Lsm3 MGI Mouse Gene Detail - MGI:1914928 - LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated

Symbol

Lsm3
Name

LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated
Synonyms

1010001J12Rik, 2610005D18Rik, 6030401D18Rik, SMX4, USS2

Feature Type

protein coding gene
IDs

MGI:1914928
NCBI Gene: 67678
Alliance

gene page
Transcription Start Sites

2 TSS

Sequence Map

Chr6:91493017-91499602 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 6, 40.58 cM, cytoband D2
Mapping Data

3 experiments

SNPs within 2kb

226 from dbSNP Build 142
Strain Annotations

17

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1914928	protein coding gene	Chr6:91492910-91499607 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0031049	protein coding gene	Chr6:93115706-93122404 (+)
A/J	MGP_AJ_G0031018	protein coding gene	Chr6:89568743-89575468 (+)
AKR/J	MGP_AKRJ_G0030949	protein coding gene	Chr6:92056122-92062813 (+)
BALB/cJ	MGP_BALBcJ_G0031029	protein coding gene	Chr6:89509617-89516310 (+)
C3H/HeJ	MGP_C3HHeJ_G0030679	protein coding gene	Chr6:92380690-92387382 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0031488	protein coding gene	Chr6:95533611-95540305 (+)
CAROLI/EiJ	no annotation
CAST/EiJ	MGP_CASTEiJ_G0030136	protein coding gene	Chr6:92166488-92175273 (+)
CBA/J	MGP_CBAJ_G0030715	protein coding gene	Chr6:99086509-99093198 (+)
DBA/2J	MGP_DBA2J_G0030868	protein coding gene	Chr6:88751004-88757699 (+)
FVB/NJ	MGP_FVBNJ_G0030822	protein coding gene	Chr6:87960009-87966682 (+)
LP/J	MGP_LPJ_G0030948	protein coding gene	Chr6:93070587-93077288 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0030856	protein coding gene	Chr6:103140332-103147025 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0031515	protein coding gene	Chr6:91894899-91901591 (+)
PWK/PhJ	MGP_PWKPhJ_G0029852	protein coding gene	Chr6:87704273-87711066 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0029681	protein coding gene	Chr6:90810699-90817269 (+)
WSB/EiJ	MGP_WSBEiJ_G0030220	protein coding gene	Chr6:92368268-92374975 (+)

Human Ortholog

LSM3, LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LSM3, LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated
Synonyms

SMX4, USS2, YLR438C
Links

HGNC:17874

NCBI Gene ID: 27258

neXtProt AC: NX_P62310

UniProt: P62310
Chr Location

3p25.1; chr3:14178817-14201122 (+) GRCh38

MGI Vertebrate Homology

Lsm3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: LSM3
Gene Tree

Lsm3

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Phenotype Summary

6 phenotypes from 1 allele in 1 genetic background
15 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

12
Endonuclease-mediated

1
Gene trapped

7
Spontaneous

1
Targeted

3
Genomic Mutations

1 involving Lsm3
Incidental Mutations

CvDC
Find Mice (IMSR)

15 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

MIce homozygous for an allele that only expresses variant 1 exhibit decreased susceptibility to VSV and influenza infection.

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All GO Annotations

22
GO References

5

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

733
Tissues

25
cDNA Data

81
Literature Summary

3

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase lsm3

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All Sequences

36
RefSeq

2
UniProt

1
CCDS

CCDS20369.1

Ensembl

ENSMUSG00000034192 (Evidence)
NCBI Gene

67678

			Length	Strain/Species	Flank
genomic	67678	NCBI Gene Model \| MGI Sequence Detail	6586	C57BL/6J	± kb
transcript	NM_026309	RefSeq \| MGI Sequence Detail	631	C57BL/6
polypeptide	P62311	UniProt \| EBI \| MGI Sequence Detail	102	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000009961 U6 snRNA-associated Sm-like protein LSm3

(term hierarchy)
InterPro Domains

IPR010920 LSM domain superfamily

IPR047575 Sm domain

IPR001163 Sm domain, eukaryotic/archaea-type

IPR034105 Sm-like protein Lsm3

IPR040002 U6 snRNA-associated Sm-like protein Lsm3

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All nucleic 84

cDNA 83

Primer pair 1

Microarray probesets 3

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MGI:1917279, MGI:2442209

Summaries

All 43

Developmental Gene Expression 3

Gene Ontology 5

Phenotypes 15
Earliest

J:93290 Araki K, et al., Exchangeable gene trap using the Cre/mutated lox system. Cell Mol Biol (Noisy-Le-Grand). 1999 Jul;45(5):737-50
Latest

J:330636 Iwata S, et al., An efficient i-GONAD method for creating and maintaining lethal mutant mice using an inversion balancer identified from the C3H/HeJJcl strain. G3 (Bethesda). 2021;11(8)

TSS for Lsm3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr57725	Chr6:91492951-91492975 (+)	-54 bp
Tssr57726	Chr6:91492988-91493040 (+)	-3 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)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/05/2024 MGI 6.24