LSM2 (LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated)

Gene

• Entrez ID: 57819
• Gene name: LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated
• Gene symbol: LSM2
• Synonyms (NCBI Gene): C6orf28, G7B, YBL026W, snRNP
• Chromosome: 6
• Chromosome location: 6p21.33
• Summary: This gene encodes a member of the LSm family of RNA-binding proteins. LSm proteins form stable heteromers that bind specifically to the 3`-terminal oligo(U) tract of U6 snRNA and may play a role in pre-mRNA splicing by mediating U4/U6 snRNP formation. Pse

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT036749	hsa-miR-760	CLASH	23622248
MIRT1121782	hsa-miR-3127-3p	CLIP-seq
MIRT1121783	hsa-miR-3144-5p	CLIP-seq
MIRT1121784	hsa-miR-3191	CLIP-seq
MIRT1121785	hsa-miR-3199	CLIP-seq
MIRT1121786	hsa-miR-3646	CLIP-seq
MIRT1121787	hsa-miR-3665	CLIP-seq
MIRT1121788	hsa-miR-3667-3p	CLIP-seq
MIRT1121789	hsa-miR-3714	CLIP-seq
MIRT1121790	hsa-miR-3938	CLIP-seq
MIRT1121791	hsa-miR-4515	CLIP-seq
MIRT1121792	hsa-miR-4652-5p	CLIP-seq
MIRT1121793	hsa-miR-4667-5p	CLIP-seq
MIRT1121794	hsa-miR-4700-5p	CLIP-seq
MIRT1121795	hsa-miR-4731-5p	CLIP-seq
MIRT1121796	hsa-miR-4736	CLIP-seq
MIRT1121797	hsa-miR-4747-5p	CLIP-seq
MIRT1121798	hsa-miR-513a-3p	CLIP-seq
MIRT1121799	hsa-miR-590-3p	CLIP-seq
MIRT1121800	hsa-miR-764	CLIP-seq
MIRT1121801	hsa-miR-940	CLIP-seq
MIRT2034448	hsa-miR-146b-3p	CLIP-seq
MIRT2034449	hsa-miR-3115	CLIP-seq
MIRT2034450	hsa-miR-3173-5p	CLIP-seq
MIRT2034451	hsa-miR-3174	CLIP-seq
MIRT1121786	hsa-miR-3646	CLIP-seq
MIRT1121788	hsa-miR-3667-3p	CLIP-seq
MIRT1121789	hsa-miR-3714	CLIP-seq
MIRT1121790	hsa-miR-3938	CLIP-seq
MIRT2034452	hsa-miR-3978	CLIP-seq
MIRT2034453	hsa-miR-4308	CLIP-seq
MIRT2034454	hsa-miR-4717-3p	CLIP-seq
MIRT2034455	hsa-miR-539	CLIP-seq
MIRT2034456	hsa-miR-548an	CLIP-seq
MIRT2034457	hsa-miR-874	CLIP-seq
MIRT2034458	hsa-miR-875-3p	CLIP-seq
MIRT2034459	hsa-miR-921	CLIP-seq
MIRT1121801	hsa-miR-940	CLIP-seq
MIRT1121782	hsa-miR-3127-3p	CLIP-seq
MIRT2390383	hsa-miR-335	CLIP-seq
MIRT2390384	hsa-miR-513c	CLIP-seq
MIRT2390385	hsa-miR-514b-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000244	Process	Spliceosomal tri-snRNP complex assembly	IDA	10523320
GO:0000398	Process	MRNA splicing, via spliceosome	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IC	11991638
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	28781166
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	30975767
GO:0000932	Component	P-body	IBA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	14667819, 15231747, 16169070, 16189514, 19628699, 21516116, 22365833, 25416956, 27107012, 28514442, 29997244, 31467278, 32296183, 32814053, 33961781, 35271311, 37398436
GO:0005634	Component	Nucleus	IDA	10523320, 26912367
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	30975767
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005681	Component	Spliceosomal complex	IPI	30975767
GO:0005688	Component	U6 snRNP	IBA
GO:0005737	Component	Cytoplasm	IDA	12515382
GO:0005829	Component	Cytosol	TAS
GO:0006397	Process	MRNA processing	IEA
GO:0006402	Process	MRNA catabolic process	IDA	12515382
GO:0008380	Process	RNA splicing	IEA
GO:0017070	Function	U6 snRNA binding	NAS	10523320
GO:0031267	Function	Small GTPase binding	IPI	24056301
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IBA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IDA	10523320, 26912367
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IPI	30975767
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	28781166
GO:0071011	Component	Precatalytic spliceosome	IBA
GO:0071013	Component	Catalytic step 2 spliceosome	IBA
GO:0071013	Component	Catalytic step 2 spliceosome	IDA	11991638
GO:0120115	Component	Lsm2-8 complex	IDA	10523320
GO:1990726	Component	Lsm1-7-Pat1 complex	IBA
GO:1990904	Component	Ribonucleoprotein complex	IEA

