Human Gene SCAF11 (ENST00000369367.8_9) from GENCODE V47lift37

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Description: SR-related CTD associated factor 11 (from RefSeq NM_004719.3)
Gencode Transcript: ENST00000369367.8_9
Gencode Gene: ENSG00000139218.18_14
Transcript (Including UTRs)
Position: hg19 chr12:46,312,914-46,384,357 Size: 71,444 Total Exon Count: 15 Strand: -
Coding Region
Position: hg19 chr12:46,315,831-46,357,950 Size: 42,120 Coding Exon Count: 14

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr12:46,312,914-46,384,357)			mRNA (may differ from genome)		Protein (1463 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	HGNC
MGI	OMIM	PubMed	UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: SCAFB_HUMAN DESCRIPTION: RecName: Full=Protein SCAF11; AltName: Full=CTD-associated SR protein 11; AltName: Full=Renal carcinoma antigen NY-REN-40; AltName: Full=SC35-interacting protein 1; AltName: Full=SR-related and CTD-associated factor 11; AltName: Full=SRSF2-interacting protein; AltName: Full=Serine/arginine-rich splicing factor 2-interacting protein; AltName: Full=Splicing factor, arginine/serine-rich 2-interacting protein; AltName: Full=Splicing regulatory protein 129; Short=SRrp129; FUNCTION: Plays a role in pre-mRNA alternative splicing by regulating spliceosome assembly. SUBUNIT: Interacts with SRSF2/SFRS2, U2AF2 and SNRNP70. SUBCELLULAR LOCATION: Nucleus. TISSUE SPECIFICITY: Widely expressed. PTM: Phosphorylated upon DNA damage, probably by ATM or ATR. SIMILARITY: Contains 1 RING-type zinc finger. SEQUENCE CAUTION: Sequence=AAC39565.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAC39565.1; Type=Frameshift; Positions=62; Sequence=AAH40951.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAH40951.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

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 D000082 Acetaminophen D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide D016604 Aflatoxin B1 D034341 Aristolochic Acids D001564 Benzo(a)pyrene D002794 Choline D003010 Clorgyline D003300 Copper D004040 Dietary Carbohydrates D004958 Estradiol more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 16.59 RPKM in Cells - EBV-transformed lymphocytes Total median expression: 301.72 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

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-97.60	243	-0.402	Picture	PostScript	Text
3' UTR	-698.80	2917	-0.240	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

InterPro Domains: Graphical view of domain structure
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

SCOP Domains:
101447 - Formin homology 2 domain (FH2 domain)
57850 - RING/U-box
57889 - Cysteine-rich domain

ModBase Predicted Comparative 3D Structure on Q99590


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003723 RNA binding GO:0005515 protein binding GO:0046872 metal ion binding Biological Process: GO:0000245 spliceosomal complex assembly GO:0000375 RNA splicing, via transesterification reactions GO:0006397 mRNA processing GO:0008380 RNA splicing Cellular Component: GO:0005634 nucleus GO:0005654 nucleoplasm GO:0005730 nucleolus GO:0016604 nuclear body

Descriptions from all associated GenBank mRNAs


	JD138026 - Sequence 119050 from Patent EP1572962. JD312747 - Sequence 293771 from Patent EP1572962. JD171122 - Sequence 152146 from Patent EP1572962. JD243272 - Sequence 224296 from Patent EP1572962. Y11251 - H.sapiens mRNA for novel member of serine-arginine domain protein, SRrp129. AF030234 - Homo sapiens splicing factor Sip1 mRNA, complete cds. JD552510 - Sequence 533534 from Patent EP1572962. JD214279 - Sequence 195303 from Patent EP1572962. JD415886 - Sequence 396910 from Patent EP1572962. JD556025 - Sequence 537049 from Patent EP1572962. JD059619 - Sequence 40643 from Patent EP1572962. JD534936 - Sequence 515960 from Patent EP1572962. JD493863 - Sequence 474887 from Patent EP1572962. JD078813 - Sequence 59837 from Patent EP1572962. JD349392 - Sequence 330416 from Patent EP1572962. AK314093 - Homo sapiens cDNA, FLJ94773, highly similar to Homo sapiens splicing factor, arginine/serine-rich 2, interacting protein (SFRS2IP), mRNA. BC141552 - Synthetic construct Homo sapiens clone IMAGE:100014549, MGC:175306 splicing factor, arginine/serine-rich 2, interacting protein (SFRS2IP) mRNA, encodes complete protein. AB463286 - Synthetic construct DNA, clone: pF1KB1891, Homo sapiens SFRS2IP gene for splicing factor, arginine/serine-rich 2, interacting protein, without stop codon, in Flexi system. BC033589 - Homo sapiens splicing factor, arginine/serine-rich 2, interacting protein, mRNA (cDNA clone IMAGE:4536747), partial cds. BC017465 - Homo sapiens splicing factor, arginine/serine-rich 2, interacting protein, mRNA (cDNA clone IMAGE:3920286). AK026473 - Homo sapiens cDNA: FLJ22820 fis, clone KAIA3937, highly similar to AF030234 Homo sapiens splicing factor Sip1 mRNA. AK302999 - Homo sapiens cDNA FLJ53255 partial cds, highly similar to SFRS2-interacting protein. AF147405 - Homo sapiens full length insert cDNA clone YP45B07. BC040951 - Homo sapiens splicing factor, arginine/serine-rich 2, interacting protein, mRNA (cDNA clone IMAGE:4429013), partial cds. JD173273 - Sequence 154297 from Patent EP1572962. JD178620 - Sequence 159644 from Patent EP1572962. BC020736 - Homo sapiens cDNA clone IMAGE:4337853. AK096682 - Homo sapiens cDNA FLJ39363 fis, clone PEBLM2006031. BC017851 - Homo sapiens splicing factor, arginine/serine-rich 2, interacting protein, mRNA (cDNA clone IMAGE:4689315), partial cds.

Other Names for This Gene


	Alternate Gene Symbols: A6NEU9, A6NLW5, CASP11, ENST00000369367.1, ENST00000369367.2, ENST00000369367.3, ENST00000369367.4, ENST00000369367.5, ENST00000369367.6, ENST00000369367.7, NM_004719, Q8IW59, Q99590, SCAFB_HUMAN, SFRS2IP, SIP1, SRSF2IP, uc318hni.1, uc318hni.2 UCSC ID: ENST00000369367.8_9 RefSeq Accession: NM_004719.3 Protein: Q99590 (aka SCAFB_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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