Length	Strain/Species	Flank
genomic	ENSMUSG00000031848	Ensembl Gene Model \| MGI Sequence Detail	5505	C57BL/6J	± kb
transcript	ENSMUST00000034311	Ensembl \| MGI Sequence Detail	925	Not Applicable
polypeptide	ENSMUSP00000034311	Ensembl \| MGI Sequence Detail	138	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000009962 U6 snRNA-associated Sm-like protein LSm4

(term hierarchy)
InterPro Domains

IPR027141 Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3

IPR010920 LSM domain superfamily

IPR047575 Sm domain

IPR001163 Sm domain, eukaryotic/archaea-type

IPR034101 Sm-like protein Lsm4

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All nucleic 125

cDNA 123

Primer pair 1

Other 1

Microarray probesets 3

Summaries

All 39

Developmental Gene Expression 3

Gene Ontology 7

Phenotypes 11
Earliest

J:59997 Hirsch E, et al., Peri-implantation lethality in mice lacking the Sm motif-containing protein Lsm4. Mol Cell Biol. 2000 Feb;20(3):1055-62
Latest

J:216429 Perez-Santangelo S, et al., Role for LSM genes in the regulation of circadian rhythms. Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15166-71

TSS for Lsm4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr77795	Chr8:71125848-71125917 (+)	-15 bp
Tssr77796	Chr8:71126014-71126078 (+)	148 bp
Tssr77797	Chr8:71126388-71126409 (+)	501 bp
Tssr77798	Chr8:71126418-71126434 (+)	528 bp
Tssr2599	Chr8:71128834-71128872 (+)	2,955 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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