Lsm4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated) - Rat Genome Database
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Gene: Lsm4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated) Mus musculus
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Symbol: Lsm4
Name: LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated
RGD ID: 1315633
MGI Page MGI
Description: Predicted to have PH domain binding activity and U6 snRNA binding activity. Predicted to be involved in P-body assembly and spliceosomal snRNP assembly. Predicted to localize to several cellular components, including Lsm2-8 complex; P-body; and nucleus. Is expressed in branchial arch; central nervous system; limb; maxillary process; and sensory organ. Orthologous to human LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LSM4 homolog, U6 small nuclear RNA associated; U6 snRNA-associated SM-like protein 4; U6 snRNA-associated Sm-like protein LSm4
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39871,124,663 - 71,131,402 (+)NCBIGRCm39mm39
GRCm38870,673,231 - 70,678,752 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl870,673,248 - 70,678,752 (+)EnsemblGRCm38mm10GRCm38
MGSCv37873,197,130 - 73,202,651 (+)NCBIGRCm37mm9NCBIm37
MGSCv36873,602,381 - 73,607,741 (+)NCBImm8
Celera873,229,842 - 73,235,362 (+)NCBICelera
Cytogenetic Map8B3.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10629062   PMID:11042159   PMID:11076861   PMID:11353399   PMID:12477932   PMID:12904583   PMID:14610273   PMID:15494374   PMID:15782199   PMID:16033648  
PMID:16141072   PMID:16141073   PMID:17967808   PMID:18799693   PMID:20059953   PMID:21267068   PMID:21677750   PMID:21873635   PMID:22639370   PMID:25288739   PMID:32325033  


Genomics

Comparative Map Data
Lsm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39871,124,663 - 71,131,402 (+)NCBIGRCm39mm39
GRCm38870,673,231 - 70,678,752 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl870,673,248 - 70,678,752 (+)EnsemblGRCm38mm10GRCm38
MGSCv37873,197,130 - 73,202,651 (+)NCBIGRCm37mm9NCBIm37
MGSCv36873,602,381 - 73,607,741 (+)NCBImm8
Celera873,229,842 - 73,235,362 (+)NCBICelera
Cytogenetic Map8B3.3NCBI
LSM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1918,306,230 - 18,323,274 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1918,306,236 - 18,323,112 (-)EnsemblGRCh38hg38GRCh38
GRCh381918,306,236 - 18,323,076 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371918,417,040 - 18,434,001 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361918,278,717 - 18,294,962 (-)NCBINCBI36hg18NCBI36
Build 341918,278,717 - 18,294,958NCBI
Celera1918,319,475 - 18,335,755 (-)NCBI
Cytogenetic Map19p13.11NCBI
HuRef1917,980,724 - 17,997,682 (-)NCBIHuRef
CHM1_11918,417,296 - 18,434,252 (-)NCBICHM1_1
Lsm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01620,506,399 - 20,511,818 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1620,506,399 - 20,511,818 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01620,363,442 - 20,368,886 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41619,261,065 - 19,266,484 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11619,261,067 - 19,266,367 (-)NCBI
Celera1618,947,390 - 18,952,806 (-)NCBICelera
Cytogenetic Map16p14NCBI
Lsm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555243,157,607 - 3,165,196 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555243,157,607 - 3,165,196 (+)NCBIChiLan1.0ChiLan1.0
LSM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11918,757,390 - 18,773,812 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1918,757,390 - 18,773,812 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01917,785,580 - 17,801,866 (-)NCBIMhudiblu_PPA_v0panPan3
LSM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2044,707,460 - 44,720,490 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12044,707,460 - 44,720,490 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Lsm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365962,903,363 - 2,916,629 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl259,498,804 - 59,517,145 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1259,499,560 - 59,513,258 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LSM4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl616,782,746 - 16,800,143 (-)Ensembl
