Human Gene SCAF4 (ENST00000286835.12_7) from GENCODE V47lift37

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Description: SR-related CTD associated factor 4, transcript variant 1 (from RefSeq NM_020706.2)
Gencode Transcript: ENST00000286835.12_7
Gencode Gene: ENSG00000156304.15_11
Transcript (Including UTRs)
Position: hg19 chr21:33,043,313-33,104,431 Size: 61,119 Total Exon Count: 20 Strand: -
Coding Region
Position: hg19 chr21:33,043,712-33,104,005 Size: 60,294 Coding Exon Count: 20

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq 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 (chr21:33,043,313-33,104,431)			mRNA (may differ from genome)		Protein (1147 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	HGNC
Malacards	MGI	OMIM	PubMed	UniProtKB	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: SFR15_HUMAN DESCRIPTION: RecName: Full=Splicing factor, arginine/serine-rich 15; AltName: Full=CTD-binding SR-like protein RA4; AltName: Full=SR-related and CTD-associated factor 4; FUNCTION: May act to physically and functionally link transcription and pre-mRNA processing (By similarity). SUBUNIT: Interacts with the repetitive C-terminal domain (CTD) of RNA polymerase II (By similarity). SUBCELLULAR LOCATION: Nucleus (By similarity). SIMILARITY: Belongs to the splicing factor SR family. SIMILARITY: Contains 1 CID domain. SIMILARITY: Contains 1 RRM (RNA recognition motif) domain. SEQUENCE CAUTION: Sequence=AAD09327.1; Type=Erroneous initiation;

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

MalaCards Disease Associations


	MalaCards Gene Search: SCAF4 Diseases sorted by gene-association score: hay-wells syndrome (4), wells syndrome (2)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl C016403 2,4-dinitrotoluene D000082 Acetaminophen D000643 Ammonium Chloride D005557 Formaldehyde D007854 Lead D016912 Levonorgestrel D008628 Mercury D012643 Selenium D013749 Tetrachlorodibenzodioxin 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: 21.28 RPKM in Testis Total median expression: 551.61 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-209.30	426	-0.491	Picture	PostScript	Text
3' UTR	-80.30	399	-0.201	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
IPR008942 - ENTH_VHS
IPR012677 - Nucleotide-bd_a/b_plait
IPR006903 - RNA_pol_II-bd
IPR006569 - RNA_polymerase_II_lsu_CTD
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF04818 - CID domain

SCOP Domains:
48464 - ENTH/VHS domain
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on O95104


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	Ensembl

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003676 nucleic acid binding GO:0003723 RNA binding Cellular Component: GO:0005634 nucleus GO:0005654 nucleoplasm

Descriptions from all associated GenBank mRNAs


	LF213665 - JP 2014500723-A/21168: Polycomb-Associated Non-Coding RNAs. AF023142 - Homo sapiens pre-mRNA splicing SR protein rA4 mRNA, partial cds. BC031898 - Homo sapiens splicing factor, arginine/serine-rich 15, mRNA (cDNA clone IMAGE:4995698), with apparent retained intron. AK027017 - Homo sapiens cDNA: FLJ23364 fis, clone HEP15601. AK025748 - Homo sapiens cDNA: FLJ22095 fis, clone HEP16878. AB032998 - Homo sapiens mRNA for KIAA1172 protein, partial cds. BC043353 - Homo sapiens splicing factor, arginine/serine-rich 15, mRNA (cDNA clone MGC:49946 IMAGE:6019414), complete cds. AL834304 - Homo sapiens mRNA; cDNA DKFZp762G014 (from clone DKFZp762G014). BC014921 - Homo sapiens splicing factor, arginine/serine-rich 15, mRNA (cDNA clone MGC:17887 IMAGE:3907610), complete cds. AK308406 - Homo sapiens cDNA, FLJ98354. BC052286 - Homo sapiens splicing factor, arginine/serine-rich 15, mRNA (cDNA clone MGC:59896 IMAGE:5442227), complete cds. BC064990 - Homo sapiens splicing factor, arginine/serine-rich 15, mRNA (cDNA clone MGC:71275 IMAGE:5432277), complete cds. JD464420 - Sequence 445444 from Patent EP1572962. JD255473 - Sequence 236497 from Patent EP1572962. JD090304 - Sequence 71328 from Patent EP1572962. AL117417 - Homo sapiens mRNA; cDNA DKFZp434E098 (from clone DKFZp434E098). AK057840 - Homo sapiens cDNA FLJ25111 fis, clone CBR01747, highly similar to CTD-BINDING SR-LIKE PROTEIN RA4. JD477079 - Sequence 458103 from Patent EP1572962. JD129042 - Sequence 110066 from Patent EP1572962. JD066036 - Sequence 47060 from Patent EP1572962. JD465830 - Sequence 446854 from Patent EP1572962. JD140887 - Sequence 121911 from Patent EP1572962. MA449242 - JP 2018138019-A/21168: Polycomb-Associated Non-Coding RNAs.

Other Names for This Gene


	Alternate Gene Symbols: C9JLZ0, ENST00000286835.1, ENST00000286835.10, ENST00000286835.11, ENST00000286835.2, ENST00000286835.3, ENST00000286835.4, ENST00000286835.5, ENST00000286835.6, ENST00000286835.7, ENST00000286835.8, ENST00000286835.9, KIAA1172 , NM_020706, O95104, Q0P5W8, Q6P1M5, Q8N3I8, Q9UFM1, Q9ULP8, SCAF4 , SCAF4_HUMAN, SFRS15 , uc317klm.1, uc317klm.2 UCSC ID: ENST00000286835.12_7 RefSeq Accession: NM_020706.2 Protein: O95104 (aka SFR15_HUMAN or SFRF_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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