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Gene: Lsm1 (LSM1 homolog, mRNA degradation associated) Rattus norvegicus

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Symbol:

Lsm1

Name:

LSM1 homolog, mRNA degradation associated

RGD ID:

1304967

Description:

Enables mRNA binding activity and pre-mRNA binding activity. Predicted to be involved in deadenylation-dependent decapping of nuclear-transcribed mRNA and histone mRNA catabolic process. Predicted to act upstream of or within negative regulation of neuron differentiation and stem cell population maintenance. Located in axon; dendrite; and neuronal cell body. Part of ribonucleoprotein complex. Orthologous to human LSM1 (LSM1 homolog, mRNA degradation associated); PARTICIPATES IN RNA degradation pathway; INTERACTS WITH 2,4-dinitrotoluene; bisphenol A; fipronil.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC364624; LSM1 homolog, U6 small nuclear RNA associated; LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae); LSM1 mRNA degradation associated; LSM1, U6 small nuclear RNA associated; U6 snRNA-associated Sm-like protein LSm1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	LSM1 (LSM1 homolog, mRNA degradation associated)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Lsm1 (LSM1 homolog, mRNA degradation associated)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Lsm1 (LSM1 homolog, mRNA degradation associated)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LSM1 (LSM1 homolog, mRNA degradation associated)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LSM1 (LSM1 homolog, mRNA degradation associated)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lsm1 (LSM1 homolog, mRNA degradation associated)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LSM1 (LSM1 homolog, mRNA degradation associated)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LSM1 (LSM1 homolog, mRNA degradation associated)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lsm1 (LSM1 homolog, mRNA degradation associated)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	LSM1 (LSM1 homolog, mRNA degradation associated)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Lsm1 (LSM1 homolog, mRNA degradation associated)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	lsm1 (LSM1, U6 small nuclear RNA associated)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	LSM1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	LSm1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	lsm-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	lsm1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	16	72,980,075 - 72,991,581 (-)	NCBI		GRCr8
mRatBN7.2	16	66,277,345 - 66,288,852 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	16	66,277,345 - 66,288,852 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	16	71,555,983 - 71,567,493 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	16	74,962,293 - 74,973,803 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	16	70,202,187 - 70,213,697 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	16	71,046,475 - 71,057,883 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	71,046,475 - 71,057,883 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	70,711,151 - 70,722,559 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	70,652,831 - 70,663,995 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	16	70,653,556 - 70,663,907 (-)	NCBI
Celera	16	64,187,220 - 64,198,747 (-)	NCBI		Celera
Cytogenetic Map	16	q12.4	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

cryptorchidism (ISO)

developmental and epileptic encephalopathy 11 (ISO)

Developmental Disabilities (ISO)

hereditary spastic paraplegia 54 (ISO)

hypogonadotropic hypogonadism 2 with or without anosmia (ISO)

paraplegia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

17beta-hydroxy-17-methylestra-4,9,11-trien-3-one (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,4-dinitrotoluene (EXP)

4,4'-sulfonyldiphenol (ISO)

acrolein (ISO)

acrylamide (ISO)

aflatoxin B1 (ISO)

alpha-pinene (ISO)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

bisphenol A (EXP,ISO)

butan-1-ol (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

Dibutyl phosphate (ISO)

dicrotophos (ISO)

fipronil (EXP)

flutamide (EXP)

folic acid (ISO)

hydrogen peroxide (ISO)

ivermectin (ISO)

levetiracetam (EXP)

manganese atom (ISO)

manganese(0) (ISO)

manganese(II) chloride (ISO)

nitrates (ISO)

ozone (ISO)

paraquat (ISO)

phenytoin (EXP)

pirinixic acid (ISO)

potassium dichromate (ISO)

rotenone (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

sodium fluoride (ISO)

succimer (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

deadenylation-dependent decapping of nuclear-transcribed mRNA (IBA)

histone mRNA catabolic process (ISO)

mRNA processing (IEA)

negative regulation of neuron differentiation (ISO)

neuron differentiation (ISO)

nuclear-transcribed mRNA catabolic process (IEA)

stem cell population maintenance (ISO)

