LSM1 (LSM1 homolog, mRNA degradation associated)

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Gene: LSM1 (LSM1 homolog, mRNA degradation associated) Chlorocebus sabaeus

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Symbol:

LSM1

Name:

LSM1 homolog, mRNA degradation associated

RGD ID:

18698239

Description:

ENCODES a protein that exhibits mRNA binding (ortholog); pre-mRNA binding (ortholog); INVOLVED IN negative regulation of neuron differentiation (ortholog); neuron differentiation (ortholog); stem cell population maintenance (ortholog); ASSOCIATED WITH cryptorchidism (ortholog); developmental and epileptic encephalopathy 11 (ortholog); Developmental Disabilities (ortholog); FOUND IN axon (ortholog); dendrite (ortholog); neuronal cell body (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

U6 snRNA-associated Sm-like protein LSm1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

ChlSab1.1 - Green Monkey 1.1 Assembly

Position:

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

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 Ontology Annotations Click to see Annotation Detail View

Biological Process

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

histone mRNA catabolic process (IEA)

mRNA processing (IEA)

negative regulation of neuron differentiation (IEA,ISO)

neuron differentiation (IEA,ISO)

nuclear-transcribed mRNA catabolic process (IEA)

stem cell population maintenance (IEA,ISO)

Cellular Component

axon (ISO)

cytoplasm (IEA)

dendrite (ISO)

Lsm1-7-Pat1 complex (IEA)

neuronal cell body (ISO)

nucleus (IEA)

P-body (IEA)

ribonucleoprotein complex (IEA,ISO)

Molecular Function

mRNA binding (IEA,ISO)

pre-mRNA binding (ISO)

protein binding (ISO)

RNA binding (IEA)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

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
(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
(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
(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
(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

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.

ectoderm	endocrine system	hemolymphoid system	mesenchyme	mesoderm	nervous system	reproductive system
76	36	20	36	36	60	20

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_007962194	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JACDXN010000020	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSCSAT00000013576 ⟹ ENSCSAP00000011571

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1 Ensembl	8	36,182,380 - 36,198,704 (-)	Ensembl

RefSeq Acc Id:

XM_007962194 ⟹ XP_007960385

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	8	36,184,928 - 36,198,689 (-)	NCBI
Vero_WHO_p1.0	NW_023666052	5,791,244 - 5,805,004 (+)	NCBI

Sequence:

show sequence

TCTGCTGCCGAGCCCCGAGAGCTGAAGGACGGAGGTCCGTGACTCTGGGGTCTCGGGAACCCGG
GGACGGGGGAAGACACCGTGTTCCTTAAGAGGGAGTATACGTTTCTTCGCCATCTATCCAATGG
AGATGCCTCTTCCCTACTTAACAGGAACAGGGAAAGGGTGTCCCCCAACCGTACGGCTGCCCCT
CCTCTTCCTGGGGGCCCGCACGTGTTACAGGAAGTGGGTGGGGGTAATATGGAGGAGCTTCCGG
CAGGCCCCGGCGGCTGAAAGCCGGGGCAGAAGTGCTGGTCTCGGTCGGGATTCCGGGCTTGGTC
CCGCCGAGGCGGCGACTGCGGTAGGAGGGAGGAGGTTTTGGACGCGCTGGCCCCCCGCCGCTGT
GCATTACAGCGTTATTTCAGTTCAAAATGAACTATATGCCCGGCACCGCCAGCCTCATCGAGGA
CATTGACAAAAAGCACTTGGTTCTGCTTCGAGATGGAAGGACCCTTATAGGCTTTTTAAGAAGC
ATTGATCAATTTGCAAACTTAGTACTACATCAGACTGTGGAGCGTATTCATGTGGGCAAAAAAT
ACGGTGATATTCCTCGAGGGATTTTTGTGGTCAGAGGAGAAAATGTGGTCCTACTAGGAGAAAT
AGACTTGGAAAAGGAGAGTGACACACCCCTCCAGCAAGTATCCATTGAAGAAATTCTAGAAGAG
CAAAGGGTAGAGCAGCAGACCAAGCTGGAAGCAGAGAAGTTGAAAGTGCAGGCCCTGAAGGACC
GAGGTCTTTCCATTCCTCGAGCAGATACTCTTGATGAGTACTAAGTCTTTTGCCCAGAGCCTGT
TGCTCTTGAAGAGTAGGGACTGTCACTGATGAAAGTGACATCCTGGCCACCTCACACATTTGAT
CAGAGACTGTAGAGTTTTGAAAAGTCACTTTTATTTTTAAGTCTTTTACACATGCAACATGAAG
AAATCGTGTAGGTGGGTTTTGTTTTTTTTTAAATAACAAAATCGTTTAAAGAAACAGTGGCATA
GACTCCTTCACACGTCACTGTGGCGCCAGCAACTACTTCTTAATATTCTTCGTATCCCAAATTA
GAGTTTACAGGGATAGTCTTCATTTACTTGTAAATAAAATATGAATGTCAAAAGTGTCA

hide sequence

Protein Sequences


Protein RefSeqs	XP_007960385	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000011571
	ENSCSAP00000011571.1

RefSeq Acc Id:	XP_007960385 ⟸ XM_007962194
- UniProtKB:	A0A0D9RSI2 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSCSAP00000011571 ⟸ ENSCSAT00000013576

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000015485	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000013576.1	UniProtKB/TrEMBL
Gene3D-CATH	2.30.30.100	UniProtKB/TrEMBL
InterPro	IPR047575	UniProtKB/TrEMBL
	Lsm1	UniProtKB/TrEMBL
	LSM_dom_euk/arc	UniProtKB/TrEMBL
	LSM_dom_sf	UniProtKB/TrEMBL
	PTHR15588	UniProtKB/TrEMBL
KEGG Report	csab:103215642	UniProtKB/TrEMBL
NCBI Gene	LSM1	ENTREZGENE
PANTHER	PTHR15588	UniProtKB/TrEMBL
	U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM1	UniProtKB/TrEMBL
Pfam	LSM	UniProtKB/TrEMBL
PROSITE	PS52002	UniProtKB/TrEMBL
SMART	SM00651	UniProtKB/TrEMBL
Superfamily-SCOP	SSF50182	UniProtKB/TrEMBL
UniProt	A0A0D9RSI2	ENTREZGENE, UniProtKB/TrEMBL

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)

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