Lsm4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated) - Rat Genome Database

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Gene: Lsm4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated) Rattus norvegicus
Analyze
Symbol: Lsm4
Name: LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated
RGD ID: 1306808
Description: Predicted to enable PH domain binding activity and U6 snRNA binding activity. Predicted to be involved in P-body assembly and spliceosomal snRNP assembly. Predicted to be located in cytosol; membrane; and nucleus. Predicted to be part of Lsm2-8 complex; U2-type precatalytic spliceosome; and spliceosomal snRNP complex. Predicted to be active in P-body. Orthologous to human LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated); PARTICIPATES IN spliceosome pathway; RNA degradation pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC290647; LSM4 homolog, U6 small nuclear RNA associated; LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae); LSM4 U6 small nuclear RNA and mRNA degradation associated; U6 snRNA-associated Sm-like protein LSm4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81618,789,466 - 18,795,164 (-)NCBIGRCr8
mRatBN7.21618,755,481 - 18,761,106 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1618,755,484 - 18,760,926 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1618,797,134 - 18,802,546 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01619,930,058 - 19,935,475 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01618,850,088 - 18,855,500 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01620,506,399 - 20,511,818 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1620,506,399 - 20,511,818 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01620,363,442 - 20,368,886 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41619,261,065 - 19,266,484 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11619,261,067 - 19,266,367 (-)NCBI
Celera1618,947,390 - 18,952,806 (-)NCBICelera
Cytogenetic Map16p14NCBI
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
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrotoluene  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-palmitoylglycerol  (ISO)
3-methylcholanthrene  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
amitrole  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
cadmium dichloride  (EXP)
chlorpyrifos  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dextran sulfate  (ISO)
diazinon  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
fenthion  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
glafenine  (EXP)
inulin  (ISO)
ivermectin  (ISO)
methidathion  (ISO)
methimazole  (EXP)
methoxychlor  (EXP)
ozone  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sulfadimethoxine  (EXP)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
triptonide  (ISO)
trovafloxacin  (EXP)
tungsten  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

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. Dendritic LSm1/CBP80-mRNPs mark the early steps of transport commitment and translational control. di Penta A, etal., J Cell Biol. 2009 Feb 9;184(3):423-35. doi: 10.1083/jcb.200807033. Epub 2009 Feb 2.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. 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.
11. Aberrantly Methylated-Differentially Expressed Genes Identify Novel Atherosclerosis Risk Subtypes. Xue Y, etal., Front Genet. 2020 Dec 14;11:569572. doi: 10.3389/fgene.2020.569572. eCollection 2020.
Additional References at PubMed
PMID:10523320   PMID:15905169   PMID:22658674   PMID:22681889   PMID:26912367   PMID:28781166  


Genomics

Comparative Map Data
Lsm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81618,789,466 - 18,795,164 (-)NCBIGRCr8
mRatBN7.21618,755,481 - 18,761,106 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1618,755,484 - 18,760,926 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1618,797,134 - 18,802,546 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01619,930,058 - 19,935,475 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01618,850,088 - 18,855,500 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01620,506,399 - 20,511,818 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1620,506,399 - 20,511,818 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01620,363,442 - 20,368,886 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41619,261,065 - 19,266,484 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11619,261,067 - 19,266,367 (-)NCBI
Celera1618,947,390 - 18,952,806 (-)NCBICelera
Cytogenetic Map16p14NCBI
LSM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381918,306,236 - 18,323,076 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1918,306,236 - 18,323,112 (-)EnsemblGRCh38hg38GRCh38
GRCh371918,417,046 - 18,433,886 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361918,278,717 - 18,294,962 (-)NCBINCBI36Build 36hg18NCBI36
Build 341918,278,717 - 18,294,958NCBI
Celera1918,319,475 - 18,335,755 (-)NCBICelera
Cytogenetic Map19p13.11NCBI
HuRef1917,980,724 - 17,997,682 (-)NCBIHuRef
CHM1_11918,417,296 - 18,434,252 (-)NCBICHM1_1
T2T-CHM13v2.01918,440,354 - 18,457,193 (-)NCBIT2T-CHM13v2.0
Lsm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39871,124,663 - 71,131,402 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl871,125,898 - 71,131,402 (+)EnsemblGRCm39 Ensembl
GRCm38870,673,231 - 70,678,752 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl870,673,248 - 70,678,752 (+)EnsemblGRCm38mm10GRCm38
MGSCv37873,197,130 - 73,202,651 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36873,602,381 - 73,607,741 (+)NCBIMGSCv36mm8
Celera873,229,842 - 73,235,362 (+)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.15NCBI
Lsm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555243,157,607 - 3,165,196 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555243,157,607 - 3,165,196 (+)NCBIChiLan1.0ChiLan1.0
LSM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22023,167,478 - 23,183,873 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11922,175,796 - 22,192,193 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01917,785,580 - 17,801,866 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11918,757,390 - 18,773,812 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1918,757,390 - 18,773,812 (-)Ensemblpanpan1.1panPan2
LSM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12044,707,460 - 44,720,490 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2044,707,460 - 44,720,490 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2044,621,620 - 44,634,648 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02045,193,083 - 45,206,148 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2045,193,083 - 45,206,124 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12044,430,435 - 44,443,463 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02044,840,880 - 44,853,912 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02045,116,311 - 45,129,341 (+)NCBIUU_Cfam_GSD_1.0
Lsm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118203,354,208 - 203,367,493 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365962,903,358 - 2,916,629 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365962,903,363 - 2,916,629 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl259,499,564 - 59,513,246 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1259,499,560 - 59,513,258 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LSM4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1616,783,566 - 16,800,116 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl616,782,746 - 16,800,143 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660742,555,195 - 2,572,041 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lsm4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249081,595,877 - 1,603,043 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249081,595,877 - 1,603,075 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lsm4
19 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:265
Count of miRNA genes:184
Interacting mature miRNAs:197
Transcripts:ENSRNOT00000026567
Prediction methods:Microtar, Miranda, Rnahybrid
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
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
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
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161572643321034895Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat

Markers in Region
RH133230  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21618,760,978 - 18,761,184 (+)MAPPERmRatBN7.2
Rnor_6.01620,511,896 - 20,512,101NCBIRnor6.0
Rnor_5.01620,368,964 - 20,369,169UniSTSRnor5.0
RGSC_v3.41619,266,562 - 19,266,767UniSTSRGSC3.4
Celera1618,952,884 - 18,953,089UniSTS
RH 3.4 Map16190.5UniSTS
Cytogenetic Map16p14UniSTS
RH141667  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21618,761,407 - 18,761,596 (+)MAPPERmRatBN7.2
Rnor_6.01620,512,325 - 20,512,513NCBIRnor6.0
Rnor_5.01620,369,393 - 20,369,581UniSTSRnor5.0
RGSC_v3.41619,266,991 - 19,267,179UniSTSRGSC3.4
Celera1618,953,313 - 18,953,501UniSTS
RH 3.4 Map16181.8UniSTS
Cytogenetic Map16p14UniSTS
RH129410  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21618,755,482 - 18,755,688 (+)MAPPERmRatBN7.2
Rnor_6.01620,506,400 - 20,506,605NCBIRnor6.0
Rnor_5.01620,363,468 - 20,363,673UniSTSRnor5.0
RGSC_v3.41619,261,066 - 19,261,271UniSTSRGSC3.4
Celera1618,947,391 - 18,947,596UniSTS
RH 3.4 Map16181.8UniSTS
Cytogenetic Map16p14UniSTS
LSM4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21618,756,161 - 18,756,298 (+)MAPPERmRatBN7.2
Rnor_6.01620,507,079 - 20,507,215NCBIRnor6.0
Rnor_5.01620,364,147 - 20,364,283UniSTSRnor5.0
RGSC_v3.41619,261,745 - 19,261,881UniSTSRGSC3.4
Celera1618,948,070 - 18,948,206UniSTS
Cytogenetic Map16p14UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000026567   ⟹   ENSRNOP00000026567
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1618,755,484 - 18,760,926 (-)Ensembl
Rnor_6.0 Ensembl1620,506,399 - 20,511,818 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000097247   ⟹   ENSRNOP00000095698
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1618,755,723 - 18,757,622 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000119396   ⟹   ENSRNOP00000083403
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1618,755,484 - 18,760,926 (-)Ensembl
RefSeq Acc Id: NM_001106073   ⟹   NP_001099543
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,789,467 - 18,794,886 (-)NCBI
mRatBN7.21618,755,482 - 18,760,901 (-)NCBI
Rnor_6.01620,506,399 - 20,511,818 (-)NCBI
Rnor_5.01620,363,442 - 20,368,886 (-)NCBI
RGSC_v3.41619,261,065 - 19,266,484 (-)RGD
Celera1618,947,390 - 18,952,806 (-)RGD
Sequence:
RefSeq Acc Id: XM_039094317   ⟹   XP_038950245
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,789,466 - 18,794,792 (-)NCBI
mRatBN7.21618,755,481 - 18,760,807 (-)NCBI
RefSeq Acc Id: XM_039094318   ⟹   XP_038950246
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,790,506 - 18,795,164 (-)NCBI
mRatBN7.21618,756,521 - 18,761,106 (-)NCBI
RefSeq Acc Id: XM_063275158   ⟹   XP_063131228
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,789,466 - 18,794,919 (-)NCBI
RefSeq Acc Id: NP_001099543   ⟸   NM_001106073
- UniProtKB: D4A2C6 (UniProtKB/TrEMBL),   A6KA13 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000026567   ⟸   ENSRNOT00000026567
RefSeq Acc Id: XP_038950245   ⟸   XM_039094317
- Peptide Label: isoform X2
- UniProtKB: A6KA14 (UniProtKB/TrEMBL),   A0A8I5ZZ77 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038950246   ⟸   XM_039094318
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000083403   ⟸   ENSRNOT00000119396
Ensembl Acc Id: ENSRNOP00000095698   ⟸   ENSRNOT00000097247
RefSeq Acc Id: XP_063131228   ⟸   XM_063275158
- Peptide Label: isoform X1
- UniProtKB: A6KA13 (UniProtKB/TrEMBL),   D4A2C6 (UniProtKB/TrEMBL)
Protein Domains
Sm

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A2C6-F1-model_v2 AlphaFold D4A2C6 1-138 view protein structure

Transcriptome

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

Promoters
RGD ID:13700020
Promoter ID:EPDNEW_R10543
Type:initiation region
Name:Lsm4_1
Description:LSM4 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_6.01620,511,688 - 20,511,748EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306808 AgrOrtholog
BioCyc Gene G2FUF-11797 BioCyc
Ensembl Genes ENSRNOG00000019572 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026567.6 UniProtKB/TrEMBL
  ENSRNOT00000097247.1 UniProtKB/TrEMBL
  ENSRNOT00000119396.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
InterPro IPR047575 UniProtKB/TrEMBL
  Lsm4 UniProtKB/TrEMBL
  LSm4/Sm_D1/D3 UniProtKB/TrEMBL
  LSM_domain UniProtKB/TrEMBL
  LSM_related_domain UniProtKB/TrEMBL
KEGG Report rno:290647 UniProtKB/TrEMBL
NCBI Gene 290647 ENTREZGENE
PANTHER PTHR23338 UniProtKB/TrEMBL
  U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PhenoGen Lsm4 PhenoGen
PROSITE PS52002 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019572 RatGTEx
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP Sm_like_riboprot UniProtKB/TrEMBL
UniProt A0A8I5ZZ77 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6APJ0_RAT UniProtKB/TrEMBL
  A6KA13 ENTREZGENE, UniProtKB/TrEMBL
  A6KA14 ENTREZGENE, UniProtKB/TrEMBL
  D4A2C6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-09 Lsm4  LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated  Lsm4  LSM4 U6 small nuclear RNA and mRNA degradation associated  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-01 Lsm4  LSM4 U6 small nuclear RNA and mRNA degradation associated  Lsm4  LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Lsm4  LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)   Lsm4_predicted  LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lsm4_predicted  LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)      Symbol and Name status set to approved 70820 APPROVED