UM
  Laboratory of RNA Biology
 | Search | Maps | UM_IntraNet |


Xie Lab


Lab Members


Research


Publications


Bookmarks


Courses


Contact


Lab Bookmarks
GOOGLE          

 Google SCHOLAR

          

UM PubMed

          

SCOPUS

          

WIKI

         

DICTIONARY

RNA/DNA: RNASociety. AberrantSplicingDB. ENSEMBL. BioMart. UCSCGenome. GenomeCoordinatesConversion. Genomic Data Viewer_NCBI. DotPlot. Reverse Complement in batch. MaxEntScan Splice Sites. Download GT/AG splice site matrices of all Ensembl-annotated species. Search for Motifs in multiple sequences(MEME).  ViennaRNA Web Service for multiple aligned RNA structures.  In silico PCR. Blastn for miRNA with your sequence. Rfam to search for U snRNAs or other non-coding RNAs. Sigma MISSION ShRNA. DAVID Functional Clustering Analysis. BatchPrimerDesign. The Cancer Genome Atlas (TCGA). COSMIC. SNP. Heatmapper_Dendrogram creator. GTExPortal. GWAS. TOPMed. FraminghamHeartStudy. UK BioBank. 

GENOME DataBases:   NCBI db  BLAST.UCSCGenome. ENSEMBL Genomes Download. Ensembl Releases

PROTEIN: Molecular weight calculation. Peptide Cutter..ProteinKinaseS..2DMobilityPlot. Protein3D..ScanSite(PredictingKinaseSites). ProteinModificationSearch.Regulated Sites.Disease-associated Sites. SwissPro. PDB.ProteinDomainSearch. MASCOT.ProteinStructureSwissModelling.TheHumanProteinAtlas. NetCTL_EpitopePrediction. AntigenicPeptidePrediction. AlphaFold Server.

BioMedJOURNALs/Archives: PubMed.SCIENCE.NATURE.CELL.Mol Cell.NEURON.PNAS.JBC..MCB. G&D. RNA.NAR. RNA Biology. ASHG. Nature Genetics. BioRxiv. arXiv.

GENERAL: TREE OF LIFE. Metazoa systematics.[RetrovirusTaxonomy]. NAS. NCBI. NIH. SFN. ATCC. AdrenalGland. JacksonLabMouse. CurrentProtocols. GeneReviews.
CIHR. ResearchNet. ResearchPortal. CCV.

University of Manitoba:UM PubMed. UManitoba.  SystemContractVendors.  SystemContractRFPnumber.   NONSysNumber. ExpenseCodes   UMeJournals. UMphysiologyFaculty. UM_IntraNet. FAST. IRIDIUM.UMFA. .UMGraduate. UMICB. LENTIVIRAL CORE SERVICE. Weather. ManitobaParkReservation.
hecla


Keywords: molecular biology, RNA, processing, alternative splicing, cryptic splicing, transcriptome integrity, hnRNP, gene regulation, gene expression, evolution, proteomic diversity, complexity, splicing factors, protein kinases, cell signaling, neurons, endocrine cells, SNP, mutation, cancer, GWAS, human health/genetic diseases

Highlights of some of the findings by the lab:

hs3ssbar


BP
Splice Site Matrices of >1000 Species/lineages

REPAG_GenomesR38R91


 REPAG
(Right-click image to view details)

The REPAG element specifically among mammals
(Sohail M., and Xie J. Molecular & Cellular Biology, 2015, 35(12): 2203-2214)

Adaptive splicing
(Right-click to view details)
Adaptive splicing

CaRRE
(Right-click image to view details)

The CaRRE element among vertebrates (Liu GD, et al., J. Biol. Chem. 2012, 287:22709–22716)

STREX model
Molecular basis of the depolarization-regulated alternative splicing of the STREX exon of the Slo1 gene

hnrnpl-prolactin
Importance of proper splicing control in hormone production: aberrant splice variant of prolactin (right) due to the loss of hnRNP L

REPA

A new group of introns: REPA element 'inserted' between the Py and 3'AG and its effects on alternative splicing

hREPAG
Consensus of 1000 human REPAG intron ends (Credit: Aydan Wang)

*Research in this lab has been supported by CIHR , NCIC, CBCF, NSERC, MMSF, MHRC and CFI.


Misce. links:



Faculty of Graduate Studies

Department of Physiology & Pathophysiology

College of Medicine

Faculty of Health Sciences

University of Manitoba