Ensembl 2013

Abstract

The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.

Figure 1.

A region of the GRCh37 human assembly showing the complete APBA1 gene. The top panel displays the GRCh37 reference sequence as originally released, and the bottom panel displays the region after the inclusion of the novel patch HSCHR9_1_CTG35. The region of difference is highlighted and marked by the ‘Assembly exception’ track, whereas the pink regions of LASTZ self-alignment provide more details about what has changed in the patch including the addition of new sequence that was missing in the originally released assembly. The green areas show the mapping between the original and the alternative sequences and demonstrate a corrected inversion at the left hand side of the patch. The patch changes the annotation such that the RNA gene RP11-548B3.3 (in purple) moves from 5′ of the APBA1 gene to within the second intron. As can be seen in the right hand side of the figure, the existence of the patch does not alter the annotation downstream of the change. Figure based on http://e68.ensembl.org/Homo_sapiens/Location/Multi?db=core;r=9:72019177-72298831;r1=HSCHR9_1_CTG35:72019384-72307679;s1=Homo_sapiens–HSCHR9_1_CTG35.

Figure 2.

Combined Segway and ChromHMM segmentation analyses within Ensembl in the region around the SLC18B1 gene on human chromosome 6. The combination process results in seven annotated segments: CTCF enriched, Predicted Weak Enhancer/Cis-reg element, Predicted Transcribed Region, Predicted Enhancer, Predicated Promoter Flank, Predicted Repressed/Low Activity or Predicted Promoter with TSS. Six of the seven segment types are shown with variability in predicted enhancer activity between the assayed cell lines. Figure based on http://e68.ensembl.org/Homo_sapiens/Location/View?r=6:133088392-133123741.