SF3A3 (splicing factor 3a subunit 3)

Gene

• Entrez ID: 10946
• Gene name: Splicing factor 3a subunit 3
• Gene symbol: SF3A3
• Synonyms (NCBI Gene): PRP9, PRPF9, SAP61, SF3a60
• Chromosome: 1
• Chromosome location: 1p34.3
• Summary: This gene encodes subunit 3 of the splicing factor 3a protein complex. The splicing factor 3a heterotrimer includes subunits 1, 2 and 3 and is necessary for the in vitro conversion of 15S U2 snRNP into an active 17S particle that performs pre-mRNA splicin

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT027169	hsa-miR-103a-3p	Sequencing	20371350
MIRT031847	hsa-miR-16-5p	Sequencing	20371350
MIRT049556	hsa-miR-92a-3p	CLASH	23622248
MIRT040150	hsa-miR-615-3p	CLASH	23622248
MIRT645628	hsa-miR-500b-3p	HITS-CLIP	23824327
MIRT645627	hsa-miR-6736-3p	HITS-CLIP	23824327
MIRT645626	hsa-miR-4267	HITS-CLIP	23824327
MIRT645625	hsa-miR-3130-3p	HITS-CLIP	23824327
MIRT618935	hsa-miR-6832-3p	HITS-CLIP	23824327
MIRT618934	hsa-miR-8055	HITS-CLIP	23824327
MIRT618933	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT618935	hsa-miR-6832-3p	HITS-CLIP	23824327
MIRT618934	hsa-miR-8055	HITS-CLIP	23824327
MIRT618933	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT528419	hsa-miR-320a	PAR-CLIP	22012620
MIRT528418	hsa-miR-320b	PAR-CLIP	22012620
MIRT528417	hsa-miR-320c	PAR-CLIP	22012620
MIRT528416	hsa-miR-320d	PAR-CLIP	22012620
MIRT528415	hsa-miR-4429	PAR-CLIP	22012620
MIRT528414	hsa-miR-4663	PAR-CLIP	22012620
MIRT645628	hsa-miR-500b-3p	HITS-CLIP	23824327
MIRT645627	hsa-miR-6736-3p	HITS-CLIP	23824327
MIRT645626	hsa-miR-4267	HITS-CLIP	23824327
MIRT645625	hsa-miR-3130-3p	HITS-CLIP	23824327
MIRT618935	hsa-miR-6832-3p	HITS-CLIP	23824327
MIRT618934	hsa-miR-8055	HITS-CLIP	23824327
MIRT618933	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT618935	hsa-miR-6832-3p	HITS-CLIP	23824327
MIRT618934	hsa-miR-8055	HITS-CLIP	23824327
MIRT618933	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT528419	hsa-miR-320a	PAR-CLIP	22012620
MIRT528418	hsa-miR-320b	PAR-CLIP	22012620
MIRT528417	hsa-miR-320c	PAR-CLIP	22012620
MIRT528416	hsa-miR-320d	PAR-CLIP	22012620
MIRT528415	hsa-miR-4429	PAR-CLIP	22012620
MIRT528414	hsa-miR-4663	PAR-CLIP	22012620
MIRT1341112	hsa-miR-103a	CLIP-seq
MIRT1341113	hsa-miR-107	CLIP-seq
MIRT1341114	hsa-miR-1184	CLIP-seq
MIRT1341115	hsa-miR-1202	CLIP-seq
MIRT1341116	hsa-miR-1245b-3p	CLIP-seq
MIRT1341117	hsa-miR-125a-5p	CLIP-seq
MIRT1341118	hsa-miR-125b	CLIP-seq
MIRT1341119	hsa-miR-1275	CLIP-seq
MIRT1341120	hsa-miR-15a	CLIP-seq
MIRT1341121	hsa-miR-15b	CLIP-seq
MIRT1341122	hsa-miR-16	CLIP-seq
MIRT1341123	hsa-miR-190	CLIP-seq
MIRT1341124	hsa-miR-190b	CLIP-seq
MIRT1341125	hsa-miR-195	CLIP-seq
MIRT1341126	hsa-miR-2110	CLIP-seq
MIRT1341127	hsa-miR-214	CLIP-seq
MIRT1341128	hsa-miR-218	CLIP-seq
MIRT1341129	hsa-miR-221	CLIP-seq
MIRT1341130	hsa-miR-222	CLIP-seq
MIRT1341131	hsa-miR-3065-5p	CLIP-seq
MIRT1341132	hsa-miR-3127-5p	CLIP-seq
MIRT1341133	hsa-miR-3153	CLIP-seq
MIRT1341134	hsa-miR-3173-3p	CLIP-seq
MIRT1341135	hsa-miR-3194-5p	CLIP-seq
MIRT1341136	hsa-miR-3199	CLIP-seq
MIRT1341137	hsa-miR-326	CLIP-seq
MIRT1341138	hsa-miR-330-5p	CLIP-seq
MIRT1341139	hsa-miR-3619-5p	CLIP-seq
MIRT1341140	hsa-miR-3942-3p	CLIP-seq
MIRT1341141	hsa-miR-3972	CLIP-seq
MIRT1341142	hsa-miR-424	CLIP-seq
MIRT1341143	hsa-miR-4252	CLIP-seq
MIRT1341144	hsa-miR-4269	CLIP-seq
MIRT1341145	hsa-miR-4270	CLIP-seq
MIRT1341146	hsa-miR-4271	CLIP-seq
MIRT1341147	hsa-miR-4319	CLIP-seq
MIRT1341148	hsa-miR-4421	CLIP-seq
MIRT1341149	hsa-miR-4438	CLIP-seq
MIRT1341150	hsa-miR-4441	CLIP-seq
MIRT1341151	hsa-miR-4525	CLIP-seq
MIRT1341152	hsa-miR-4650-5p	CLIP-seq
MIRT1341153	hsa-miR-4665-5p	CLIP-seq
MIRT1341154	hsa-miR-4667-5p	CLIP-seq
MIRT1341155	hsa-miR-4690-5p	CLIP-seq
MIRT1341156	hsa-miR-4700-5p	CLIP-seq
MIRT1341157	hsa-miR-4713-3p	CLIP-seq
MIRT1341158	hsa-miR-4723-5p	CLIP-seq
MIRT1341159	hsa-miR-4725-3p	CLIP-seq
MIRT1341160	hsa-miR-4727-5p	CLIP-seq
MIRT1341161	hsa-miR-4732-3p	CLIP-seq
MIRT1341162	hsa-miR-4769-3p	CLIP-seq
MIRT1341163	hsa-miR-4779	CLIP-seq
MIRT1341164	hsa-miR-491-5p	CLIP-seq
MIRT1341165	hsa-miR-497	CLIP-seq
MIRT1341166	hsa-miR-5095	CLIP-seq
MIRT1341167	hsa-miR-562	CLIP-seq
MIRT1341168	hsa-miR-583	CLIP-seq
MIRT1341169	hsa-miR-593	CLIP-seq
MIRT1341170	hsa-miR-610	CLIP-seq
MIRT1341171	hsa-miR-625	CLIP-seq
MIRT1341172	hsa-miR-636	CLIP-seq
MIRT1341173	hsa-miR-637	CLIP-seq
MIRT1341174	hsa-miR-670	CLIP-seq
MIRT1341175	hsa-miR-761	CLIP-seq
MIRT1341176	hsa-miR-943	CLIP-seq
MIRT1341117	hsa-miR-125a-5p	CLIP-seq
MIRT1341118	hsa-miR-125b	CLIP-seq
MIRT1341129	hsa-miR-221	CLIP-seq
MIRT1341130	hsa-miR-222	CLIP-seq
MIRT1341147	hsa-miR-4319	CLIP-seq
MIRT1341161	hsa-miR-4732-3p	CLIP-seq
MIRT1341170	hsa-miR-610	CLIP-seq
MIRT1341174	hsa-miR-670	CLIP-seq
MIRT2100971	hsa-miR-1200	CLIP-seq
MIRT2100972	hsa-miR-1205	CLIP-seq
MIRT2100973	hsa-miR-139-5p	CLIP-seq
MIRT2100974	hsa-miR-150	CLIP-seq
MIRT2100975	hsa-miR-1976	CLIP-seq
MIRT1341136	hsa-miR-3199	CLIP-seq
MIRT2100976	hsa-miR-3659	CLIP-seq
MIRT2100977	hsa-miR-4264	CLIP-seq
MIRT2100978	hsa-miR-4324	CLIP-seq
MIRT2100979	hsa-miR-4641	CLIP-seq
MIRT2100980	hsa-miR-4658	CLIP-seq
MIRT2100981	hsa-miR-4667-3p	CLIP-seq
MIRT2100982	hsa-miR-4722-3p	CLIP-seq
MIRT2100983	hsa-miR-544b	CLIP-seq
MIRT2100984	hsa-miR-574-5p	CLIP-seq
MIRT1341168	hsa-miR-583	CLIP-seq
MIRT2100985	hsa-miR-622	CLIP-seq
MIRT1341112	hsa-miR-103a	CLIP-seq
MIRT1341113	hsa-miR-107	CLIP-seq
MIRT1341114	hsa-miR-1184	CLIP-seq
MIRT2325494	hsa-miR-1208	CLIP-seq
MIRT1341117	hsa-miR-125a-5p	CLIP-seq
MIRT1341118	hsa-miR-125b	CLIP-seq
MIRT2100974	hsa-miR-150	CLIP-seq
MIRT1341120	hsa-miR-15a	CLIP-seq
MIRT1341121	hsa-miR-15b	CLIP-seq
MIRT1341122	hsa-miR-16	CLIP-seq
MIRT1341125	hsa-miR-195	CLIP-seq
MIRT2100975	hsa-miR-1976	CLIP-seq
MIRT1341127	hsa-miR-214	CLIP-seq
MIRT1341129	hsa-miR-221	CLIP-seq
MIRT1341130	hsa-miR-222	CLIP-seq
MIRT2325495	hsa-miR-224	CLIP-seq
MIRT1341131	hsa-miR-3065-5p	CLIP-seq
MIRT1341132	hsa-miR-3127-5p	CLIP-seq
MIRT1341134	hsa-miR-3173-3p	CLIP-seq
MIRT1341136	hsa-miR-3199	CLIP-seq
MIRT2325496	hsa-miR-320e	CLIP-seq
MIRT1341139	hsa-miR-3619-5p	CLIP-seq
MIRT1341142	hsa-miR-424	CLIP-seq
MIRT1341144	hsa-miR-4269	CLIP-seq
MIRT1341145	hsa-miR-4270	CLIP-seq
MIRT1341147	hsa-miR-4319	CLIP-seq
MIRT1341148	hsa-miR-4421	CLIP-seq
MIRT1341149	hsa-miR-4438	CLIP-seq
MIRT1341150	hsa-miR-4441	CLIP-seq
MIRT1341152	hsa-miR-4650-5p	CLIP-seq
MIRT2100981	hsa-miR-4667-3p	CLIP-seq
MIRT1341155	hsa-miR-4690-5p	CLIP-seq
MIRT1341157	hsa-miR-4713-3p	CLIP-seq
MIRT2100982	hsa-miR-4722-3p	CLIP-seq
MIRT1341161	hsa-miR-4732-3p	CLIP-seq
MIRT2325497	hsa-miR-4746-5p	CLIP-seq
MIRT1341163	hsa-miR-4779	CLIP-seq
MIRT1341165	hsa-miR-497	CLIP-seq
MIRT1341166	hsa-miR-5095	CLIP-seq
MIRT1341167	hsa-miR-562	CLIP-seq
MIRT1341170	hsa-miR-610	CLIP-seq
MIRT1341174	hsa-miR-670	CLIP-seq
MIRT1341175	hsa-miR-761	CLIP-seq
MIRT1341117	hsa-miR-125a-5p	CLIP-seq
MIRT1341118	hsa-miR-125b	CLIP-seq
MIRT2394276	hsa-miR-202	CLIP-seq
MIRT1341129	hsa-miR-221	CLIP-seq
MIRT1341130	hsa-miR-222	CLIP-seq
MIRT2394277	hsa-miR-3915	CLIP-seq
MIRT2394278	hsa-miR-3928	CLIP-seq
MIRT1341147	hsa-miR-4319	CLIP-seq
MIRT2394279	hsa-miR-4710	CLIP-seq
MIRT1341161	hsa-miR-4732-3p	CLIP-seq
MIRT2394280	hsa-miR-4792	CLIP-seq
MIRT2394281	hsa-miR-4802-5p	CLIP-seq
MIRT2394282	hsa-miR-561	CLIP-seq
MIRT1341170	hsa-miR-610	CLIP-seq
MIRT1341174	hsa-miR-670	CLIP-seq
MIRT2621170	hsa-miR-1182	CLIP-seq
MIRT1341117	hsa-miR-125a-5p	CLIP-seq
MIRT1341118	hsa-miR-125b	CLIP-seq
MIRT2621171	hsa-miR-193a-5p	CLIP-seq
MIRT2100975	hsa-miR-1976	CLIP-seq
MIRT1341129	hsa-miR-221	CLIP-seq
MIRT1341130	hsa-miR-222	CLIP-seq
MIRT2621172	hsa-miR-3121-3p	CLIP-seq
MIRT2621173	hsa-miR-3162-5p	CLIP-seq
MIRT2621174	hsa-miR-3658	CLIP-seq
MIRT2621175	hsa-miR-3672	CLIP-seq
MIRT2621176	hsa-miR-3689a-3p	CLIP-seq
MIRT2621177	hsa-miR-3689c	CLIP-seq
MIRT2621178	hsa-miR-376c	CLIP-seq
MIRT2621179	hsa-miR-378g	CLIP-seq
MIRT1341147	hsa-miR-4319	CLIP-seq
MIRT2621180	hsa-miR-4425	CLIP-seq
MIRT2621181	hsa-miR-4474-5p	CLIP-seq
MIRT2100981	hsa-miR-4667-3p	CLIP-seq
MIRT2621182	hsa-miR-4715-3p	CLIP-seq
MIRT2100982	hsa-miR-4722-3p	CLIP-seq
MIRT1341161	hsa-miR-4732-3p	CLIP-seq
MIRT2621183	hsa-miR-491-3p	CLIP-seq
MIRT2621184	hsa-miR-513c	CLIP-seq
MIRT2621185	hsa-miR-514b-5p	CLIP-seq
MIRT2621186	hsa-miR-532-5p	CLIP-seq
MIRT2621187	hsa-miR-539	CLIP-seq
MIRT2621188	hsa-miR-548p	CLIP-seq
MIRT1341170	hsa-miR-610	CLIP-seq
MIRT2621189	hsa-miR-645	CLIP-seq
MIRT2621190	hsa-miR-659	CLIP-seq
