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	27258
Gene name	LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated
Gene symbol	LSM3
Synonyms (NCBI Gene)	SMX4USS2YLR438C
Chromosome	3
Chromosome location	3p25.1
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

204

Show/Hide all (204)

miRTarBase ID	miRNA	Experiments	Reference
MIRT021014	hsa-miR-155-5p	Proteomics	18668040
MIRT030252	hsa-miR-26b-5p	Microarray	19088304
MIRT048272	hsa-miR-196a-5p	CLASH	23622248
MIRT045864	hsa-miR-128-3p	CLASH	23622248
MIRT695106	hsa-miR-8063	HITS-CLIP	23313552
MIRT695105	hsa-miR-4698	HITS-CLIP	23313552
MIRT695104	hsa-miR-3665	HITS-CLIP	23313552
MIRT695103	hsa-miR-657	HITS-CLIP	23313552
MIRT695102	hsa-miR-889-3p	HITS-CLIP	23313552
MIRT695101	hsa-miR-675-3p	HITS-CLIP	23313552
MIRT695099	hsa-miR-4768-5p	HITS-CLIP	23313552
MIRT695100	hsa-miR-6833-3p	HITS-CLIP	23313552
MIRT695098	hsa-miR-6809-3p	HITS-CLIP	23313552
MIRT664235	hsa-miR-106a-5p	HITS-CLIP	23824327
MIRT664234	hsa-miR-106b-5p	HITS-CLIP	23824327
MIRT664233	hsa-miR-17-5p	HITS-CLIP	23824327
MIRT664232	hsa-miR-20a-5p	HITS-CLIP	23824327
MIRT664231	hsa-miR-20b-5p	HITS-CLIP	23824327
MIRT664230	hsa-miR-519d-3p	HITS-CLIP	23824327
MIRT664229	hsa-miR-526b-3p	HITS-CLIP	23824327
MIRT664228	hsa-miR-93-5p	HITS-CLIP	23824327
MIRT664227	hsa-miR-302a-3p	HITS-CLIP	23824327
MIRT664226	hsa-miR-302b-3p	HITS-CLIP	23824327
MIRT664225	hsa-miR-302c-3p	HITS-CLIP	23824327
MIRT664224	hsa-miR-302d-3p	HITS-CLIP	23824327
MIRT664223	hsa-miR-302e	HITS-CLIP	23824327
MIRT664222	hsa-miR-372-3p	HITS-CLIP	23824327
MIRT664221	hsa-miR-373-3p	HITS-CLIP	23824327
MIRT664220	hsa-miR-520a-3p	HITS-CLIP	23824327
MIRT664219	hsa-miR-520b	HITS-CLIP	23824327
MIRT664218	hsa-miR-520c-3p	HITS-CLIP	23824327
MIRT664217	hsa-miR-520d-3p	HITS-CLIP	23824327
MIRT664216	hsa-miR-520e	HITS-CLIP	23824327
MIRT518054	hsa-miR-4438	HITS-CLIP	23824327
MIRT664215	hsa-miR-512-3p	HITS-CLIP	23824327
MIRT518053	hsa-miR-654-3p	HITS-CLIP	23824327
MIRT518052	hsa-miR-6504-3p	HITS-CLIP	23824327
MIRT664214	hsa-miR-520g-3p	HITS-CLIP	23824327
MIRT664213	hsa-miR-520h	HITS-CLIP	23824327
MIRT518051	hsa-miR-3190-5p	HITS-CLIP	23824327
MIRT518050	hsa-miR-3176	HITS-CLIP	23824327
MIRT518049	hsa-miR-3922-3p	HITS-CLIP	23824327
MIRT664212	hsa-miR-4731-5p	HITS-CLIP	23824327
MIRT518048	hsa-miR-3136-3p	HITS-CLIP	23824327
MIRT518047	hsa-miR-7155-3p	HITS-CLIP	23824327
MIRT518046	hsa-miR-5095	HITS-CLIP	23824327
MIRT518045	hsa-miR-7151-3p	HITS-CLIP	23824327
MIRT518044	hsa-miR-6807-5p	HITS-CLIP	23824327
MIRT518043	hsa-miR-1231	HITS-CLIP	23824327
MIRT354736	hsa-miR-944	PAR-CLIP	20371350
MIRT354743	hsa-miR-4433b-3p	PAR-CLIP	20371350
MIRT354741	hsa-miR-4768-3p	PAR-CLIP	20371350
MIRT354740	hsa-miR-4459	PAR-CLIP	20371350
MIRT354739	hsa-miR-4433a-3p	PAR-CLIP	20371350
MIRT571261	hsa-miR-4707-5p	PAR-CLIP	20371350
MIRT571260	hsa-miR-5587-3p	PAR-CLIP	20371350
MIRT571259	hsa-miR-7-5p	PAR-CLIP	20371350
MIRT571258	hsa-miR-6077	PAR-CLIP	20371350
