Lsm5l1 (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated like 1) - Rat Genome Database

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Gene: Lsm5l1 (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated like 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Lsm5l1 (Ensembl: LOC103693862)
Name: LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated like 1 (Ensembl:U6 snRNA-associated Sm-like protein LSm5 pseudogene)
RGD ID: 9247050
Description: Predicted to enable RNA binding activity. Predicted to be involved in RNA splicing and mRNA processing. Predicted to be part of spliceosomal complex.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC103693862; LOC679753; similar to LSM5 homolog, U6 small nuclear RNA associated; U6 snRNA-associated Sm-like protein LSm5; U6 snRNA-associated Sm-like protein LSm5 pseudogene
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2161,339,769 - 1,340,198 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,339,784 - 1,340,056 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0162,061,590 - 2,061,900 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0162,037,216 - 2,037,517 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4161,374,435 - 1,374,707 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera161,316,308 - 1,316,618 (+)NCBICelera
Cytogenetic Map16p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function
RNA binding  (IBA,IEA)

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Lsm5l1
4 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2325838Bp347Blood pressure QTL 3470.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1613080679Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)163802452995463Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
12903278Am16Aortic mass QTL 160.019aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)168323802995225Rat
12903279Cm115Cardiac mass QTL 1150.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)168323802995225Rat
12903281Cm116Cardiac mass QTL 1160.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)168323802995225Rat
12903952Cm117Cardiac mass QTL 1170.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)168323802995225Rat
12903954Bw186Body weight QTL 1860.011body mass (VT:0001259)body weight (CMO:0000012)168323802995225Rat
2301404Bp321Blood pressure QTL 3210.05arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)168323802995225Rat
12903955Kidm69Kidney mass QTL 690.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)168323804227609Rat


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_039094931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JACYVU010000273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000091719   ⟹   ENSRNOP00000085219
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,339,784 - 1,340,056 (+)Ensembl
Rnor_6.0 Ensembl162,061,613 - 2,061,882 (+)Ensembl
RefSeq Acc Id: XM_039094931   ⟹   XP_038950859
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2161,339,769 - 1,340,198 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038950859 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000029367.3
  ENSRNOP00000085219
  ENSRNOP00000085219.1
Reference Protein Sequences
RefSeq Acc Id: XP_038950859   ⟸   XM_039094931
- UniProtKB: A0A8I6A168 (UniProtKB/TrEMBL),   A6JDZ7 (UniProtKB/TrEMBL),   D3ZD76 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000085219   ⟸   ENSRNOT00000091719
Protein Domains
Sm

Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-12267 BioCyc
Ensembl Genes ENSRNOG00000027305 UniProtKB/TrEMBL
  ENSRNOG00000056629 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038594.3 UniProtKB/TrEMBL
  ENSRNOT00000091719 ENTREZGENE
  ENSRNOT00000091719.2 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
InterPro IPR047575 UniProtKB/TrEMBL
  LSm5 UniProtKB/TrEMBL
  LSM_dom_euk/arc UniProtKB/TrEMBL
  LSM_dom_sf UniProtKB/TrEMBL
NCBI Gene LOC103693862 ENTREZGENE
PANTHER PTHR20971 UniProtKB/TrEMBL
  U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PhenoGen Lsm5l1 PhenoGen
PROSITE PS52002 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027305 RatGTEx
  ENSRNOG00000056629 RatGTEx
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP SSF50182 UniProtKB/TrEMBL
UniProt A0A8I6A168 ENTREZGENE, UniProtKB/TrEMBL
  A6JDZ7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZD76 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Lsm5l1  LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated like 1  LOC103693862  U6 snRNA-associated Sm-like protein LSm5 pseudogene  Symbol and Name Changed 1299863 APPROVED
2015-07-29 LOC103693862  U6 snRNA-associated Sm-like protein LSm5 pseudogene  LOC679753  similar to LSM5 homolog, U6 small nuclear RNA associated  Data merged from RGD:1584789 737654 PROVISIONAL
2014-08-25 LOC103693862  U6 snRNA-associated Sm-like protein LSm5 pseudogene      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC679753  similar to LSM5 homolog, U6 small nuclear RNA associated      Symbol and Name status set to provisional 70820 PROVISIONAL