Cellular Component

axon (IDA)

cytoplasm (IEA,ISO)

dendrite (IDA)

Lsm1-7-Pat1 complex (IBA)

neuronal cell body (IDA)

nucleus (ISO)

P-body (IBA,IEA,ISO)

ribonucleoprotein complex (IDA,IEA)

Molecular Function

mRNA binding (IBA,IDA)

pre-mRNA binding (IDA)

protein binding (ISO)

RNA binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

RNA degradation pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	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.
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.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
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:18172165	PMID:18559850	PMID:18719247	PMID:22658674	PMID:22681889	PMID:25456498

Genomics

Comparative Map Data

Lsm1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	16	72,980,075 - 72,991,581 (-)	NCBI		GRCr8
mRatBN7.2	16	66,277,345 - 66,288,852 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	16	66,277,345 - 66,288,852 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	16	71,555,983 - 71,567,493 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	16	74,962,293 - 74,973,803 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	16	70,202,187 - 70,213,697 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	16	71,046,475 - 71,057,883 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	71,046,475 - 71,057,883 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	70,711,151 - 70,722,559 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	70,652,831 - 70,663,995 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	16	70,653,556 - 70,663,907 (-)	NCBI
Celera	16	64,187,220 - 64,198,747 (-)	NCBI		Celera
Cytogenetic Map	16	q12.4	NCBI

LSM1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	8	38,163,321 - 38,176,730 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	8	38,163,335 - 38,176,730 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	8	38,020,839 - 38,034,248 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	8	38,140,014 - 38,153,183 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	8	38,140,013 - 38,153,183	NCBI
Celera	8	36,973,393 - 36,986,562 (-)	NCBI		Celera
Cytogenetic Map	8	p11.23	NCBI
HuRef	8	36,555,756 - 36,568,636 (-)	NCBI		HuRef
CHM1_1	8	38,222,844 - 38,236,249 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	8	38,440,300 - 38,453,709 (-)	NCBI		T2T-CHM13v2.0

Lsm1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	26,275,326 - 26,294,003 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	8	26,275,316 - 26,294,003 (+)	Ensembl		GRCm39 Ensembl
GRCm38	8	25,785,318 - 25,803,975 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	25,785,288 - 25,803,975 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	8	26,896,063 - 26,914,447 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	8	27,250,852 - 27,269,520 (+)	NCBI		MGSCv36	mm8
Celera	8	27,253,809 - 27,272,186 (+)	NCBI		Celera
Cytogenetic Map	8	A2	NCBI
cM Map	8	14.17	NCBI

Lsm1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955463	13,773,869 - 13,788,784 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955463	13,775,639 - 13,788,784 (-)	NCBI	ChiLan1.0	ChiLan1.0

LSM1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	7	56,726,906 - 56,739,998 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	8	32,443,915 - 32,457,154 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	8	37,465,986 - 37,479,186 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	8	34,642,938 - 34,656,142 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	8	34,642,938 - 34,656,142 (-)	Ensembl	panpan1.1		panPan2

LSM1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	16	27,304,257 - 27,315,389 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	16	27,304,198 - 27,315,233 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	16	27,821,271 - 27,832,688 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	16	29,203,163 - 29,214,621 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	16	29,203,401 - 29,214,465 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	16	27,425,471 - 27,436,928 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	16	28,002,718 - 28,014,129 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	16	28,041,959 - 28,053,408 (+)	NCBI		UU_Cfam_GSD_1.0