Other IDs

• MIM: 607282
• HGNC: 13940
• e!Ensembl: ENSG00000204392

Protein

• UniProt ID: Q9Y333
• Protein name: U6 snRNA-associated Sm-like protein LSm2 (Protein G7b) (Small nuclear ribonuclear protein D homolog) (snRNP core Sm-like protein Sm-x5)
• Protein function: Plays a role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex
• PDB: 3JCR, 5O9Z, 6AH0, 6AHD, 6QW6, 6QX9, 7ABG, 8H6E, 8H6J, 8H6K, 8H6L, 8QO9, 8QXD, 8QZS, 8R08, 8R09, 8R0A, 8R0B, 8RM5
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01423	LSM	5 → 72	LSM domain	Domain

• Sequence:

  MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC
  FIRGSVVRYVQLPADEVDTQLLQDAARKEALQQKQ

• Sequence length: 95

Pathways

KEGG:

RNA degradation
Spliceosome

Reactome:

mRNA decay by 5' to 3' exoribonuclease
mRNA Splicing - Major Pathway
mRNA Splicing - Minor Pathway

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	24773620	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	BEFREE	25625564, 25735748		★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	BEFREE	30912329		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	12440236, 20500824, 21233219		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	6203115	Associate	★☆☆☆☆ Found in Text Mining only
Autoimmune Lymphoproliferative Syndrome	Autoimmune Lymphoproliferative Disorder	BEFREE	21233219		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	29938207		★☆☆☆☆ Found in Text Mining only
Connective Tissue Diseases	Connective Tissue Disease	BEFREE	12218166		★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down Syndrome	BEFREE	11197177		★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down syndrome	Pubtator	24773620	Associate	★☆☆☆☆ Found in Text Mining only
Dysautonomia, Familial	Dysautonomia	BEFREE	28592461		★☆☆☆☆ Found in Text Mining only
Frontotemporal Lobar Degeneration	Frontotemporal dementia	BEFREE	24023061		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	28304396	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	11439168, 6203115	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	11069087, 21632208, 29156741, 2932224, 6203115, 6226047, 7481563		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	29938207		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	24788092		★☆☆☆☆ Found in Text Mining only
Melanoma Cutaneous Malignant	Melanoma	Pubtator	36371223	Stimulate	★☆☆☆☆ Found in Text Mining only
Melanoma Cutaneous Malignant	Melanoma	Pubtator	37312186	Associate	★☆☆☆☆ Found in Text Mining only
MICROCEPHALIC OSTEODYSPLASTIC PRIMORDIAL DWARFISM, TYPE I	Microcephalic osteodysplastic primordial dwarfism	BEFREE	24865609		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	31671093		★☆☆☆☆ Found in Text Mining only
Miller Dieker syndrome	Miller Dieker Syndrome	BEFREE	25311244		★☆☆☆☆ Found in Text Mining only
Mixed Connective Tissue Disease	Mixed connective tissue disease	Pubtator	11439168, 6203115	Associate	★☆☆☆☆ Found in Text Mining only
Motor Neuron Disease	Motor Neuron Disease	BEFREE	25735748		★☆☆☆☆ Found in Text Mining only
MYELODYSPLASTIC SYNDROME	Myelodysplastic Syndrome	BEFREE	25311244		★☆☆☆☆ Found in Text Mining only
Myoclonic Epilepsies, Progressive	Myoclonic epilepsy	BEFREE	8660980		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	24023061		★☆☆☆☆ Found in Text Mining only
Neurofibromatosis 1	Neurofibromatosis	BEFREE	19292874		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	26755624		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	34793589	Associate	★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	24023061		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	11867543	Associate	★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	17934474, 18334927, 21549338, 24419317, 25383878, 28515276, 31445970		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa 18	Retinitis Pigmentosa	BEFREE	17932117		★☆☆☆☆ Found in Text Mining only
Spinal Muscular Atrophy	Spinal Muscular Atrophy	BEFREE	10500148, 15964810, 16204184, 17473171, 17895963, 18629520, 19329542, 21098506, 21816274, 21957043, 22302308, 22813737, 24645792, 25483032, 27557711, 28642865, 28879433, 28981879, 30012555, 30398641, 31799625, 9323129		★☆☆☆☆ Found in Text Mining only
Teratoma	Teratoma	BEFREE	2974536		★☆☆☆☆ Found in Text Mining only
Unverricht-Lundborg Syndrome	Myoclonic Epilepsy	BEFREE	8660980		★☆☆☆☆ Found in Text Mining only