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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SCAF1 Gene

protein-coding   GIFtS: 45
GCID: GC19P050145

SR-Related CTD-Associated Factor 1

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
SR-Related CTD-Associated Factor 11 2     SR-Related-CTD-Associated Factor2 3
Serine Arginine-Rich Pre-MRNA Splicing Factor SR-A12 3     Splicing Factor, Arginine/Serine-Rich 192
SCAF2 3     SFRS193
SRA12 3     SR-A13
SR-Related And CTD-Associated Factor 12 3     

External Ids:    HGNC: 304031   Entrez Gene: 585062   Ensembl: ENSG000001264617   UniProtKB: Q9H7N43   

Export aliases for SCAF1 gene to outside databases

Previous GC identifers: GC19P054832 GC19P046523


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for SCAF1 Gene: 
SCAF1 (SR-related CTD-associated factor 1) is a protein-coding gene. Diseases associated with SCAF1 include colon cancer, and ovarian cancer. GO annotations related to this gene include RNA binding and protein domain specific binding. An important paralog of this gene is PHRF1.

UniProtKB/Swiss-Prot: SFR19_HUMAN, Q9H7N4
Function: May function in pre-mRNA splicing (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NT_011109.16  NC_018930.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SCAF1 gene promoter:
         Elk-1   p53   Egr-1   Ik-3   LCR-F1   YY1   Max   COMP1   NF-kappaB1   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): SCAF1 promoter sequence
   Search SABiosciences Chromatin IP Primers for SCAF1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SCAF1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.3-q13.4   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.3-q13.4

SCAF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCAF1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P050145:  view genomic region     (about GC identifiers)

Start:
50,145,382 bp from pter      End:
50,161,906 bp from pter
Size:
16,525 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SFR19_HUMAN, Q9H7N4 (See protein sequence)
Recommended Name: Splicing factor, arginine/serine-rich 19  
Size: 1312 amino acids; 139270 Da
Subunit: Interacts with POLR2A
Subcellular location: Nucleus (Probable)
Sequence caution: Sequence=BAB15734.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: Q7Z5V7 Q8WVA1 Q9NR59

Explore the universe of human proteins at neXtProt for SCAF1: NX_Q9H7N4

Explore proteomics data for SCAF1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9H7N4

  • SCAF1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SCAF1 Protein Expression
    REFSEQ proteins: NP_067051.2  
    ENSEMBL proteins: 
     ENSP00000353769   ENSP00000473210   ENSP00000472649   ENSP00000472276  

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    Cloud-Clone Corp. Proteins for SCAF1 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    SCAF1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ProtoNet protein and cluster: Q9H7N4

    UniProtKB/Swiss-Prot: SFR19_HUMAN, Q9H7N4
    Similarity: Belongs to the splicing factor SR family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SFR19_HUMAN, Q9H7N4
    Function: May function in pre-mRNA splicing (By similarity)
    Induction: Up-regulated by estrogens, androgens and glucocorticoids

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding IEA--
    GO:0019904protein domain specific binding IEA--
         
    SCAF1 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SCAF1:
     Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for SCAF1 
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    SwitchGear 3'UTR luciferase reporter plasmidSCAF1 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SCAF1

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    5/6 Interacting proteins for SCAF1 (Q9H7N42, 3 ENSP000003537694) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBQLN4Q9NRR52, 3, ENSP000003572924MINT-2875516 I2D: score=3 STRING: ENSP00000357292
    ALBP027683, ENSP000002958974I2D: score=1 STRING: ENSP00000295897
    IGHG1P018573, ENSP000003749904I2D: score=1 STRING: ENSP00000374990
    MAP4K4O958193I2D: score=2 
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006366transcription from RNA polymerase II promoter IEA--
    GO:0006397mRNA processing IEA--
    GO:0008380RNA splicing IEA--

    SCAF1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SCAF1 (SFR19)

    Search CenterWatch for drugs/clinical trials and news about SCAF1 / SFR19

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SCAF1 gene: 
    NM_021228.2  

    Unigene Cluster for SCAF1:

    SR-related CTD-associated factor 1
    Hs.103521  [show with all ESTs]
    Unigene Representative Sequence: NM_021228
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000360565(uc002poq.3) ENST00000598359 ENST00000601038 ENST00000595242

    miRNA
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    hsa-miR-877* hsa-miR-433 hsa-miR-4283 hsa-miR-198 hsa-miR-1236 hsa-miR-1207-5p hsa-miR-181a-2* hsa-miR-4301
    SwitchGear 3'UTR luciferase reporter plasmidSCAF1 3' UTR sequence
    Inhib. RNA
    Products:
         
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SCAF1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SCAF1

    Additional mRNA sequence: 

    AK024444.1 BC011662.2 BC018398.1 BC023628.2 BC053992.1 

    5 DOTS entries:

    DT.100714257  DT.101956698  DT.75189907  DT.92040703  DT.95169150 

    24/148 AceView cDNA sequences (see all 148):

    BU736329 AK024444 BE887481 BM708194 CA425278 BU625013 AW298066 CN483928 
    BQ066514 BE797361 BM976751 NM_021228 BU185377 BU175132 AA515273 BC053992 
    BM713366 BM551884 BC023628 BM916118 BM558264 BM561276 BM697966 BM674705 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SCAF1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SCAF1 Expression
    About this image


    See SCAF1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SCAF1

    SOURCE GeneReport for Unigene cluster: Hs.103521

    UniProtKB/Swiss-Prot: SFR19_HUMAN, Q9H7N4
    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

        SABiosciences Custom PCR Arrays for SCAF1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCAF1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for SCAF1 gene from 6/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Scaf11 , 5 SR-related CTD-associated factor 11, 5 82.03(n)1
    89.6(a)1
      7 (29.07 cM)5
    2332081  NM_001008422.11  NP_001008422.11 
     450029485 
    lizard
    (Anolis carolinensis)
    Reptilia SCAF16
    Uncharacterized protein
    44(a)
    1 ↔ 1
    6(80596962-80611064)
    African clawed frog
    (Xenopus laevis)
    Amphibia BJ075050.12   -- 81.64(n)    BJ075050.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.190862 Transcribed sequence with weak similarity to protein more 76.51(n)    BQ450406.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG29266
    --
    5(a)
    1 → many
    3R(1405023-1414097)
    corn
    (Zea mays)
    Liliopsida Zm.101492 Zea mays clone cbn10.pk0055.e11, mRNA sequence 74.14(n)    AY105067.1 


    ENSEMBL Gene Tree for SCAF1 (if available)
    TreeFam Gene Tree for SCAF1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SCAF1 gene
    PHRF12  SCAF112  

    SCAF1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/370 SNPs in SCAF1 are shown (see all 370)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs597560971,2
    C--50145799(+) TGGCCT/CGGATC 1 -- int12Minor allele frequency- C:0.13WA EA 122
    rs1893490941,2
    --50145900(+) TATGTC/TCCAGG 1 -- int10--------
    rs1821734581,2
    --50145901(+) ATGTCC/TCAGGG 1 -- int10--------
    rs1496353371,2
    --50146069(+) CAAGGA/GCTAAG 1 -- int10--------
    rs1147285631,2
    F--50146098(+) TAGGGG/CGTTGG 1 -- int11Minor allele frequency- C:0.08WA 118
    rs1851096001,2
    --50146134(+) AAATAC/TTGAGA 1 -- int10--------
    rs1444163821,2
    C--50146141(+) GAGATA/GTACTG 1 -- int10--------
    rs1901853001,2
    --50146328(+) AATACG/TGAAAG 1 -- int10--------
    rs607580831,2
    C--50146453(+) ATCTAC/TATTAG 1 -- int12Minor allele frequency- T:0.04WA 120
    rs1483492981,2
    --50146562(+) TTTCAC/TTGAGA 1 -- int10--------

    HapMap Linkage Disequilibrium report for SCAF1 (50145382 - 50161906 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/11 variations for SCAF1 (see all 11):    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv912269CNV Loss21882294
    dgv3973n71CNV Loss21882294
    nsv912266CNV Loss21882294
    dgv3972n71CNV Loss21882294
    nsv828578CNV Loss20364138
    nsv470150CNV Gain18288195
    nsv833864CNV Gain17160897
    nsv817854CNV Gain17921354
    nsv9739CNV Gain+Loss18304495
    nsv833865CNV Gain+Loss17160897

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    4 diseases for SCAF1:    About MalaCards
    colon cancer    ovarian cancer    breast cancer    leukemia


    SCAF1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): SCAF1
    Human Genome Epidemiology (HuGE) Navigator: SCAF1 (4 documents)

    Export disorders for SCAF1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SCAF1 gene, integrated from 9 sources (see all 31):
    (articles sorted by number of sources associating them with SCAF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    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. (PubMed id 11461075)1, 2, 3, 9 Scorilas A.... Diamandis E.P. (2001)
    2. Expression analysis and prognostic significance of the SRA1 gene, in ovarian cancer. (PubMed id 16631123)1, 2, 9 Leoutsakou T.... Scorilas A. (2006)
    3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
    4. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (2010)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. Proteome-wide identification of ubiquitylation sites b y conjugation of engineered lysine-less ubiquitin. (PubMed id 22053931)1 Oshikawa K....Nakayama K.I. (2012)
    7. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (2012)
    8. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    9. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    10. Toward an understanding of the protein interaction net work of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    NCBI Bookshelf
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 58506 HGNC: 30403 AceView: SR-A1 Ensembl:ENSG00000126461 euGenes: HUgn58506
    ECgene: SCAF1 H-InvDB: SCAF1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SCAF1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SCAF1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SCAF1 gene:
    Search GeneIP for patents involving SCAF1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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