Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	9584
Gene name	RNA binding motif protein 39
Gene symbol	RBM39
Synonyms (NCBI Gene)	CAPERCAPERalphaFSAP59HCC1RNPC2
Chromosome	20
Chromosome location	20q11.22
Summary	This gene encodes a member of the U2AF65 family of proteins. The encoded protein is found in the nucleus, where it co-localizes with core spliceosomal proteins. It has been shown to play a role in both steroid hormone receptor-mediated transcription and a

182

Show/Hide all (182)

miRTarBase ID	miRNA	Experiments	Reference
MIRT023844	hsa-miR-1-3p	Proteomics	18668040
MIRT050471	hsa-miR-22-3p	CLASH	23622248
MIRT050133	hsa-miR-26a-5p	CLASH	23622248
MIRT046886	hsa-miR-221-3p	CLASH	23622248
MIRT041834	hsa-miR-484	CLASH	23622248
MIRT439802	hsa-miR-382-5p	HITS-CLIP	24374217
MIRT439801	hsa-miR-369-5p	HITS-CLIP	24374217
MIRT439802	hsa-miR-382-5p	HITS-CLIP	24374217
MIRT439801	hsa-miR-369-5p	HITS-CLIP	24374217
MIRT1296097	hsa-miR-1273d	CLIP-seq
MIRT1296098	hsa-miR-3655	CLIP-seq
MIRT1296099	hsa-miR-3658	CLIP-seq
MIRT1296100	hsa-miR-431	CLIP-seq
MIRT1296101	hsa-miR-4452	CLIP-seq
MIRT1296102	hsa-miR-4475	CLIP-seq
MIRT1296103	hsa-miR-4658	CLIP-seq
MIRT1296104	hsa-miR-4758-5p	CLIP-seq
MIRT1296105	hsa-miR-513c	CLIP-seq
MIRT1296106	hsa-miR-514b-5p	CLIP-seq
MIRT1296107	hsa-miR-603	CLIP-seq
MIRT1296108	hsa-miR-626	CLIP-seq
MIRT1296109	hsa-miR-1321	CLIP-seq
MIRT1296110	hsa-miR-2909	CLIP-seq
MIRT1296111	hsa-miR-3162-5p	CLIP-seq
MIRT1296112	hsa-miR-4654	CLIP-seq
MIRT1296113	hsa-miR-4699-3p	CLIP-seq
MIRT1296114	hsa-miR-4739	CLIP-seq
MIRT1296115	hsa-miR-4756-5p	CLIP-seq
MIRT1296116	hsa-miR-4769-5p	CLIP-seq
MIRT1296099	hsa-miR-3658	CLIP-seq
MIRT1296103	hsa-miR-4658	CLIP-seq
MIRT1296104	hsa-miR-4758-5p	CLIP-seq
MIRT2088010	hsa-miR-1273f	CLIP-seq
MIRT2088011	hsa-miR-129-3p	CLIP-seq
MIRT2088012	hsa-miR-143	CLIP-seq
MIRT2088013	hsa-miR-203	CLIP-seq
MIRT2088014	hsa-miR-3152-5p	CLIP-seq
MIRT2088015	hsa-miR-3157-5p	CLIP-seq
MIRT2088016	hsa-miR-329	CLIP-seq
MIRT2088017	hsa-miR-337-3p	CLIP-seq
MIRT2088018	hsa-miR-3606	CLIP-seq
MIRT2088019	hsa-miR-362-3p	CLIP-seq
MIRT2088020	hsa-miR-362-5p	CLIP-seq
MIRT2088021	hsa-miR-3685	CLIP-seq
MIRT2088022	hsa-miR-384	CLIP-seq
MIRT2088023	hsa-miR-3942-3p	CLIP-seq
MIRT1296100	hsa-miR-431	CLIP-seq
MIRT2088024	hsa-miR-4330	CLIP-seq
MIRT1296102	hsa-miR-4475	CLIP-seq