MIRT354738	hsa-miR-3190-3p	PAR-CLIP	20371350
MIRT354742	hsa-miR-6763-3p	PAR-CLIP	20371350
MIRT518054	hsa-miR-4438	PAR-CLIP	23446348
MIRT518053	hsa-miR-654-3p	PAR-CLIP	23446348
MIRT518052	hsa-miR-6504-3p	PAR-CLIP	23446348
MIRT518051	hsa-miR-3190-5p	PAR-CLIP	23446348
MIRT518050	hsa-miR-3176	PAR-CLIP	23446348
MIRT518049	hsa-miR-3922-3p	PAR-CLIP	23446348
MIRT518048	hsa-miR-3136-3p	PAR-CLIP	23446348
MIRT518047	hsa-miR-7155-3p	PAR-CLIP	23446348
MIRT518046	hsa-miR-5095	PAR-CLIP	23446348
MIRT518045	hsa-miR-7151-3p	PAR-CLIP	23446348
MIRT518044	hsa-miR-6807-5p	PAR-CLIP	23446348
MIRT518043	hsa-miR-1231	PAR-CLIP	23446348
MIRT695106	hsa-miR-8063	HITS-CLIP	23313552
MIRT695105	hsa-miR-4698	HITS-CLIP	23313552
MIRT695104	hsa-miR-3665	HITS-CLIP	23313552
MIRT695103	hsa-miR-657	HITS-CLIP	23313552
MIRT695102	hsa-miR-889-3p	HITS-CLIP	23313552
MIRT695101	hsa-miR-675-3p	HITS-CLIP	23313552
MIRT695099	hsa-miR-4768-5p	HITS-CLIP	23313552
MIRT695100	hsa-miR-6833-3p	HITS-CLIP	23313552
MIRT695098	hsa-miR-6809-3p	HITS-CLIP	23313552
MIRT664235	hsa-miR-106a-5p	HITS-CLIP	23824327
MIRT664234	hsa-miR-106b-5p	HITS-CLIP	23824327
MIRT664233	hsa-miR-17-5p	HITS-CLIP	23824327
MIRT664232	hsa-miR-20a-5p	HITS-CLIP	23824327
MIRT664231	hsa-miR-20b-5p	HITS-CLIP	23824327
MIRT664230	hsa-miR-519d-3p	HITS-CLIP	23824327
MIRT664229	hsa-miR-526b-3p	HITS-CLIP	23824327
MIRT664228	hsa-miR-93-5p	HITS-CLIP	23824327
MIRT664227	hsa-miR-302a-3p	HITS-CLIP	23824327
MIRT664226	hsa-miR-302b-3p	HITS-CLIP	23824327
MIRT664225	hsa-miR-302c-3p	HITS-CLIP	23824327
MIRT664224	hsa-miR-302d-3p	HITS-CLIP	23824327
MIRT664223	hsa-miR-302e	HITS-CLIP	23824327
MIRT664222	hsa-miR-372-3p	HITS-CLIP	23824327
MIRT664221	hsa-miR-373-3p	HITS-CLIP	23824327
MIRT664220	hsa-miR-520a-3p	HITS-CLIP	23824327
MIRT664219	hsa-miR-520b	HITS-CLIP	23824327
MIRT664218	hsa-miR-520c-3p	HITS-CLIP	23824327
MIRT664217	hsa-miR-520d-3p	HITS-CLIP	23824327
MIRT664216	hsa-miR-520e	HITS-CLIP	23824327
MIRT518054	hsa-miR-4438	HITS-CLIP	23824327
MIRT664215	hsa-miR-512-3p	HITS-CLIP	23824327
MIRT518053	hsa-miR-654-3p	HITS-CLIP	23824327
MIRT518052	hsa-miR-6504-3p	HITS-CLIP	23824327
MIRT664214	hsa-miR-520g-3p	HITS-CLIP	23824327
MIRT664213	hsa-miR-520h	HITS-CLIP	23824327
MIRT518051	hsa-miR-3190-5p	HITS-CLIP	23824327
MIRT518050	hsa-miR-3176	HITS-CLIP	23824327
MIRT518049	hsa-miR-3922-3p	HITS-CLIP	23824327
MIRT664212	hsa-miR-4731-5p	HITS-CLIP	23824327
MIRT518048	hsa-miR-3136-3p	HITS-CLIP	23824327
MIRT518047	hsa-miR-7155-3p	HITS-CLIP	23824327
MIRT518046	hsa-miR-5095	HITS-CLIP	23824327
MIRT518045	hsa-miR-7151-3p	HITS-CLIP	23824327
MIRT518044	hsa-miR-6807-5p	HITS-CLIP	23824327
MIRT518043	hsa-miR-1231	HITS-CLIP	23824327
MIRT354736	hsa-miR-944	PAR-CLIP	20371350
MIRT354743	hsa-miR-4433b-3p	PAR-CLIP	20371350
MIRT354741	hsa-miR-4768-3p	PAR-CLIP	20371350
MIRT354740	hsa-miR-4459	PAR-CLIP	20371350
MIRT354739	hsa-miR-4433a-3p	PAR-CLIP	20371350
MIRT571261	hsa-miR-4707-5p	PAR-CLIP	20371350
MIRT571260	hsa-miR-5587-3p	PAR-CLIP	20371350
