LSM6 (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated)

Gene

• Entrez ID: 11157
• Gene name: LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated
• Gene symbol: LSM6
• Synonyms (NCBI Gene): YDR378C
• Chromosome: 4
• Chromosome location: 4q31.22
• Summary: Sm-like proteins were identified in a variety of organisms based on sequence homology with the Sm protein family (see SNRPD2; MIM 601061). Sm-like proteins contain the Sm sequence motif, which consists of 2 regions separated by a linker of variable length

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT032421	hsa-let-7b-5p	Proteomics	18668040
MIRT1121945	hsa-miR-105	CLIP-seq
MIRT1121946	hsa-miR-1179	CLIP-seq
MIRT1121947	hsa-miR-202	CLIP-seq
MIRT1121948	hsa-miR-203	CLIP-seq
MIRT1121949	hsa-miR-3133	CLIP-seq
MIRT1121950	hsa-miR-3646	CLIP-seq
MIRT1121951	hsa-miR-3686	CLIP-seq
MIRT1121952	hsa-miR-4476	CLIP-seq
MIRT1121953	hsa-miR-4738-3p	CLIP-seq
MIRT1121954	hsa-miR-4778-5p	CLIP-seq
MIRT1121955	hsa-miR-513b	CLIP-seq
MIRT1121956	hsa-miR-549	CLIP-seq
MIRT1121957	hsa-miR-568	CLIP-seq
MIRT1121958	hsa-miR-605	CLIP-seq
MIRT1121959	hsa-miR-643	CLIP-seq
MIRT2034487	hsa-miR-511	CLIP-seq
MIRT2034488	hsa-miR-944	CLIP-seq
MIRT1121947	hsa-miR-202	CLIP-seq
MIRT1121952	hsa-miR-4476	CLIP-seq
MIRT2034487	hsa-miR-511	CLIP-seq
MIRT1121959	hsa-miR-643	CLIP-seq
MIRT2563953	hsa-miR-223	CLIP-seq
MIRT1121949	hsa-miR-3133	CLIP-seq
MIRT2563954	hsa-miR-3163	CLIP-seq
MIRT2563955	hsa-miR-340	CLIP-seq
MIRT2563956	hsa-miR-3680	CLIP-seq
MIRT2563957	hsa-miR-4276	CLIP-seq
MIRT2563958	hsa-miR-4697-3p	CLIP-seq
MIRT2563959	hsa-miR-4717-3p	CLIP-seq
MIRT2563960	hsa-miR-4719	CLIP-seq
MIRT2563961	hsa-miR-4729	CLIP-seq
MIRT1121953	hsa-miR-4738-3p	CLIP-seq
MIRT2563962	hsa-miR-4798-3p	CLIP-seq
MIRT1121955	hsa-miR-513b	CLIP-seq
MIRT2563963	hsa-miR-548c-3p	CLIP-seq
MIRT2563964	hsa-miR-550b	CLIP-seq
MIRT1121957	hsa-miR-568	CLIP-seq
MIRT2563965	hsa-miR-583	CLIP-seq
MIRT1121958	hsa-miR-605	CLIP-seq
MIRT2563953	hsa-miR-223	CLIP-seq
MIRT1121949	hsa-miR-3133	CLIP-seq
MIRT2563956	hsa-miR-3680	CLIP-seq
MIRT2563957	hsa-miR-4276	CLIP-seq
MIRT2563958	hsa-miR-4697-3p	CLIP-seq
MIRT2563959	hsa-miR-4717-3p	CLIP-seq
MIRT2563961	hsa-miR-4729	CLIP-seq
MIRT1121953	hsa-miR-4738-3p	CLIP-seq
MIRT2563962	hsa-miR-4798-3p	CLIP-seq
MIRT1121955	hsa-miR-513b	CLIP-seq
MIRT2563963	hsa-miR-548c-3p	CLIP-seq
MIRT2563964	hsa-miR-550b	CLIP-seq
MIRT1121957	hsa-miR-568	CLIP-seq
MIRT1121958	hsa-miR-605	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000398	Process	MRNA splicing, via spliceosome	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	28781166
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	30975767
GO:0000932	Component	P-body	IBA
GO:0003723	Function	RNA binding	HDA	22681889
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	15231747, 19628699, 22365833, 25416956, 28514442, 32296183, 33961781, 35271311
GO:0005634	Component	Nucleus	IDA	26912367
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	30975767
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:0005730	Component	Nucleolus	IBA
GO:0005732	Component	Sno(s)RNA-containing ribonucleoprotein complex	IBA
GO:0005737	Component	Cytoplasm	IDA	12515382
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006364	Process	RRNA processing	IEA
GO:0006397	Process	MRNA processing	IEA
GO:0006402	Process	MRNA catabolic process	IDA	12515382
GO:0008033	Process	TRNA processing	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0008380	Process	RNA splicing	TAS	10523320
GO:0030490	Process	Maturation of SSU-rRNA	IBA
GO:0030532	Component	Small nuclear ribonucleoprotein complex	TAS	10523320
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IBA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IDA	26912367
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IPI	30975767
GO:0046982	Function	Protein heterodimerization activity	IDA	12515382
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	28781166
GO:0120115	Component	Lsm2-8 complex	IDA	10523320
GO:0120115	Component	Lsm2-8 complex	IEA
GO:1990904	Component	Ribonucleoprotein complex	IEA

Other IDs

• MIM: 607286
• HGNC: 17017
• e!Ensembl: ENSG00000164167

Protein

• UniProt ID: P62312
• Protein name: U6 snRNA-associated Sm-like protein LSm6
• 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	10 → 75	LSM domain	Domain

• Sequence:

  MSLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKY
  GDAFIRGNNVLYISTQKRRM

• Sequence length: 80

Pathways

KEGG:

RNA degradation
Spliceosome

Reactome:

mRNA decay by 5' to 3' exoribonuclease
mRNA Splicing - Major 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
ATRIAL FIBRILLATION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Relationship Type	References	Evidence Score
Carcinoma Non Small Cell Lung	Associate	26755624	★☆☆☆☆ Found in Text Mining only