MIRT2088025	hsa-miR-4494	CLIP-seq
MIRT2088026	hsa-miR-4691-3p	CLIP-seq
MIRT2088027	hsa-miR-4696	CLIP-seq
MIRT1296113	hsa-miR-4699-3p	CLIP-seq
MIRT2088028	hsa-miR-4708-5p	CLIP-seq
MIRT2088029	hsa-miR-4738-3p	CLIP-seq
MIRT2088030	hsa-miR-4770	CLIP-seq
MIRT2088031	hsa-miR-4774-3p	CLIP-seq
MIRT2088032	hsa-miR-4789-3p	CLIP-seq
MIRT2088033	hsa-miR-499a-5p	CLIP-seq
MIRT2088034	hsa-miR-500b	CLIP-seq
MIRT1296105	hsa-miR-513c	CLIP-seq
MIRT1296106	hsa-miR-514b-5p	CLIP-seq
MIRT2088035	hsa-miR-520d-5p	CLIP-seq
MIRT2088036	hsa-miR-524-5p	CLIP-seq
MIRT2088037	hsa-miR-544	CLIP-seq
MIRT1296108	hsa-miR-626	CLIP-seq
MIRT2088038	hsa-miR-643	CLIP-seq
MIRT2088039	hsa-miR-767-3p	CLIP-seq
MIRT2088040	hsa-miR-921	CLIP-seq
MIRT2088014	hsa-miR-3152-5p	CLIP-seq
MIRT2088020	hsa-miR-362-5p	CLIP-seq
MIRT2432468	hsa-miR-4645-3p	CLIP-seq
MIRT2088034	hsa-miR-500b	CLIP-seq
MIRT2432469	hsa-miR-502-5p	CLIP-seq
MIRT2432470	hsa-miR-936	CLIP-seq
MIRT2088013	hsa-miR-203	CLIP-seq
MIRT2457913	hsa-miR-892a	CLIP-seq
MIRT2088010	hsa-miR-1273f	CLIP-seq
MIRT2088011	hsa-miR-129-3p	CLIP-seq
MIRT2088012	hsa-miR-143	CLIP-seq
MIRT2609135	hsa-miR-1909	CLIP-seq
MIRT2088013	hsa-miR-203	CLIP-seq
MIRT2609136	hsa-miR-204	CLIP-seq
MIRT2609137	hsa-miR-208a	CLIP-seq
MIRT2609138	hsa-miR-208b	CLIP-seq
MIRT2609139	hsa-miR-211	CLIP-seq
MIRT2609140	hsa-miR-2117	CLIP-seq
MIRT2609141	hsa-miR-3149	CLIP-seq
MIRT2088014	hsa-miR-3152-5p	CLIP-seq
MIRT2609142	hsa-miR-323-3p	CLIP-seq
MIRT2088017	hsa-miR-337-3p	CLIP-seq
MIRT2609143	hsa-miR-346	CLIP-seq
MIRT2609144	hsa-miR-3617	CLIP-seq
MIRT2088020	hsa-miR-362-5p	CLIP-seq
MIRT1296099	hsa-miR-3658	CLIP-seq
MIRT2609145	hsa-miR-3663-5p	CLIP-seq
MIRT2609146	hsa-miR-3673	CLIP-seq
MIRT2609147	hsa-miR-3714	CLIP-seq
MIRT2609148	hsa-miR-375	CLIP-seq
MIRT2609149	hsa-miR-383	CLIP-seq
MIRT2609150	hsa-miR-3925-5p	CLIP-seq
MIRT2609151	hsa-miR-4273	CLIP-seq
MIRT2609152	hsa-miR-4279	CLIP-seq
MIRT2609153	hsa-miR-4287	CLIP-seq
MIRT2609154	hsa-miR-4292	CLIP-seq
MIRT2609155	hsa-miR-4308	CLIP-seq
MIRT1296100	hsa-miR-431	CLIP-seq
MIRT2609156	hsa-miR-4328	CLIP-seq
MIRT1296101	hsa-miR-4452	CLIP-seq
MIRT2609157	hsa-miR-4469	CLIP-seq
MIRT1296102	hsa-miR-4475	CLIP-seq
MIRT2609158	hsa-miR-4527	CLIP-seq
MIRT2432468	hsa-miR-4645-3p	CLIP-seq
MIRT2609159	hsa-miR-4677-5p	CLIP-seq
MIRT2609160	hsa-miR-4685-3p	CLIP-seq
MIRT2088027	hsa-miR-4696	CLIP-seq
MIRT2088028	hsa-miR-4708-5p	CLIP-seq
MIRT2088030	hsa-miR-4770	CLIP-seq
MIRT2609161	hsa-miR-4772-5p	CLIP-seq
MIRT2609162	hsa-miR-4773	CLIP-seq
MIRT2609163	hsa-miR-4775	CLIP-seq
MIRT2609164	hsa-miR-4799-5p	CLIP-seq
MIRT2609165	hsa-miR-494	CLIP-seq
MIRT2609166	hsa-miR-499-5p	CLIP-seq
MIRT2088034	hsa-miR-500b	CLIP-seq
MIRT2432469	hsa-miR-502-5p	CLIP-seq
MIRT1296105	hsa-miR-513c	CLIP-seq
MIRT1296106	hsa-miR-514b-5p	CLIP-seq
MIRT2609167	hsa-miR-548ac	CLIP-seq
MIRT2609168	hsa-miR-548ae	CLIP-seq
MIRT2609169	hsa-miR-548aj	CLIP-seq
MIRT2609170	hsa-miR-548am	CLIP-seq
MIRT2609171	hsa-miR-548an	CLIP-seq
MIRT2609172	hsa-miR-548d-3p	CLIP-seq
MIRT2609173	hsa-miR-548x	CLIP-seq
MIRT2609174	hsa-miR-548z	CLIP-seq
MIRT2609175	hsa-miR-568	CLIP-seq
MIRT2609176	hsa-miR-578	CLIP-seq
MIRT2609177	hsa-miR-590-3p	CLIP-seq
MIRT1296108	hsa-miR-626	CLIP-seq
MIRT2609178	hsa-miR-641	CLIP-seq
MIRT2088038	hsa-miR-643	CLIP-seq
MIRT2609179	hsa-miR-873	CLIP-seq
MIRT2432470	hsa-miR-936	CLIP-seq
MIRT2609135	hsa-miR-1909	CLIP-seq
MIRT2609140	hsa-miR-2117	CLIP-seq
MIRT2088014	hsa-miR-3152-5p	CLIP-seq
MIRT2609142	hsa-miR-323-3p	CLIP-seq
MIRT2088017	hsa-miR-337-3p	CLIP-seq
MIRT2609143	hsa-miR-346	CLIP-seq
MIRT2088020	hsa-miR-362-5p	CLIP-seq
MIRT2609145	hsa-miR-3663-5p	CLIP-seq
MIRT2609146	hsa-miR-3673	CLIP-seq
MIRT2609147	hsa-miR-3714	CLIP-seq
MIRT2609148	hsa-miR-375	CLIP-seq
MIRT2609151	hsa-miR-4273	CLIP-seq
MIRT2609152	hsa-miR-4279	CLIP-seq
MIRT2609154	hsa-miR-4292	CLIP-seq
MIRT2609155	hsa-miR-4308	CLIP-seq
MIRT1296101	hsa-miR-4452	CLIP-seq
MIRT1296102	hsa-miR-4475	CLIP-seq
MIRT2609158	hsa-miR-4527	CLIP-seq
MIRT2432468	hsa-miR-4645-3p	CLIP-seq
MIRT2609159	hsa-miR-4677-5p	CLIP-seq
MIRT2609163	hsa-miR-4775	CLIP-seq
MIRT2609164	hsa-miR-4799-5p	CLIP-seq
MIRT2609165	hsa-miR-494	CLIP-seq
MIRT2088034	hsa-miR-500b	CLIP-seq
MIRT2432469	hsa-miR-502-5p	CLIP-seq
MIRT1296105	hsa-miR-513c	CLIP-seq
MIRT1296106	hsa-miR-514b-5p	CLIP-seq
MIRT2609167	hsa-miR-548ac	CLIP-seq
MIRT2609168	hsa-miR-548ae	CLIP-seq
MIRT2609169	hsa-miR-548aj	CLIP-seq
MIRT2609170	hsa-miR-548am	CLIP-seq
MIRT2609171	hsa-miR-548an	CLIP-seq
MIRT2609172	hsa-miR-548d-3p	CLIP-seq
MIRT2609173	hsa-miR-548x	CLIP-seq
MIRT2609174	hsa-miR-548z	CLIP-seq
MIRT2609177	hsa-miR-590-3p	CLIP-seq
MIRT2609179	hsa-miR-873	CLIP-seq
MIRT2432470	hsa-miR-936	CLIP-seq

Show/Hide all (21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	15798186, 17389360, 22365833, 23602568, 25416956, 26871637, 28437394, 32296183, 32707033, 32814053, 33961781, 35271311
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS	8227358
GO:0006396	Process	RNA processing	TAS	8227358
GO:0006397	Process	MRNA processing	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0015630	Component	Microtubule cytoskeleton	IDA
GO:0016607	Component	Nuclear speck	IDA
GO:0016607	Component	Nuclear speck	IEA
GO:0016607	Component	Nuclear speck	IMP	28437394
GO:0032991	Component	Protein-containing complex	IMP	28437394
GO:0034451	Component	Centriolar satellite	IDA
GO:0048024	Process	Regulation of mRNA splicing, via spliceosome	IDA	15694343
GO:0048024	Process	Regulation of mRNA splicing, via spliceosome	IEA
GO:0048024	Process	Regulation of mRNA splicing, via spliceosome	IMP	28302793, 28437394
GO:0050733	Function	RS domain binding	IEA
GO:1990446	Function	U1 snRNP binding	IBA

MIM	HGNC	e!Ensembl
604739	15923	ENSG00000131051

Q14498

Protein name

RNA-binding protein 39 (CAPER alpha) (CAPERalpha) (Hepatocellular carcinoma protein 1) (RNA-binding motif protein 39) (RNA-binding region-containing protein 2) (Splicing factor HCC1)

Protein function

RNA-binding protein that acts as a pre-mRNA splicing factor (PubMed:15694343, PubMed:24795046, PubMed:28302793, PubMed:28437394, PubMed:31271494). Acts by promoting exon inclusion via regulation of exon cassette splicing (PubMed:31271494). Also

PDB

2JRS , 2MHN , 4OO6 , 4OZ0 , 4OZ1 , 4YUD , 6PAI , 6Q0R , 6Q0V , 6Q0W , 6SJ7 , 6UD7 , 6UE5 , 7Q33

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00076	RRM_1	155 → 223	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	Domain
PF00076	RRM_1	252 → 322	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	Domain
PF15519	RBM39linker	341 → 442	linker between RRM2 and RRM3 domains in RBM39 protein	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. Highly expressed in pancreas, skeletal muscle, lung and brain (PubMed:8227358). Expressed at intermediate level in kidney, liver and heart (PubMed:8227358). {ECO:0000269|PubMed:8227358}.

Sequence

MADDIDIEAMLEAPYKKDENKLSSANGHEERSKKRKKSKSRSRSHERKRSKSKERKRSRD
RERKKSKSRERKRSRSKERRRSRSRSRDRRFRGRYRSPYSGPKFNSAIRGKIGLPHSIKL
SRRRSRSKSPFRKDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVR
DVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMAN
NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD
SECAKKALEQLNGFELAGRPMKVGHVTERTDASSASSFLDSDELERTGIDLGTTGRLQLM
ARLAEGTGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAAASVQP
LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPS
IAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR

Sequence length

530

Interactions

View interactions

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.
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOBLASTOMA MULTIFORME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, KNEE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (28)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adenocarcinoma of pancreas	Pancreatic adenocarcinoma	BEFREE	11356193		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenoma of large intestine	Colorectal adenoma	BEFREE	22711543		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	19342371, 24621503		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	26934653	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	24643682, 35989423	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	26934653	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	24643682, 29022480		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Familial Idiopathic	Cardiomyopathy	BEFREE	24621503		★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic kidney disease stage 5	Kidney Disease	BEFREE	8551235		★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic Kidney Diseases	Kidney Disease	BEFREE	8551235		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	22711543		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	22711543	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathies	Diabetic neuropathy	Pubtator	37986381	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Invasive Ductal Breast Carcinoma	Invasive Duct and Lobular Carcinoma	BEFREE	24621503		★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Failure, Chronic	Kidney Failure	BEFREE	8551235		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	30889374	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	30799057		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukocyte adhesion deficiency type 1	Leukocyte adhesion deficiency	Pubtator	26934653	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	11356193, 29075151, 29472529, 29497780		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	24643682	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	19342371, 24621503		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	24643682, 29022480		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	24643682, 30889374, 31289203		★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	BEFREE	31289203		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	21731718, 22009261, 22711543		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	35296644	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	24643682		★★★★★ ★☆☆☆☆ Found in Text Mining only
Noninfiltrating Intraductal Carcinoma	Ductal carcinoma	BEFREE	19342371, 24621503		★★★★★ ★☆☆☆☆ Found in Text Mining only

RBM39 (RNA binding motif protein 39)