Human Gene SREK1 (ENST00000334121.11_7) from GENCODE V47lift37
  Description: splicing regulatory glutamic acid and lysine rich protein 1, transcript variant 7 (from RefSeq NM_001323533.2)
Gencode Transcript: ENST00000334121.11_7
Gencode Gene: ENSG00000153914.16_13
Transcript (Including UTRs)
   Position: hg19 chr5:65,440,128-65,479,443 Size: 39,316 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr5:65,440,205-65,474,696 Size: 34,492 Coding Exon Count: 12 

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 (chr5:65,440,128-65,479,443)mRNA (may differ from genome)Protein (624 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SREK1_HUMAN
DESCRIPTION: RecName: Full=Splicing regulatory glutamine/lysine-rich protein 1; AltName: Full=Serine/arginine-rich-splicing regulatory protein 86; Short=SRrp86; AltName: Full=Splicing factor, arginine/serine-rich 12; AltName: Full=Splicing regulatory protein 508; Short=SRrp508;
FUNCTION: Participates in the regulation of alternative splicing by modulating the activity of other splice facors. Inhibits the splicing activity of SFRS1, SFRS2 and SFRS6. Augments the splicing activity of SFRS3 (By similarity).
SUBUNIT: Homodimer. Binds SFRS1, SFRS2, SFRS3 and SFRS6. Interacts with the spliceosome (By similarity). Interacts with SREK1IP1.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the splicing factor SR family.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SEQUENCE CAUTION: Sequence=AAH47322.1; 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           more ... click here to view the complete list

+  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: 22.68 RPKM in Thyroid
Total median expression: 591.16 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -30.9077-0.401 Picture PostScript Text
3' UTR -1163.304747-0.245 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q8WXA9
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-  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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000381 regulation of alternative mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AK308287 - Homo sapiens cDNA, FLJ98235.
BC017000 - Homo sapiens splicing factor, arginine/serine-rich 12, mRNA (cDNA clone IMAGE:4422249), with apparent retained intron.
AK091758 - Homo sapiens cDNA FLJ34439 fis, clone HLUNG2001146, highly similar to Splicing factor, arginine/serine-rich 12.
AX747166 - Sequence 691 from Patent EP1308459.
BC047322 - Homo sapiens, Similar to expressed sequence AI450757, clone IMAGE:5415800, mRNA, partial cds.
BC067770 - Homo sapiens splicing factor, arginine/serine-rich 12, mRNA (cDNA clone MGC:87089 IMAGE:4827589), complete cds.
AF459094 - Homo sapiens splicing factor, arginine/serine-rich 12 (SFRS12) mRNA, complete cds.
JD384874 - Sequence 365898 from Patent EP1572962.
AL832888 - Homo sapiens mRNA; cDNA DKFZp667P103 (from clone DKFZp667P103).
JD490584 - Sequence 471608 from Patent EP1572962.
BC112343 - Homo sapiens splicing factor, arginine/serine-rich 12, mRNA (cDNA clone MGC:133045 IMAGE:40008558), complete cds.
JD154398 - Sequence 135422 from Patent EP1572962.
KJ895563 - Synthetic construct Homo sapiens clone ccsbBroadEn_04957 SREK1 gene, encodes complete protein.
AB209694 - Homo sapiens mRNA for splicing factor, arginine/serine-rich 12 variant protein.
AK125893 - Homo sapiens cDNA FLJ43905 fis, clone TESTI4010475, weakly similar to Rattus norvegicus serine-arginine-rich splicing regulatory protein 86 (Srrp86).
JD259059 - Sequence 240083 from Patent EP1572962.
JD437465 - Sequence 418489 from Patent EP1572962.
JD362769 - Sequence 343793 from Patent EP1572962.
JD452522 - Sequence 433546 from Patent EP1572962.
JD315064 - Sequence 296088 from Patent EP1572962.
JD410460 - Sequence 391484 from Patent EP1572962.
JD330255 - Sequence 311279 from Patent EP1572962.
JD513062 - Sequence 494086 from Patent EP1572962.
JD269036 - Sequence 250060 from Patent EP1572962.
JD530706 - Sequence 511730 from Patent EP1572962.
JD202807 - Sequence 183831 from Patent EP1572962.
JD243845 - Sequence 224869 from Patent EP1572962.
JD243097 - Sequence 224121 from Patent EP1572962.
AL049309 - Homo sapiens mRNA; cDNA DKFZp564B176 (from clone DKFZp564B176).
JD249489 - Sequence 230513 from Patent EP1572962.
JD168526 - Sequence 149550 from Patent EP1572962.
JD498955 - Sequence 479979 from Patent EP1572962.
JD142729 - Sequence 123753 from Patent EP1572962.
JD268865 - Sequence 249889 from Patent EP1572962.
JD044008 - Sequence 25032 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A4FTW3, ENST00000334121.1, ENST00000334121.10, ENST00000334121.2, ENST00000334121.3, ENST00000334121.4, ENST00000334121.5, ENST00000334121.6, ENST00000334121.7, ENST00000334121.8, ENST00000334121.9, NM_001323533, Q2M1J0, Q86X37, Q8WXA9, SFRS12, SREK1_HUMAN, SRRP86, uc317tvq.1, uc317tvq.2
UCSC ID: ENST00000334121.11_7
RefSeq Accession: NM_001077199.3
Protein: Q8WXA9 (aka SREK1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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