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Ensembl MapView

Introduction

The Ensembl 'MapView' page displays an ideogram of a single chromosome. To the left, feature density plots for genes, GC contents, repetitive sequences and SNPs are shown.

Clicking on any chromosomal band or anywhere along one of the density plots will redirect you to Ensembl 'ContigView'. Alternatively, you can use one of the navigation tools in the right hand box.

• Chromosome - Some basic statistics about the chromosome are shown top right:

  • Length is estimated total length of the chromosome.

  • Gene Count is the total number of 'known', 'novel' and 'pseudogenes' predicted by the Ensembl analysis and annotation pipeline.

  • Known Gene Count gives the number of 'known' genes that Ensembl has predicted on this chromosome. 'Known' genes have been mapped by Ensembl to near-full-length species-specific protein sequences already available in the public sequence databases.

  • Novel Gene Count the number of 'novel' genes that Ensembl has predicted on this chromosome. 'Novel' genes, although predicted on the basis of similarity to protein or cDNA sequences and/or ESTs, could not be mapped with confidence to existing entries.

  • Non-coding RNA genes Ensembl annotates several sub-classes of non-coding RNA genes. Counts per RNA gene class are also available from this page.

  • Please note: Gene counts presented per chromosome on Ensembl 'MapView' pages will not neccessarily add up to the numbers presented for the whole genome on the species-specific Ensembl pages. This is due to extra-chromosomal sequences, which are annotated with genes but not always accessible via 'MapView' and also due to the fact that pseudo-autosomal regions (PAR) on the human X and Y chromosomes count towards the whole-genome statistics only once.

  • SNP Count lists the number of SNPs that Ensembl has placed on this chromosome.

• Change Chromsome - Display another chromsome of the same oranism in Ensembl 'MapView'.

• Jump to ContigView - A region for display in Ensembl 'ContigView' can be selected entering two STS marker names into the boxes. Please note that while 'ContigView' displays are limited to 1 Mb, larger regions can be examined in Ensembl 'CytoView'.

The search box at the top of the page allows you to search for any identifier present in Ensembl. For detailed instructions see the Ensembl 'TextView' page.