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	6633
Gene name	Small nuclear ribonucleoprotein D2 polypeptide
Gene symbol	SNRPD2
Synonyms (NCBI Gene)	SMD2SNRPD1Sm-D2
Chromosome	19
Chromosome location	19q13.32
Summary	The protein encoded by this gene belongs to the small nuclear ribonucleoprotein core protein family. It is required for pre-mRNA splicing and small nuclear ribonucleoprotein biogenesis. Multiple transcript variants encoding different isoforms have been fo

Show/Hide all (39)

miRTarBase ID	miRNA	Experiments	Reference
MIRT045600	hsa-miR-149-5p	CLASH	23622248
MIRT044703	hsa-miR-320a	CLASH	23622248
MIRT041764	hsa-miR-484	CLASH	23622248
MIRT038465	hsa-miR-296-3p	CLASH	23622248
MIRT1376222	hsa-miR-1197	CLIP-seq
MIRT1376223	hsa-miR-3174	CLIP-seq
MIRT1376224	hsa-miR-3591-3p	CLIP-seq
MIRT1376225	hsa-miR-376a	CLIP-seq
MIRT1376226	hsa-miR-376b	CLIP-seq
MIRT1376227	hsa-miR-4795-3p	CLIP-seq
MIRT1376228	hsa-miR-513c	CLIP-seq
MIRT1376229	hsa-miR-514b-5p	CLIP-seq
MIRT1376230	hsa-miR-885-3p	CLIP-seq
MIRT1376222	hsa-miR-1197	CLIP-seq
MIRT1376223	hsa-miR-3174	CLIP-seq
MIRT1376224	hsa-miR-3591-3p	CLIP-seq
MIRT1376225	hsa-miR-376a	CLIP-seq
MIRT1376226	hsa-miR-376b	CLIP-seq
MIRT1376230	hsa-miR-885-3p	CLIP-seq
MIRT1376222	hsa-miR-1197	CLIP-seq
MIRT1376223	hsa-miR-3174	CLIP-seq
MIRT1376224	hsa-miR-3591-3p	CLIP-seq
MIRT1376225	hsa-miR-376a	CLIP-seq
MIRT1376226	hsa-miR-376b	CLIP-seq
MIRT2335142	hsa-miR-421	CLIP-seq
MIRT2335143	hsa-miR-4709-5p	CLIP-seq
MIRT1376227	hsa-miR-4795-3p	CLIP-seq
MIRT2335144	hsa-miR-505	CLIP-seq
MIRT1376228	hsa-miR-513c	CLIP-seq
MIRT1376229	hsa-miR-514b-5p	CLIP-seq
MIRT1376230	hsa-miR-885-3p	CLIP-seq
MIRT1376222	hsa-miR-1197	CLIP-seq
MIRT1376224	hsa-miR-3591-3p	CLIP-seq
MIRT1376225	hsa-miR-376a	CLIP-seq
MIRT1376226	hsa-miR-376b	CLIP-seq
MIRT1376227	hsa-miR-4795-3p	CLIP-seq
MIRT1376228	hsa-miR-513c	CLIP-seq
MIRT1376229	hsa-miR-514b-5p	CLIP-seq
MIRT1376230	hsa-miR-885-3p	CLIP-seq

