Transcript Information Encoding in Biological Molecules: DNA and

Ensembl Web
Erin Pleasance
Canada’s Michael Smith Genome Sciences Centre, Vancouver
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Homepage at http://www.ensembl.org
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Species-specific homepage
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chromosome
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Site Map
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Text search
caspase-3
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GeneView
ContigView of
gene
ContigView of gene and
surrounding region
ProteinView
TransView
of transcript
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ExonView
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GeneView
(On the same page)
GeneView of
homologues
References
provided by
SWISSPROT
via GeneDAS
ExportView
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GeneSNPView 8
GeneView
(On the same
page)
Information
provided for each
transcript
individually
Links to external
databases
AlignView of gene against
external sequence
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GeneView
GOView: Gene Ontology
classification of function
DomainView of
functional domains
FamilyView of other
proteins in same family
TransView
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ProteinView
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TransView
ExonView
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ExonView
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GeneView
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ProteinView
Links to external
databases
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GeneView
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ContigView
Chromosome
and bands
Sequence
contigs
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ContigView
Detailed View
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chromosome
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sequences
link to external
databases
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ContigView
Basepair View
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strand
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strand
• DNA sequence
• 6-frame translation
• Enzyme sites
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ContigView
Single nucleotide
polymorphisms
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SNPView
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ContigView
Markers
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MarkerView
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ContigView
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Forward
strand
ContigView
of surrounding region
caspase-3
Nearby
genes
Reverse
strand
“Unstranded”
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ContigView
Feature tracks
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menu options
available!
Informs that
other tracks are
available
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ContigView
Feature tracks
Repeats appear in
new track
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Exporting
From ContigView
From GeneView
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ExportView
• Flatfile (EMBL or
GenBank) with
features
• FASTA sequence only
• Feature list in a table
• Image of region
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ExportView
Flatfile
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Click Back to
ExportView
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EnsMart Data Mining
“EnsMart is a powerful
data mining toolset for
retrieving customised
data sets from
annotated genomes,
using criteria from
Ensembl and third
party databases.”
To export:
• Genes
• SNPs
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MartView: Start
Indicates current
query progress
Refine query
Reviews current
query, indicates
number of objects
to be retrieved
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MartView: Filter
4
186139601
186339601
Upload gene lists
Specify query
requirements
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MartView: Output
Can also output Output
sequence, SNP
info, gene structure
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of entries 34
to
be retrieved
MartView: Results
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Similarity searching
BLAST: for distantly
related or protein
sequences; slow
SSAHA: for nearly
identical sequences; fast
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Similarity searching: SSAHA
Copy-and-paste
sequence OR
upload file
(my_sequence.txt)
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Similarity searching: SSAHA
Similar
sequences on
chromosomes
List of
results
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Similarity searching: SSAHA
Results shown
in ContigView
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Other access methods: AnchorView
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Other access methods: Disease View
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Other access methods: KaryoView
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Exercises
Single nucleotide variations in the gene HFE have been
associated with the disease hemochromatosis.
• What types of annotations represent this gene (eg.
Ensembl novel gene, etc.)? How many Ensembl
transcripts are annotated for this gene?
• How many coding SNPs are in the transcript for the
longest protein product of this gene?
• What is the mouse homologue of this gene? Obtain a
GenBank-format file of this homologue.
• How many EST transcripts appear to be equivalent to
this gene? What markers overlap this gene? What is
one type or repeat found in the 3’ UTR of this gene?
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