MIRT571259	hsa-miR-7-5p	PAR-CLIP	20371350
MIRT571258	hsa-miR-6077	PAR-CLIP	20371350
MIRT354738	hsa-miR-3190-3p	PAR-CLIP	20371350
MIRT354742	hsa-miR-6763-3p	PAR-CLIP	20371350
MIRT518054	hsa-miR-4438	PAR-CLIP	23446348
MIRT518053	hsa-miR-654-3p	PAR-CLIP	23446348
MIRT518052	hsa-miR-6504-3p	PAR-CLIP	23446348
MIRT518051	hsa-miR-3190-5p	PAR-CLIP	23446348
MIRT518050	hsa-miR-3176	PAR-CLIP	23446348
MIRT518049	hsa-miR-3922-3p	PAR-CLIP	23446348
MIRT518048	hsa-miR-3136-3p	PAR-CLIP	23446348
MIRT518047	hsa-miR-7155-3p	PAR-CLIP	23446348
MIRT518046	hsa-miR-5095	PAR-CLIP	23446348
MIRT518045	hsa-miR-7151-3p	PAR-CLIP	23446348
MIRT518044	hsa-miR-6807-5p	PAR-CLIP	23446348
MIRT518043	hsa-miR-1231	PAR-CLIP	23446348
MIRT1121802	hsa-miR-1270	CLIP-seq
MIRT1121803	hsa-miR-1279	CLIP-seq
MIRT1121804	hsa-miR-1303	CLIP-seq
MIRT1121805	hsa-miR-185	CLIP-seq
MIRT1121806	hsa-miR-2052	CLIP-seq
MIRT1121807	hsa-miR-21	CLIP-seq
MIRT1121808	hsa-miR-323-5p	CLIP-seq
MIRT1121809	hsa-miR-3646	CLIP-seq
MIRT1121810	hsa-miR-3647-3p	CLIP-seq
MIRT1121811	hsa-miR-3653	CLIP-seq
MIRT1121812	hsa-miR-3658	CLIP-seq
MIRT1121813	hsa-miR-3662	CLIP-seq
MIRT1121814	hsa-miR-382	CLIP-seq
MIRT1121815	hsa-miR-4252	CLIP-seq
MIRT1121816	hsa-miR-4306	CLIP-seq
MIRT1121817	hsa-miR-4307	CLIP-seq
MIRT1121818	hsa-miR-4424	CLIP-seq
MIRT1121819	hsa-miR-4531	CLIP-seq
MIRT1121820	hsa-miR-4644	CLIP-seq
MIRT1121821	hsa-miR-4717-5p	CLIP-seq
MIRT1121822	hsa-miR-4720-3p	CLIP-seq
MIRT1121823	hsa-miR-4753-3p	CLIP-seq
MIRT1121824	hsa-miR-520d-5p	CLIP-seq
MIRT1121825	hsa-miR-524-5p	CLIP-seq
MIRT1121826	hsa-miR-539	CLIP-seq
MIRT1121827	hsa-miR-580	CLIP-seq
MIRT1121828	hsa-miR-590-5p	CLIP-seq
MIRT1121829	hsa-miR-620	CLIP-seq
MIRT1121802	hsa-miR-1270	CLIP-seq
MIRT1121804	hsa-miR-1303	CLIP-seq
MIRT1121805	hsa-miR-185	CLIP-seq
MIRT1121806	hsa-miR-2052	CLIP-seq
MIRT1121807	hsa-miR-21	CLIP-seq
MIRT2034460	hsa-miR-2276	CLIP-seq
MIRT1121811	hsa-miR-3653	CLIP-seq
MIRT1121812	hsa-miR-3658	CLIP-seq
MIRT1121814	hsa-miR-382	CLIP-seq
MIRT1121815	hsa-miR-4252	CLIP-seq
MIRT1121816	hsa-miR-4306	CLIP-seq
MIRT1121817	hsa-miR-4307	CLIP-seq
MIRT1121818	hsa-miR-4424	CLIP-seq
MIRT2034461	hsa-miR-4436a	CLIP-seq
MIRT1121819	hsa-miR-4531	CLIP-seq
MIRT1121820	hsa-miR-4644	CLIP-seq
MIRT2034462	hsa-miR-4686	CLIP-seq
MIRT2034463	hsa-miR-4700-3p	CLIP-seq
MIRT1121821	hsa-miR-4717-5p	CLIP-seq
MIRT1121822	hsa-miR-4720-3p	CLIP-seq
MIRT1121823	hsa-miR-4753-3p	CLIP-seq
MIRT2034464	hsa-miR-4772-3p	CLIP-seq
MIRT1121828	hsa-miR-590-5p	CLIP-seq
MIRT1121829	hsa-miR-620	CLIP-seq
MIRT1121804	hsa-miR-1303	CLIP-seq
MIRT1121806	hsa-miR-2052	CLIP-seq
MIRT2034460	hsa-miR-2276	CLIP-seq
MIRT1121815	hsa-miR-4252	CLIP-seq
MIRT1121817	hsa-miR-4307	CLIP-seq
MIRT2034462	hsa-miR-4686	CLIP-seq
MIRT2034463	hsa-miR-4700-3p	CLIP-seq
MIRT1121821	hsa-miR-4717-5p	CLIP-seq
MIRT2034464	hsa-miR-4772-3p	CLIP-seq
MIRT1121824	hsa-miR-520d-5p	CLIP-seq
MIRT1121825	hsa-miR-524-5p	CLIP-seq
MIRT2264939	hsa-miR-587	CLIP-seq

