SCAF1 Gene (Protein Coding)

SR-Related CTD Associated Factor 1

GC19P049645
GIFtS:
32
See more...

Aliases for SCAF1 Gene

Aliases for SCAF1 Gene

  • SR-Related CTD Associated Factor 1 2 3 5
  • Serine Arginine-Rich Pre-MRNA Splicing Factor SR-A1 3 4
  • SR-Related C-Terminal Domain-Associated Factor 1 3 4
  • Splicing Factor, Arginine/Serine-Rich 19 3 4
  • SR-Related And CTD-Associated Factor 1 3 4
  • SR-Related-CTD-Associated Factor 3 4
  • SR-A1 2 4
  • SRA1 3 4
  • SCAF 3 4
  • FLJ00034 2
  • SFRS19 4
  • SCAF1 5

External Ids for SCAF1 Gene

Previous GeneCards Identifiers for SCAF1 Gene

  • GC19P054832
  • GC19P050145
  • GC19P046523
  • GC19P049642

Summaries for SCAF1 Gene

GeneCards Summary for SCAF1 Gene

SCAF1 (SR-Related CTD Associated Factor 1) is a Protein Coding gene. Diseases associated with SCAF1 include Spinocerebellar Ataxia, Autosomal Recessive 3. Gene Ontology (GO) annotations related to this gene include RNA binding and protein domain specific binding. An important paralog of this gene is SCAF11.

UniProtKB/Swiss-Prot Summary for SCAF1 Gene

Additional gene information for SCAF1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCAF1 Gene

Genomics for SCAF1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SCAF1 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 SCAF1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCAF1

Top Transcription factor binding sites by QIAGEN in the SCAF1 gene promoter:
  • c-Myc
  • COMP1
  • Egr-1
  • Elk-1
  • Ik-3
  • LCR-F1
  • Max
  • NF-kappaB1
  • p53
  • YY1

Genomic Locations for SCAF1 Gene

Genomic Locations for SCAF1 Gene
chr19:49,640,481-49,658,642
(GRCh38/hg38)
Size:
18,162 bases
Orientation:
Plus strand
chr19:50,145,382-50,161,906
(GRCh37/hg19)
Size:
16,525 bases
Orientation:
Plus strand

Genomic View for SCAF1 Gene

Genes around SCAF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCAF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCAF1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SCAF1 Gene

Proteins for SCAF1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for SCAF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H7N4-SFR19_HUMAN
    Recommended name:
    Splicing factor, arginine/serine-rich 19
    Protein Accession:
    Q9H7N4
    Secondary Accessions:
    • Q7Z5V7
    • Q8WVA1
    • Q9NR59

    Protein attributes for SCAF1 Gene

    Size:
    1312 amino acids
    Molecular mass:
    139270 Da
    Quaternary structure:
    • Interacts with POLR2A.
    SequenceCaution:
    • Sequence=BAB15734.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

neXtProt entry for SCAF1 Gene

Protein Expression for SCAF1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SCAF1 Gene

  • Ubiquitination at Lys55, Lys158, and Lys1123
  • Modification sites at PhosphoSitePlus

Other Protein References for SCAF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SCAF1 Gene

Domains & Families for SCAF1 Gene

Gene Families for SCAF1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SCAF1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SCAF1 Gene

GenScript: Design optimal peptide antigens:
  • SCAF1 protein (Q7Z6I4_HUMAN)
  • Serine arginine-rich pre-mRNA splicing factor SR-A1 (SFR19_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H7N4

UniProtKB/Swiss-Prot:

SFR19_HUMAN :
  • Belongs to the splicing factor SR family.
Family:
  • Belongs to the splicing factor SR family.
genes like me logo Genes that share domains with SCAF1: view

Function for SCAF1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for SCAF1 Gene

UniProtKB/Swiss-Prot Function:
May function in pre-mRNA splicing.
UniProtKB/Swiss-Prot Induction:
Up-regulated by estrogens, androgens and glucocorticoids.

Phenotypes From GWAS Catalog for SCAF1 Gene

Gene Ontology (GO) - Molecular Function for SCAF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0019904 protein domain specific binding IEA --
GO:0099122 RNA polymerase II C-terminal domain binding IPI 15992770
genes like me logo Genes that share ontologies with SCAF1: view
genes like me logo Genes that share phenotypes with SCAF1: view

Animal Model Products

CRISPR Products

miRNA for SCAF1 Gene

miRTarBase miRNAs that target SCAF1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCAF1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SCAF1 Gene

Localization for SCAF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCAF1 Gene

Nucleus.

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 SCAF1 gene
Compartment Confidence
nucleus 5
cytosol 3
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCAF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with SCAF1: view

Pathways & Interactions for SCAF1 Gene

PathCards logo

SuperPathways for SCAF1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCAF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006366 transcription by RNA polymerase II IEA --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SCAF1: view

No data available for Pathways by source and SIGNOR curated interactions for SCAF1 Gene

Drugs & Compounds for SCAF1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SCAF1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SCAF1 Gene

1 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
4 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 SCAF1

Alternative Splicing Database (ASD) splice patterns (SP) for SCAF1 Gene

No ASD Table

Relevant External Links for SCAF1 Gene

GeneLoc Exon Structure for
SCAF1

Expression for SCAF1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCAF1 Gene

mRNA expression in normal human tissues for SCAF1 Gene
mRNA expression by BioGPS for SCAF1 GenemRNA expression by GTEx for SCAF1 Gene

Protein differential expression in normal tissues from HIPED for SCAF1 Gene

This gene is overexpressed in Liver, secretome (12.9), Cerebrospinal fluid (11.2), and Peripheral blood mononuclear cells (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SCAF1 Gene



Protein tissue co-expression partners for SCAF1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCAF1

SOURCE GeneReport for Unigene cluster for SCAF1 Gene:

Hs.103521

mRNA Expression by UniProt/SwissProt for SCAF1 Gene:

Q9H7N4-SFR19_HUMAN
Tissue specificity: Ubiquitous. Highly expressed in fetal brain and liver, poorly expressed in salivary gland, heart, skin and ovary. Expressed in colorectal carcinomas and ovarian cancers. Overexpressed in colorectal carcinomas as compared to normal colonic mucosa.

Evidence on tissue expression from TISSUES for SCAF1 Gene

  • Liver(4.4)
  • Spleen(4.2)
  • Lung(4.2)
  • Eye(4.2)
  • Nervous system(2.6)
  • Heart(2.5)
  • Muscle(2.5)
genes like me logo Genes that share expression patterns with SCAF1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCAF1 Gene

Orthologs for SCAF1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SCAF1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SCAF1 30 31
  • 96.78 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia SCAF1 30 31
  • 89.8 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia SCAF1 30 31
  • 89.26 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Scaf1 31
  • 78 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia SCAF1 31
  • 38 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia SCAF1 31
  • 40 (a)
 OneToOne
Zebrafish
(Danio rerio)
 Actinopterygii scaf1 31
  • 21 (a)
 OneToOne
Dr.19086 30
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.10928 30
Fruit Fly
(Drosophila melanogaster)
 Insecta CG2926 31
  • 8 (a)
 OneToMany
Corn
(Zea mays)
 Liliopsida Zm.10149 30
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 8 (a)
 OneToMany
Species where no ortholog for SCAF1 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)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SCAF1 Gene

ENSEMBL:
Gene Tree for SCAF1 (if available)
TreeFam:
Gene Tree for SCAF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCAF1: view image

Paralogs for SCAF1 Gene

Paralogs for SCAF1 Gene

genes like me logo Genes that share paralogs with SCAF1: view

Variants for SCAF1 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCAF1 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
710861 Benign: not provided 49,645,079(+) G/A MISSENSE_VARIANT
710946 Benign: not provided 49,646,556(+) G/T MISSENSE_VARIANT
769038 Benign: not provided 49,645,071(+) G/C SYNONYMOUS_VARIANT
790762 Benign: not provided 49,654,723(+) G/A SYNONYMOUS_VARIANT
rs2304208 - p.Met1146Thr

Additional dbSNP identifiers (rs#s) for SCAF1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SCAF1 Gene

Variant ID Type Subtype PubMed ID
nsv1160655 CNV deletion 26073780
nsv469715 CNV gain+loss 16826518
nsv470150 CNV gain 18288195
nsv579908 CNV loss 21841781
nsv579909 CNV loss 21841781
nsv817854 CNV gain 17921354
nsv828578 CNV loss 20364138
nsv833864 CNV gain 17160897
nsv833865 CNV gain+loss 17160897
nsv953600 CNV deletion 24416366
nsv9739 CNV gain+loss 18304495

Variation tolerance for SCAF1 Gene

Residual Variation Intolerance Score: 42.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.03; 68.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCAF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCAF1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCAF1 Gene

Disorders for SCAF1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SCAF1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
spinocerebellar ataxia, autosomal recessive 3
  • scar3
- elite association - COSMIC cancer census association via MalaCards
Search SCAF1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SCAF1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SCAF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCAF1 Gene

Publications for SCAF1 Gene

  1. Cloning of a gene (SR-A1), encoding for a new member of the human Ser/Arg-rich family of pre-mRNA splicing factors: overexpression in aggressive ovarian cancer. (PMID: 11461075) Scorilas A … Diamandis EP (British journal of cancer 2001) 2 3 4 23
  2. Expression analysis and prognostic significance of the SRA1 gene, in ovarian cancer. (PMID: 16631123) Leoutsakou T … Scorilas A (Biochemical and biophysical research communications 2006) 3 4 23
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  5. Expression of the C-terminal domain of novel human SR-A1 protein: interaction with the CTD domain of RNA polymerase II. (PMID: 15992770) Katsarou ME … Scorilas A (Biochemical and biophysical research communications 2005) 3 4

ExternalLinks

View latest publications for SCAF1 gene in Mastermind

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Sources for SCAF1 Gene