SCAF4 Gene
protein-coding GIFtS: 46
GCID: GC21M033044
|
|
SR-related CTD-associated factor 4(Previous names: splicing factor, arginine/serine-rich 15 )
(Previous symbol: SFRS15)
| |
Aliases
for SCAF4 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| SR-Related CTD-Associated Factor 41 2 | | SR-Related And CTD-Associated Factor 42 3 | | SFRS151 2 3 | | DKFZp434E0981 | | SRA41 2 | | Pre-MRNA Splicing SR Protein RA42 | | Splicing Factor, Arginine/Serine-Rich 151 2 | | Splicing Factor Serine Alanine 152 | | KIAA11721 3 | | SR-Like CTD-Associated Factor 42 | | CTD-Binding SR-Like Protein RA42 3 | | |
Export aliases for SCAF4 gene to outside databases |
Summaries
for SCAF4 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for SCAF4:
This gene likely encodes a member of the arginine/serine-rich splicing factor family. A similar protein in Rat appearsto 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)
UniProtKB/Swiss-Prot: SFR15_HUMAN, O95104Function: May act to physically and functionally link transcription and pre-mRNA processing (By similarity)
|
Genomic Views
for SCAF4 gene
(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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000021.8 NC_018932.1 NT_011512.11
Regulatory elements:
 Search SABiosciences Regulatory transcription factor binding sites for SCAF4
Other transcription factors
Search SABiosciences Chromatin IP Primers for SCAF4
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SCAF4 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 21q22.1 Ensembl cytogenetic band: 21q22.11 HGNC cytogenetic band: 21q22.1SCAF4 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 21 GeneLoc Exon Structure GeneLoc location for GC21M033044: view genomic region
(about GC identifiers)
Start:
|
33,043,313 bp from pter |
End:
|
33,104,431 bp from pter |
Size:
|
61,119 bases |
Orientation:
|
minus strand |
|
Proteins
for SCAF4 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
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
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: SFR15_HUMAN, O95104 (See
protein sequence)Recommended Name: Splicing factor, arginine/serine-rich 15 Size: 1147 amino acids; 125869 Da
Subunit: Interacts with the repetitive C-terminal domain (CTD) of RNA polymerase II (By similarity)
Subcellular location: Nucleus (By similarity)
Sequence caution: Sequence=AAD09327.1; Type=Erroneous initiation;
Secondary accessions: Q0P5W8 Q6P1M5 Q8N3I8 Q9UFM1 Q9ULP8Alternative splicing: 2 isoforms: O95104-1 O95104-2 (No experimental confirmation available)Explore the universe of human proteins at neXtProt for SCAF4: NX_O95104
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_O95104
SCAF4 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (3 alternative transcripts):
NP_001138916.1 NP_001138917.1 NP_065757.1
ENSEMBL proteins: ENSP00000286835 ENSP00000382703 ENSP00000402377
Human Recombinant Protein Products for SCAF4:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
SCAF4 for ontologies About GeneDecksing
SCAF4 Antibody Products:
Assay Products for SCAF4: |
Protein
Domains /
Families
for SCAF4 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
SCAF4 for domains About GeneDecksing
5 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry O95104ProtoNet protein and cluster: O95104 2 Blocks protein families: IPB000504 RNA-binding region RNP-1 (RNA recognition motif) IPB006569 Regulation of nuclear pre-mRNA protein
UniProtKB/Swiss-Prot: SFR15_HUMAN, O95104Similarity: Belongs to the splicing factor SR familySimilarity: Contains 1 CID domainSimilarity: Contains 1 RRM (RNA recognition motif) domain |
Function
for SCAF4 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
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,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Molecular Function:
UniProtKB/Swiss-Prot Summary: SFR15_HUMAN, O95104Function: May act to physically and functionally link transcription and pre-mRNA processing (By similarity) Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view): About this table
SCAF4 for ontologies About GeneDecksing
Phenotypes:
1 GenomeRNAi human phenotype for SCAF4:
Animal Models:
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SCAF4 (see all 3)
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
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Synthesis Service for SCAF4 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SCAF4 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCAF4 |
|
Pathways & Interactions
for SCAF4 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
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 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SCAF4
STRING Interaction
Network Preview (showing 4 interactants - click image to see more details)
4 Interacting proteins for SCAF4 (O951042, 3 ENSP000002868354) via UniProtKB, MINT, STRING, and/or I2DAbout this table
Gene Ontology (GO): 1 biological process term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0006397 | mRNA processing |
-- | -- |
SCAF4 for ontologies About GeneDecksing
|
Drugs & Compounds
for SCAF4 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for SCAF4
Search CenterWatch for drugs/clinical trials and news about SCAF4 / SFR15
|
Transcripts
for SCAF4 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
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,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for SCAF4 gene (3 alternative transcripts): NM_001145444.1 NM_001145445.1 NM_020706.2 Unigene Cluster for SCAF4: SR-related CTD-associated factor 4 Hs.17255 [show with all ESTs]Unigene Representative Sequence: NM_0207066 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000286835 ENST00000399804 ENST00000467731(uc002ypf.1) ENST00000472318
ENST00000485790(uc002ypg.2) ENST00000434667(uc002ypd.2 uc002ype.2 uc010glu.2)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SCAF4 (see all 5)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SCAF4 (see all 3)
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector (see all 3): SCAF4 (NM_020706) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for SCAF4 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SCAF4 |
Additional cDNA sequence: AB032998.1 AF023142.1 AK025748.1 AK027017.1 AK057840.1 AK308406.1 AL117417.1 AL834304.1 BC014921.1 BC031898.1 BC043353.1 BC052286.1 BC064990.1 12 DOTS entries: DT.99986720 DT.109029 DT.309228 DT.100022693 DT.308140 DT.92045672 DT.92427206 DT.95276510 DT.407010 DT.309229 DT.95276512 DT.99994556 24/125 AceView cDNA sequences (see all 125): BC014921 AL834304 AB032998 AI041854 CR603649 AA481081 BM461730 BC064990 BM560729 AI377920 AI352477 AK025748 AI478410 BG942498 BM463597 AA283161 BC052286 AK057840 AJ712295 BC031898 BG941180 NM_020706 CB154024 AA768387
GeneLoc Exon Structure
5/13 Alternative Splicing Database (ASD) splice patterns (SP) for SCAF4 (see all 13) About this scheme
| 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: | | | | | | | | | | | | | | | | | | | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| ExUns: | 16a | · | 16b | ^ | 17 | ^ | 18 | ^ | 19a | · | 19b | · | 19c | ^ | 20a | · | 20b | · | 20c |
|---|
|
| SP1: | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | | | | | | | | | | | |
| SP3: | | | | | | | | | | | | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | | | | | | | | |
ECgene alternative splicing isoforms for SCAF4
|
Expression
for SCAF4 gene
(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
| SCAF4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GCCCCTTTGT
About this image
See SCAF4 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SCAF4
SOURCE GeneReport for Unigene cluster: Hs.17255
SABiosciences Custom PCR Arrays for SCAF4
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SCAF4
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat SCAF4 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SCAF4 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SCAF4 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCAF4 |
Orthologs
for SCAF4 gene
(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 animals.
Orthologs for SCAF4 gene from 5/19 species (see all 19) About this table
ENSEMBL Gene Tree for SCAF4 (if available)
TreeFam Gene Tree for SCAF4 (if available) |
Paralogs
for SCAF4 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for SCAF4 gene
- SCAF82
3 SIMAP similar genes for SCAF4 using alignment to 2 protein entries: SFR15_HUMAN (see all proteins):SFRS15 RBM16 SCAF8
SCAF4 for paralogs About GeneDecksing
|
Genomic Variants
for SCAF4 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, 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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 21 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for SCAF4 (33043313 - 33104431 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for SCAF4: -- | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SCAF4 |
|
Disorders
/ Diseases
for SCAF4 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
SCAF4 for disorders About GeneDecksing
5  diseases for SCAF4: About MalaCardshay-wells syndrome wells syndrome nephropathy meningioma
leukemia
Export disorders for SCAF4 gene to outside databases
|
Publications
for SCAF4 gene (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 SCAF4 gene, integrated from 9 sources (see all 33):
(articles sorted by number of sources associating them with SCAF4) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain. (PubMed id 10574461)1, 2, 3 Hirosawa M.... Ohara O. (1999)
- Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
- The DNA sequence of human chromosome 21. (PubMed id 10830953)1, 2 Hattori M....Yaspo M.L. (2000)
- A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
- Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (2012)
- 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)
- Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
- 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)
- Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
|
External Searches for SCAF4 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing SCAF4 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing SCAF4 gene
(According to HUGE)
About This Section
| |
Specialized Databases showing SCAF4 gene(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
|
| Name | Description |
| PharmGKB entry for SCAF4 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for SCAF4 gene:
Search GeneIP for patents involving SCAF4
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for SCAF4 gene(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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
|
 | |
 | |
 |
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| |
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat SCAF4 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SCAF4 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SCAF4 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SCAF4 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SCAF4 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SCAF4 |
| |
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| |  |  |  |  | | | | |
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 | | | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCAF4 |
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| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SCAF4 |
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