ChlSab1.1616,783,566 - 16,800,116 (-)NCBI
Lsm4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249081,595,877 - 1,603,075 (-)NCBI

Position Markers
Lsm4  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38870,677,849 - 70,678,688UniSTSGRCm38
MGSCv37873,201,748 - 73,202,587UniSTSGRCm37
Celera873,234,459 - 73,235,298UniSTS
Cytogenetic Map8B3.3UniSTS
cM Map8 UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558870Eae36_mexperimental allergic encephalomyelitis susceptibility 36 (mouse)Not determined81472316071045600Mouse
1357811Orq3_movulation rate QTL 3 (mouse)Not determined83201654471287993Mouse
4141437W10q14_mweight 10 weeks QTL 14 (mouse)Not determined3201654471287993Mouse
4141172W6q9_mweight 6 weeks QTL 9 (mouse)Not determined3201654471287993Mouse
4140966Egq12_mearly growth QTL 12 (mouse)Not determined3201654471287993Mouse
4140967Bmd39_mbone mineral density 39 (mouse)Not determined832016544117238700Mouse
1558875Eae31_mexperimental allergic encephalomyelitis susceptibility 31 (mouse)Not determined834642776114837007Mouse
1301013Capsq4_mcapsaicin sensitivity related QTL 4 (mouse)Not determined83616300092728652Mouse
27226754Femd6_mfemur midshaft diameter 6, 10 week (mouse)837400000109600000Mouse
12904744Carcdq1_mcardiac collagen deposition QTL 1 (mouse)83970925694689598Mouse
1301544Iba3_minduction of brown adipocytes 3 (mouse)Not determined84429488078295025Mouse
1301717Adip4_madiposity 4 (mouse)Not determined84763703081637146Mouse
10766453Char11_mP. chabaudi malaria resistance QTL 11 (mouse)84763703081637146Mouse
1301441Skull11_mskull morphology 11 (mouse)Not determined84773713481737254Mouse
1357715Alaa3_malopecia areata 3 (mouse)Not determined84879293982793021Mouse
14746987Manh64_mmandible shape 64 (mouse)85005330684053306Mouse
14747005Mancz7_mmandible centroid size 7 (mouse)85005330684053306Mouse
14700686Civq3_mcerebral infarct volume QTL 3 (mouse)85188219185882191Mouse
1301506Aevm1_mautoimmune extremity vasculitis in MRL mice 1 (mouse)Not determined85428781788287993Mouse
1301952Im3_mimmunoregulatory 3 (mouse)Not determined85470661488706763Mouse
10412287Carg3_mCandida albicans resistance gene 3 (mouse)Not determined85554502889545028Mouse
11353828Gf7_mgonadal fat pad weight 7 (mouse)85820147992201479Mouse
10043975Obq31_mobesity QTL 31 (mouse)Not determined85840977692409776Mouse
1301688Orch6_mautoimmune orchitis resistance 6 (mouse)Not determined86078685094786976Mouse
4141285Tgq18_mtriglyceride QTL 18 (mouse)Not determined6346010797460107Mouse
4141797Skmw16_mskeletal muscle weight 16 (mouse)Not determined86393954797939696Mouse
1357787Vtbt5_mvertebral trabecular bone trait 5 (mouse)Not determined86535776899357920Mouse
10043992Hbnr11_mHeligmosomoides bakeri nematode resistance 11 (mouse)Not determined86560020799600347Mouse
10766466Char12_mP. chabaudi malaria resistance QTL 12 (mouse)86826982782600347Mouse
1301767Fcsa2_mfemoral cross-sectional area 2 (mouse)Not determined870305375104305495Mouse
4142283Imraq2_mimmune response to AAV2 QTL 2 (mouse)Not determined870305375104305495Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:588
Count of miRNA genes:347
Interacting mature miRNAs:393
Transcripts:ENSMUST00000034311, ENSMUST00000146972, ENSMUST00000153689
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001359042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_015816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_030243665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC162446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC166931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ249439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK003847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK010910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK089028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK143470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK167784 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK179003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK185496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC026747 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CA322716 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CD776868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466569 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000034311   ⟹   ENSMUSP00000034311
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl870,673,248 - 70,678,752 (+)Ensembl
RefSeq Acc Id: ENSMUST00000146972   ⟹   ENSMUSP00000121019
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl870,673,379 - 70,678,116 (+)Ensembl
RefSeq Acc Id: ENSMUST00000153689
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl870,677,665 - 70,678,116 (+)Ensembl
RefSeq Acc Id: ENSMUST00000210071   ⟹   ENSMUSP00000147320
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl870,673,385 - 70,678,519 (+)Ensembl
RefSeq Acc Id: ENSMUST00000210987   ⟹   ENSMUSP00000147637
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl870,673,432 - 70,678,746 (+)Ensembl
RefSeq Acc Id: NM_001359042   ⟹   NP_001345971
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39871,125,881 - 71,131,402 (+)NCBI
GRCm38870,673,231 - 70,678,752 (+)NCBI
Sequence:
RefSeq Acc Id: NM_015816   ⟹   NP_056631
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39871,125,881 - 71,131,402 (+)NCBI
GRCm38870,673,231 - 70,678,752 (+)ENTREZGENE
MGSCv37873,197,130 - 73,202,651 (+)RGD
Celera873,229,842 - 73,235,362 (+)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_030243665   ⟹   XP_030099525
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39871,124,663 - 71,131,402 (+)NCBI
GRCm38870,673,231 - 70,678,752 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_056631   ⟸   NM_015816
- Peptide Label: isoform 1
- UniProtKB: Q9QXA5 (UniProtKB/Swiss-Prot),   Q9CY46 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_030099525   ⟸   XM_030243665
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001345971   ⟸   NM_001359042
- Peptide Label: isoform 2
RefSeq Acc Id: ENSMUSP00000034311   ⟸   ENSMUST00000034311
RefSeq Acc Id: ENSMUSP00000121019   ⟸   ENSMUST00000146972
RefSeq Acc Id: ENSMUSP00000147637   ⟸   ENSMUST00000210987
RefSeq Acc Id: ENSMUSP00000147320   ⟸   ENSMUST00000210071
Protein Domains
Sm

Promoters
RGD ID:8667333
Promoter ID:EPDNEW_M11698
Type:initiation region
Name:Lsm4_1
Description:Mus musculus LSM4 homolog, U6 small nuclear RNA and mRNA degradationassociated , transcript variant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38870,673,379 - 70,673,439EPDNEW
RGD ID:6843420
Promoter ID:MM_KWN:54726
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_015816,   OTTMUST00000074175,   UC009MBD.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36873,197,056 - 73,197,627 (+)MPROMDB
RGD ID:6843419
Promoter ID:MM_KWN:54727
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney,   Spleen
Transcripts:OTTMUST00000074176
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36873,201,616 - 73,202,116 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1354692 AgrOrtholog
Ensembl Genes ENSMUSG00000031848 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000034311 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000121019 UniProtKB/TrEMBL
  ENSMUSP00000147320 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000147637 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000034311 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000146972 UniProtKB/TrEMBL
  ENSMUST00000210071 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000210987 UniProtKB/TrEMBL
InterPro Lsm4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LSm4/Sm_D1/D3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LSM_dom_euk/arc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LSM_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:50783 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:1354692 ENTREZGENE
NCBI Gene 50783 ENTREZGENE
PANTHER PTHR23338 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam LSM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lsm4 PhenoGen
SMART SM00651 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50182 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Mm.248188 ENTREZGENE
UniProt A0A1B0GQZ9_MOUSE UniProtKB/TrEMBL
  A0A1B0GRR9_MOUSE UniProtKB/TrEMBL
  D3YTP8_MOUSE UniProtKB/TrEMBL
  LSM4_MOUSE UniProtKB/Swiss-Prot
  Q9CY46 ENTREZGENE, UniProtKB/TrEMBL
  Q9D181_MOUSE UniProtKB/TrEMBL
  Q9QXA5 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-02 Lsm4  LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated    LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED