Lsm5 (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated) - Rat Genome Database

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Gene: Lsm5 (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated) Rattus norvegicus
Analyze
Symbol: Lsm5
Name: LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated
RGD ID: 1308655
Description: Predicted to enable protein heterodimerization activity. Predicted to contribute to RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to act upstream of or within mRNA catabolic process and response to bacterium. Predicted to be located in cytoplasm and nucleus. Predicted to be part of several cellular components, including Lsm1-7-Pat1 complex; Lsm2-8 complex; and spliceosomal snRNP complex. Orthologous to human LSM5 (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated); PARTICIPATES IN RNA degradation pathway; spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC306222; LSM5 homolog, U6 small nuclear RNA associated; LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae); LSM5 U6 small nuclear RNA and mRNA degradation associated; U6 snRNA-associated Sm-like protein LSm5
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
GRCr8487,281,260 - 87,284,476 (-)NCBIGRCr8
mRatBN7.2485,951,073 - 85,954,289 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl485,951,073 - 85,954,289 (-)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl6104,652,477 - 104,654,165 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx491,185,666 - 91,188,888 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0486,961,092 - 86,964,314 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0485,361,949 - 85,365,179 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0487,016,003 - 87,019,219 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl487,016,003 - 87,019,219 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,831,108 - 108,832,796 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04151,668,265 - 151,671,481 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4485,656,850 - 85,660,066NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera480,789,492 - 80,792,716 (-)NCBICelera
Cytogenetic Map4q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction 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. 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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
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
Additional References at PubMed
PMID:10523320   PMID:12515382   PMID:23012479   PMID:26912367   PMID:28781166  


Genomics

Comparative Map Data
Lsm5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8487,281,260 - 87,284,476 (-)NCBIGRCr8
mRatBN7.2485,951,073 - 85,954,289 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl485,951,073 - 85,954,289 (-)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl6104,652,477 - 104,654,165 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx491,185,666 - 91,188,888 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0486,961,092 - 86,964,314 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0485,361,949 - 85,365,179 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0487,016,003 - 87,019,219 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl487,016,003 - 87,019,219 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,831,108 - 108,832,796 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04151,668,265 - 151,671,481 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4485,656,850 - 85,660,066NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera480,789,492 - 80,792,716 (-)NCBICelera
Cytogenetic Map4q24NCBI
LSM5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38732,485,338 - 32,495,283 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl732,485,338 - 32,495,283 (-)EnsemblGRCh38hg38GRCh38
GRCh37732,524,950 - 32,534,895 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36732,492,942 - 32,496,502 (-)NCBINCBI36Build 36hg18NCBI36
Build 34732,299,658 - 32,303,217NCBI
Celera732,508,861 - 32,518,784 (-)NCBICelera
Cytogenetic Map7p14.3NCBI
HuRef732,402,581 - 32,412,511 (-)NCBIHuRef
CHM1_1732,524,639 - 32,534,553 (-)NCBICHM1_1
T2T-CHM13v2.0732,624,513 - 32,634,448 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2732,570,144 - 32,580,067 (-)NCBI
Lsm5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39656,678,048 - 56,681,684 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl656,678,048 - 56,681,695 (-)EnsemblGRCm39 Ensembl
GRCm38656,701,063 - 56,704,699 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl656,701,063 - 56,704,710 (-)EnsemblGRCm38mm10GRCm38
MGSCv37656,651,057 - 56,654,693 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36656,630,641 - 56,634,261 (-)NCBIMGSCv36mm8
Celera657,464,070 - 57,467,706 (-)NCBICelera
Cytogenetic Map6B3NCBI
cM Map627.72NCBI
Lsm5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495561742,447 - 47,999 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495561742,829 - 47,999 (-)NCBIChiLan1.0ChiLan1.0
LSM5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2637,294,240 - 37,302,526 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1785,618,972 - 85,627,239 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0733,094,545 - 33,104,489 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LSM5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11444,857,882 - 44,860,929 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1444,857,930 - 44,860,821 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1444,292,332 - 44,295,390 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01444,795,728 - 44,798,786 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1444,795,782 - 44,798,694 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11444,900,836 - 44,903,891 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01444,581,381 - 44,584,439 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01444,955,444 - 44,958,504 (-)NCBIUU_Cfam_GSD_1.0
Lsm5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511889,329,568 - 89,333,605 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364788,540,330 - 8,545,348 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364788,541,293 - 8,545,280 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1840,752,461 - 40,755,906 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11840,752,390 - 40,755,909 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21844,736,388 - 44,739,868 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LSM5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12125,921,288 - 25,925,237 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604278,816,172 - 78,826,302 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lsm5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248963,079,196 - 3,083,433 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248963,079,167 - 3,083,380 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lsm5
15 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:319
Count of miRNA genes:166
Interacting mature miRNAs:186
Transcripts:ENSRNOT00000038594, ENSRNOT00000065625
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
631556Bp135Blood pressure QTL 1350.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)478881294117676292Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473169846132642728Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462879517107879517Rat
631662Hcar2Hepatocarcinoma resistance QTL 23.10.0003liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)478878504123878504Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738015Pia9Pristane induced arthritis QTL 94.50.048joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)480694870125694870Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711443291360801Rat
634334Xhs3X-ray hypersensitivity QTL 310intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)484728680129854654Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)470808386115808386Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)470808386115808386Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)457486946102486946Rat
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
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45843213392991462Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)460220938105220938Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)460220938105220938Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)485253748148090731Rat
1641919Alc22Alcohol consumption QTL 220.0005drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)481192555126192555Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470362013132642728Rat
61364Iddm2Insulin dependent diabetes mellitus QTL 2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)478885890102684881Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
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
724522Bp146Blood pressure QTL 1462.20.0021arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)473630210118630210Rat
2302051Pia28Pristane induced arthritis QTL 285.30.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)473630210118630210Rat
2306899Bp338Blood pressure QTL 3380.071arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)481006124120102625Rat
2312569Pur19Proteinuria QTL 193.40.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)46588210796130297Rat
2306794Ean2Experimental allergic neuritis QTL 26.4nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)48342841995853334Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
70167Bw22Body weight QTL 223.1body mass (VT:0001259)body weight (CMO:0000012)476647384117676292Rat
1357342Bw40Body weight QTL 400.001body mass (VT:0001259)body weight (CMO:0000012)476647384117676292Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)462933508114921294Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)485253748150276390Rat
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
2300179Bmd50Bone mineral density QTL 505.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)460928534105928534Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46293326987483707Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658103194791Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658115089733Rat

Markers in Region
RH137282  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2161,339,914 - 1,340,094 (+)MAPPERmRatBN7.2
Rnor_6.0162,061,744 - 2,061,923NCBIRnor6.0
Rnor_5.0162,037,359 - 2,037,538UniSTSRnor5.0
RGSC_v3.4161,374,566 - 1,374,745UniSTSRGSC3.4
Celera161,316,462 - 1,316,641UniSTS
RH 3.4 Map1616.3UniSTS
Cytogenetic Map16p16UniSTS
Cytogenetic Map4q24UniSTS


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 54 38 19 38 8 10 74 35 38 11 8
Low 3 10 31 15 19 15 8 9 24 12 16 11 8
Below cutoff 15 7 7 7 3 16 8 15

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000038594   ⟹   ENSRNOP00000029367
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6104,652,477 - 104,654,165 (+)Ensembl
Rnor_6.0 Ensembl6108,831,108 - 108,832,796 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000065625   ⟹   ENSRNOP00000062832
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl485,951,073 - 85,954,289 (-)Ensembl
Rnor_6.0 Ensembl487,016,003 - 87,019,219 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101731   ⟹   ENSRNOP00000078939
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl485,951,073 - 85,954,238 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114266   ⟹   ENSRNOP00000081351
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl485,951,073 - 85,953,072 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118324   ⟹   ENSRNOP00000083668
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl485,951,378 - 85,954,289 (-)Ensembl
RefSeq Acc Id: NM_001107289   ⟹   NP_001100759
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8487,281,260 - 87,284,476 (-)NCBI
mRatBN7.2485,951,073 - 85,954,289 (-)NCBI
Rnor_6.0487,016,003 - 87,019,219 (-)NCBI
Rnor_5.04151,668,265 - 151,671,481 (-)NCBI
RGSC_v3.4485,656,850 - 85,660,066 (-)RGD
Celera480,789,492 - 80,792,716 (-)RGD
Sequence:
RefSeq Acc Id: XM_063285928   ⟹   XP_063141998
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8487,281,262 - 87,284,354 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001100759   ⟸   NM_001107289
- UniProtKB: A6K112 (UniProtKB/TrEMBL),   A6JDZ7 (UniProtKB/TrEMBL),   D3ZD76 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000029367   ⟸   ENSRNOT00000038594
RefSeq Acc Id: ENSRNOP00000062832   ⟸   ENSRNOT00000065625
RefSeq Acc Id: ENSRNOP00000078939   ⟸   ENSRNOT00000101731
RefSeq Acc Id: ENSRNOP00000081351   ⟸   ENSRNOT00000114266
RefSeq Acc Id: ENSRNOP00000083668   ⟸   ENSRNOT00000118324
RefSeq Acc Id: XP_063141998   ⟸   XM_063285928
- Peptide Label: isoform X1
Protein Domains
Sm

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZD76-F1-model_v2 AlphaFold D3ZD76 1-92 view protein structure

Transcriptome

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

Promoters
RGD ID:13693078
Promoter ID:EPDNEW_R3602
Type:single initiation site
Name:Lsm5_1
Description:LSM5 homolog, U6 small nuclear RNA and mRNA degradation 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_6.0487,019,183 - 87,019,243EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308655 AgrOrtholog
BioCyc Gene G2FUF-44714 BioCyc
Ensembl Genes ENSRNOG00000027305 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000042126 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038594.3 UniProtKB/TrEMBL
  ENSRNOT00000065625.2 UniProtKB/TrEMBL
  ENSRNOT00000101731.1 UniProtKB/TrEMBL
  ENSRNOT00000114266.1 UniProtKB/TrEMBL
  ENSRNOT00000118324 ENTREZGENE
  ENSRNOT00000118324.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
InterPro IPR047575 UniProtKB/TrEMBL
  LSm5 UniProtKB/TrEMBL
  LSM_domain UniProtKB/TrEMBL
  LSM_related_domain UniProtKB/TrEMBL
KEGG Report rno:306222 UniProtKB/TrEMBL
NCBI Gene 306222 ENTREZGENE
PANTHER PTHR20971 UniProtKB/TrEMBL
  U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PhenoGen Lsm5 PhenoGen
PROSITE PS52002 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027305 RatGTEx
  ENSRNOG00000042126 RatGTEx
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP Sm_like_riboprot UniProtKB/TrEMBL
UniProt A0A8I5ZRU9_RAT UniProtKB/TrEMBL
  A0A8I5ZVR9_RAT UniProtKB/TrEMBL
  A0A8I6G476_RAT UniProtKB/TrEMBL
  A6JDZ7 ENTREZGENE, UniProtKB/TrEMBL
  A6K112 ENTREZGENE, UniProtKB/TrEMBL
  D3ZBJ0_RAT UniProtKB/TrEMBL
  D3ZD76 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-09 Lsm5  LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated  Lsm5  LSM5 U6 small nuclear RNA and mRNA degradation associated  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-01 Lsm5  LSM5 U6 small nuclear RNA and mRNA degradation associated  Lsm5  LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Lsm5  LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)   Lsm5_predicted  LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lsm5_predicted  LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)      Symbol and Name status set to approved 70820 APPROVED