MIRT2621191	hsa-miR-661	CLIP-seq
MIRT1341174	hsa-miR-670	CLIP-seq
MIRT2621192	hsa-miR-671-5p	CLIP-seq
MIRT2621170	hsa-miR-1182	CLIP-seq
MIRT1341117	hsa-miR-125a-5p	CLIP-seq
MIRT1341118	hsa-miR-125b	CLIP-seq
MIRT2621171	hsa-miR-193a-5p	CLIP-seq
MIRT1341129	hsa-miR-221	CLIP-seq
MIRT1341130	hsa-miR-222	CLIP-seq
MIRT2621172	hsa-miR-3121-3p	CLIP-seq
MIRT2621173	hsa-miR-3162-5p	CLIP-seq
MIRT2621174	hsa-miR-3658	CLIP-seq
MIRT2621175	hsa-miR-3672	CLIP-seq
MIRT2621176	hsa-miR-3689a-3p	CLIP-seq
MIRT2621177	hsa-miR-3689c	CLIP-seq
MIRT2621178	hsa-miR-376c	CLIP-seq
MIRT2621179	hsa-miR-378g	CLIP-seq
MIRT2690537	hsa-miR-4256	CLIP-seq
MIRT1341147	hsa-miR-4319	CLIP-seq
MIRT2621180	hsa-miR-4425	CLIP-seq
MIRT1341161	hsa-miR-4732-3p	CLIP-seq
MIRT2621187	hsa-miR-539	CLIP-seq
MIRT2621188	hsa-miR-548p	CLIP-seq
MIRT1341170	hsa-miR-610	CLIP-seq
MIRT2621190	hsa-miR-659	CLIP-seq
MIRT2621191	hsa-miR-661	CLIP-seq
MIRT1341174	hsa-miR-670	CLIP-seq
MIRT2621192	hsa-miR-671-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000375	Process	RNA splicing, via transesterification reactions	TAS	7816610
GO:0000389	Process	MRNA 3'-splice site recognition	TAS	15647371
GO:0000398	Process	MRNA splicing, via spliceosome	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IC	9731529, 11991638
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	29360106, 32494006, 34822310, 36797247
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	21349847, 31744343
GO:0003676	Function	Nucleic acid binding	IEA
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	17098193, 17332742, 22190034, 22365833, 25277244, 25416956, 28514442, 30021884, 31515488, 32814053, 33961781, 35271311
GO:0005634	Component	Nucleus	IDA	21349847, 29360106
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	31744343
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IBA
GO:0005681	Component	Spliceosomal complex	IDA	9731529
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005681	Component	Spliceosomal complex	NAS	31744343
GO:0005684	Component	U2-type spliceosomal complex	IDA	32494006, 34822310, 36797247
GO:0005684	Component	U2-type spliceosomal complex	IPI	10882114
GO:0005686	Component	U2 snRNP	IDA	11533230
GO:0005686	Component	U2 snRNP	IEA
GO:0005686	Component	U2 snRNP	NAS	31744343
GO:0006397	Process	MRNA processing	IEA
GO:0006397	Process	MRNA processing	IMP	15647371
GO:0008270	Function	Zinc ion binding	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0016607	Component	Nuclear speck	IDA	8022796
GO:0016607	Component	Nuclear speck	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	8022796, 29360106
GO:0071013	Component	Catalytic step 2 spliceosome	IDA	11991638
GO:1903241	Process	U2-type prespliceosome assembly	IDA	11533230
GO:1903241	Process	U2-type prespliceosome assembly	NAS	31744343

Other IDs

• MIM: 605596
• HGNC: 10767
• e!Ensembl: ENSG00000183431

Protein

• UniProt ID: Q12874
• Protein name: Splicing factor 3A subunit 3 (SF3a60) (Spliceosome-associated protein 61) (SAP 61)
• Protein function: Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs (PubMed:10882114, PubMed:11533230, PubMed:32494006, PubMed:34822310, PubMed:8022796). The 17S U2 SnRNP co
• PDB: 2DT7, 5Z56, 5Z57, 5Z58, 6AH0, 6AHD, 6FF7, 6QX9, 6Y50, 6Y53, 6Y5Q, 7ABG, 7ABH, 7ABI, 7EVO, 7ONB, 7Q3L, 7Q4O, 7Q4P, 7QTT, 7VPX, 8CH6, 8H6E, 8H6J, 8H6K, 8H6L, 8HK1, 8I0P, 8I0R, 8I0S, 8I0T, 8I0U, 8QO9, 8QXD, 8QZS, 8R08, 8R09, 8R0A, 8R0B, 8RM5
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF12108	SF3a60_bindingd	74 → 100	Splicing factor SF3a60 binding domain	Domain
  PF16837	SF3A3	129 → 207	Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9	Domain
  PF13297	Telomere_Sde2_2	244 → 303		Domain
  PF11931	DUF3449	323 → 500	Domain of unknown function (DUF3449)	Family

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:7816610}.
• Sequence:

  METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDL
  YDDKDGLRKEELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENP
  SEEAQNLVEFTDEEGYGRYLDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNA
  EYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQAEFEKKWENGTFPGWPKETSSALTHA
  GAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEERAQRLFSTKGKSLESLDTSL
  FAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTGEEREEEE
  EEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
  AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYE
  DSSGNVVNKKTYEDLKRQGLL

• Sequence length: 501

Pathways

KEGG:

Spliceosome

Reactome:

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
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL ADENOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
THYROIDITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	40424306	Associate	★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	34281234	Associate	★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	28296343		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	37929350	Associate	★☆☆☆☆ Found in Text Mining only