Lsm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404943	49,909,516 - 49,915,246 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936710	1,545,790 - 1,552,394 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936710	1,546,027 - 1,551,685 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LSM1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	48,348,648 - 48,365,106 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	15	48,348,653 - 48,360,004 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	55,604,059 - 55,615,385 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LSM1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	8	36,184,928 - 36,198,689 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	8	36,182,380 - 36,198,704 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666052	5,791,244 - 5,805,004 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lsm1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624780	5,473,041 - 5,483,300 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624780	5,473,172 - 5,483,584 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Lsm1
29 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	427
Count of miRNA genes:	217
Interacting mature miRNAs:	255
Transcripts:	ENSRNOT00000020721
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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2300163	Bmd64	Bone mineral density QTL 64	5.3	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	16	37752156	82752156	Rat
1600378	Arunc4	Aerobic running capacity QTL 4		0.03	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	16	380245	80345693	Rat
70215	Niddm29	Non-insulin dependent diabetes mellitus QTL 29	3.54		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	16	19004435	75226532	Rat
1578768	Stresp22	Stress response QTL 22	2.8		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	16	35288870	80288870	Rat
2302057	Pia29	Pristane induced arthritis QTL 29	3.6	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	16	21735975	66735975	Rat
7205510	Activ5	Activity QTL 5	3.78	0.00028	locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	16	42396345	84729064	Rat
631525	Pia14	Pristane induced arthritis QTL 14	4.4		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	16	55711087	83402471	Rat
8694453	Bw172	Body weight QTL 172	8.33	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	16	24325513	69325513	Rat
7411648	Foco22	Food consumption QTL 22	15	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	16	52726464	84729064	Rat
6903294	Stl30	Serum triglyceride level QTL 30	2.6	0.0013	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	16	25152793	70152793	Rat
2293690	Bss45	Bone structure and strength QTL 45	5.13	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	16	37752156	82752156	Rat
8694364	Abfw7	Abdominal fat weight QTL 7	12.22	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	16	52726464	84729064	Rat
8694429	Bw164	Body weight QTL 164	5	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	16	52726464	84729064	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor diameter (CMO:0001889)	16	17696791	82635055	Rat

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

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

Nucleotide Sequences


RefSeq Transcripts	NM_001108876	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473970	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ216033	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220497	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000016	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000020721 ⟹ ENSRNOP00000020721

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	66,277,345 - 66,288,852 (-)	Ensembl
Rnor_6.0 Ensembl	16	71,046,475 - 71,057,883 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000118602 ⟹ ENSRNOP00000089972

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	66,277,345 - 66,283,881 (-)	Ensembl

RefSeq Acc Id:

NM_001108876 ⟹ NP_001102346

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	16	72,980,075 - 72,991,581 (-)	NCBI
mRatBN7.2	16	66,277,345 - 66,288,852 (-)	NCBI
Rnor_6.0	16	71,046,475 - 71,057,883 (-)	NCBI
Rnor_5.0	16	70,711,151 - 70,722,559 (-)	NCBI
RGSC_v3.4	16	70,652,831 - 70,663,995 (-)	RGD
Celera	16	64,187,220 - 64,198,747 (-)	RGD

Sequence:

show sequence

CGCCGAGTGCCGAGCGGTCATGGACTGTACGGATCAACCCGGGCCTCGGAGCAGGAAAGCGAGG
CGAGGGACAGCGCTTGTCACGAGTGAGGAAACGCCTATTCTCCGCCCTTCCGACCTGGACTTCA
CTTCACTGACTAGAAAGGAAGAAAACGTTGTCTGCGACCGAACGCCCGGCACGCCTTTTTCAGT
GGATGGACAGGCGATACCGGAAGTGGGTGGGGTTACCTGAAACGCTTCCGGCGACTAGCGGTGT
TTGAGTTGCAGGTGAGCGGCGGGTTCCCGTCCGCGTCCCGCCGACGGGCGATTGGACGCCCTCG
CGGCCGTCCAGTGCAGCCTTGCGAGAGCTCAAAATGAACTATATGCCCGGCACCGCCAGCCTCA
TCGAGGACATCGACAAAAAGCACTTGGTCCTACTTCGAGATGGAAGGACACTTATAGGTTTTTT
AAGAAGCATTGATCAATTTGCTAACCTAGTGCTCCATCAGACTGTGGAGCGAATTCACGTGGGC
AGAAAGTACGGTGATATTCCTCGAGGGATTTTCGTGGTCAGAGGAGAAAATGTGGTCCTACTAG
GAGAAATAGACTTGGAAAAGGAAAGTGACACGCCACTTCAGCAAGTCTCCATTGAAGAGATCCT
GGAGGAACAGAGGGTAGAGCAGCAGAGCAGGCTGGAGGCAGAGAAGCTGAAGGTCCAGGCCCTT
AAAGACCGGGGTCTCTCCATTCCTCGTGCAGACACTCTGGATGAGTACTGAGTCCTTGCTTAGA
GACTGCTTCAGAGAGCAGGTGCTGTCACCTGGTCACCTCACATCTGACCAGAGTATCACACTGA
AAAGTGATCTTATTCTTTCACAGATGCCAACATGAAGAAATCATGGGATTTGTTTTGTTTTTGT
TTGTTTTTTTTACACAATCATTGTATATTAGTTTTGCCTTTTTCTTCAAACAGTCTCAACACAT
AGTCCTGGCTGACCTAGAACTCACTATGTAAACCAGGATGCCCTCTAGCTTGTGGGATTTCAGG
TGGGCTCTACCATCCCAGCTTTGCTGTTTAAAGAAACAGTGGCATGACCTCCCCTCAACACGTC
ACTGTGGAGCCAAGAACCGTGTCTTTATATTGCTTTTCTTATCTCAGAGTTTACATTTCTTTTC
AAAACATATTTCATTTACTTGTAAATAAAAAAAATGAAGCTCAGAACTGTCATCTTCATAAAAT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102346	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM09069	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000020721
	ENSRNOP00000020721.4
	ENSRNOP00000089972.1

RefSeq Acc Id:	NP_001102346 ⟸ NM_001108876
- UniProtKB:	D3ZWB1 (UniProtKB/TrEMBL), A6IW03 (UniProtKB/TrEMBL), A0A8I6GHU0 (UniProtKB/TrEMBL)
- Sequence:	show sequence MNYMPGTASLIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGRKYGDIPRGIF VVRGENVVLLGEIDLEKESDTPLQQVSIEEILEEQRVEQQSRLEAEKLKVQALKDRGLSIPRAD TLDEY hide sequence

Ensembl Acc Id:

ENSRNOP00000020721 ⟸ ENSRNOT00000020721

Ensembl Acc Id:

ENSRNOP00000089972 ⟸ ENSRNOT00000118602

Protein Domains

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZWB1-F1-model_v2	AlphaFold	D3ZWB1	1-133	view protein structure

Transcriptome

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

Promoters

RGD ID:

13700166

Promoter ID:

EPDNEW_R10690

Type:

initiation region

Name:

Lsm1_1

Description:

LSM1 homolog, 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	16	71,057,642 - 71,057,702	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1304967	AgrOrtholog
BioCyc Gene	G2FUF-10976	BioCyc
Ensembl Genes	ENSRNOG00000015375	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000020721	ENTREZGENE
	ENSRNOT00000020721.6	UniProtKB/TrEMBL
	ENSRNOT00000118602.1	UniProtKB/TrEMBL
Gene3D-CATH	2.30.30.100	UniProtKB/TrEMBL
InterPro	IPR047575	UniProtKB/TrEMBL
	Lsm1	UniProtKB/TrEMBL
	LSM_domain	UniProtKB/TrEMBL
	LSM_related_domain	UniProtKB/TrEMBL
	PTHR15588	UniProtKB/TrEMBL
KEGG Report	rno:364624	UniProtKB/TrEMBL
NCBI Gene	364624	ENTREZGENE
PANTHER	PTHR15588	UniProtKB/TrEMBL
	U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM1	UniProtKB/TrEMBL
Pfam	LSM	UniProtKB/TrEMBL
PhenoGen	Lsm1	PhenoGen
PROSITE	PS52002	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000015375	RatGTEx
SMART	SM00651	UniProtKB/TrEMBL
Superfamily-SCOP	Sm_like_riboprot	UniProtKB/TrEMBL
UniProt	A0A8I6GHU0	ENTREZGENE, UniProtKB/TrEMBL
	A6IW03	ENTREZGENE, UniProtKB/TrEMBL
	D3ZWB1	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-07-09	Lsm1	LSM1 homolog, mRNA degradation associated	Lsm1	LSM1 mRNA degradation associated	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-07-01	Lsm1	LSM1 mRNA degradation associated	Lsm1	LSM1, U6 small nuclear RNA associated	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2014-03-07	Lsm1	LSM1, U6 small nuclear RNA associated	Lsm1	LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Lsm1	LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)	Lsm1_predicted	LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Lsm1_predicted	LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)