Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	25804
Gene name	LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated
Gene symbol	LSM4
Synonyms (NCBI Gene)	GRPYER112W
Chromosome	19
Chromosome location	19p13.11
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. Alt

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miRTarBase ID	miRNA	Experiments	Reference
MIRT042595	hsa-miR-423-3p	CLASH	23622248
MIRT039176	hsa-miR-769-5p	CLASH	23622248
MIRT572313	hsa-miR-125a-5p	PAR-CLIP	20371350
MIRT572312	hsa-miR-125b-5p	PAR-CLIP	20371350
MIRT572311	hsa-miR-4319	PAR-CLIP	20371350
MIRT572310	hsa-miR-4324	PAR-CLIP	20371350
MIRT572309	hsa-miR-4251	PAR-CLIP	20371350
MIRT572308	hsa-miR-18a-3p	PAR-CLIP	20371350
MIRT572307	hsa-miR-589-5p	PAR-CLIP	20371350
MIRT572306	hsa-miR-146a-5p	PAR-CLIP	20371350
MIRT572305	hsa-miR-146b-5p	PAR-CLIP	20371350
MIRT572303	hsa-miR-7153-5p	PAR-CLIP	20371350
MIRT572304	hsa-miR-7976	PAR-CLIP	20371350
MIRT572302	hsa-miR-3173-5p	PAR-CLIP	20371350
MIRT572301	hsa-miR-6799-3p	PAR-CLIP	20371350
MIRT572300	hsa-miR-146b-3p	PAR-CLIP	20371350
MIRT572299	hsa-miR-6882-3p	PAR-CLIP	20371350
MIRT572298	hsa-miR-874-3p	PAR-CLIP	20371350
MIRT572313	hsa-miR-125a-5p	PAR-CLIP	27292025
MIRT572312	hsa-miR-125b-5p	PAR-CLIP	27292025
MIRT572306	hsa-miR-146a-5p	PAR-CLIP	27292025
MIRT572300	hsa-miR-146b-3p	PAR-CLIP	27292025
MIRT572305	hsa-miR-146b-5p	PAR-CLIP	27292025
MIRT572308	hsa-miR-18a-3p	PAR-CLIP	27292025
MIRT572302	hsa-miR-3173-5p	PAR-CLIP	27292025
MIRT572309	hsa-miR-4251	PAR-CLIP	27292025
MIRT572311	hsa-miR-4319	PAR-CLIP	27292025
MIRT572310	hsa-miR-4324	PAR-CLIP	27292025
MIRT572307	hsa-miR-589-5p	PAR-CLIP	27292025
MIRT572301	hsa-miR-6799-3p	PAR-CLIP	27292025
MIRT572299	hsa-miR-6882-3p	PAR-CLIP	27292025
MIRT572303	hsa-miR-7153-5p	PAR-CLIP	27292025
MIRT572304	hsa-miR-7976	PAR-CLIP	27292025
MIRT572298	hsa-miR-874-3p	PAR-CLIP	27292025
MIRT572313	hsa-miR-125a-5p	PAR-CLIP	20371350
MIRT572312	hsa-miR-125b-5p	PAR-CLIP	20371350
MIRT572311	hsa-miR-4319	PAR-CLIP	20371350
MIRT572310	hsa-miR-4324	PAR-CLIP	20371350
MIRT572309	hsa-miR-4251	PAR-CLIP	20371350
MIRT572308	hsa-miR-18a-3p	PAR-CLIP	20371350
MIRT572307	hsa-miR-589-5p	PAR-CLIP	20371350
MIRT572306	hsa-miR-146a-5p	PAR-CLIP	20371350
MIRT572305	hsa-miR-146b-5p	PAR-CLIP	20371350
MIRT572303	hsa-miR-7153-5p	PAR-CLIP	20371350
MIRT572304	hsa-miR-7976	PAR-CLIP	20371350
MIRT572302	hsa-miR-3173-5p	PAR-CLIP	20371350
MIRT572301	hsa-miR-6799-3p	PAR-CLIP	20371350
MIRT572300	hsa-miR-146b-3p	PAR-CLIP	20371350
MIRT572299	hsa-miR-6882-3p	PAR-CLIP	20371350
MIRT572298	hsa-miR-874-3p	PAR-CLIP	20371350
MIRT1121830	hsa-miR-1207-5p	CLIP-seq
MIRT1121831	hsa-miR-1247	CLIP-seq
MIRT1121832	hsa-miR-1254	CLIP-seq
MIRT1121833	hsa-miR-125b	CLIP-seq
MIRT1121834	hsa-miR-1293	CLIP-seq
MIRT1121835	hsa-miR-146a	CLIP-seq
MIRT1121836	hsa-miR-2467-5p	CLIP-seq
