PHF5A (PHD finger protein 5A)

Gene

• Entrez ID: 84844
• Gene name: PHD finger protein 5A
• Gene symbol: PHF5A
• Synonyms (NCBI Gene): INI, Rds3, SAP14b, SF3B7, SF3b14b, bK223H9.2
• Chromosome: 22
• Chromosome location: 22q13.2
• Summary: This gene encodes a subunit of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-m

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT052678	hsa-miR-1260b	CLASH	23622248
MIRT532634	hsa-miR-6838-3p	PAR-CLIP	22012620
MIRT532633	hsa-miR-6734-3p	PAR-CLIP	22012620
MIRT532632	hsa-miR-20b-3p	PAR-CLIP	22012620
MIRT532631	hsa-miR-4297	PAR-CLIP	22012620
MIRT532630	hsa-miR-5581-5p	PAR-CLIP	22012620
MIRT532629	hsa-miR-1537-5p	PAR-CLIP	22012620
MIRT532627	hsa-miR-4718	PAR-CLIP	22012620
MIRT532628	hsa-miR-4999-5p	PAR-CLIP	22012620
MIRT532626	hsa-miR-4529-5p	PAR-CLIP	22012620
MIRT532624	hsa-miR-4540	PAR-CLIP	22012620
MIRT532625	hsa-miR-202-5p	PAR-CLIP	22012620
MIRT532623	hsa-miR-3187-3p	PAR-CLIP	22012620
MIRT462643	hsa-miR-204-3p	PAR-CLIP	23592263
MIRT462642	hsa-miR-4646-5p	PAR-CLIP	23592263
MIRT462641	hsa-miR-3192-5p	PAR-CLIP	23592263
MIRT462640	hsa-miR-619-5p	PAR-CLIP	23592263
MIRT462639	hsa-miR-6506-5p	PAR-CLIP	23592263
MIRT462638	hsa-miR-3160-3p	PAR-CLIP	23592263
MIRT462637	hsa-miR-558	PAR-CLIP	23592263
MIRT462636	hsa-miR-4487	PAR-CLIP	23592263
MIRT462635	hsa-miR-377-5p	PAR-CLIP	23592263
MIRT462634	hsa-miR-6086	PAR-CLIP	23592263
MIRT462633	hsa-miR-924	PAR-CLIP	23592263
MIRT462632	hsa-miR-6499-3p	PAR-CLIP	23592263
MIRT462631	hsa-miR-4747-5p	PAR-CLIP	23592263
MIRT462630	hsa-miR-5196-5p	PAR-CLIP	23592263
MIRT462629	hsa-miR-4314	PAR-CLIP	23592263
MIRT462628	hsa-miR-627-5p	PAR-CLIP	23592263
MIRT462627	hsa-miR-455-3p	PAR-CLIP	23592263
MIRT462626	hsa-miR-6516-5p	PAR-CLIP	23592263
MIRT532634	hsa-miR-6838-3p	PAR-CLIP	22012620
MIRT532633	hsa-miR-6734-3p	PAR-CLIP	22012620
MIRT532632	hsa-miR-20b-3p	PAR-CLIP	22012620
MIRT532631	hsa-miR-4297	PAR-CLIP	22012620
MIRT532630	hsa-miR-5581-5p	PAR-CLIP	22012620
MIRT532629	hsa-miR-1537-5p	PAR-CLIP	22012620
MIRT532627	hsa-miR-4718	PAR-CLIP	22012620
MIRT532628	hsa-miR-4999-5p	PAR-CLIP	22012620
MIRT532626	hsa-miR-4529-5p	PAR-CLIP	22012620
MIRT532624	hsa-miR-4540	PAR-CLIP	22012620
MIRT532625	hsa-miR-202-5p	PAR-CLIP	22012620
MIRT532623	hsa-miR-3187-3p	PAR-CLIP	22012620
MIRT462643	hsa-miR-204-3p	PAR-CLIP	23592263
MIRT462642	hsa-miR-4646-5p	PAR-CLIP	23592263
MIRT462641	hsa-miR-3192-5p	PAR-CLIP	23592263
MIRT462640	hsa-miR-619-5p	PAR-CLIP	23592263
MIRT462639	hsa-miR-6506-5p	PAR-CLIP	23592263
MIRT462638	hsa-miR-3160-3p	PAR-CLIP	23592263
MIRT462637	hsa-miR-558	PAR-CLIP	23592263
MIRT462636	hsa-miR-4487	PAR-CLIP	23592263
MIRT462635	hsa-miR-377-5p	PAR-CLIP	23592263
MIRT462634	hsa-miR-6086	PAR-CLIP	23592263
MIRT462633	hsa-miR-924	PAR-CLIP	23592263
MIRT462632	hsa-miR-6499-3p	PAR-CLIP	23592263
MIRT462631	hsa-miR-4747-5p	PAR-CLIP	23592263
MIRT462630	hsa-miR-5196-5p	PAR-CLIP	23592263
MIRT462629	hsa-miR-4314	PAR-CLIP	23592263
MIRT462628	hsa-miR-627-5p	PAR-CLIP	23592263
MIRT462627	hsa-miR-455-3p	PAR-CLIP	23592263
MIRT462626	hsa-miR-6516-5p	PAR-CLIP	23592263
MIRT1231128	hsa-miR-1183	CLIP-seq
MIRT1231129	hsa-miR-1231	CLIP-seq
MIRT1231130	hsa-miR-1262	CLIP-seq
MIRT1231131	hsa-miR-1268	CLIP-seq
MIRT1231132	hsa-miR-1268b	CLIP-seq
MIRT1231133	hsa-miR-1275	CLIP-seq
MIRT1231134	hsa-miR-128	CLIP-seq
MIRT1231135	hsa-miR-187	CLIP-seq
MIRT1231136	hsa-miR-223	CLIP-seq
MIRT1231137	hsa-miR-2276	CLIP-seq
MIRT1231138	hsa-miR-27a	CLIP-seq
MIRT1231139	hsa-miR-27b	CLIP-seq
MIRT1231140	hsa-miR-298	CLIP-seq
MIRT1231141	hsa-miR-3137	CLIP-seq
MIRT1231142	hsa-miR-3147	CLIP-seq
MIRT1231143	hsa-miR-3162-3p	CLIP-seq
MIRT1231144	hsa-miR-3179	CLIP-seq
MIRT1231145	hsa-miR-3202	CLIP-seq
MIRT1231146	hsa-miR-4277	CLIP-seq
MIRT1231147	hsa-miR-4307	CLIP-seq
MIRT1231148	hsa-miR-4326	CLIP-seq
MIRT1231149	hsa-miR-4420	CLIP-seq
MIRT1231150	hsa-miR-4425	CLIP-seq
MIRT1231151	hsa-miR-4476	CLIP-seq
MIRT1231152	hsa-miR-4486	CLIP-seq
MIRT1231153	hsa-miR-4638-3p	CLIP-seq
MIRT1231154	hsa-miR-4665-5p	CLIP-seq
MIRT1231155	hsa-miR-4696	CLIP-seq
MIRT1231156	hsa-miR-4701-3p	CLIP-seq
MIRT1231157	hsa-miR-4723-5p	CLIP-seq
MIRT1231158	hsa-miR-4781-3p	CLIP-seq
MIRT1231159	hsa-miR-500a	CLIP-seq
MIRT1231160	hsa-miR-501-5p	CLIP-seq
MIRT1231161	hsa-miR-5096	CLIP-seq
MIRT1231162	hsa-miR-513a-5p	CLIP-seq
MIRT1231163	hsa-miR-585	CLIP-seq
MIRT1231164	hsa-miR-587	CLIP-seq
MIRT2067824	hsa-miR-103a	CLIP-seq
MIRT2067825	hsa-miR-107	CLIP-seq
MIRT2067826	hsa-miR-1184	CLIP-seq
MIRT2067827	hsa-miR-22	CLIP-seq
MIRT2067828	hsa-miR-31	CLIP-seq
MIRT2067829	hsa-miR-3128	CLIP-seq
MIRT1231144	hsa-miR-3179	CLIP-seq
MIRT1231145	hsa-miR-3202	CLIP-seq
MIRT2067830	hsa-miR-3688-5p	CLIP-seq
MIRT2067831	hsa-miR-3977	CLIP-seq
MIRT1231147	hsa-miR-4307	CLIP-seq
MIRT2067832	hsa-miR-4434	CLIP-seq
MIRT1231151	hsa-miR-4476	CLIP-seq
MIRT2067833	hsa-miR-4494	CLIP-seq
MIRT2067834	hsa-miR-4499	CLIP-seq
MIRT2067835	hsa-miR-4516	CLIP-seq
MIRT2067836	hsa-miR-4531	CLIP-seq
MIRT2067837	hsa-miR-4704-5p	CLIP-seq
MIRT2067838	hsa-miR-4712-5p	CLIP-seq
MIRT2067839	hsa-miR-4720-5p	CLIP-seq
MIRT1231157	hsa-miR-4723-5p	CLIP-seq
MIRT2067840	hsa-miR-4771	CLIP-seq
MIRT2067841	hsa-miR-4773	CLIP-seq
MIRT2067842	hsa-miR-4799-3p	CLIP-seq
MIRT2067843	hsa-miR-4802-5p	CLIP-seq
MIRT2067844	hsa-miR-770-5p	CLIP-seq
MIRT2067845	hsa-miR-885-3p	CLIP-seq
MIRT2067846	hsa-miR-922	CLIP-seq
MIRT2067824	hsa-miR-103a	CLIP-seq
MIRT2067825	hsa-miR-107	CLIP-seq
MIRT2067826	hsa-miR-1184	CLIP-seq
MIRT2295286	hsa-miR-1244	CLIP-seq
MIRT2295287	hsa-miR-138	CLIP-seq
MIRT2067827	hsa-miR-22	CLIP-seq
MIRT2067829	hsa-miR-3128	CLIP-seq
MIRT1231147	hsa-miR-4307	CLIP-seq
MIRT1231148	hsa-miR-4326	CLIP-seq
MIRT2067833	hsa-miR-4494	CLIP-seq
MIRT2067834	hsa-miR-4499	CLIP-seq
MIRT2295288	hsa-miR-4690-5p	CLIP-seq
MIRT2067837	hsa-miR-4704-5p	CLIP-seq
MIRT2067838	hsa-miR-4712-5p	CLIP-seq
MIRT2067839	hsa-miR-4720-5p	CLIP-seq
MIRT2067840	hsa-miR-4771	CLIP-seq
MIRT2067842	hsa-miR-4799-3p	CLIP-seq
MIRT2295289	hsa-miR-544	CLIP-seq
MIRT2067844	hsa-miR-770-5p	CLIP-seq
MIRT2067845	hsa-miR-885-3p	CLIP-seq
MIRT2067846	hsa-miR-922	CLIP-seq
MIRT1231131	hsa-miR-1268	CLIP-seq
MIRT1231132	hsa-miR-1268b	CLIP-seq
MIRT1231134	hsa-miR-128	CLIP-seq
MIRT1231136	hsa-miR-223	CLIP-seq
MIRT1231138	hsa-miR-27a	CLIP-seq
MIRT1231139	hsa-miR-27b	CLIP-seq
MIRT1231140	hsa-miR-298	CLIP-seq
MIRT1231146	hsa-miR-4277	CLIP-seq
MIRT1231148	hsa-miR-4326	CLIP-seq
MIRT1231149	hsa-miR-4420	CLIP-seq
MIRT1231152	hsa-miR-4486	CLIP-seq
MIRT1231162	hsa-miR-513a-5p	CLIP-seq
MIRT1231163	hsa-miR-585	CLIP-seq
MIRT1231131	hsa-miR-1268	CLIP-seq
MIRT1231132	hsa-miR-1268b	CLIP-seq
MIRT1231134	hsa-miR-128	CLIP-seq
MIRT1231137	hsa-miR-2276	CLIP-seq
MIRT1231138	hsa-miR-27a	CLIP-seq
MIRT1231139	hsa-miR-27b	CLIP-seq
MIRT1231147	hsa-miR-4307	CLIP-seq
MIRT1231149	hsa-miR-4420	CLIP-seq
MIRT1231152	hsa-miR-4486	CLIP-seq
MIRT1231155	hsa-miR-4696	CLIP-seq
MIRT2592893	hsa-miR-4715-3p	CLIP-seq
MIRT1231161	hsa-miR-5096	CLIP-seq
MIRT1231162	hsa-miR-513a-5p	CLIP-seq
MIRT1231163	hsa-miR-585	CLIP-seq
MIRT1231131	hsa-miR-1268	CLIP-seq
MIRT1231132	hsa-miR-1268b	CLIP-seq
MIRT1231134	hsa-miR-128	CLIP-seq
MIRT1231136	hsa-miR-223	CLIP-seq
MIRT1231137	hsa-miR-2276	CLIP-seq
MIRT1231138	hsa-miR-27a	CLIP-seq
MIRT1231139	hsa-miR-27b	CLIP-seq
MIRT1231146	hsa-miR-4277	CLIP-seq
MIRT1231147	hsa-miR-4307	CLIP-seq
MIRT1231149	hsa-miR-4420	CLIP-seq
MIRT1231152	hsa-miR-4486	CLIP-seq
MIRT1231155	hsa-miR-4696	CLIP-seq
MIRT2592893	hsa-miR-4715-3p	CLIP-seq
MIRT1231161	hsa-miR-5096	CLIP-seq
MIRT1231162	hsa-miR-513a-5p	CLIP-seq
MIRT1231163	hsa-miR-585	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000398	Process	MRNA splicing, via spliceosome	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	12234937, 27720643, 29360106, 32494006, 34822310, 36797247
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	31744343
GO:0003677	Function	DNA binding	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IDA	27720643
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	17332742, 24981860, 27720643, 32814053, 33961781
GO:0005634	Component	Nucleus	IDA	27720643, 28541300, 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	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	27720643
GO:0005686	Component	U2 snRNP	IBA
GO:0005686	Component	U2 snRNP	IDA	12234937
GO:0005686	Component	U2 snRNP	NAS	31744343
GO:0005689	Component	U12-type spliceosomal complex	IDA	15146077
GO:0006397	Process	MRNA processing	IEA
GO:0008270	Function	Zinc ion binding	IDA	28541300
GO:0008380	Process	RNA splicing	IEA
GO:0016363	Component	Nuclear matrix	IEA
GO:0016607	Component	Nuclear speck	IEA
GO:0016607	Component	Nuclear speck	ISS
GO:0045893	Process	Positive regulation of DNA-templated transcription	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0048863	Process	Stem cell differentiation	IEA
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	29360106
GO:0071011	Component	Precatalytic spliceosome	IBA
GO:1903241	Process	U2-type prespliceosome assembly	NAS	31744343

