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] See more...

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 4
  • SR-Related And CTD-Associated Factor 4 3 4
  • CTD-Binding SR-Like Protein RA4 3 4
  • KIAA1172 2 4
  • SFRS15 3 4
  • SRA4 2 3
  • Splicing Factor Serine Alanine 15 3
  • Pre-MRNA Splicing SR Protein RA4 3
  • SR-Like CTD-Associated Factor 4 3
  • DKFZp434E098 2
  • SCAF4 5

External Ids for SCAF4 Gene

Previous HGNC Symbols for SCAF4 Gene

  • SFRS15

Previous GeneCards Identifiers for SCAF4 Gene

  • GC21M033044
  • GC21M031671

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 Ankyloblepharon-Ectodermal Defects-Cleft Lip/Palate and Wells Syndrome. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is SCAF8.

UniProtKB/Swiss-Prot Summary for SCAF4 Gene

  • 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-functional truncated proteins (PubMed:31104839). Mechanistically, associates with the phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit (POLR2A), and subsequently binds nascent RNA upstream of early polyadenylation sites to prevent premature mRNA transcript cleavage and polyadenylation (PubMed:31104839). Independently of SCAF8, also acts as a suppressor of transcriptional readthrough (PubMed:31104839).

Additional gene information for SCAF4 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCAF4 Gene

Genomics for SCAF4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SCAF4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCAF4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCAF4

Genomic Locations for SCAF4 Gene

Genomic Locations for SCAF4 Gene
chr21:31,668,987-31,732,118
(GRCh38/hg38)
Size:
63,132 bases
Orientation:
Minus strand
chr21:33,043,313-33,104,431
(GRCh37/hg19)
Size:
61,119 bases
Orientation:
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:
    O95104-SCAF4_HUMAN
    Recommended name:
    SR-related and CTD-associated factor 4
    Protein Accession:
    O95104
    Secondary Accessions:
    • C9JLZ0
    • Q0P5W8
    • Q6P1M5
    • Q8N3I8
    • Q9UFM1
    • Q9ULP8

    Protein attributes for SCAF4 Gene

    Size:
    1147 amino acids
    Molecular mass:
    125869 Da
    Quaternary structure:
    • Interacts with POLR2A; via C-terminal heptapeptide repeat domain (CTD) phosphorylated at 'Ser-2' and 'Ser-5'.
    SequenceCaution:
    • Sequence=AAD09327.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SCAF4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCAF4 Gene

Post-translational modifications for SCAF4 Gene

  • Ubiquitination at Lys119 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

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

Protein Domains for SCAF4 Gene

InterPro:
Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)
  • Regulation of nuclear pre-mRNA protein
ProtoNet:

Suggested Antigen Peptide Sequences for SCAF4 Gene

GenScript: Design optimal peptide antigens:
  • Splicing factor, arginine/serine-rich 15 (Q0P607_HUMAN)
  • SR-related and CTD-associated factor 4 (SFR15_HUMAN)
genes like me logo Genes that share domains with SCAF4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SCAF4 Gene

Function for SCAF4 Gene

Molecular function for SCAF4 Gene

UniProtKB/Swiss-Prot 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-functional truncated proteins (PubMed:31104839). Mechanistically, associates with the phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit (POLR2A), and subsequently binds nascent RNA upstream of early polyadenylation sites to prevent premature mRNA transcript cleavage and polyadenylation (PubMed:31104839). Independently of SCAF8, also acts as a suppressor of transcriptional readthrough (PubMed:31104839).

Phenotypes From GWAS Catalog for SCAF4 Gene

Gene Ontology (GO) - Molecular Function for SCAF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,IDA 31104839
GO:0008022 protein C-terminus binding IEA --
GO:1990269 RNA polymerase II C-terminal domain phosphoserine binding IDA 31104839
genes like me logo Genes that share ontologies with SCAF4: view
genes like me logo Genes that share phenotypes with SCAF4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCAF4

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

COMPARTMENTS
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
extracellular 1
cytoskeleton 1
cytosol 1

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,IDA 31104839
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with SCAF4: view

Pathways & Interactions for SCAF4 Gene

PathCards logo

SuperPathways for SCAF4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCAF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006397 mRNA processing IEA --
GO:2000805 negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled IDA 31104839
genes like me logo Genes that share ontologies with SCAF4: view

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

mRNA/cDNA for SCAF4 Gene

3 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCAF4

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 ^
SP1:
SP2: -
SP3: -
SP4: - - -
SP5: -
SP6:
SP7: -
SP8: -
SP9: -
SP10:
SP11:
SP12:
SP13:

ExUns: 16a · 16b ^ 17 ^ 18 ^ 19a · 19b · 19c ^ 20a · 20b · 20c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11: -
SP12: - -
SP13:

Relevant External Links for SCAF4 Gene

GeneLoc Exon Structure for
SCAF4

Expression for SCAF4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for SCAF4 Gene



Protein tissue co-expression partners for SCAF4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCAF4

SOURCE GeneReport for Unigene cluster for SCAF4 Gene:

Hs.17255

Evidence on tissue expression from TISSUES for SCAF4 Gene

  • Nervous system(4.7)
  • Liver(4.4)
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
Chimpanzee
(Pan troglodytes)
Mammalia SCAF4 30 31
  • 99.85 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SCAF4 30 31
  • 92.24 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SCAF4 30 31
  • 90.51 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SCAF4 31
  • 89 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Scaf4 30 17 31
  • 88.3 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Scaf4 30
  • 83.63 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SCAF4 31
  • 80 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SCAF4 31
  • 81 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SCAF4 31
  • 68 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia scaf4 30
  • 71.13 (n)
Zebrafish
(Danio rerio)
Actinopterygii scaf4a 31
  • 49 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG4266 31
  • 26 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea nrd-1 31
  • 27 (a)
OneToMany
Species where no ortholog for SCAF4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for SCAF4 (if available)
TreeFam:
Gene Tree for SCAF4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCAF4: view image

Paralogs for SCAF4 Gene

Paralogs for SCAF4 Gene

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

  • SFR15_HUMAN
genes like me logo Genes that share paralogs with SCAF4: view

Variants for SCAF4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCAF4 Gene

SNP ID Clinical significance and condition Chr 21 pos Variation AA Info Type
rs386352359 Uncertain Significance: not provided 31,692,445(-) G/A SYNONYMOUS_VARIANT
rs12152067 - p.Ser846Tyr

Additional dbSNP identifiers (rs#s) for SCAF4 Gene

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
esv3324185 CNV insertion 20981092
esv3394837 CNV insertion 20981092
esv3450908 CNV insertion 20981092
esv3575385 CNV gain 25503493
esv992169 CNV gain 20482838
nsv1067151 CNV gain 25217958
nsv1123552 CNV deletion 24896259
nsv510792 CNV deletion 20534489
nsv519899 CNV gain 19592680
nsv820180 CNV gain 19587683
nsv834079 CNV loss 17160897
nsv953354 CNV duplication 24416366

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)

Additional Variant Information for SCAF4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCAF4

SNP Genotyping and Copy Number Assay Products

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

Disorders for SCAF4 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SCAF4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
ankyloblepharon-ectodermal defects-cleft lip/palate
  • aec
wells syndrome
  • bullous cellulitis with eosinophilia
amyotrophic lateral sclerosis 1
  • als1
- elite association - COSMIC cancer census association via MalaCards
Search SCAF4 in MalaCards View complete list of genes associated with diseases
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
  2. SCAF4 and SCAF8, mRNA Anti-Terminator Proteins. (PMID: 31104839) Gregersen LH … Svejstrup JQ (Cell 2019) 3 4
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4
  4. 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
  5. The DNA sequence of human chromosome 21. (PMID: 10830953) Hattori M … Chromosome 21 mapping and sequencing consortium (Nature 2000) 3 4

Products for SCAF4 Gene

Sources for SCAF4 Gene