Show/Hide all (36)

GO ID	Ontology	Definition	Evidence	Reference
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	10369684, 10523320
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	22658674, 22681889
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	14667819, 15231747, 16169070, 16189514, 19060904, 19628699, 21516116, 21988832, 22365833, 23986595, 25416956, 26871637, 27107012, 28514442, 29997244, 31467278, 32296183, 32814053, 33961781, 35271311, 37398436
GO:0005634	Component	Nucleus	IDA	26912367
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	30975767
GO:0005634	Component	Nucleus	TAS	10369684
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:0005829	Component	Cytosol	TAS
GO:0006397	Process	MRNA processing	IEA
GO:0006397	Process	MRNA processing	TAS	10369684
GO:0008380	Process	RNA splicing	IEA
GO:0030629	Function	U6 snRNA 3'-end binding	IDA	10369684, 10523320
GO:0033962	Process	P-body assembly	IBA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IBA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IDA	10369684, 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:0120115	Component	Lsm2-8 complex	IEA
GO:1990726	Component	Lsm1-7-Pat1 complex	IBA
GO:1990904	Component	Ribonucleoprotein complex	IEA

MIM	HGNC	e!Ensembl
607283	17874	ENSG00000170860

P62310

Protein name

U6 snRNA-associated Sm-like protein LSm3

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	19 → 97	LSM domain	Domain

Sequence

MADDVDQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEET
VTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLRVG

Sequence length

102

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 (7)

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.
CARDIOMYOPATHY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHOROIDAL MELANOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DILATED CARDIOMYOPATHY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEART FAILURE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTROPHIC CARDIOMYOPATHY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UVEAL MELANOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (6)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Alzheimer Disease	Associate	36195955	★★★★★ ★☆☆☆☆ Found in Text Mining only
Calcinosis Cutis	Associate	17054779	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Non Small Cell Lung	Associate	26755624	★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Associate	37559353	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Associate	17054779	★★★★★ ★☆☆☆☆ Found in Text Mining only
Xeroderma Pigmentosum Complementation Group C	Associate	37109656	★★★★★ ★☆☆☆☆ Found in Text Mining only

LSM3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated)