SRSF1

gene
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Also known as ASFSF2SRp30aSF2p33MGC5228

Summary

SRSF1 (serine and arginine rich splicing factor 1, HGNC:10780) is a protein-coding gene on chromosome 17q22, encoding Serine/arginine-rich splicing factor 1 (Q07955). Plays a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines) and haploinsufficient (ClinGen: sufficient evidence).

This gene encodes a member of the arginine/serine-rich splicing factor protein family. The encoded protein can either activate or repress splicing, depending on its phosphorylation state and its interaction partners. Multiple transcript variants have been found for this gene. There is a pseudogene of this gene on chromosome 13.

Source: NCBI Gene 6426 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder with dysmorphic facies and behavioral abnormalities (Strong, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 20 total — 7 pathogenic, 1 likely-pathogenic
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • Transcription factor: yes — 13 downstream targets (CollecTRI)
  • MANE Select transcript: NM_006924

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10780
Approved symbolSRSF1
Nameserine and arginine rich splicing factor 1
Location17q22
Locus typegene with protein product
StatusApproved
AliasesASF, SF2, SRp30a, SF2p33, MGC5228
Ensembl geneENSG00000136450
Ensembl biotypeprotein_coding
OMIM600812
Entrez6426

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding, 3 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000258962, ENST00000578430, ENST00000581497, ENST00000581979, ENST00000582730, ENST00000583741, ENST00000584668, ENST00000584773, ENST00000585096

RefSeq mRNA: 2 — MANE Select: NM_006924 NM_001078166, NM_006924

CCDS: CCDS11600, CCDS58580

Canonical transcript exons

ENST00000258962 — 4 exons

ExonStartEnd
ENSE000034931105800634358006527
ENSE000036560615800091958005600
ENSE000036742175800580158005973
ENSE000036856255800694458007246

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 99.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 116.9632 / max 975.9728, expressed in 1825 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
167173108.16431825
1671672.23621034
1671751.6219701
1671701.0666647
1671690.9846568
1671660.8035492
1671680.7943439
1671710.4835247
2082760.4425219
1671740.3657161

Top tissues by expression

296 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402399.12gold quality
ventricular zoneUBERON:000305399.07gold quality
colonic epitheliumUBERON:000039798.71gold quality
cortical plateUBERON:000534398.46gold quality
left ovaryUBERON:000211998.21gold quality
body of uterusUBERON:000985398.10gold quality
rectumUBERON:000105298.03gold quality
adrenal tissueUBERON:001830397.96gold quality
calcaneal tendonUBERON:000370197.93gold quality
right ovaryUBERON:000211897.92gold quality
endocervixUBERON:000045897.87gold quality
right uterine tubeUBERON:000130297.68gold quality
muscle layer of sigmoid colonUBERON:003580597.68gold quality
monocyteCL:000057697.65gold quality
left uterine tubeUBERON:000130397.62gold quality
adenohypophysisUBERON:000219697.62gold quality
ectocervixUBERON:001224997.61gold quality
left lobe of thyroid glandUBERON:000112097.58gold quality
esophagogastric junction muscularis propriaUBERON:003584197.46gold quality
right lobe of thyroid glandUBERON:000111997.43gold quality
minor salivary glandUBERON:000183097.36gold quality
lower esophagusUBERON:001347397.34gold quality
lower esophagus muscularis layerUBERON:003583397.34gold quality
left adrenal gland cortexUBERON:003582597.32gold quality
right coronary arteryUBERON:000162597.28gold quality
small intestine Peyer’s patchUBERON:000345497.27gold quality
left adrenal glandUBERON:000123497.25gold quality
transverse colonUBERON:000115797.23gold quality
mononuclear cellCL:000084297.21gold quality
metanephros cortexUBERON:001053397.21gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-10yes16.72
E-ANND-3yes10.71
E-MTAB-6819no1442.81
E-GEOD-93593no6.73

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

13 targets.

TargetRegulation
AURKA
AURKB
COL1A1
HNRNPH1
HNRNPL
MYCUnknown
NFKB1Repression
RRM2
RSRC2
SRSF1
SRSF2
SRSF7
VIM

Upstream regulators (CollecTRI, top): E2F6, MYC, NR5A1, SRSF1, SRSF2

miRNA regulators (miRDB)

265 targeting SRSF1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3646100.0073.565283
HSA-MIR-3064-3P100.0070.091254
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-5692A100.0074.406850
HSA-MIR-5193100.0067.261744
HSA-MIR-188-3P100.0068.761240
HSA-MIR-4713-3P100.0065.92505
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-9-5P100.0072.282361
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-548P99.9872.253784
HSA-MIR-23B-5P99.9866.07587
HSA-MIR-477599.9875.006394
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-520D-5P99.9873.344883

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 40)

  • encodes for a repressor domain required for its inhibitor activity on pre-mRNA splicing (PMID:11801589)
  • acts as a potent regulator of G alpha(s) isoform expression (PMID:11825891)
  • ASF/SF2 plays an important role in viral RNA expression and splicing at the proximal 3’ splice site. (PMID:12525645)
  • c-Src splicing activation by SF2/ASF is dependent on the N1 exon enhancer element. The activity of these exonic splicing regulators, SF2/ASF and hnRNP A1, is linked to the splicing of an exon primarily controlled by intronic factors. (PMID:12612063)
  • SR proteins 9G8, SC35, ASF/SF2, and SRp40 have effects on the utilization of the A1 to A5 splicing sites of HIV-1 RNA (PMID:15123677)
  • activates the ESE (exon splicing enhancer) which regulates HIV-1 rev, env, vpu, and nef gene expression (PMID:15163745)
  • hypophosphorylation of ASF in mRNPs coincides with its higher affinity for TAP (PMID:15184380)
  • splicing of beta-tropomyosin exon 6B is repressed by hnRNP A1, and activated by ASF/SF2 and SC35 (PMID:15208309)
  • SR proteins 9G8 and ASF/SF2 exhibit higher affinity for TAP/NXF1 when hypophosphorylated (PMID:15210956)
  • SF2/ASF is part of a complex that forms upon the 79-nucleotide negative regulatory element (NRE) that is thought to be pivotal in posttranscriptional regulation of late gene expression in human papillomavirus type 16 (PMID:15367627)
  • SR proteins ASF/SF2, SC35 and 9G8 can down-regulate the late steps of HIV-1 replication via negative impact on RNA splicing and virion production. (PMID:15907217)
  • The vivo depletion of ASF/SF2 results in a hypermutation phenotype likely due to DNA rearrangements, reflected in the rapid appearance of DNA double-strand breaks and high-molecular-weight DNA fragments. (PMID:16096057)
  • Data suggest that RS-domain phosphorylation may influence the association of splicing factor 2/alternative splicing factor with mRNA, whereas RRM2 may play an important role in mediating protein-protein interactions during translation. (PMID:16210245)
  • ASF/SF2 is phosphorylated by SRPK1 and Clk/Sty (PMID:16223727)
  • ASF/SF2 inactivation results in a G2-phase cell cycle arrest and subsequent programmed cell death; however, internucleosomal DNA fragmentation is not detected. (PMID:16260492)
  • identified SRp30a as an RNA trans-acting factor that functions as a major regulator of caspase-9 pre-mRNA processing and is required for ceramide to mediate the alternative splicing of caspase-9 (PMID:16505493)
  • In this work we report the identification of a strong SF2/ASF binding site within exon 7 of the human fibrinogen Bbeta-chain gene (FGB). (PMID:16611940)
  • Data demonstrate that CDC2L5 is located in the nucleoplasm, where it directly interacts with the ASF/SF2-associated protein p32, a protein involved in splicing regulation. (PMID:16721827)
  • Splicing factor SF2/ASF is upregulated in various human tumors, in part due to amplification of its gene, SFRS1. (PMID:17310252)
  • a novel role for SR proteins in promoting RSV polyadenylation in the context of the NRS-3’ splice site complex, which is thought to bridge the long distance between the NRS and poly(A) site. (PMID:17670832)
  • data provide additional evidence that the SF2/ASF RS domain is not strictly required for constitutive splicing in vitro, contrary to prevailing models for how the domains of SR proteins function to promote splicing (PMID:17786225)
  • RNPS1 is able to function together with ASF/SF2 to form ribonucleoprotein complexes on nascent transcripts, and thereby prevent formation of transcriptional R-loops. (PMID:17959926)
  • These studies reveal that SRPK1 docks near the C-terminus of the RS1 segment of ASF protein and then moves in an N-terminal direction along the RS domain. (PMID:18155240)
  • Increased TAP binding correlates with increased SF2/ASF binding, but not increased REF/Aly or Y14 binding. (PMID:18243119)
  • ASF/SF2 and SRp55 appear to interact with the variable TF exon 5 through exonic splicing enhancers at bases 39 and 87-117. Weakening of the above ESE modulates splicing of TF exon 5. (PMID:18315555)
  • SF2/ASF promotes translation initiation of bound mRNAs; this activity requires the presence of the cytoplasmic cap-binding protein eIF4E. (PMID:18439897)
  • poly(ADP-ribose) targeting of topoisomerase I and ASF/SF2 functions may participate in the regulation of gene expression (PMID:18495665)
  • Growth hormone deficiency and splicing fidelity: two serine/arginine-rich proteins, ASF/SF2 and SC35, act antagonistically (PMID:18586677)
  • Data show that adaptable molecular interactions guide phosphorylation of the SR protein ASF/SF2 by SRPK1. (PMID:18687337)
  • SF2/ASF splicing factor activates the mTORC1 branch of the pathway (PMID:18832178)
  • data presented here indicate that SF2/ASF has the capacity to co-regulate the nuclear and cytoplasmic processing of specific mRNAs and provide further evidence that the nuclear history of an mRNA may influence its cytoplasmic fate (PMID:18841201)
  • The authors demonstrate that the HPV16 E2 transcription factor transactivates the SF2/ASF promoter. (PMID:18945764)
  • ASF/SF2 and PPAR-gamma determines the ratio of UCP3 isoforms. (PMID:19073146)
  • These research data identify APC mutation c.1918C>G (pR640G) as pathogenic and indicate a mechanism involving disruption of an ASF/SF2 exonic splicing enhancer element. (PMID:19111562)
  • SFRS1 may broadly influence the post-transcriptional control of gene expression in vivo. (PMID:19116412)
  • ASF/SF2, associate with interphase chromatin, is released from hyperphosphorylated mitotic chromosomes, but reassociate with chromatin late in M-phase (PMID:19250906)
  • role for SF2/ASF as a regulator of alternative translation, meaning the generation of different proteins by the balance among two translation initiation mechanisms (PMID:19441081)
  • confirm the interactions of eEF1A1, p54(nrb), hnRNP-L, GAPDH and ASF/SF2 with the right terminal stem-loop domain of HDV genomic RNA in vitro (PMID:19464723)
  • while local RS/SR content steers regional preferences in the RS domain, distal contacts with SRPK1 guide initiation and directional phosphorylation within these regions. (PMID:19477182)
  • ASF/SF2 and SRp20 are two antagonistic splicing factors regulating Rac1b expression in colorectal tumor cells. (PMID:19602482)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosrsf1bENSDARG00000017843
danio_reriosrsf1aENSDARG00000057691
mus_musculusSrsf1ENSMUSG00000018379
rattus_norvegicusSrsf1ENSRNOG00000050323

Paralogs (8): SRSF5 (ENSG00000100650), RSRC2 (ENSG00000111011), SRSF9 (ENSG00000111786), SRSF3 (ENSG00000112081), SRSF7 (ENSG00000115875), SRSF4 (ENSG00000116350), RSRP1 (ENSG00000117616), SRSF6 (ENSG00000124193)

Protein

Protein identifiers

Serine/arginine-rich splicing factor 1Q07955 (reviewed: Q07955)

Alternative names: Alternative-splicing factor 1, Splicing factor, arginine/serine-rich 1, pre-mRNA-splicing factor SF2, P33 subunit

All UniProt accessions (5): Q07955, J3KSR8, J3KSW7, J3KTL2, J3QQV5

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5’- and 3’-splice site binding components, U1 snRNP and U2AF. Can stimulate binding of U1 snRNP to a 5’-splice site-containing pre-mRNA. Binds to purine-rich RNA sequences, either the octamer, 5’-RGAAGAAC-3’ (r=A or G) or the decamers, AGGACAGAGC/AGGACGAAGC. Binds preferentially to the 5’-CGAGGCG-3’ motif in vitro. Three copies of the octamer constitute a powerful splicing enhancer in vitro, the ASF/SF2 splicing enhancer (ASE) which can specifically activate ASE-dependent splicing. Isoform ASF-2 and isoform ASF-3 act as splicing repressors. May function as export adapter involved in mRNA nuclear export through the TAP/NXF1 pathway.

Subunit / interactions. Consists of two polypeptides of p32 and p33. Identified in the spliceosome C complex. Component of a ribonucleoprotein complex containing mRNAs and RNA-binding proteins including DDX5, HNRNPH2 and SRSF1 as well as splicing regulator ARVCF. In vitro, self-associates and binds SRSF2, SNRNP70 and U2AF1 but not U2AF2. Binds SREK1/SFRS12. Interacts with SAFB/SAFB1. Interacts with PSIP1/LEDGF. Interacts with RSRC1 (via Arg/Ser-rich domain). Interacts with ZRSR2/U2AF1-RS2. Interacts with CCDC55 (via C-terminus). Interacts with SRPK1 and a sliding docking interaction is essential for its sequential and processive phosphorylation by SRPK1. Interacts with NXF1. Interacts with CCNL1, CCNL2 and CDK11B. Interacts with RRP1B. Interacts (when phosphorylated in its RS domain) with TNPO3; promoting nuclear import. Interacts with ILDR1 (via C-terminus) and ILDR2.

Subcellular location. Cytoplasm. Nucleus speckle.

Post-translational modifications. Phosphorylated by CLK1, CLK2, CLK3 and CLK4. Phosphorylated by SRPK1 at multiple serines in its RS domain via a directional (C-terminal to N-terminal) and a dual-track mechanism incorporating both processive phosphorylation (in which the kinase stays attached to the substrate after each round of phosphorylation) and distributive phosphorylation steps (in which the kinase and substrate dissociate after each phosphorylation event). The RS domain of SRSF1 binds to a docking groove in the large lobe of the kinase domain of SRPK1 and this induces certain structural changes in SRPK1 and/or RRM 2 domain of SRSF1, allowing RRM 2 to bind the kinase and initiate phosphorylation. The cycles continue for several phosphorylation steps in a processive manner (steps 1-8) until the last few phosphorylation steps (approximately steps 9-12). During that time, a mechanical stress induces the unfolding of the beta-4 motif in RRM 2, which then docks at the docking groove of SRPK1. This also signals RRM 2 to begin to dissociate, which facilitates SRSF1 dissociation after phosphorylation is completed. Asymmetrically dimethylated at arginines, probably by PRMT1, methylation promotes localization to nuclear speckles.

Disease relevance. Neurodevelopmental disorder with dysmorphic facies and behavioral abnormalities (NEDFBA) [MIM:620489] An autosomal dominant disorder characterized by developmental delay, intellectual disability, speech delay, hypotonia, behavioral abnormalities, and non-specific dysmorphic facial features. Some patients have variable skeletal and cardiac anomalies. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The RRM 2 domain plays an important role in governing both the binding mode and the phosphorylation mechanism of the RS domain by SRPK1. RS domain and RRM 2 are uniquely positioned to initiate a highly directional (C-terminus to N-terminus) phosphorylation reaction in which the RS domain slides through an extended electronegative channel separating the docking groove of SRPK1 and the active site. RRM 2 binds toward the periphery of the active site and guides the directional phosphorylation mechanism. Both the RS domain and an RRM domain are required for nucleocytoplasmic shuttling.

Miscellaneous. May be due to intron retention.

Similarity. Belongs to the splicing factor SR family.

Isoforms (3)

UniProt IDNamesCanonical?
Q07955-1ASF-1yes
Q07955-2ASF-2
Q07955-3ASF-3

RefSeq proteins (2): NP_001071634, NP_008855* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000504RRM_domDomain
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR029538SRSF1_RRM2Domain
IPR034520SRSF1_RRM1Domain
IPR035979RBD_domain_sfHomologous_superfamily
IPR050374RRT5_SRSF_SRFamily

Pfam: PF00076

UniProt features (84 total): modified residue 21, strand 16, mutagenesis site 15, sequence variant 11, helix 6, splice variant 3, region of interest 3, domain 2, cross-link 2, compositionally biased region 2, initiator methionine 1, chain 1, turn 1

Structure

Experimental structures (PDB)

10 structures.

PDBMethodResolution (Å)
4C0OX-RAY DIFFRACTION2.56
3BEGX-RAY DIFFRACTION2.9
8QO9ELECTRON MICROSCOPY5.29
7ABGELECTRON MICROSCOPY7.8
9R8VELECTRON MICROSCOPY8.5
1X4ASOLUTION NMR
2M7SSOLUTION NMR
2M8DSOLUTION NMR
2O3DSOLUTION NMR
6HPJSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q07955-F171.990.37

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (23): 2, 38, 93, 93, 97, 97, 109, 109, 111, 133, 179, 199, 201, 202, 205, 207, 209, 231, 234, 238 …

Mutagenesis-validated functional residues (15):

PositionPhenotype
58–59in fv1; loss of ability to activate splicing. slight reduction in splice site switching activity and no effect on rna-bi
93predominantly localizes to cytoplasm and fails to modulate splicing of endogenous pre-mrnas; when associated with ala-97
97predominantly localizes to cytoplasm and fails to modulate splicing of endogenous pre-mrnas; when associated with ala-93
109predominantly localizes to cytoplasm and fails to modulate splicing of endogenous pre-mrnas; when associated with ala-93
162–163in fv2; loss of ability to activate splicing. great reduction in splice site switching activity and rna-binding.
162in av; loss of ability to activate splicing. great reduction in splice site switching activity and no effect on rna-bind
162reduced nucleocytoplasmic shuttling; when associated with d-190.
180reduced nucleocytoplasmic shuttling; when associated with d-162.
182–248in mr-b; strongly inhibits splicing.
182–199in mr-e; loss of ability to activate splicing.
192–248in mr-a; loss of ability to activate splicing.
192–199in mr-d; loss of ability to activate splicing.
199–224in rs-a; loss of ability to activate splicing but retains splice site switching.
215–248in rs-c; loss of ability to activate splicing but retains splice site switching.
226–248in rs-b; retains both splice activation and splice site switching activity.

Function

Pathways and Gene Ontology

Reactome pathways

13 pathways

IDPathway
R-HSA-159236Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-72163mRNA Splicing - Major Pathway
R-HSA-72165mRNA Splicing - Minor Pathway
R-HSA-72187mRNA 3’-end processing
R-HSA-72203Processing of Capped Intron-Containing Pre-mRNA
R-HSA-9770562mRNA Polyadenylation
R-HSA-9918481Dengue Virus-Host Interactions
R-HSA-73856RNA Polymerase II Transcription Termination
R-HSA-72172mRNA Splicing
R-HSA-72202Transport of Mature Transcript to Cytoplasm
R-HSA-73857RNA Polymerase II Transcription
R-HSA-74160Gene expression (Transcription)
R-HSA-8953854Metabolism of RNA

MSigDB gene sets: 496 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, E2F_Q4, MORF_DNMT1, ELVIDGE_HYPOXIA_DN, E2F_Q4_01, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, MORF_SMC1L1, TGCGCANK_UNKNOWN, E2F4DP1_01, GOBP_CIRCULATORY_SYSTEM_PROCESS, MORF_BUB1, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, BASSO_B_LYMPHOCYTE_NETWORK

GO Biological Process (20): alternative mRNA splicing, via spliceosome (GO:0000380), regulation of alternative mRNA splicing, via spliceosome (GO:0000381), mRNA 5’-splice site recognition (GO:0000395), mRNA splicing, via spliceosome (GO:0000398), in utero embryonic development (GO:0001701), mRNA splice site recognition (GO:0006376), mRNA processing (GO:0006397), signal transduction involved in regulation of gene expression (GO:0023019), positive regulation of RNA splicing (GO:0033120), protein localization to nucleus (GO:0034504), regulation of RNA splicing (GO:0043484), mRNA stabilization (GO:0048255), oligodendrocyte differentiation (GO:0048709), mRNA transport (GO:0051028), cardiac muscle contraction (GO:0060048), interleukin-17-mediated signaling pathway (GO:0097400), liver regeneration (GO:0097421), protein localization to P-body (GO:0110012), RNA splicing (GO:0008380), cellular response to interleukin-17 (GO:0097398)

GO Molecular Function (7): RNA binding (GO:0003723), mRNA binding (GO:0003729), protein kinase B binding (GO:0043422), DNA topoisomerase binding (GO:0044547), RS domain binding (GO:0050733), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (8): nucleus (GO:0005634), nuclear envelope (GO:0005635), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear speck (GO:0016607), catalytic step 2 spliceosome (GO:0071013), spliceosomal complex (GO:0005681), exon-exon junction complex (GO:0035145)

Reactome top-level categories

Rollup of top-8 pathways:

CategoryPathways
Processing of Capped Intron-Containing Pre-mRNA3
mRNA Splicing2
Transport of Mature Transcript to Cytoplasm1
Metabolism of RNA1
mRNA 3’-end processing1
Dengue Virus Infection1
RNA Polymerase II Transcription1
Gene expression (Transcription)1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
regulation of gene expression2
RNA splicing2
protein localization to organelle2
binding2
cellular anatomical structure2
nuclear protein-containing complex2
mRNA splicing, via spliceosome1
alternative mRNA splicing, via spliceosome1
regulation of mRNA splicing, via spliceosome1
mRNA splice site recognition1
mRNA cis splicing, via spliceosome1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
chordate embryonic development1
spliceosomal complex assembly1
protein-RNA complex assembly1
mRNA metabolic process1
signal transduction1
positive regulation of gene expression1
regulation of RNA splicing1
regulation of primary metabolic process1
regulation of mRNA stability1
RNA stabilization1
negative regulation of mRNA catabolic process1
central nervous system development1
glial cell differentiation1
RNA transport1
striated muscle contraction1
heart contraction1
cytokine-mediated signaling pathway1
cellular response to interleukin-171
liver development1
animal organ regeneration1
cellular response to cytokine stimulus1
response to interleukin-171
nucleic acid binding1
RNA binding1
protein kinase binding1
enzyme binding1

Protein interactions and networks

STRING

4722 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SRSF1H3C1P02295988
SRSF1SNRNP70P08621985
SRSF1H3-3AP06351981
SRSF1PSIP1O75475953
SRSF1H3-4Q16695952
SRSF1H3-7Q5TEC6952
SRSF1H3-5Q6NXT2952
SRSF1H3C14Q71DI3950
SRSF1SRPK1Q96SB4949
SRSF1U2AF2P26368942
SRSF1TNPO3Q9Y5L0940
SRSF1U2AF1Q01081938
SRSF1HNRNPA1P09651935
SRSF1SRSF2Q01130930
SRSF1NXF1Q9UBU9913

IntAct

323 interactions, top by confidence:

ABTypeScore
NFYANFYBpsi-mi:“MI:0915”(physical association)0.840
NFYANFYBpsi-mi:“MI:0914”(association)0.840
SRSF1NXF1psi-mi:“MI:0915”(physical association)0.810
NXF1SRSF1psi-mi:“MI:0915”(physical association)0.810
SCYL1SEC31Apsi-mi:“MI:0914”(association)0.710
SNRPD2GEMIN2psi-mi:“MI:0914”(association)0.710
RRP1BSRSF1psi-mi:“MI:0915”(physical association)0.650
RRP1BSRSF1psi-mi:“MI:0403”(colocalization)0.650
EIF4A3HNRNPA1psi-mi:“MI:0914”(association)0.640
NCBP1KPNA3psi-mi:“MI:0914”(association)0.640
U2AF1SRSF1psi-mi:“MI:0915”(physical association)0.620
U2AF1SRSF1psi-mi:“MI:2364”(proximity)0.620
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
SNRNP70SRSF1psi-mi:“MI:0915”(physical association)0.600
SNRNP70SRSF1psi-mi:“MI:2364”(proximity)0.600
SRSF1psi-mi:“MI:0403”(colocalization)0.600
SRSF1psi-mi:“MI:0915”(physical association)0.600
SRSF1psi-mi:“MI:0403”(colocalization)0.600
NFYASRSF1psi-mi:“MI:0915”(physical association)0.600

BioGRID (783): SRSF1 (Affinity Capture-MS), SRSF1 (Affinity Capture-Western), SRSF1 (Affinity Capture-RNA), SRSF1 (Affinity Capture-RNA), SRSF1 (Affinity Capture-RNA), SRSF1 (Affinity Capture-MS), SRSF1 (Affinity Capture-MS), SRSF1 (Affinity Capture-MS), SRSF1 (Affinity Capture-MS), SRSF1 (Affinity Capture-MS), SRSF1 (Affinity Capture-MS), SRSF1 (Affinity Capture-MS), SRSF1 (Affinity Capture-MS), SRSF1 (Affinity Capture-MS), LNX1 (Two-hybrid)

ESM2 similar proteins: A2RVS6, F4JHI7, O22315, O75494, O81126, O81127, P30352, P84103, P84104, P92964, P92965, P92966, Q01130, Q06A98, Q07955, Q09511, Q0VCY7, Q10021, Q13242, Q13595, Q16629, Q18409, Q23120, Q23121, Q3MHR5, Q3SZR8, Q3T106, Q3YLA6, Q5PPI1, Q5R1W5, Q5R7H2, Q62093, Q69KL9, Q6DII2, Q6K4N0, Q6K9C3, Q6NYA0, Q6PDM2, Q6PDU1, Q6PFR5

Diamond homologs: A0A0D1DZT6, A2RVS6, A5A6M3, D4AE41, F4JHI7, G3V6S8, O22315, O22703, O35326, O75494, O81127, O93235, P19682, P26686, P28644, P30352, P33240, P38159, P60824, P60825, P60826, P78814, P84103, P84104, P84586, P92964, Q01130, Q02427, Q04836, Q06AT9, Q07955, Q08170, Q09167, Q0VCY7, Q10021, Q13242, Q13243, Q13247, Q14011, Q16629

SIGNOR signaling

14 interactions.

AEffectBMechanism
DYRK1AunknownSRSF1phosphorylation
PRKACAup-regulatesSRSF1phosphorylation
SRSF1up-regulatesAlternative_Splicing_Regulation
IRAK2“down-regulates activity”SRSF1phosphorylation
NEK2“down-regulates activity”SRSF1phosphorylation
CDK11B“up-regulates activity”SRSF1phosphorylation
CLK1“up-regulates activity”SRSF1phosphorylation
SRPK2“up-regulates activity”SRSF1phosphorylation
SRPK1up-regulatesSRSF1phosphorylation
SRP54“up-regulates activity”SRSF1binding
CLK2“up-regulates activity”SRSF1phosphorylation
CLK3“up-regulates activity”SRSF1phosphorylation
CLK4“up-regulates activity”SRSF1phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 179 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex527.1×4e-05
Metabolism of non-coding RNA525.6×5e-05
Abortive elongation of HIV-1 transcript in the absence of Tat520.0×1e-04
RNA Polymerase II Transcription Termination814.2×5e-06
Formation of the Early Elongation Complex513.5×5e-04
Formation of the HIV-1 Early Elongation Complex513.5×5e-04
HIV Transcription Elongation513.5×5e-04
RHO GTPases activate PKNs512.8×6e-04

GO biological processes:

GO termPartnersFoldFDR
negative regulation of transcription elongation by RNA polymerase II525.0×2e-04
spliceosomal snRNP assembly622.8×4e-05
mRNA export from nucleus713.5×1e-04
regulation of alternative mRNA splicing, via spliceosome812.8×4e-05
autophagosome maturation511.5×7e-03
mitophagy510.4×8e-03
mRNA splicing, via spliceosome1710.2×9e-10
regulation of RNA splicing710.0×6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

20 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic7
Likely pathogenic1
Uncertain significance10
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (8)

Variant IDHGVSClassification
2429775NM_006924.5(SRSF1):c.377_378del (p.Ser126fs)Pathogenic
2429776NM_006924.5(SRSF1):c.208G>A (p.Ala70Thr)Pathogenic
2429777NM_006924.5(SRSF1):c.231T>G (p.Tyr77Ter)Pathogenic
2429778NM_006924.5(SRSF1):c.251T>G (p.Leu84Arg)Pathogenic
2429784NM_006924.5(SRSF1):c.82C>T (p.Arg28Ter)Pathogenic
2429786NM_006924.5(SRSF1):c.119G>T (p.Gly40Val)Pathogenic
2429787NM_006924.5(SRSF1):c.97G>T (p.Glu33Ter)Pathogenic
3377265NM_006924.5(SRSF1):c.366_367del (p.Arg122fs)Likely pathogenic

SpliceAI

1144 predictions. Top by Δscore:

VariantEffectΔscore
17:58005969:CAGTC:Cacceptor_gain1.0000
17:58005970:AGTC:Aacceptor_gain1.0000
17:58005971:GTC:Gacceptor_gain1.0000
17:58005972:TC:Tacceptor_gain1.0000
17:58005973:CC:Cacceptor_gain1.0000
17:58005974:C:CCacceptor_gain1.0000
17:58006338:CTCA:Cdonor_loss1.0000
17:58006339:TCACC:Tdonor_loss1.0000
17:58006340:CA:Cdonor_loss1.0000
17:58006341:A:ACdonor_gain1.0000
17:58006341:A:AGdonor_loss1.0000
17:58006342:C:Adonor_loss1.0000
17:58006342:C:CCdonor_gain1.0000
17:58006523:CGTCT:Cacceptor_gain1.0000
17:58006526:CT:Cacceptor_gain1.0000
17:58006537:C:CTacceptor_gain1.0000
17:58006909:ATTT:Adonor_gain1.0000
17:58006942:A:ACdonor_gain1.0000
17:58006943:C:CCdonor_gain1.0000
17:58006961:A:ACdonor_gain1.0000
17:58006962:A:Cdonor_gain1.0000
17:58003773:C:CTacceptor_gain0.9900
17:58004012:A:Tacceptor_gain0.9900
17:58005794:AACCT:Adonor_loss0.9900
17:58005796:CCT:Cdonor_loss0.9900
17:58005797:CTACC:Cdonor_loss0.9900
17:58005798:TAC:Tdonor_loss0.9900
17:58005799:AC:Adonor_loss0.9900
17:58005819:A:ACdonor_gain0.9900
17:58005982:G:Cacceptor_gain0.9900

AlphaMissense

1587 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:58005806:G:CH183D1.000
17:58005813:A:CF180L1.000
17:58005813:A:TF180L1.000
17:58005814:A:GF180S1.000
17:58005815:A:GF180L1.000
17:58005829:A:GL175P1.000
17:58005841:G:TA171E1.000
17:58005867:A:CF162L1.000
17:58005867:A:TF162L1.000
17:58005868:A:CF162C1.000
17:58005868:A:GF162S1.000
17:58005869:A:GF162L1.000
17:58005880:C:TG158D1.000
17:58005881:C:GG158R1.000
17:58005904:G:TA150D1.000
17:58005905:C:GA150P1.000
17:58005913:A:TV147E1.000
17:58005919:C:AG145V1.000
17:58005919:C:TG145D1.000
17:58005920:C:GG145R1.000
17:58005928:C:GR142P1.000
17:58005929:G:AR142C1.000
17:58005929:G:TR142S1.000
17:58005935:G:CH140D1.000
17:58005936:A:CD139E1.000
17:58005936:A:TD139E1.000
17:58005937:T:AD139V1.000
17:58005937:T:CD139G1.000
17:58005937:T:GD139A1.000
17:58005938:C:GD139H1.000

dbSNP variants (sampled 300 via entrez): RS1000187288 (17:57996837 A>C,G), RS1000191054 (17:57994134 A>G), RS1000255549 (17:57990028 T>C), RS1000286552 (17:57990465 C>A), RS1000313370 (17:57993579 G>T), RS1000390268 (17:58005730 AC>A), RS1000891438 (17:58007666 C>G), RS1000894838 (17:57996609 T>G), RS1000962650 (17:57988574 C>A,T), RS1001078570 (17:57988680 C>G,T), RS1001243110 (17:58003465 C>A,T), RS1001474886 (17:58003020 A>G), RS1001551336 (17:58007470 C>A,T), RS1001775426 (17:58009217 C>T), RS1001836922 (17:57992021 A>G)

Disease associations

OMIM: gene MIM:600812 | disease phenotypes: MIM:620489

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorder with dysmorphic facies and behavioral abnormalitiesStrongAutosomal dominant

Mondo (3): intellectual disability (MONDO:0001071), neurodevelopmental disorder with dysmorphic facies and behavioral abnormalities (MONDO:0957583), autism spectrum disorder (MONDO:0005258)

Orphanet (2): NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658), NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST010396_130Gut microbiota (bacterial taxa, hurdle binary method)2.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007874gut microbiome measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4295805 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1232461MOLIBRESIB21,538

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

6 potent at pChembl≥5 of 6 total, top 6 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.25Kd56.22nMCHEMBL5653589
7.25ED5056.22nMCHEMBL5653589
5.58Kd2650nMMOLIBRESIB
5.40IC504000nMMOLIBRESIB
5.04Kd9124nMCHEMBL3752910
5.04ED509124nMCHEMBL3752910

PubChem BioAssay actives

4 with measured affinity, of 12 total; 3 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149490: Binding affinity to human SRSF1 incubated for 45 mins by Kinobead based pull down assaykd0.0562uM
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide2179156: Binding affinity against SFRS1 (unknown origin) assessed as apparent dissociation constant incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysiskd2.6500uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149490: Binding affinity to human SRSF1 incubated for 45 mins by Kinobead based pull down assaykd9.1245uM

CTD chemical–gene interactions

83 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression5
cobaltous chloridedecreases expression3
Cadmium Chlorideincreases methylation, decreases expression, increases abundance, increases expression3
bisphenol Adecreases expression, increases expression2
sodium arsenitedecreases expression, increases expression2
Acetaminophendecreases expression2
Cisplatinincreases expression2
Copperaffects binding, decreases expression2
Doxorubicindecreases expression, increases response to substance2
Estradiolincreases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
biochanin Adecreases expression1
methylmercuric chloridedecreases expression1
alpha-pineneincreases oxidation, increases abundance, affects cotreatment1
deoxynivalenolincreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, decreases expression1
hexamethylene bisacetamideincreases expression1
arseniteaffects binding, decreases reaction1
methylparabendecreases expression1
afimoxifenedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
perfluorooctanoic aciddecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
coumarindecreases phosphorylation1
methacrylaldehydeincreases oxidation, increases abundance, affects cotreatment1
diallyl trisulfideincreases expression1
cyclic 3’,5’-uridine monophosphateaffects binding1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1

ChEMBL screening assays

9 unique, capped per target: 9 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4155373BindingBinding affinity to serine/arginine-rich-splicing factor 1 in human A549 cells at 0.15 mM after 4 hrs by HPLC-MS based pull down assay relative to controlSynthesis, cytotoxic evaluation and target identification of thieno[2,3-d]pyrimidine derivatives with a dithiocarbamate side chain at C2 position. — Eur J Med Chem

Clinical trials (associated diseases)

197 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459Not specifiedACTIVE_NOT_RECRUITINGAutism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081Not specifiedCOMPLETEDDevelopment and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502Not specifiedCOMPLETEDEnhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277Not specifiedCOMPLETEDDiabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754Not specifiedCOMPLETEDWeight Management for Adolescents With IDD
NCT02591446Not specifiedCOMPLETEDTranscranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868Not specifiedCOMPLETEDEvaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394Not specifiedUNKNOWNFCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614Not specifiedCOMPLETEDPsychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405Not specifiedCOMPLETEDTMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders