Human Gene U2SURP (ENST00000473835.7_9) from GENCODE V47lift37
  Description: U2 snRNP associated SURP domain containing, transcript variant 4 (from RefSeq NM_001320222.2)
Gencode Transcript: ENST00000473835.7_9
Gencode Gene: ENSG00000163714.18_19
Transcript (Including UTRs)
   Position: hg19 chr3:142,720,412-142,779,567 Size: 59,156 Total Exon Count: 28 Strand: +
Coding Region
   Position: hg19 chr3:142,720,471-142,775,292 Size: 54,822 Coding Exon Count: 28 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:142,720,412-142,779,567)mRNA (may differ from genome)Protein (1029 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SR140_HUMAN
DESCRIPTION: RecName: Full=U2 snRNP-associated SURP motif-containing protein; AltName: Full=140 kDa Ser/Arg-rich domain protein; AltName: Full=U2-associated protein SR140;
SUBUNIT: Interacts with ERBB4.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the splicing factor SR family.
SIMILARITY: Contains 1 CID domain.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SIMILARITY: Contains 1 SURP motif repeat.
SEQUENCE CAUTION: Sequence=AAH16323.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAI05605.1; 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: 23.56 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 563.57 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 -18.4059-0.312 Picture PostScript Text
3' UTR -989.504275-0.231 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
IPR013170 - mRNA_splic_Cwf21
IPR012677 - Nucleotide-bd_a/b_plait
IPR006569 - RNA_polymerase_II_lsu_CTD
IPR000504 - RRM_dom
IPR000061 - Surp

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF01805 - Surp module
PF04818 - CID domain
PF08312 - cwf21 domain

SCOP Domains:
48464 - ENTH/VHS domain
109905 - Surp module (SWAP domain)
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on O15042
FrontTopSide
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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGD  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:0000398 mRNA splicing, via spliceosome
GO:0006396 RNA processing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  BC111692 - Homo sapiens U2-associated SR140 protein, mRNA (cDNA clone MGC:133197 IMAGE:40028600), complete cds.
LF384581 - JP 2014500723-A/192084: Polycomb-Associated Non-Coding RNAs.
AK296440 - Homo sapiens cDNA FLJ60621 complete cds.
BC028110 - Homo sapiens U2-associated SR140 protein, mRNA (cDNA clone IMAGE:5309735), with apparent retained intron.
AB383852 - Synthetic construct DNA, clone: pF1KSDA0332, Homo sapiens SR140 gene for U2-associated protein SR140, complete cds, without stop codon, in Flexi system.
BC006474 - Homo sapiens, clone IMAGE:2820942, mRNA, partial cds.
AB002330 - Homo sapiens mRNA for KIAA0332 gene, partial cds.
MA620158 - JP 2018138019-A/192084: Polycomb-Associated Non-Coding RNAs.
BC062727 - Homo sapiens U2-associated SR140 protein, mRNA (cDNA clone IMAGE:6616571).
BC105604 - Homo sapiens U2-associated SR140 protein, mRNA (cDNA clone IMAGE:6649019), partial cds.
BC016323 - Homo sapiens U2-associated SR140 protein, mRNA (cDNA clone IMAGE:4092985), partial cds.
LF378114 - JP 2014500723-A/185617: Polycomb-Associated Non-Coding RNAs.
MA613691 - JP 2018138019-A/185617: Polycomb-Associated Non-Coding RNAs.
AK074327 - Homo sapiens cDNA FLJ23747 fis, clone HEP16095.
KJ902331 - Synthetic construct Homo sapiens clone ccsbBroadEn_11725 U2SURP gene, encodes complete protein.
AK057679 - Homo sapiens cDNA FLJ33117 fis, clone TRACH2001341, weakly similar to MNN4 PROTEIN.
AF087979 - Homo sapiens full length insert cDNA clone YW27H04.
JD299219 - Sequence 280243 from Patent EP1572962.
JD203087 - Sequence 184111 from Patent EP1572962.
JD537812 - Sequence 518836 from Patent EP1572962.
JD359826 - Sequence 340850 from Patent EP1572962.
JD313925 - Sequence 294949 from Patent EP1572962.
JD231419 - Sequence 212443 from Patent EP1572962.
JD316614 - Sequence 297638 from Patent EP1572962.
JD160508 - Sequence 141532 from Patent EP1572962.
JD304300 - Sequence 285324 from Patent EP1572962.
JD280191 - Sequence 261215 from Patent EP1572962.
BC045744 - Homo sapiens U2-associated SR140 protein, mRNA (cDNA clone IMAGE:5261770).
JD147435 - Sequence 128459 from Patent EP1572962.
JD491165 - Sequence 472189 from Patent EP1572962.
JD362773 - Sequence 343797 from Patent EP1572962.
JD051808 - Sequence 32832 from Patent EP1572962.
JD376204 - Sequence 357228 from Patent EP1572962.
JD507076 - Sequence 488100 from Patent EP1572962.
JD110020 - Sequence 91044 from Patent EP1572962.
JD282530 - Sequence 263554 from Patent EP1572962.
JD417513 - Sequence 398537 from Patent EP1572962.
JD417514 - Sequence 398538 from Patent EP1572962.
JD475682 - Sequence 456706 from Patent EP1572962.
JD261588 - Sequence 242612 from Patent EP1572962.
JD491021 - Sequence 472045 from Patent EP1572962.
JD414013 - Sequence 395037 from Patent EP1572962.
JD562947 - Sequence 543971 from Patent EP1572962.
JD289789 - Sequence 270813 from Patent EP1572962.
JD410996 - Sequence 392020 from Patent EP1572962.
JD524414 - Sequence 505438 from Patent EP1572962.
JD509738 - Sequence 490762 from Patent EP1572962.
JD223011 - Sequence 204035 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O15042 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A0PJ60, ENST00000473835.1, ENST00000473835.2, ENST00000473835.3, ENST00000473835.4, ENST00000473835.5, ENST00000473835.6, KIAA0332, NM_001320222, O15042, Q0D2M1, Q2NKQ7, Q9BR70, SR140, SR140_HUMAN, uc321rmw.1, uc321rmw.2
UCSC ID: ENST00000473835.7_9
RefSeq Accession: NM_001080415.2
Protein: O15042 (aka SR140_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.