ENCODE Data

Introductory Page

Updated Data from the PDG - Summary Pages also in the Right Bar The primary sequences from 33 loci are not in the human sequence databases. BLAST finds human homologues for all but 19 of the isoforms. 13 sequences have their whole sequence covered by a PDB structure, 81 more have part of the sequence in the PDB. 587 sequences find at least one PDB template structure with BLAST. 269 of the 409 alternate isoforms split PFAM Domains by insertion of deletion. - Summary of Sequence Data - Human homologues, PDB structures, Pfam domains and links to annotated sequences Institute of Enzymology Predictions 67 Encode proteins are listed where at least 40% of a domain is missing. - MisPred Predictions EBI Prediction Data PDBsum, exons, functional residues, model structures and preliminary analysis using ProFunc. - Results from Janet Thornton's EBI Group - ProFunc Analysis CBS Prediction Results 31 loci have transcripts with variation in predicted signal peptide. 47 loci vary in propeptide prediction. - SignalP, TargetP, TMHMM, NetNGlyc, NetOGlyc, ProP, NetAcet, NetNES, NetPhos Predictions - CBS Data With Links to Annotated Sequences Bologna Group 1D Feature Prediction Bologna Biocomputing Group 1D Features have been predicted with a range of prediction methods. Difference between isoforms are highlighted. - Signal Peptides, Transmembrane Helices and Cysteine Bond Prediction Bioinformatics Unit Fold Prediction Folds have been predicted for the sequences in the GENCODE set. - mGenTHREADER Fold Predictions Biocomputing Model Structures Domain and exon boundaries have been mapped onto model structures. - Model Structures The Original GENCODE Data Set All the data generated in the GENCODE project are linked below. - GENCODE Data Set

Talks at Biosapiens Meeting, Barcelona - EBI - Andreas Kahari - Biocomputing Group - Anna Tramontano - EBI - Gabrielle Reeves - EBI - Henning Hermjakob - Institute of Enzymology - Laszlo Patthy - PDG - Michael Tress - Bologna - Rita Casadio - CBS - Soeren Brunak Data Pages from the PDG Summary Pages - Main Summary Page - Best Human, Mouse and Zebra Fish Homologues - GO Functional Terms - PDB Structures - Manual vs. "Randomly" Selected Regions - Domains and Splice Variants - Transfrag Homologues Data Pages - with links to annotations - Human Homologue Sequences - PDB Structures - CBS Prediction Data Tab-Delimited Data Pages - these may be slow to load - Collected Data - Human Homologous Sequences - GO Functional Terms - PDB Structures and Models - Transfrag Homologues