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	57466
Gene name	SR-related CTD associated factor 4
Gene symbol	SCAF4
Synonyms (NCBI Gene)	FZSSFRS15SRA4
Chromosome	21
Chromosome location	21q22.11
Summary	This gene likely encodes a member of the arginine/serine-rich splicing factor family. A similar protein in Rat appears to bind the large subunit of RNA polymerase II and provide a link between transcription and pre-mRNA splicing. Alternatively spliced tra

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Show/Hide all (154)

miRTarBase ID	miRNA	Experiments	Reference
MIRT031980	hsa-miR-16-5p	Proteomics	18668040
MIRT032458	hsa-let-7b-5p	Proteomics	18668040
MIRT031980	hsa-miR-16-5p	CLASH	23622248
MIRT050312	hsa-miR-25-3p	CLASH	23622248
MIRT043389	hsa-miR-331-3p	CLASH	23622248
MIRT521187	hsa-miR-369-3p	PAR-CLIP	23446348
MIRT521186	hsa-miR-5692b	PAR-CLIP	23446348
MIRT521185	hsa-miR-5692c	PAR-CLIP	23446348
MIRT521183	hsa-miR-4508	PAR-CLIP	23446348
MIRT521184	hsa-miR-17-3p	PAR-CLIP	23446348
MIRT521182	hsa-miR-744-5p	PAR-CLIP	23446348
MIRT521180	hsa-miR-6090	PAR-CLIP	23446348
MIRT521181	hsa-miR-6829-5p	PAR-CLIP	23446348
MIRT521179	hsa-miR-185-3p	PAR-CLIP	23446348
MIRT521178	hsa-miR-374c-5p	PAR-CLIP	23446348
MIRT521177	hsa-miR-655-3p	PAR-CLIP	23446348
MIRT439657	hsa-miR-374a-5p	PAR-CLIP	23446348
MIRT521176	hsa-miR-374b-5p	PAR-CLIP	23446348
MIRT439657	hsa-miR-374a-5p	HITS-CLIP	22473208
MIRT439657	hsa-miR-374a-5p	HITS-CLIP	22473208
MIRT521187	hsa-miR-369-3p	PAR-CLIP	23446348
MIRT521186	hsa-miR-5692b	PAR-CLIP	23446348
MIRT521185	hsa-miR-5692c	PAR-CLIP	23446348
MIRT521183	hsa-miR-4508	PAR-CLIP	23446348
MIRT521184	hsa-miR-17-3p	PAR-CLIP	23446348
MIRT521182	hsa-miR-744-5p	PAR-CLIP	23446348
MIRT521180	hsa-miR-6090	PAR-CLIP	23446348
MIRT521181	hsa-miR-6829-5p	PAR-CLIP	23446348
MIRT521179	hsa-miR-185-3p	PAR-CLIP	23446348
MIRT521178	hsa-miR-374c-5p	PAR-CLIP	23446348
MIRT521177	hsa-miR-655-3p	PAR-CLIP	23446348
MIRT439657	hsa-miR-374a-5p	PAR-CLIP	23446348
MIRT521176	hsa-miR-374b-5p	PAR-CLIP	23446348
MIRT1327725	hsa-miR-1224-5p	CLIP-seq
MIRT1327726	hsa-miR-1304	CLIP-seq
MIRT1327727	hsa-miR-2052	CLIP-seq
MIRT1327728	hsa-miR-28-5p	CLIP-seq
MIRT1327729	hsa-miR-3139	CLIP-seq
MIRT1327730	hsa-miR-3150b-3p	CLIP-seq
MIRT1327731	hsa-miR-3915	CLIP-seq
MIRT1327732	hsa-miR-4689	CLIP-seq
MIRT1327733	hsa-miR-4784	CLIP-seq
MIRT1327734	hsa-miR-5096	CLIP-seq
MIRT1327735	hsa-miR-708	CLIP-seq
MIRT1327736	hsa-miR-1207-3p	CLIP-seq
MIRT1327725	hsa-miR-1224-5p	CLIP-seq
MIRT1327737	hsa-miR-1226	CLIP-seq
MIRT1327738	hsa-miR-1279	CLIP-seq
MIRT1327726	hsa-miR-1304	CLIP-seq
MIRT1327739	hsa-miR-1323	CLIP-seq
MIRT1327727	hsa-miR-2052	CLIP-seq
MIRT1327740	hsa-miR-2277-5p	CLIP-seq
MIRT1327741	hsa-miR-2355-5p	CLIP-seq
MIRT1327728	hsa-miR-28-5p	CLIP-seq
MIRT1327742	hsa-miR-3120-3p	CLIP-seq
MIRT1327729	hsa-miR-3139	CLIP-seq
MIRT1327730	hsa-miR-3150b-3p	CLIP-seq
MIRT1327743	hsa-miR-374a	CLIP-seq
MIRT1327744	hsa-miR-374b	CLIP-seq
MIRT1327745	hsa-miR-374c	CLIP-seq
MIRT1327731	hsa-miR-3915	CLIP-seq
MIRT1327746	hsa-miR-4286	CLIP-seq
MIRT1327747	hsa-miR-4634	CLIP-seq
MIRT1327732	hsa-miR-4689	CLIP-seq
MIRT1327733	hsa-miR-4784	CLIP-seq
MIRT1327748	hsa-miR-545	CLIP-seq
MIRT1327749	hsa-miR-548o	CLIP-seq
MIRT1327750	hsa-miR-548p	CLIP-seq
MIRT1327751	hsa-miR-655	CLIP-seq
MIRT1327752	hsa-miR-664	CLIP-seq
MIRT1327735	hsa-miR-708	CLIP-seq
MIRT1327753	hsa-miR-744	CLIP-seq
MIRT1327738	hsa-miR-1279	CLIP-seq
MIRT1327754	hsa-miR-129-5p	CLIP-seq
MIRT1327739	hsa-miR-1323	CLIP-seq
MIRT1327755	hsa-miR-2113	CLIP-seq
MIRT1327756	hsa-miR-30a	CLIP-seq
MIRT1327757	hsa-miR-30b	CLIP-seq
MIRT1327758	hsa-miR-30c	CLIP-seq
MIRT1327759	hsa-miR-30d	CLIP-seq
MIRT1327760	hsa-miR-30e	CLIP-seq
MIRT1327761	hsa-miR-4474-3p	CLIP-seq
MIRT1327749	hsa-miR-548o	CLIP-seq
MIRT1327752	hsa-miR-664	CLIP-seq
MIRT1327736	hsa-miR-1207-3p	CLIP-seq
MIRT1327737	hsa-miR-1226	CLIP-seq
MIRT1327740	hsa-miR-2277-5p	CLIP-seq
MIRT1327742	hsa-miR-3120-3p	CLIP-seq
MIRT1327743	hsa-miR-374a	CLIP-seq
MIRT1327744	hsa-miR-374b	CLIP-seq
MIRT1327745	hsa-miR-374c	CLIP-seq
MIRT1327746	hsa-miR-4286	CLIP-seq
MIRT1327747	hsa-miR-4634	CLIP-seq
MIRT2097291	hsa-miR-508-5p	CLIP-seq
MIRT1327748	hsa-miR-545	CLIP-seq
MIRT1327750	hsa-miR-548p	CLIP-seq
MIRT1327751	hsa-miR-655	CLIP-seq
MIRT2097292	hsa-miR-665	CLIP-seq
MIRT1327753	hsa-miR-744	CLIP-seq
MIRT2321625	hsa-miR-1208	CLIP-seq
MIRT1327740	hsa-miR-2277-5p	CLIP-seq
MIRT2321626	hsa-miR-23a	CLIP-seq
MIRT2321627	hsa-miR-23b	CLIP-seq
MIRT2321628	hsa-miR-23c	CLIP-seq
MIRT1327742	hsa-miR-3120-3p	CLIP-seq
MIRT2321629	hsa-miR-3121-3p	CLIP-seq
MIRT1327743	hsa-miR-374a	CLIP-seq
MIRT1327744	hsa-miR-374b	CLIP-seq
MIRT1327745	hsa-miR-374c	CLIP-seq
MIRT1327747	hsa-miR-4634	CLIP-seq
MIRT2097291	hsa-miR-508-5p	CLIP-seq
MIRT1327734	hsa-miR-5096	CLIP-seq
MIRT2321630	hsa-miR-597	CLIP-seq
MIRT1327751	hsa-miR-655	CLIP-seq
MIRT2097292	hsa-miR-665	CLIP-seq
MIRT2321631	hsa-miR-668	CLIP-seq
MIRT1327753	hsa-miR-744	CLIP-seq
MIRT1327742	hsa-miR-3120-3p	CLIP-seq
MIRT1327743	hsa-miR-374a	CLIP-seq
MIRT1327744	hsa-miR-374b	CLIP-seq
MIRT1327745	hsa-miR-374c	CLIP-seq
MIRT1327751	hsa-miR-655	CLIP-seq
MIRT1327736	hsa-miR-1207-3p	CLIP-seq
MIRT1327725	hsa-miR-1224-5p	CLIP-seq
MIRT1327737	hsa-miR-1226	CLIP-seq
MIRT1327726	hsa-miR-1304	CLIP-seq
MIRT1327727	hsa-miR-2052	CLIP-seq
MIRT1327741	hsa-miR-2355-5p	CLIP-seq
MIRT1327728	hsa-miR-28-5p	CLIP-seq
MIRT1327729	hsa-miR-3139	CLIP-seq
MIRT1327730	hsa-miR-3150b-3p	CLIP-seq
MIRT2617971	hsa-miR-3200-3p	CLIP-seq
MIRT1327731	hsa-miR-3915	CLIP-seq
MIRT1327746	hsa-miR-4286	CLIP-seq
MIRT1327747	hsa-miR-4634	CLIP-seq
MIRT1327732	hsa-miR-4689	CLIP-seq
MIRT2617972	hsa-miR-4724-3p	CLIP-seq
MIRT1327733	hsa-miR-4784	CLIP-seq
MIRT1327734	hsa-miR-5096	CLIP-seq
MIRT2617973	hsa-miR-582-5p	CLIP-seq
MIRT2617974	hsa-miR-600	CLIP-seq
MIRT1327735	hsa-miR-708	CLIP-seq
MIRT1327725	hsa-miR-1224-5p	CLIP-seq
MIRT1327726	hsa-miR-1304	CLIP-seq
MIRT1327727	hsa-miR-2052	CLIP-seq
MIRT1327728	hsa-miR-28-5p	CLIP-seq
MIRT1327729	hsa-miR-3139	CLIP-seq
MIRT1327730	hsa-miR-3150b-3p	CLIP-seq
MIRT1327731	hsa-miR-3915	CLIP-seq
MIRT1327732	hsa-miR-4689	CLIP-seq
MIRT2617972	hsa-miR-4724-3p	CLIP-seq
MIRT1327733	hsa-miR-4784	CLIP-seq
MIRT1327734	hsa-miR-5096	CLIP-seq
MIRT1327735	hsa-miR-708	CLIP-seq

Show/Hide all (15)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	HDA	22681889
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IDA	31104839
GO:0003723	Function	RNA binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	31104839
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:1990269	Function	RNA polymerase II C-terminal domain phosphoserine binding	IBA
GO:1990269	Function	RNA polymerase II C-terminal domain phosphoserine binding	IDA	31104839
GO:1990269	Function	RNA polymerase II C-terminal domain phosphoserine binding	IEA
GO:2000805	Process	Negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled	IBA
GO:2000805	Process	Negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled	IDA	31104839
GO:2000805	Process	Negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled	IEA

MIM	HGNC	e!Ensembl
616023	19304	ENSG00000156304

O95104

Protein name

SR-related and CTD-associated factor 4 (CTD-binding SR-like protein RA4) (Splicing factor, arginine/serine-rich 15)

Protein function

Anti-terminator protein required to prevent early mRNA termination during transcription (PubMed:31104839). Together with SCAF8, acts by suppressing the use of early, alternative poly(A) sites, thereby preventing the accumulation of non-functiona

PDB

6XKB

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04818	CID	5 → 131	CID domain	Domain
PF00076	RRM_1	510 → 576	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	Domain

Sequence

MDAVNAFNQELFSLMDMKPPISRAKMILITKAAIKAIKLYKHVVQIVEKFIKKCKPEYKV
PGLYVIDSIVRQSRHQFGTDKDVFGPRFSKNITATFQYLYLCPSEDKSKIVRVLNLWQKN
GVFKIEIIQPLLDMAAGTSNAAPVAENVTNNEGSPPPPVKVSSEPPTQATPNSVPAVPQL
PSSDAFAAVAQLFQTTQGQQLQQILQTFQQPPKPQSPALDNAVMAQVQAITAQLKTTPTQ
PSEQKAAFPPPEQKTAFDKKLLDRFDYDDEPEAVEESKKEDTTAVTTTAPAAAVPPAPTA
TVPAAAAPAAASPPPPQAPFGFPGDGMQQPAYTQHQNMDQFQPRMMGIQQDPMHHQVPLP
PNGQMPGFGLLPTPPFPPMAQPVIPPTPPVQQPFQASFQAQNEPLTQKPHQQEMEVEQPC
IQEVKRHMSDNRKSRSRSASRSPKRRRSRSGSRSRRSRHRRSRSRSRDRRRHSPRSRSQE
RRDREKERERRQKGLPQVKPETASVCSTTLWVGQLDKRTTQQDVASLLEEFGPIESINMI
PPRGCAYIVMVHRQDAYRALQKLSRGNYKVNQKSIKIAWALNKGIKADYKQYWDVELGVT
YIPWDKVKPEELESFCEGGMLDSDTLNPDWKGIPKKPENEVAQNGGAETSHTEPVSPIPK
PLPVPVPPIPVPAPITVPPPQVPPHQPGPPVVGALQPPAFTPPLGIPPPGFGPGVPPPPP
PPPFLRPGFNPMHLPPGFLPPGPPPPITPPVSIPPPHTPPISIPNSTIAGINEDTTKDLS
IGNPIPTVVSGARGNAESGDSVKMYGSAVPPAAPTNLPTPPVTQPVSLLGTQGVAPGPVI
GLQAPSTGLLGARPGLIPLQRPPGMPPPHLQRFPLMPPRPMPPHMMHRGPPPGPGGFAMP
PPHGMKGPFPPHGPFVRPGGMPGLGGPGPGPGGPEDRDGRQQPPQQPQQQPQPQAPQQPQ
QQQQQQPPPSQQPPPTQQQPQQFRNDNRQQFNSGRDQERFGRRSFGNRVENDRERYGNRN
DDRDNSNRDRREWGRRSPDRDRHRDLEERNRRSSGHRDRERDSRDRESRREKEEARGKEK
PEVTDRAGGNKTVEPPISQVGNVDTASELEKGVSEAAVLKPSEELPAEATSSVEPEKDSG
SAAEAPR

Sequence length

1147

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 Causal Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the kidney	Pathogenic	rs2516765465	RCV002468778	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Complex neurodevelopmental disorder	Pathogenic	rs2123578933	RCV002272959	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Fliedner-Zweier syndrome	Pathogenic; Likely pathogenic	rs2123586296, rs868454222, rs2516753687, rs2516811789, rs2516811028, rs2516811898, rs2516724533, rs2516760777, rs2050589119, rs2050182643	RCV003328485 RCV003328495 RCV003448511 RCV003494048 RCV003596250 RCV003595848 RCV004437808 RCV004566481 RCV003328481 RCV003328482	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Intellectual disability	Pathogenic	rs2123557653, rs2516774500	RCV001843812 RCV002287610	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Multicystic kidney dysplasia	Pathogenic	rs2516765465	RCV002468778	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies	Likely pathogenic	rs2516760898	RCV003444181	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rare syndromic intellectual disability	Pathogenic	rs2123586296	RCV001814626	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SCAF4-associated mental retardation	Pathogenic	rs2050538888	RCV001250423	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SCAF4-related disorder	Likely pathogenic	rs2516779304, rs770737101, rs2516777715	RCV003399714 RCV003416704 RCV003400447	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (8)

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.
AMYOTROPHIC LATERAL SCLEROSIS 1	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL ANOMALY OF THE KIDNEY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neurodevelopmental disorder	Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCAF4-associated Neurodevelopmental disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (7)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Amyotrophic Lateral Sclerosis	Associate	35034660	★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Associate	37891035	★★★★★ ★☆☆☆☆ Found in Text Mining only
DNA Virus Infections	Associate	27184836	★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Associate	37891035	★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Associate	34400640	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Associate	17914031	★★★★★ ★☆☆☆☆ Found in Text Mining only
Seizures	Associate	37891035	★★★★★ ★☆☆☆☆ Found in Text Mining only

SCAF4 (SR-related CTD associated factor 4)