Lsm1 (LSM1 homolog, mRNA degradation associated) - Rat Genome Database

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Gene: Lsm1 (LSM1 homolog, mRNA degradation associated) Heterocephalus glaber
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Symbol: Lsm1
Name: LSM1 homolog, mRNA degradation associated
RGD ID: 18928110
Description: ENCODES a protein that exhibits mRNA binding (ortholog); pre-mRNA binding (ortholog); INVOLVED IN histone mRNA catabolic process (ortholog); negative regulation of neuron differentiation (ortholog); neuron differentiation (ortholog); ASSOCIATED WITH cryptorchidism (ortholog); developmental and epileptic encephalopathy 11 (ortholog); Developmental Disabilities (ortholog); FOUND IN axon (ortholog); dendrite (ortholog); neuronal cell body (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LSM1 homolog, U6 small nuclear RNA associated; U6 snRNA-associated Sm-like protein LSm1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247805,473,041 - 5,483,300 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247805,473,172 - 5,483,584 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:21993625   PMID:30032202  


Genomics

Comparative Map Data
Lsm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247805,473,041 - 5,483,300 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247805,473,172 - 5,483,584 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
LSM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38838,163,321 - 38,176,730 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl838,163,335 - 38,176,730 (-)EnsemblGRCh38hg38GRCh38
GRCh37838,020,839 - 38,034,248 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36838,140,014 - 38,153,183 (-)NCBINCBI36Build 36hg18NCBI36
Build 34838,140,013 - 38,153,183NCBI
Celera836,973,393 - 36,986,562 (-)NCBICelera
Cytogenetic Map8p11.23NCBI
HuRef836,555,756 - 36,568,636 (-)NCBIHuRef
CHM1_1838,222,844 - 38,236,249 (-)NCBICHM1_1
T2T-CHM13v2.0838,440,300 - 38,453,709 (-)NCBIT2T-CHM13v2.0
Lsm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39826,275,326 - 26,294,003 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl826,275,316 - 26,294,003 (+)EnsemblGRCm39 Ensembl
GRCm38825,785,318 - 25,803,975 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl825,785,288 - 25,803,975 (+)EnsemblGRCm38mm10GRCm38
MGSCv37826,896,063 - 26,914,447 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36827,250,852 - 27,269,520 (+)NCBIMGSCv36mm8
Celera827,253,809 - 27,272,186 (+)NCBICelera
Cytogenetic Map8A2NCBI
cM Map814.17NCBI
Lsm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81672,980,075 - 72,991,581 (-)NCBIGRCr8
mRatBN7.21666,277,345 - 66,288,852 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1666,277,345 - 66,288,852 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1671,555,983 - 71,567,493 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01674,962,293 - 74,973,803 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01670,202,187 - 70,213,697 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01671,046,475 - 71,057,883 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1671,046,475 - 71,057,883 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01670,711,151 - 70,722,559 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41670,652,831 - 70,663,995 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11670,653,556 - 70,663,907 (-)NCBI
Celera1664,187,220 - 64,198,747 (-)NCBICelera
Cytogenetic Map16q12.4NCBI
Lsm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546313,773,869 - 13,788,784 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495546313,775,639 - 13,788,784 (-)NCBIChiLan1.0ChiLan1.0
LSM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2756,726,906 - 56,739,998 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1832,443,915 - 32,457,154 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0837,465,986 - 37,479,186 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1834,642,938 - 34,656,142 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl834,642,938 - 34,656,142 (-)Ensemblpanpan1.1panPan2
LSM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11627,304,257 - 27,315,389 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1627,304,198 - 27,315,233 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1627,821,271 - 27,832,688 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01629,203,163 - 29,214,621 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1629,203,401 - 29,214,465 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11627,425,471 - 27,436,928 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01628,002,718 - 28,014,129 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01628,041,959 - 28,053,408 (+)NCBIUU_Cfam_GSD_1.0
Lsm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494349,909,516 - 49,915,246 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367101,545,790 - 1,552,394 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367101,546,027 - 1,551,685 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1548,348,648 - 48,365,106 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11548,348,653 - 48,360,004 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21555,604,059 - 55,615,385 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LSM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1836,184,928 - 36,198,689 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl836,182,380 - 36,198,704 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660525,791,244 - 5,805,004 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSHGLT00000007972   ⟹   ENSHGLP00000007884
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046247805,473,041 - 5,483,300 (+)Ensembl
Ensembl Acc Id: ENSHGLT00000007973   ⟹   ENSHGLP00000007885
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046247805,473,366 - 5,483,014 (+)Ensembl
RefSeq Acc Id: XM_004855367   ⟹   XP_004855424
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046247805,473,425 - 5,483,584 (+)NCBI
RefSeq Acc Id: XM_004855368   ⟹   XP_004855425
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046247805,473,172 - 5,483,584 (+)NCBI
RefSeq Acc Id: XM_021236812   ⟹   XP_021092471
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046247805,473,172 - 5,483,584 (+)NCBI
Protein Sequences
Protein RefSeqs XP_004855424 (Get FASTA)   NCBI Sequence Viewer  
  XP_004855425 (Get FASTA)   NCBI Sequence Viewer  
  XP_021092471 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EHB02716 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000007884
  ENSHGLP00000043855
  ENSHGLP00100054972
GenBank Protein JAO01252 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_021092471   ⟸   XM_021236812
- Peptide Label: isoform X2
RefSeq Acc Id: XP_004855425   ⟸   XM_004855368
- Peptide Label: isoform X3
- UniProtKB: G5B0A5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004855424   ⟸   XM_004855367
- Peptide Label: isoform X1
Ensembl Acc Id: ENSHGLP00000007885   ⟸   ENSHGLT00000007973
Ensembl Acc Id: ENSHGLP00000007884   ⟸   ENSHGLT00000007972


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000005711 Ensembl, ENTREZGENE
  ENSHGLG00000048140 UniProtKB/TrEMBL
  ENSHGLG00100046599 UniProtKB/TrEMBL
Ensembl Transcript ENSHGLT00000007972 ENTREZGENE
  ENSHGLT00000079457 UniProtKB/TrEMBL
  ENSHGLT00100091173 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
InterPro IPR047575 UniProtKB/TrEMBL
  Lsm1 UniProtKB/TrEMBL
  LSM_dom_euk/arc UniProtKB/TrEMBL
  LSM_dom_sf UniProtKB/TrEMBL
  PTHR15588 UniProtKB/TrEMBL
NCBI Gene Lsm1 ENTREZGENE
PANTHER PTHR15588 UniProtKB/TrEMBL
  U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM1 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PROSITE PS52002 UniProtKB/TrEMBL
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP SSF50182 UniProtKB/TrEMBL
UniProt G5B0A5 ENTREZGENE, UniProtKB/TrEMBL