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) Rattus norvegicus
Analyze
Symbol: Lsm7
Name: LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated
RGD ID: 1305354
Description: Predicted to contribute to RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleus. Predicted to be part of several cellular components, including Lsm1-7-Pat1 complex; spliceosomal complex; and spliceosomal snRNP complex. Orthologous to human LSM7 (LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated); PARTICIPATES IN spliceosome pathway; RNA degradation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; Brodifacoum.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC362829; LSM7 homolog, U6 small nuclear RNA associated; LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae); LSM7 U6 small nuclear RNA and mRNA degradation associated; U6 snRNA-associated Sm-like protein LSm7
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
mRatBN7.278,856,666 - 8,859,119 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,856,489 - 8,859,119 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx711,740,650 - 11,743,084 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0713,616,154 - 13,618,588 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0711,482,686 - 11,485,120 (+)NCBIRnor_WKY
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
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

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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. 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:26912367   PMID:28781166  


Genomics

Comparative Map Data
Lsm7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.278,856,666 - 8,859,119 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,856,489 - 8,859,119 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx711,740,650 - 11,743,084 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0713,616,154 - 13,618,588 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0711,482,686 - 11,485,120 (+)NCBIRnor_WKY
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38192,321,521 - 2,328,586 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 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
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
PanPan1.1192,302,280 - 2,309,344 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl192,302,280 - 2,313,255 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0191,330,469 - 1,337,610 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365881,390,456 - 1,393,940 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
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
(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
5 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:127
Count of miRNA genes:101
Interacting mature miRNAs:106
Transcripts:ENSRNOT00000026551
Prediction methods:Microtar, Miranda, Rnahybrid, 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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat


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 39 57 41 19 41 2 5 74 35 40 11 2
Low 4 6 6 1 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026551   ⟹   ENSRNOP00000026551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl78,856,489 - 8,859,119 (+)Ensembl
Rnor_6.0 Ensembl711,724,962 - 11,727,388 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108930   ⟹   ENSRNOP00000079263
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl78,856,715 - 8,859,094 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109513   ⟹   ENSRNOP00000084004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl78,856,715 - 8,858,640 (+)Ensembl
RefSeq Acc Id: NM_001108732   ⟹   NP_001102202
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,856,693 - 8,859,119 (+)NCBI
Rnor_6.0711,724,962 - 11,727,388 (+)NCBI
Rnor_5.0711,892,648 - 11,895,103 (+)NCBI
RGSC_v3.4710,367,329 - 10,369,755 (+)RGD
Celera77,040,813 - 7,043,237 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240958   ⟹   XP_006241020
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,856,701 - 8,859,113 (+)NCBI
Rnor_6.0711,724,969 - 11,727,382 (+)NCBI
Rnor_5.0711,892,648 - 11,895,103 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765118   ⟹   XP_008763340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,856,666 - 8,859,113 (+)NCBI
Rnor_6.0711,724,932 - 11,727,382 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001102202   ⟸   NM_001108732
- UniProtKB: D4A2D8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241020   ⟸   XM_006240958
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008763340   ⟸   XM_008765118
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000026551   ⟸   ENSRNOT00000026551
RefSeq Acc Id: ENSRNOP00000084004   ⟸   ENSRNOT00000109513
RefSeq Acc Id: ENSRNOP00000079263   ⟸   ENSRNOT00000108930
Protein Domains
Sm

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A2D8-F1-model_v2 AlphaFold D4A2D8 1-103 view protein structure

Transcriptome

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

Promoters
RGD ID:13695000
Promoter ID:EPDNEW_R5524
Type:multiple initiation site
Name:Lsm7_1
Description:LSM7 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_6.0711,724,969 - 11,725,029EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305354 AgrOrtholog
BioCyc Gene G2FUF-34973 BioCyc
Ensembl Genes ENSRNOG00000019552 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026551 ENTREZGENE
  ENSRNOP00000026551.5 UniProtKB/TrEMBL
  ENSRNOP00000079263.1 UniProtKB/TrEMBL
  ENSRNOP00000084004.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026551 ENTREZGENE
  ENSRNOT00000026551.6 UniProtKB/TrEMBL
  ENSRNOT00000108930.1 UniProtKB/TrEMBL
  ENSRNOT00000109513.1 UniProtKB/TrEMBL
InterPro Lsm7/SmG-like UniProtKB/TrEMBL
  LSM_domain UniProtKB/TrEMBL
  LSM_related_domain UniProtKB/TrEMBL
  U6_snRNA_Lsm7 UniProtKB/TrEMBL
KEGG Report rno:362829 UniProtKB/TrEMBL
NCBI Gene 362829 ENTREZGENE
PANTHER PTHR10553 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PhenoGen Lsm7 PhenoGen
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP Sm_like_riboprot UniProtKB/TrEMBL
UniProt A0A8I5ZMR4_RAT UniProtKB/TrEMBL
  A0A8I6A0C6_RAT UniProtKB/TrEMBL
  D4A2D8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-09 Lsm7  LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated  Lsm7  LSM7 U6 small nuclear RNA and mRNA degradation associated  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-01 Lsm7  LSM7 U6 small nuclear RNA and mRNA degradation associated  Lsm7  LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Lsm7  LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)   Lsm7_predicted  LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lsm7_predicted  LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)      Symbol and Name status set to approved 70820 APPROVED