Show/Hide all (57)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000245	Process	Spliceosomal complex assembly	TAS	7527560
GO:0000387	Process	Spliceosomal snRNP assembly	IBA
GO:0000387	Process	Spliceosomal snRNP assembly	IDA	18984161
GO:0000398	Process	MRNA splicing, via spliceosome	IC	11991638
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	28076346, 32494006, 36797247
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	15564372, 30975767, 31744343, 33677607
GO:0003723	Function	RNA binding	HDA	22658674
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	9417867, 10500148, 11714716, 11748230, 12065586, 14667819, 15231747, 15848170, 15939020, 17332742, 18984161, 22365833, 25416956, 28514442, 30021884, 31799625, 32296183, 32814053, 33961781, 35271311
GO:0005634	Component	Nucleus	IDA	28076346
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	21113136, 30975767, 31744343
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005681	Component	Spliceosomal complex	IPI	30975767, 33677607
GO:0005681	Component	Spliceosomal complex	NAS	31744343
GO:0005681	Component	Spliceosomal complex	TAS	1701240
GO:0005682	Component	U5 snRNP	IBA
GO:0005682	Component	U5 snRNP	NAS	15564372
GO:0005684	Component	U2-type spliceosomal complex	IDA	32494006, 36797247
GO:0005685	Component	U1 snRNP	IBA
GO:0005685	Component	U1 snRNP	IDA	21113136, 25555158
GO:0005685	Component	U1 snRNP	IPI	33677607
GO:0005685	Component	U1 snRNP	NAS	15564372
GO:0005686	Component	U2 snRNP	IBA
GO:0005686	Component	U2 snRNP	NAS	15564372, 31744343
GO:0005687	Component	U4 snRNP	IDA	21516107
GO:0005687	Component	U4 snRNP	NAS	15564372
GO:0005689	Component	U12-type spliceosomal complex	IDA	15146077
GO:0005689	Component	U12-type spliceosomal complex	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA	18984161
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006397	Process	MRNA processing	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0008380	Process	RNA splicing	TAS	1701240
GO:0030532	Component	Small nuclear ribonucleoprotein complex	IEA
GO:0030532	Component	Small nuclear ribonucleoprotein complex	TAS	1701240
GO:0034709	Component	Methylosome	IDA	18984161
GO:0034715	Component	PICln-Sm protein complex	IBA
GO:0034715	Component	PICln-Sm protein complex	IDA	18984161
GO:0034719	Component	SMN-Sm protein complex	IDA	18984161
GO:0036261	Process	7-methylguanosine cap hypermethylation	NAS	15564372
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:0070062	Component	Extracellular exosome	HDA	20458337
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	28781166
GO:0071007	Component	U2-type catalytic step 2 spliceosome	IDA	28076346
GO:0071011	Component	Precatalytic spliceosome	IBA
GO:0071013	Component	Catalytic step 2 spliceosome	IBA
GO:0071013	Component	Catalytic step 2 spliceosome	IDA	11991638
GO:0097525	Component	Spliceosomal snRNP complex	IEA
GO:1903241	Process	U2-type prespliceosome assembly	NAS	31744343
GO:1990904	Component	Ribonucleoprotein complex	IEA

MIM	HGNC	e!Ensembl
601061	11159	ENSG00000125743

P62316

Protein name

Small nuclear ribonucleoprotein Sm D2 (Sm-D2) (snRNP core protein D2)

Protein function

Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23333303, Pu

PDB

1B34 , 3CW1 , 3JCR , 3PGW , 4F7U , 4PJO , 4V98 , 4WZJ , 5MQF , 5O9Z , 5XJC , 5XJL , 5XJQ , 5XJR , 5XJS , 5XJT , 5XJU , 5YZG , 5Z56 , 5Z57 , 5Z58 , 6AH0 , 6AHD , 6FF7 , 6ICZ , 6ID0 , 6ID1 , 6QDV , 6QW6 , 6QX9 , 6Y53 , 6Y5Q , 7A5P , 7ABG , 7ABI , 7B0Y , 7DVQ , 7EVO , 7QTT , 7VPX , 7W59 , 7W5A , 7W5B , 8C6J , 8CH6 , 8H6E , 8H6J , 8H6K , 8H6L , 8HK1 , 8I0P

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01423	LSM	33 → 111	LSM domain	Domain

Sequence

MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD
RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK

Sequence length

118

Interactions

View interactions

	KEGG		Reactome
	Spliceosome		snRNP Assembly mRNA Splicing - Major Pathway mRNA Splicing - Minor 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 (4)

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.
CORONARY ARTERY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUPUS ERYTHEMATOSUS, SYSTEMIC	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEPHROLITHIASIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Alzheimer Disease	Associate	34461609	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cognitive Dysfunction	Associate	34461609	★★★★★ ★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Associate	34426508	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COVID 19	Associate	35277538, 35657140	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	38166541	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Stimulate	39684842	★★★★★ ★☆☆☆☆ Found in Text Mining only
Optic Neuropathy Ischemic	Stimulate	39273537	★★★★★ ★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Associate	38166541	★★★★★ ★☆☆☆☆ Found in Text Mining only

SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide)