SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide)

Gene

• Entrez ID: 6633
• Gene name: Small nuclear ribonucleoprotein D2 polypeptide
• Gene symbol: SNRPD2
• Synonyms (NCBI Gene): SMD2, SNRPD1, Sm-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

miRNA

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

Gene ontology (GO)

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

Other IDs

• MIM: 601061
• HGNC: 11159
• e!Ensembl: ENSG00000125743

Protein

• UniProt ID: 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

Pathways

KEGG:

Spliceosome

Reactome:

snRNP Assembly
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
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

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alopecia	Alopecia	BEFREE	28790444		★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	34461609	Associate	★☆☆☆☆ Found in Text Mining only
Amyotrophic Lateral Sclerosis	Amyotrophic lateral sclerosis	Pubtator	39486415	Inhibit	★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	14524621		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	14524621	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	37098488	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	37014321	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of larynx	Laryngeal carcinoma	BEFREE	23981752		★☆☆☆☆ Found in Text Mining only
Cognitive Dysfunction	Cognition disorder	Pubtator	34461609	Associate	★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	Pubtator	34426508	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Exanthema	Exanthema	Pubtator	28790444	Associate	★☆☆☆☆ Found in Text Mining only
Heart Diseases	Heart disease	Pubtator	12176801	Associate	★☆☆☆☆ Found in Text Mining only
Idiopathic pulmonary arterial hypertension	Pulmonary arterial hypertension	BEFREE	28790444		★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	BEFREE	28790444		★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney disease	Pubtator	28790444	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	11120828, 12176801, 28790444	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	28790444, 29151171, 9175921, 9631751		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant neoplasm of breast	Breast Cancer	BEFREE	23358685		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	16247014	Associate	★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	23358685		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	23251412	Associate	★☆☆☆☆ Found in Text Mining only
Optic Neuropathy Ischemic	Optic neuropathy	Pubtator	39273537	Stimulate	★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	32666642, 38166541	Associate	★☆☆☆☆ Found in Text Mining only
Post-Traumatic Stress Disorder	Stress Disorder	BEFREE	28151992		★☆☆☆☆ Found in Text Mining only
Pulmonary arterial hypertension	Pulmonary arterial hypertension	BEFREE	28790444		★☆☆☆☆ Found in Text Mining only
Pulmonary Arterial Hypertension	Pulmonary arterial hypertension	Pubtator	28790444	Associate	★☆☆☆☆ Found in Text Mining only
RING DERMOID OF CORNEA	Ring Dermoid Of Cornea	BEFREE	28790444		★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	28790444	Associate	★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	BEFREE	30210166		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	40082221	Associate	★☆☆☆☆ Found in Text Mining only