Human Gene SCAF1 (ENST00000360565.8_7) from GENCODE V47lift37
  Description: SR-related CTD associated factor 1 (from RefSeq NM_021228.3)
Gencode Transcript: ENST00000360565.8_7
Gencode Gene: ENSG00000126461.15_12
Transcript (Including UTRs)
   Position: hg19 chr19:50,145,466-50,161,899 Size: 16,434 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr19:50,148,284-50,161,656 Size: 13,373 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:50,145,466-50,161,899)mRNA (may differ from genome)Protein (1312 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SFR19_HUMAN
DESCRIPTION: RecName: Full=Splicing factor, arginine/serine-rich 19; AltName: Full=SR-related and CTD-associated factor 1; AltName: Full=SR-related-CTD-associated factor; Short=SCAF; AltName: Full=Serine arginine-rich pre-mRNA splicing factor SR-A1; Short=SR-A1;
FUNCTION: May function in pre-mRNA splicing (By similarity).
SUBUNIT: Interacts with POLR2A.
SUBCELLULAR LOCATION: Nucleus (Probable).
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.
INDUCTION: Up-regulated by estrogens, androgens and glucocorticoids.
SIMILARITY: Belongs to the splicing factor SR family.
SEQUENCE CAUTION: Sequence=BAB15734.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.58 RPKM in Brain - Cortex
Total median expression: 1028.89 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -16.7040-0.418 Picture PostScript Text
3' UTR -59.80243-0.246 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  SCOP Domains:
48371 - ARM repeat

ModBase Predicted Comparative 3D Structure on Q9H7N4
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0019904 protein domain specific binding

Biological Process:
GO:0006366 transcription from RNA polymerase II promoter
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK024444 - Homo sapiens FLJ00034 mRNA for FLJ00034 protein.
BC011662 - Homo sapiens SR-related CTD-associated factor 1, mRNA (cDNA clone IMAGE:4137959), complete cds.
JD187171 - Sequence 168195 from Patent EP1572962.
BC053992 - Homo sapiens SR-related CTD-associated factor 1, mRNA (cDNA clone MGC:45499 IMAGE:5578439), complete cds.
AB463288 - Synthetic construct DNA, clone: pF1KF0034, Homo sapiens SCAF1 gene for SR-related CTD-associated factor 1, without stop codon, in Flexi system.
KY849380 - Homo sapiens SR-related CTD associated factor 1 transcript variant 2 (SCAF1) mRNA, partial sequence.
KY849381 - Homo sapiens SR-related CTD associated factor 1 transcript variant 3 (SCAF1) mRNA, complete cds.
KY849382 - Homo sapiens SR-related CTD associated factor 1 transcript variant 4 (SCAF1) mRNA, complete cds.
KY849383 - Homo sapiens SR-related CTD associated factor 1 transcript variant 5 (SCAF1) mRNA, partial sequence.
KY849384 - Homo sapiens SR-related CTD associated factor 1 transcript variant 6 (SCAF1) mRNA, complete cds.
KY849385 - Homo sapiens SR-related CTD associated factor 1 transcript variant 7 (SCAF1) mRNA, partial sequence.
KY849386 - Homo sapiens SR-related CTD associated factor 1 transcript variant 8 (SCAF1) mRNA, partial sequence.
KY849387 - Homo sapiens SR-related CTD associated factor 1 transcript variant 9 (SCAF1) mRNA, partial sequence.
KY849388 - Homo sapiens SR-related CTD associated factor 1 transcript variant 10 (SCAF1) mRNA, partial sequence.
KY849389 - Homo sapiens SR-related CTD associated factor 1 transcript variant 11 (SCAF1) mRNA, complete cds.
KY849390 - Homo sapiens SR-related CTD associated factor 1 transcript variant 12 (SCAF1) mRNA, partial sequence.
KY849391 - Homo sapiens SR-related CTD associated factor 1 transcript variant 13 (SCAF1) mRNA, complete cds.
KY849392 - Homo sapiens SR-related CTD associated factor 1 transcript variant 14 (SCAF1) mRNA, partial sequence.
KY849393 - Homo sapiens SR-related CTD associated factor 1 transcript variant 15 (SCAF1) mRNA, complete cds.
KY849394 - Homo sapiens splicing factor, arginine/serine-rich 19 isoform 8 (SCAF1) mRNA, complete cds.
BC023628 - Homo sapiens SR-related CTD-associated factor 1, mRNA (cDNA clone IMAGE:4763654).
BC018398 - Homo sapiens SR-related CTD-associated factor 1, mRNA (cDNA clone IMAGE:3881197), partial cds.
JD408479 - Sequence 389503 from Patent EP1572962.
JD401015 - Sequence 382039 from Patent EP1572962.
JD553248 - Sequence 534272 from Patent EP1572962.
JD559403 - Sequence 540427 from Patent EP1572962.
JD065040 - Sequence 46064 from Patent EP1572962.
JD335786 - Sequence 316810 from Patent EP1572962.
JD416899 - Sequence 397923 from Patent EP1572962.
JD390593 - Sequence 371617 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000360565.1, ENST00000360565.2, ENST00000360565.3, ENST00000360565.4, ENST00000360565.5, ENST00000360565.6, ENST00000360565.7, NM_021228, Q7Z5V7, Q8WVA1, Q9H7N4, Q9NR59, SFR19_HUMAN, SFRS19, SRA1, uc318bpv.1, uc318bpv.2
UCSC ID: ENST00000360565.8_7
RefSeq Accession: NM_021228.3
Protein: Q9H7N4 (aka SFR19_HUMAN)

-  Gene Model Information
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.