Lsm3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated) - Rat Genome Database
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Gene: Lsm3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated) Mus musculus
Analyze
Symbol: Lsm3
Name: LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated
RGD ID: 1314319
MGI Page MGI
Description: Is expressed in brain; central nervous system ganglion; and cerebral cortex ventricular layer. Orthologous to human LSM3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 1,2-dimethylhydrazine; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 1010001J12Rik; 2610005D18Rik; 6030401D18Rik; LSM3 homolog, U6 small nuclear RNA associated; RIKEN cDNA 2610005D18 gene; SMX; SMX4; U6 snRNA-associated Sm-like protein LSm3; US; USS2
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gm46510  
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39691,493,017 - 91,499,602 (+)NCBIGRCm39mm39
GRCm39 Ensembl691,492,910 - 91,499,607 (+)Ensembl
GRCm38691,516,035 - 91,522,620 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl691,515,928 - 91,522,625 (+)EnsemblGRCm38mm10GRCm38
MGSCv37691,466,029 - 91,472,614 (+)NCBIGRCm37mm9NCBIm37
MGSCv36691,481,539 - 91,488,124 (+)NCBImm8
Celera693,409,326 - 93,415,908 (+)NCBICelera
Cytogenetic Map6D1NCBI
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
References

Additional References at PubMed
PMID:10349636   PMID:10512203   PMID:10922068   PMID:11042159   PMID:11076861   PMID:12477932   PMID:12520002   PMID:14610273   PMID:15489334   PMID:15840001   PMID:16033648   PMID:16141072  
PMID:16141073   PMID:18799693   PMID:19521500   PMID:21267068   PMID:21677750   PMID:21873635   PMID:29706547   PMID:32325033  


Genomics

Comparative Map Data
Lsm3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39691,493,017 - 91,499,602 (+)NCBIGRCm39mm39
GRCm39 Ensembl691,492,910 - 91,499,607 (+)Ensembl
GRCm38691,516,035 - 91,522,620 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl691,515,928 - 91,522,625 (+)EnsemblGRCm38mm10GRCm38
MGSCv37691,466,029 - 91,472,614 (+)NCBIGRCm37mm9NCBIm37
MGSCv36691,481,539 - 91,488,124 (+)NCBImm8
Celera693,409,326 - 93,415,908 (+)NCBICelera
Cytogenetic Map6D1NCBI
LSM3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl314,178,817 - 14,201,122 (+)EnsemblGRCh38hg38GRCh38
GRCh38314,178,817 - 14,201,122 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37314,220,317 - 14,242,622 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36314,195,341 - 14,214,842 (+)NCBINCBI36hg18NCBI36
Build 34314,195,340 - 14,214,840NCBI
Celera314,158,457 - 14,178,097 (+)NCBI
Cytogenetic Map3p25.1NCBI
HuRef314,155,207 - 14,174,845 (+)NCBIHuRef
CHM1_1314,170,613 - 14,190,252 (+)NCBICHM1_1
Lsm3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24124,021,023 - 124,027,269 (+)NCBI
Rnor_6.0 Ensembl4123,162,086 - 123,168,330 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04123,162,086 - 123,168,330 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04187,377,370 - 187,383,614 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44125,700,026 - 125,706,270 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14125,945,303 - 125,950,751 (+)NCBI
Celera4112,940,482 - 112,946,726 (+)NCBICelera
Cytogenetic Map4q34NCBI
Lsm3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542916,968,490 - 16,977,517 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542916,968,490 - 16,977,517 (+)NCBIChiLan1.0ChiLan1.0
LSM3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1314,437,497 - 14,456,727 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl314,437,497 - 14,456,726 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0314,097,035 - 14,165,942 (+)NCBIMhudiblu_PPA_v0panPan3
LSM3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl204,329,038 - 4,342,859 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1204,328,930 - 4,342,731 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Lsm3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936602140,014 - 147,000 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1370,336,900 - 70,348,652 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11370,339,685 - 70,349,802 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21377,737,428 - 77,746,329 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LSM3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12250,121,674 - 50,141,071 (+)NCBI
Lsm3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248721,428,885 - 1,438,633 (-)NCBI

Position Markers
Lsm3  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38434,281,892 - 34,282,441UniSTSGRCm38
Celera434,031,204 - 34,031,753UniSTS
Cytogenetic Map6D2UniSTS
cM Map6 UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
25440480Moaq2_mmodifier of alien QTL 2 (mouse)61117500000Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139100000Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396656149Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396656149Mouse
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396656149Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396656149Mouse
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63866962592607450Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645314059128835032Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46935985136423692Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648720000125360000Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648720000148450000Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648726556125356785Mouse
1357683Igf1sl1_mIGF-1 serum levels 1 (mouse)Not determined652161713116155267Mouse
1558977Skmw10_mskeletal muscle weight 10 (mouse)Not determined65844758392447710Mouse
10043972Obq28_mobesity QTL 28 (mouse)Not determined65854043392540433Mouse
1301740Bwq2_mbody weight QTL 2 (mouse)Not determined66005768094057799Mouse
1301369Im4_mimmunoregulatory 4 (mouse)Not determined66348473897484905Mouse
1300650Bw18_mbody weight QTL 18 (mouse)Not determined666713869100714031Mouse
1301876Bits2_mbitterness sensitivity 2 (mouse)Not determined670425898104426034Mouse
1301813Skl3_mskeletal size (tail length) 3 (mouse)Not determined670425898104426034Mouse
1301034Egrm2_mearly growth rate (mouse)Not determined670425898104426034Mouse
1302020Bbaa20_mB.burgdorferi-associated arthritis 20 (mouse)Not determined67132262193464093Mouse
1300869Stheal5_msoft tissue heal 5 (mouse)Not determined671575060105575178Mouse
1300954Fcsa1_mfemoral cross-sectional area 1 (mouse)Not determined671981024105981170Mouse
1301521Pas1c_mpulmonary adenoma susceptibility 1c (mouse)Not determined671981024105981170Mouse
13506930Recrq9_mrecombination rate in male meiosis QTL 9 (mouse)673500000134700000Mouse
1301320Ots1_movarian teratoma susceptibility 1 (mouse)Not determined675447583104503555Mouse
1301571Arrd1_mage-related retinal degeneration 1 (mouse)Not determined67554435692607450Mouse
1300674Nidd3n_mnon-insulin-dependent diabetes mellitus 3 in NSY (mouse)Not determined67554435694225955Mouse
10412195Efw_mepididymal fat weight (mouse)Not determined67554435694225955Mouse
10043901Pfat5_mpredicted fat percentage 5 (mouse)Not determined675607306109607450Mouse
10412208Cypr4_mcytokine production 4 (mouse)Not determined675716503109716697Mouse
1357875Pfat2_mpredicted fat percentage 2 (mouse)Not determined676463949110464093Mouse
13824985Alh1_mamplitude of lateral head displacement 1 (mouse)67800000097000000Mouse
4141376Dbm1_mdiabetes modifier 1 (mouse)Not determined678629504121115387Mouse
14696731Pairq1_mP. aeruginosa infection resistance QTL 1 (mouse)681500000102200000Mouse
10043864T2dm4sa_mtype 2 diabetes mellitus 4 in SMXA RI mice (mouse)Not determined683713869147052561Mouse
11251720Ewc4_methanol withdrawal and consumption 4 (mouse)684122513118122513Mouse
1301687Mnic2_mmacronutrient intake (mouse)Not determined686806805113544602Mouse
1301744Hdlq11_mHDL QTL 11 (mouse)Not determined687503360121503555Mouse
1301262Gasa3_mgastritis type A susceptibility locus 3 (mouse)Not determined689005405123005603Mouse
1301244Ichs_mimmediate cutaneous hypersensitivity QTL (mouse)Not determined690795610124795846Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:433
Count of miRNA genes:324
Interacting mature miRNAs:347
Transcripts:ENSMUST00000040607, ENSMUST00000123569, ENSMUST00000126253
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


Reference Sequences
RefSeq Acc Id: ENSMUST00000040607   ⟹   ENSMUSP00000044178
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl691,515,928 - 91,522,625 (+)Ensembl
RefSeq Acc Id: ENSMUST00000123569
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl691,516,047 - 91,517,519 (+)Ensembl
RefSeq Acc Id: ENSMUST00000126253
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl691,515,957 - 91,519,835 (+)Ensembl
RefSeq Acc Id: ENSMUST00000205609
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl691,515,977 - 91,518,008 (+)Ensembl
RefSeq Acc Id: ENSMUST00000206947   ⟹   ENSMUSP00000145568
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl691,516,048 - 91,522,620 (+)Ensembl
RefSeq Acc Id: NM_026309   ⟹   NP_080585
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39691,493,017 - 91,499,602 (+)NCBI
GRCm38691,516,035 - 91,522,620 (+)ENTREZGENE
MGSCv37691,466,029 - 91,472,614 (+)RGD
Celera693,409,326 - 93,415,908 (+)RGD
cM Map6 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_080585 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH54368 (Get FASTA)   NCBI Sequence Viewer  
  BAB22585 (Get FASTA)   NCBI Sequence Viewer  
  BAB25303 (Get FASTA)   NCBI Sequence Viewer  
  EDK99304 (Get FASTA)   NCBI Sequence Viewer  
  P62311 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_080585   ⟸   NM_026309
- UniProtKB: P62311 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000145568   ⟸   ENSMUST00000206947
RefSeq Acc Id: ENSMUSP00000044178   ⟸   ENSMUST00000040607

Promoters
RGD ID:6839593
Promoter ID:MM_KWN:46925
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:OTTMUST00000059034,   OTTMUST00000059035,   OTTMUST00000059036,   OTTMUST00000059041,   OTTMUST00000059042
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36691,465,654 - 91,466,154 (+)MPROMDB
RGD ID:6890454
Promoter ID:EPDNEW_M8678
Type:multiple initiation site
Name:Lsm3_1
Description:Mus musculus LSM3 homolog, U6 small nuclear RNA and mRNA degradationassociated , 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
GRCm38691,516,044 - 91,516,104EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1914928 AgrOrtholog
Ensembl Genes ENSMUSG00000034192 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000044178 UniProtKB/Swiss-Prot
  ENSMUSP00000145568 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000040607 UniProtKB/Swiss-Prot
  ENSMUST00000206947 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Lsm3 UniProtKB/Swiss-Prot
  LSM_dom_euk/arc UniProtKB/Swiss-Prot
  LSM_dom_sf UniProtKB/Swiss-Prot
  Sm-like_LSM3 UniProtKB/Swiss-Prot
KEGG Report mmu:67678 UniProtKB/Swiss-Prot
MGD MGI:1914928 ENTREZGENE
NCBI Gene 67678 ENTREZGENE
PANTHER PTHR13110 UniProtKB/Swiss-Prot
Pfam LSM UniProtKB/Swiss-Prot
PhenoGen Lsm3 PhenoGen
SMART SM00651 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50182 UniProtKB/Swiss-Prot
UniProt LSM3_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9Y4Z1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-05 Lsm3  LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated  2610005D18Rik  RIKEN cDNA 2610005D18 gene  Data Merged 737654 PROVISIONAL
2016-02-02 Lsm3  LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated    LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED