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) Chinchilla lanigera
Analyze
Symbol: Lsm4
Name: LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated
RGD ID: 8991966
Description: ENCODES a protein that exhibits PH domain binding (ortholog); INVOLVED IN mRNA splicing, via spliceosome (ortholog); PARTICIPATES IN spliceosome pathway; ASSOCIATED WITH atherosclerosis (ortholog); genetic disease (ortholog); Megalencephaly-Polymicrogyria-Polydactyly-Hydrocephalus Syndrome 1 (ortholog); FOUND IN cytosol (ortholog); Lsm2-8 complex (ortholog); membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LSM4 homolog, U6 small nuclear RNA associated; U6 snRNA-associated Sm-like protein LSm4
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381918,306,236 - 18,323,076 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1918,306,236 - 18,323,112 (-)EnsemblGRCh38hg38GRCh38
GRCh371918,417,046 - 18,433,886 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361918,278,717 - 18,294,962 (-)NCBINCBI36Build 36hg18NCBI36
Build 341918,278,717 - 18,294,958NCBI
Celera1918,319,475 - 18,335,755 (-)NCBICelera
Cytogenetic Map19p13.11NCBI
HuRef1917,980,724 - 17,997,682 (-)NCBIHuRef
CHM1_11918,417,296 - 18,434,252 (-)NCBICHM1_1
T2T-CHM13v2.01918,440,354 - 18,457,193 (-)NCBIT2T-CHM13v2.0
Lsm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39871,124,663 - 71,131,402 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl871,125,898 - 71,131,402 (+)EnsemblGRCm39 Ensembl
GRCm38870,673,231 - 70,678,752 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl870,673,248 - 70,678,752 (+)EnsemblGRCm38mm10GRCm38
MGSCv37873,197,130 - 73,202,651 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36873,602,381 - 73,607,741 (+)NCBIMGSCv36mm8
Celera873,229,842 - 73,235,362 (+)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.15NCBI
Lsm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81618,789,466 - 18,795,164 (-)NCBIGRCr8
mRatBN7.21618,755,481 - 18,761,106 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1618,755,484 - 18,760,926 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1618,797,134 - 18,802,546 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01619,930,058 - 19,935,475 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01618,850,088 - 18,855,500 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11619,261,067 - 19,266,367 (-)NCBI
Celera1618,947,390 - 18,952,806 (-)NCBICelera
Cytogenetic Map16p14NCBI
LSM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22023,167,478 - 23,183,873 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11922,175,796 - 22,192,193 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01917,785,580 - 17,801,866 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11918,757,390 - 18,773,812 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1918,757,390 - 18,773,812 (-)Ensemblpanpan1.1panPan2
LSM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12044,707,460 - 44,720,490 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2044,707,460 - 44,720,490 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2044,621,620 - 44,634,648 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02045,193,083 - 45,206,148 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2045,193,083 - 45,206,124 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12044,430,435 - 44,443,463 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02044,840,880 - 44,853,912 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02045,116,311 - 45,129,341 (+)NCBIUU_Cfam_GSD_1.0
Lsm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118203,354,208 - 203,367,493 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365962,903,358 - 2,916,629 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365962,903,363 - 2,916,629 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl259,499,564 - 59,513,246 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1259,499,560 - 59,513,258 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LSM4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1616,783,566 - 16,800,116 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl616,782,746 - 16,800,143 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660742,555,195 - 2,572,041 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lsm4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249081,595,877 - 1,603,043 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249081,595,877 - 1,603,075 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSCLAT00000015916   ⟹   ENSCLAP00000015753
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049555243,157,607 - 3,165,196 (+)Ensembl
RefSeq Acc Id: ENSCLAT00000015917   ⟹   ENSCLAP00000015754
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049555243,157,715 - 3,164,879 (+)Ensembl
RefSeq Acc Id: ENSCLAT00000015918   ⟹   ENSCLAP00000015755
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049555243,161,897 - 3,164,879 (+)Ensembl
RefSeq Acc Id: XM_005409570   ⟹   XP_005409627
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049555243,157,607 - 3,165,196 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013507313   ⟹   XP_013362767
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049555243,159,581 - 3,165,196 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005409627 (Get FASTA)   NCBI Sequence Viewer  
  XP_013362767 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000015753
  ENSCLAP00000015753.1
  ENSCLAP00000015754.1
  ENSCLAP00000015755.1
Reference Protein Sequences
RefSeq Acc Id: XP_005409627   ⟸   XM_005409570
- Peptide Label: isoform X1
- UniProtKB: A0A8C2VN39 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013362767   ⟸   XM_013507313
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSCLAP00000015754   ⟸   ENSCLAT00000015917
RefSeq Acc Id: ENSCLAP00000015753   ⟸   ENSCLAT00000015916
RefSeq Acc Id: ENSCLAP00000015755   ⟸   ENSCLAT00000015918
Protein Domains
Sm


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000010828 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000015916 ENTREZGENE
  ENSCLAT00000015916.1 UniProtKB/TrEMBL
  ENSCLAT00000015917.1 UniProtKB/TrEMBL
  ENSCLAT00000015918.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
InterPro IPR047575 UniProtKB/TrEMBL
  Lsm4 UniProtKB/TrEMBL
  LSm4/Sm_D1/D3 UniProtKB/TrEMBL
  LSM_dom_euk/arc UniProtKB/TrEMBL
  LSM_dom_sf UniProtKB/TrEMBL
NCBI Gene Lsm4 ENTREZGENE
PANTHER PTHR23338 UniProtKB/TrEMBL
  U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PROSITE PS52002 UniProtKB/TrEMBL
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP SSF50182 UniProtKB/TrEMBL
UniProt A0A8C2VHP7_CHILA UniProtKB/TrEMBL
  A0A8C2VN39 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-08-25 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