LSM7 (LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated) - Rat Genome Database

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Gene: LSM7 (LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated) Sus scrofa
Analyze
Symbol: LSM7
Name: LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated
RGD ID: 14025833
Description: ENCODES a protein that exhibits RNA binding (inferred); INVOLVED IN mRNA splicing, via spliceosome (inferred); nuclear-transcribed mRNA catabolic process (inferred); PARTICIPATES IN spliceosome pathway; ASSOCIATED WITH genetic disease (ortholog); leukodystrophy (ortholog); Neurodevelopmental Disorders (ortholog); FOUND IN U4/U6 x U5 tri-snRNP complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LSM7 homolog, U6 small nuclear RNA associated; U6 snRNA-associated Sm-like protein LSm7
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl276,247,058 - 76,252,598 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1276,247,010 - 76,251,824 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2276,798,931 - 76,813,621 (+)NCBISscrofa10.2Sscrofa10.2susScr3
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

Molecular Function
protein binding  (ISO)
RNA binding  (IBA,IEA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
LSM7
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl276,247,058 - 76,252,598 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1276,247,010 - 76,251,824 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2276,798,931 - 76,813,621 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LSM7
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38192,321,521 - 2,328,586 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl192,321,520 - 2,328,611 (-)EnsemblGRCh38hg38GRCh38
GRCh37192,321,520 - 2,328,585 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36192,272,520 - 2,279,574 (-)NCBINCBI36Build 36hg18NCBI36
Build 34192,272,521 - 2,279,574NCBI
Celera192,255,614 - 2,262,707 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef192,092,206 - 2,099,305 (-)NCBIHuRef
CHM1_1192,321,133 - 2,328,227 (-)NCBICHM1_1
T2T-CHM13v2.0192,295,189 - 2,302,259 (-)NCBIT2T-CHM13v2.0
Lsm7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391080,688,659 - 80,691,043 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1080,688,655 - 80,691,043 (-)EnsemblGRCm39 Ensembl
GRCm381080,852,825 - 80,855,209 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,852,821 - 80,855,209 (-)EnsemblGRCm38mm10GRCm38
MGSCv371080,315,570 - 80,317,954 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361080,255,954 - 80,258,338 (-)NCBIMGSCv36mm8
Celera1081,871,623 - 81,874,007 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Lsm7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr879,507,373 - 9,509,787 (+)NCBIGRCr8
mRatBN7.278,856,698 - 8,859,113 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,856,489 - 8,859,119 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx711,740,650 - 11,743,084 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,616,154 - 13,618,588 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0711,482,686 - 11,485,120 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,724,932 - 11,732,020 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,724,962 - 11,727,388 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0711,892,648 - 11,895,103 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,367,329 - 10,369,755 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1710,367,331 - 10,369,731 (+)NCBI
Celera77,040,813 - 7,043,237 (+)NCBICelera
Cytogenetic Map7q11NCBI
Lsm7
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554955,829,247 - 5,836,900 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554955,829,976 - 5,836,785 (+)NCBIChiLan1.0ChiLan1.0
LSM7
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2206,704,626 - 6,711,749 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1195,933,968 - 5,941,103 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0191,330,469 - 1,337,610 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1192,302,280 - 2,309,344 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl192,302,280 - 2,313,255 (-)Ensemblpanpan1.1panPan2
LSM7
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12056,730,476 - 56,735,115 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2056,730,486 - 56,735,112 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2056,526,078 - 56,530,718 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02057,463,885 - 57,468,524 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2057,463,177 - 57,468,521 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12056,515,964 - 56,520,602 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02057,001,211 - 57,005,850 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02057,201,524 - 57,206,163 (+)NCBIUU_Cfam_GSD_1.0
Lsm7
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118216,440,803 - 216,444,325 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365881,390,459 - 1,394,004 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365881,390,456 - 1,393,940 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM7
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.162,108,212 - 2,121,547 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl62,108,212 - 2,121,571 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660816,588,042 - 6,594,735 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lsm7
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248286,576,708 - 6,584,303 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248286,576,672 - 6,584,303 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LSM7
92 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 10 4 3 5 2 23 2 3 3
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000014708   ⟹   ENSSSCP00000014311
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl276,247,058 - 76,252,598 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000071368   ⟹   ENSSSCP00000068380
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl276,247,150 - 76,252,598 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000090383   ⟹   ENSSSCP00000073302
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl276,247,117 - 76,252,598 (+)Ensembl
RefSeq Acc Id: XM_003123024   ⟹   XP_003123072
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1276,247,010 - 76,251,824 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_003123072 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00000014311.4
  ENSSSCP00000068380.2
  ENSSSCP00000073302.1
Reference Protein Sequences
RefSeq Acc Id: XP_003123072   ⟸   XM_003123024
- Sequence:
RefSeq Acc Id: ENSSSCP00000073302   ⟸   ENSSSCT00000090383
RefSeq Acc Id: ENSSSCP00000068380   ⟸   ENSSSCT00000071368
RefSeq Acc Id: ENSSSCP00000014311   ⟸   ENSSSCT00000014708
Protein Domains
Sm


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000013463 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000014708.5 UniProtKB/TrEMBL
  ENSSSCT00000071368.2 UniProtKB/TrEMBL
  ENSSSCT00000090383.2 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
InterPro IPR047575 UniProtKB/TrEMBL
  Lsm7 UniProtKB/TrEMBL
  Lsm7/SmG-like UniProtKB/TrEMBL
  LSM_dom_euk/arc UniProtKB/TrEMBL
  LSM_dom_sf UniProtKB/TrEMBL
NCBI Gene LSM7 ENTREZGENE
PANTHER PTHR10553 UniProtKB/TrEMBL
  U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PIRSF U6_snRNA_Lsm7 UniProtKB/TrEMBL
PROSITE PS52002 UniProtKB/TrEMBL
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP SSF50182 UniProtKB/TrEMBL
UniProt A0A5G2QW54_PIG UniProtKB/TrEMBL
  A0A5G2RF09_PIG UniProtKB/TrEMBL
  F1S8H0_PIG UniProtKB/TrEMBL
VGNC ID VGNC:89876 ENTREZGENE