MIRT1121837	hsa-miR-2964a-3p	CLIP-seq
MIRT1121838	hsa-miR-3116	CLIP-seq
MIRT1121839	hsa-miR-3125	CLIP-seq
MIRT1121840	hsa-miR-3148	CLIP-seq
MIRT1121841	hsa-miR-3177-3p	CLIP-seq
MIRT1121842	hsa-miR-324-5p	CLIP-seq
MIRT1121843	hsa-miR-331-3p	CLIP-seq
MIRT1121844	hsa-miR-3620	CLIP-seq
MIRT1121845	hsa-miR-3916	CLIP-seq
MIRT1121846	hsa-miR-3918	CLIP-seq
MIRT1121847	hsa-miR-4263	CLIP-seq
MIRT1121848	hsa-miR-4318	CLIP-seq
MIRT1121849	hsa-miR-4459	CLIP-seq
MIRT1121850	hsa-miR-4483	CLIP-seq
MIRT1121851	hsa-miR-4488	CLIP-seq
MIRT1121852	hsa-miR-451b	CLIP-seq
MIRT1121853	hsa-miR-4640-5p	CLIP-seq
MIRT1121854	hsa-miR-4685-5p	CLIP-seq
MIRT1121855	hsa-miR-4697-5p	CLIP-seq
MIRT1121856	hsa-miR-4722-5p	CLIP-seq
MIRT1121857	hsa-miR-4726-5p	CLIP-seq
MIRT1121858	hsa-miR-4731-3p	CLIP-seq
MIRT1121859	hsa-miR-4736	CLIP-seq
MIRT1121860	hsa-miR-4763-3p	CLIP-seq
MIRT1121861	hsa-miR-4766-3p	CLIP-seq
MIRT1121862	hsa-miR-4779	CLIP-seq
MIRT1121863	hsa-miR-4801	CLIP-seq
MIRT1121864	hsa-miR-488	CLIP-seq
MIRT1121865	hsa-miR-495	CLIP-seq
MIRT1121866	hsa-miR-548c-3p	CLIP-seq
MIRT1121867	hsa-miR-576-5p	CLIP-seq
MIRT1121868	hsa-miR-587	CLIP-seq
MIRT1121869	hsa-miR-589	CLIP-seq
MIRT1121870	hsa-miR-874	CLIP-seq
MIRT1121871	hsa-miR-875-3p	CLIP-seq
MIRT1121833	hsa-miR-125b	CLIP-seq
MIRT1121835	hsa-miR-146a	CLIP-seq
MIRT1121869	hsa-miR-589	CLIP-seq
MIRT1121870	hsa-miR-874	CLIP-seq
MIRT2034465	hsa-miR-1236	CLIP-seq
MIRT1121833	hsa-miR-125b	CLIP-seq
MIRT1121835	hsa-miR-146a	CLIP-seq
MIRT1121843	hsa-miR-331-3p	CLIP-seq
MIRT2034466	hsa-miR-3679-3p	CLIP-seq
MIRT2034467	hsa-miR-4303	CLIP-seq
MIRT2034468	hsa-miR-4468	CLIP-seq
MIRT2034469	hsa-miR-4762-3p	CLIP-seq
MIRT2034470	hsa-miR-4763-5p	CLIP-seq
MIRT2034471	hsa-miR-4800-3p	CLIP-seq
MIRT1121864	hsa-miR-488	CLIP-seq
MIRT2034472	hsa-miR-566	CLIP-seq
MIRT1121869	hsa-miR-589	CLIP-seq
MIRT1121870	hsa-miR-874	CLIP-seq
MIRT1121831	hsa-miR-1247	CLIP-seq
MIRT1121832	hsa-miR-1254	CLIP-seq
MIRT1121833	hsa-miR-125b	CLIP-seq
MIRT1121835	hsa-miR-146a	CLIP-seq
MIRT1121836	hsa-miR-2467-5p	CLIP-seq
MIRT1121837	hsa-miR-2964a-3p	CLIP-seq
MIRT1121838	hsa-miR-3116	CLIP-seq
MIRT2264940	hsa-miR-3143	CLIP-seq
MIRT1121840	hsa-miR-3148	CLIP-seq
MIRT2264941	hsa-miR-3591-3p	CLIP-seq
MIRT1121847	hsa-miR-4263	CLIP-seq
MIRT1121864	hsa-miR-488	CLIP-seq
MIRT1121865	hsa-miR-495	CLIP-seq
MIRT2264942	hsa-miR-543	CLIP-seq
MIRT1121867	hsa-miR-576-5p	CLIP-seq
MIRT1121869	hsa-miR-589	CLIP-seq
MIRT2264943	hsa-miR-802	CLIP-seq
MIRT1121870	hsa-miR-874	CLIP-seq
MIRT1121871	hsa-miR-875-3p	CLIP-seq
MIRT2563931	hsa-miR-1302	CLIP-seq
MIRT2563932	hsa-miR-3122	CLIP-seq
MIRT2563933	hsa-miR-3913-5p	CLIP-seq
MIRT2563934	hsa-miR-4298	CLIP-seq
MIRT2563935	hsa-miR-4328	CLIP-seq
MIRT2563936	hsa-miR-4676-5p	CLIP-seq
MIRT2563937	hsa-miR-575	CLIP-seq
MIRT2563935	hsa-miR-4328	CLIP-seq
MIRT2563936	hsa-miR-4676-5p	CLIP-seq
MIRT2563937	hsa-miR-575	CLIP-seq