Other IDs

• MIM: 617846
• HGNC: 18000
• e!Ensembl: ENSG00000100410

Protein

• UniProt ID: Q7RTV0
• Protein name: PHD finger-like domain-containing protein 5A (PHD finger-like domain protein 5A) (Splicing factor 3B-associated 14 kDa protein) (SF3b14b)
• Protein function: Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs (PubMed:12234937, PubMed:27720643, PubMed:28541300, PubMed:32494006, PubMed:34822310). The 17S U2 SnRNP c
• PDB: 5IFE, 5O9Z, 5SYB, 5Z56, 5Z57, 5Z58, 5ZYA, 6AH0, 6AHD, 6EN4, 6FF4, 6FF7, 6QX9, 6Y50, 6Y5Q, 7ABG, 7ABH, 7ABI, 7B0I, 7B91, 7B92, 7B9C, 7DVQ, 7EVN, 7EVO, 7OMF, 7ONB, 7OPI, 7Q3L, 7Q4O, 7Q4P, 7QTT, 7VPX, 8CH6, 8H6E, 8H6J, 8H6K, 8H6L, 8HK1, 8I0P, 8I0R, 8I0S, 8I0T, 8I0U, 8I0V, 8QO9, 8QXD, 8QZS, 8R08, 8R09, 8R0A
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF03660	PHF5	1 → 104	PHF5-like protein	Family

• Sequence:

  MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVI
  CGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR

• Sequence length: 110

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
ASTHMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHILDHOOD ONSET ASTHMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RESPIRATORY SYSTEM DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	29566713, 30932358		★☆☆☆☆ Found in Text Mining only
Adult Medulloblastoma	Medulloblastoma	BEFREE	26109171		★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	GWASCAT_DG	30929738		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Atypical Teratoid Rhabdoid Tumor	Teratoid Rhabdoid Tumor	BEFREE	26109171		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain Neoplasms	BEFREE	23651857		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	29700004, 30932358		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	30932358	Associate	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	37845358	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	30766880	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	30932358		★☆☆☆☆ Found in Text Mining only
Childhood Medulloblastoma	Medulloblastoma	BEFREE	26109171		★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	31054974		★☆☆☆☆ Found in Text Mining only
Congenital Microtia	Congenital microtia	Pubtator	33811463	Associate	★☆☆☆☆ Found in Text Mining only
Ewings sarcoma-primitive neuroectodermal tumor (PNET)	Ewing sarcoma	BEFREE	26109171		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	30932358		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	30932358	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	23651857, 30932358		★☆☆☆☆ Found in Text Mining only
Kidney Neoplasms	Kidney neoplasm	Pubtator	25638191	Associate	★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	30766880		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	29700004, 30932358		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	30932358		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28427184, 29700004, 31054974		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	31054974		★☆☆☆☆ Found in Text Mining only
Medulloblastoma	Medulloblastoma	BEFREE	26109171		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	23651857, 29566713, 31455041		★☆☆☆☆ Found in Text Mining only
Neuroectodermal Tumor, Primitive	Neuroectodermal Tumors	BEFREE	26109171		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	29566713, 30932358		★☆☆☆☆ Found in Text Mining only
Respiratory Distress Syndrome, Newborn	Congenital alveolar dysplasia	BEFREE	29456694		★☆☆☆☆ Found in Text Mining only
Rhabdoid Tumor	Rhabdoid Tumor	BEFREE	18580682		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	11443520		★☆☆☆☆ Found in Text Mining only
Schwannomatosis	Schwannomatosis	Pubtator	35732500	Associate	★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	37434235	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	36609277	Associate	★☆☆☆☆ Found in Text Mining only
Thoracic Diseases	Thoracic disease	Pubtator	33811463	Associate	★☆☆☆☆ Found in Text Mining only