Lsm8 (LSM8 homolog, U6 small nuclear RNA associated) - Rat Genome Database

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Gene: Lsm8 (LSM8 homolog, U6 small nuclear RNA associated) Rattus norvegicus
Analyze
Symbol: Lsm8
Name: LSM8 homolog, U6 small nuclear RNA associated
RGD ID: 1308442
Description: Predicted to enable mRNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleus. Predicted to be part of Lsm2-8 complex; U2-type precatalytic spliceosome; and spliceosomal snRNP complex. Orthologous to human LSM8 (LSM8 homolog, U6 small nuclear RNA associated); PARTICIPATES IN spliceosome pathway; INTERACTS WITH benzo[a]pyrene; bisphenol A; flutamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC296913; LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae); N-alpha-acetyltransferase 38, NatC auxiliary subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8448,272,128 - 48,277,994 (+)NCBIGRCr8
mRatBN7.2447,306,259 - 47,312,125 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl447,306,295 - 47,314,293 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx452,288,762 - 52,294,635 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0448,209,920 - 48,215,793 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0446,638,575 - 46,644,463 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0445,555,077 - 45,560,943 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl445,555,077 - 45,560,943 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0443,016,688 - 43,022,554 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4444,717,003 - 44,722,869 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1444,947,578 - 44,953,397 (-)NCBI
Celera442,561,436 - 42,567,302 (+)NCBICelera
Cytogenetic Map4q22NCBI
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. Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. Chen YI, etal., Nucleic Acids Res. 2007;35(12):3928-44. Epub 2007 May 30.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, etal., Cell. 2009 Feb 20;136(4):701-18. doi: 10.1016/j.cell.2009.02.009.
Additional References at PubMed
PMID:10523320   PMID:12477932   PMID:22658674   PMID:22681889   PMID:26912367   PMID:28781166   PMID:31505169  


Genomics

Comparative Map Data
Lsm8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8448,272,128 - 48,277,994 (+)NCBIGRCr8
mRatBN7.2447,306,259 - 47,312,125 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl447,306,295 - 47,314,293 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx452,288,762 - 52,294,635 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0448,209,920 - 48,215,793 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0446,638,575 - 46,644,463 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0445,555,077 - 45,560,943 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl445,555,077 - 45,560,943 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0443,016,688 - 43,022,554 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4444,717,003 - 44,722,869 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1444,947,578 - 44,953,397 (-)NCBI
Celera442,561,436 - 42,567,302 (+)NCBICelera
Cytogenetic Map4q22NCBI
LSM8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387118,184,164 - 118,204,035 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7118,184,144 - 118,204,035 (+)EnsemblGRCh38hg38GRCh38
GRCh377117,824,218 - 117,844,089 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367117,611,322 - 117,620,116 (+)NCBINCBI36Build 36hg18NCBI36
Build 347117,418,169 - 117,426,827NCBI
Celera7112,633,566 - 112,653,561 (+)NCBICelera
Cytogenetic Map7q31.31NCBI
HuRef7112,190,045 - 112,210,037 (+)NCBIHuRef
CHM1_17117,757,651 - 117,777,658 (+)NCBICHM1_1
T2T-CHM13v2.07119,499,900 - 119,519,771 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27117,219,509 - 117,239,504 (+)NCBI
Lsm8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39618,848,634 - 18,854,051 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl618,848,578 - 18,855,750 (+)EnsemblGRCm39 Ensembl
GRCm38618,848,635 - 18,854,052 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl618,848,579 - 18,855,751 (+)EnsemblGRCm38mm10GRCm38
MGSCv37618,798,635 - 18,804,052 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36618,798,636 - 18,804,053 (+)NCBIMGSCv36mm8
Celera618,915,775 - 18,921,192 (+)NCBICelera
Cytogenetic Map6A2NCBI
cM Map68.16NCBI
Lsm8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543223,818,227 - 23,823,382 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543223,818,036 - 23,823,550 (+)NCBIChiLan1.0ChiLan1.0
LSM8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26155,010,418 - 155,019,137 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan177,020,642 - 7,029,394 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07110,150,584 - 110,160,864 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17122,844,848 - 122,856,577 (+)NCBIpanpan1.1PanPan1.1panPan2
LSM8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11855,715,008 - 55,715,562 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1855,715,105 - 55,715,395 (+)EnsemblCanFam3.1canFam3CanFam3.1
Lsm8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511845,576,455 - 45,584,161 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365891,105,341 - 1,113,452 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365891,107,534 - 1,113,439 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1828,108,308 - 28,130,330 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11828,124,116 - 28,130,375 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21829,761,550 - 29,767,808 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LSM8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12186,838,350 - 86,846,675 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2186,838,375 - 86,846,517 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604216,871,635 - 16,880,717 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lsm8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248271,192,380 - 1,201,994 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lsm8
27 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43258419952754138Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat


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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 10 74 35 41 11 8
Low 1
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000089007   ⟹   ENSRNOP00000073002
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl445,555,077 - 45,560,943 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115943   ⟹   ENSRNOP00000079477
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl447,306,295 - 47,314,293 (+)Ensembl
RefSeq Acc Id: NM_001106585   ⟹   NP_001100055
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8448,272,128 - 48,277,994 (+)NCBI
mRatBN7.2447,306,259 - 47,312,125 (+)NCBI
Rnor_6.0445,555,077 - 45,560,943 (+)NCBI
Rnor_5.0443,016,688 - 43,022,554 (+)NCBI
RGSC_v3.4444,717,003 - 44,722,869 (-)RGD
Celera442,561,436 - 42,567,302 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100055 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI67094 (Get FASTA)   NCBI Sequence Viewer  
  EDM15129 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000079477
  ENSRNOP00000079477.1
RefSeq Acc Id: NP_001100055   ⟸   NM_001106585
- UniProtKB: B2RZB6 (UniProtKB/TrEMBL),   A6IE42 (UniProtKB/TrEMBL),   A0A8I5ZNK7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073002   ⟸   ENSRNOT00000089007
RefSeq Acc Id: ENSRNOP00000079477   ⟸   ENSRNOT00000115943
Protein Domains
Sm

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2RZB6-F1-model_v2 AlphaFold B2RZB6 1-96 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13692895
Promoter ID:EPDNEW_R3419
Type:initiation region
Name:Lsm8_1
Description:LSM8 homolog, U6 small nuclear RNA associated
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0445,555,191 - 45,555,251EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308442 AgrOrtholog
BioCyc Gene G2FUF-45534 BioCyc
Ensembl Genes ENSRNOG00000058677 Ensembl
  ENSRNOG00000070946 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000115943 ENTREZGENE
  ENSRNOT00000115943.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7462085 IMAGE-MGC_LOAD
InterPro IPR047575 UniProtKB/TrEMBL
  Lsm8 UniProtKB/TrEMBL
  LSM_domain UniProtKB/TrEMBL
  LSM_related_domain UniProtKB/TrEMBL
  PTHR15588 UniProtKB/TrEMBL
KEGG Report rno:296913 UniProtKB/TrEMBL
MGC_CLONE MGC:189529 IMAGE-MGC_LOAD
NCBI Gene 296913 ENTREZGENE
PANTHER PTHR15588 UniProtKB/TrEMBL
  U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM8 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PhenoGen Lsm8 PhenoGen
PROSITE PS52002 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000058677 RatGTEx
  ENSRNOG00000070946 RatGTEx
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP Sm_like_riboprot UniProtKB/TrEMBL
UniProt A0A8I5ZNK7 ENTREZGENE, UniProtKB/TrEMBL
  A6IE42 ENTREZGENE, UniProtKB/TrEMBL
  B2RZB6 ENTREZGENE
UniProt Secondary B2RZB6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-01-23 Lsm8  LSM8 homolog, U6 small nuclear RNA associated  Naa38  N(alpha)-acetyltransferase 38, NatC auxiliary subunit  Name and Symbol changed 629549 APPROVED
2011-08-02 Naa38  N(alpha)-acetyltransferase 38, NatC auxiliary subunit  Lsm8  LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Lsm8  LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae)   Lsm8_predicted  LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lsm8_predicted  LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)      Symbol and Name status set to approved 70820 APPROVED