Show/Hide all (35)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000387	Process	Spliceosomal snRNP assembly	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:0000956	Process	Nuclear-transcribed mRNA catabolic process	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	15231747, 15905169, 16189514, 19628699, 20584987, 20696395, 21988832, 22365833, 25416956, 32296183, 33961781
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:0005688	Component	U6 snRNP	TAS	10369684
GO:0005829	Component	Cytosol	IDA	15905169
GO:0005829	Component	Cytosol	TAS
GO:0006396	Process	RNA processing	IEA
GO:0006397	Process	MRNA processing	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0008380	Process	RNA splicing	TAS	10523320
GO:0016020	Component	Membrane	IDA	15905169
GO:0017070	Function	U6 snRNA binding	IBA
GO:0032991	Component	Protein-containing complex	IDA	15905169
GO:0033962	Process	P-body assembly	IBA
GO:0042731	Function	PH domain binding	IDA	15905169
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:0071005	Component	U2-type precatalytic spliceosome	IDA	28781166
GO:0097526	Component	Spliceosomal tri-snRNP complex	IBA
GO:0120115	Component	Lsm2-8 complex	IDA	10523320
GO:0120115	Component	Lsm2-8 complex	IEA
GO:1990904	Component	Ribonucleoprotein complex	IEA

MIM	HGNC	e!Ensembl
607284	17259	ENSG00000130520

Q9Y4Z0

Protein name

U6 snRNA-associated Sm-like protein LSm4 (Glycine-rich protein) (GRP)

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 → 71	LSM domain	Domain

Sequence

MLPLSLLKTAQNHPMLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECY
IRGSTIKYLRIPDEIIDMVKEEVVAKGRGRGGLQQQKQQKGRGMGGAGRGVFGGRGRGGI
PGTGRGQPEKKPGRQAGKQ

Sequence length

139

Interactions

View interactions

	KEGG		Reactome
	RNA degradation Spliceosome		mRNA decay by 5' to 3' exoribonuclease mRNA Splicing - Major Pathway

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)

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
AUTOIMMUNE DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOTHYROIDISM	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POST-TRAUMATIC STRESS DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (4)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Astrocytoma	Astrocytoma	BEFREE	17663465		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	34341433	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Melanoma Cutaneous Malignant	Melanoma	Pubtator	36371223	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Atrophy Spinal	Spinal muscular atrophy	Pubtator	11720283	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated)