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Aliases for SCAF4 Gene

Aliases for SCAF4 Gene

  • SR-Related CTD Associated Factor 4 2 3 5
  • Splicing Factor, Arginine/Serine-Rich 15 2 3
  • CTD-Binding SR-Like Protein RA4 3 4
  • SFRS15 3 4
  • SR-Related And CTD-Associated Factor 4 4
  • Splicing Factor Serine Alanine 15 3
  • Pre-MRNA Splicing SR Protein RA4 3
  • SR-Like CTD-Associated Factor 4 3
  • KIAA1172 4
  • SRA4 3

External Ids for SCAF4 Gene

Previous HGNC Symbols for SCAF4 Gene

  • SFRS15

Previous GeneCards Identifiers for SCAF4 Gene

  • GC21M033044

Summaries for SCAF4 Gene

Entrez Gene Summary for SCAF4 Gene

  • 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 transcript variants have been described. [provided by RefSeq, Feb 2009]

GeneCards Summary for SCAF4 Gene

SCAF4 (SR-Related CTD Associated Factor 4) is a Protein Coding gene. Diseases associated with SCAF4 include Hay-Wells Syndrome and Wells Syndrome. GO annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is SCAF8.

UniProtKB/Swiss-Prot for SCAF4 Gene

  • May act to physically and functionally link transcription and pre-mRNA processing.

Additional gene information for SCAF4 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCAF4 Gene

Genomics for SCAF4 Gene

Regulatory Elements for SCAF4 Gene

Enhancers for SCAF4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH21H032492 1.4 Ensembl ENCODE dbSUPER 89.1 -762.6 -762563 4.6 PKNOX1 ZNF493 ZFP64 FEZF1 BATF RFX5 EGR1 ZNF350 FOS EGR2 PAXBP1 TMEM50B SCAF4 EVA1C C21orf59 URB1 MIS18A C21orf62-AS1 ENSG00000238390 ENSG00000252045
GH21H032258 1.2 Ensembl ENCODE 80.9 -526.4 -526383 0.6 RB1 ZNF493 ZFP64 RAD21 ZNF354C SCRT2 ZNF143 RUNX3 DEK ZNF202 PAXBP1 SCAF4 EVA1C C21orf59 URB1 MIS18A PAXBP1-AS1 C21orf62-AS1 LINC00846 ENSG00000238390
GH21H032726 1.1 ENCODE 61.6 -995.7 -995668 2.7 HDGF PKNOX1 ARNT ZFP64 ARID4B SIN3A YY1 SLC30A9 ZNF143 SP3 PAXBP1 SCAF4 SON TMEM50B MIS18A DONSON EVA1C C21orf62-AS1 GART SYNJ1
GH21H031730 1.4 FANTOM5 ENCODE 40 0.0 -32 4.1 HDGF PKNOX1 ARNT SIN3A DMAP1 ZNF766 CBX5 ZNF207 ZNF143 SP3 SCAF4 MIS18A URB1 ENSG00000238390 EVA1C SOD1 ENSG00000273091
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SCAF4 on UCSC Golden Path with GeneCards custom track

Promoters for SCAF4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000141335 618 2601 ATF1 SIN3A DMAP1 GLI4 ETS1 ZNF121 ZNF766 CBX5 ELK1 ZNF207

Genomic Locations for SCAF4 Gene

Genomic Locations for SCAF4 Gene
61,119 bases
Minus strand

Genomic View for SCAF4 Gene

Genes around SCAF4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCAF4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCAF4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCAF4 Gene

Proteins for SCAF4 Gene

  • Protein details for SCAF4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Splicing factor, arginine/serine-rich 15
    Protein Accession:
    Secondary Accessions:
    • C9JLZ0
    • Q0P5W8
    • Q6P1M5
    • Q8N3I8
    • Q9UFM1
    • Q9ULP8

    Protein attributes for SCAF4 Gene

    1147 amino acids
    Molecular mass:
    125869 Da
    Quaternary structure:
    • Interacts with the repetitive C-terminal domain (CTD) of RNA polymerase II.
    • Sequence=AAD09327.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SCAF4 Gene


neXtProt entry for SCAF4 Gene

Post-translational modifications for SCAF4 Gene

  • Ubiquitination at isoforms=2, 3119 and Lys583
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SCAF4 Gene

Domains & Families for SCAF4 Gene

Gene Families for SCAF4 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for SCAF4 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the splicing factor SR family.
  • Belongs to the splicing factor SR family.
genes like me logo Genes that share domains with SCAF4: view

Function for SCAF4 Gene

Molecular function for SCAF4 Gene

UniProtKB/Swiss-Prot Function:
May act to physically and functionally link transcription and pre-mRNA processing.

Phenotypes From GWAS Catalog for SCAF4 Gene

Gene Ontology (GO) - Molecular Function for SCAF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA,IEA 22681889
genes like me logo Genes that share ontologies with SCAF4: view
genes like me logo Genes that share phenotypes with SCAF4: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SCAF4 Gene

Localization for SCAF4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCAF4 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCAF4 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SCAF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with SCAF4: view

Pathways & Interactions for SCAF4 Gene

SuperPathways for SCAF4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCAF4 Gene


No data available for Pathways by source and SIGNOR curated interactions for SCAF4 Gene

Drugs & Compounds for SCAF4 Gene

No Compound Related Data Available

Transcripts for SCAF4 Gene

Unigene Clusters for SCAF4 Gene

SR-related CTD-associated factor 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCAF4 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b · 7c ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b · 12c · 12d ^ 13 ^ 14 ^ 15a · 15b · 15c ^
SP2: -
SP3: -
SP4: - - -
SP5: -
SP7: -
SP8: -
SP9: -

ExUns: 16a · 16b ^ 17 ^ 18 ^ 19a · 19b · 19c ^ 20a · 20b · 20c
SP11: -
SP12: - -

Relevant External Links for SCAF4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCAF4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCAF4 Gene

Protein differential expression in normal tissues from HIPED for SCAF4 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.1), Urine (8.1), and Blymphocyte (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SCAF4 Gene

Protein tissue co-expression partners for SCAF4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SCAF4 Gene:


SOURCE GeneReport for Unigene cluster for SCAF4 Gene:


Evidence on tissue expression from TISSUES for SCAF4 Gene

  • Nervous system(4.6)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with SCAF4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCAF4 Gene

Orthologs for SCAF4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SCAF4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SCAF4 33 34
  • 99.85 (n)
(Canis familiaris)
Mammalia SCAF4 33 34
  • 92.24 (n)
(Bos Taurus)
Mammalia SCAF4 33 34
  • 90.51 (n)
(Monodelphis domestica)
Mammalia SCAF4 34
  • 89 (a)
(Mus musculus)
Mammalia Scaf4 33 16 34
  • 88.3 (n)
(Rattus norvegicus)
Mammalia Scaf4 33
  • 83.63 (n)
(Ornithorhynchus anatinus)
Mammalia SCAF4 34
  • 80 (a)
(Gallus gallus)
Aves SCAF4 34
  • 81 (a)
(Anolis carolinensis)
Reptilia SCAF4 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia scaf4 33
  • 71.13 (n)
(Danio rerio)
Actinopterygii scaf4a 34
  • 49 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG4266 34
  • 26 (a)
(Caenorhabditis elegans)
Secernentea nrd-1 34
  • 27 (a)
Species where no ortholog for SCAF4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SCAF4 Gene

Gene Tree for SCAF4 (if available)
Gene Tree for SCAF4 (if available)

Paralogs for SCAF4 Gene

Paralogs for SCAF4 Gene

(2) SIMAP similar genes for SCAF4 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SCAF4: view

Variants for SCAF4 Gene

Sequence variations from dbSNP and Humsavar for SCAF4 Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
rs386352359 Uncertain significance 31,692,445(-) GTTTG(C/T)AGTAC reference, synonymous-codon
rs1000028384 -- 31,729,262(+) CTTTT(C/T)AGCAC intron-variant
rs1000078094 -- 31,693,796(+) TACTA(C/T)TGTTA intron-variant
rs1000151364 -- 31,708,614(+) TGAAA(A/G)GGGAT intron-variant
rs1000178624 -- 31,690,042(+) GTGAT(C/G/T)TTCCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SCAF4 Gene

Variant ID Type Subtype PubMed ID
esv2520415 CNV deletion 19546169
esv3306440 CNV mobile element insertion 20981092
esv3309278 CNV mobile element insertion 20981092
nsv953354 CNV duplication 24416366
nsv834079 CNV loss 17160897
nsv820180 CNV gain 19587683
nsv519899 CNV gain 19592680
nsv510792 CNV deletion 20534489
nsv1123552 CNV deletion 24896259
nsv1067151 CNV gain 25217958
esv992169 CNV gain 20482838
esv3575385 CNV gain 25503493
esv3450908 CNV insertion 20981092
esv3394837 CNV insertion 20981092
esv3324185 CNV insertion 20981092

Variation tolerance for SCAF4 Gene

Residual Variation Intolerance Score: 6.49% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.20; 39.81% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SCAF4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCAF4 Gene

Disorders for SCAF4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SCAF4 Gene - From: GeneCards

Disorder Aliases PubMed IDs
hay-wells syndrome
  • ankyloblepharon-ectodermal defects-cleft lip/palate syndrome
wells syndrome
  • bullous cellulitis with eosinophilia
- elite association - COSMIC cancer census association via MalaCards
Search SCAF4 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SCAF4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SCAF4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCAF4 Gene

Publications for SCAF4 Gene

  1. Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain. (PMID: 10574461) Hirosawa M … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 60
  2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 60
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  4. The DNA sequence of human chromosome 21. (PMID: 10830953) Hattori M … Chromosome 21 mapping and sequencing consortium (Nature 2000) 3 4 60
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60

Products for SCAF4 Gene

Sources for SCAF4 Gene

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