Gene Passport

The Gene Passport collects all the information about a gene, its location and structure, functional annotations, sequences, homology, and expression.

Opening the Gene Passport

In the Graph View, gene annotations are shown as blue bands at the bottom of each graph track. Click a gene annotation to open its Gene Passport in the left sidebar. If several genes overlap at the clicked position, a dropdown at the top lets you switch between them. The gene name (and any alias) can be copied to the clipboard.

TIP

To move directly to a gene by name instead of scrolling to it, use Navigate to gene in the Navigation Menu or in the Genome View.

Summary

The Summary panel lists the core facts about the gene:

• Name and Gene alias - alternative identifiers, if aliases have been uploaded
• Assembly - the genome the gene belongs to
• Position on that genome
• Strand - forward or reverse
• Length
• Functional description

Gene Function

The Gene Function panel shows functional annotations, where available, as links to the corresponding external databases:

• GO terms
• InterPro
• Pfam
• Superfamily
• Prosite
• Uniprot

Any additional annotations attached to the gene — for example Gene3D or PANTHER — are listed alongside these as plain text.

Sequences

The Sequences panel gives access to the gene sequence and its transcript sequences. You can view, copy and download them.

It also lists the gene's transcripts. Each transcript is drawn as a small diagram of its exon/intron structure and offers the following actions:

• Switch between the protein sequence, the coding sequence (CDS) and the DNA sequence (exons in capital letters, introns in lowercase)
• View the transcript sequence
• Copy the transcript sequence to the clipboard
• Download the transcript sequence as a FASTA file

Homology

If orthology information has been computed for the dataset, the Homology panel shows the gene's ortholog group:

• The homology group and the number of homologous genes it contains
• A gene-count barplot for the group (with zoom in/out), followed by the gene identifier of each assembly in the group

Phylogenetic tree of homologous genes

Below the Homology panel, the Phylogenetic tree of homologous genes panel shows the gene tree of the homology groups side by side with the aligned protein sequences. A dropdown allows users to select from different homology groups, if available. Each leaf of the tree is one transcript, labelled Assembly@GeneID (for example Wm82v2@glyma.Wm82.gnm2.Glyma.08G265200.1), and the alignment row to its right shows that sequence as a colored bar above the amino acid letters.

Controls

• Search - find a sequence by its label or a residue motif in the alignment
• Trim on search - reduce the alignment to the region matching the search, so that the matching columns are visible without scrolling
• Amino acid coloring - choose the coloring scheme for the residues
• Variable branch lengths - when off, the tree is drawn as a cladogram with branches of equal length; when on, branches are drawn to scale according to the branch lengths of the tree

Navigating the view

• Drag or scroll to move the tree and the alignment, Ctrl/⌘ + scroll to zoom
• The magnifier buttons zoom out and in step by step; the percentage next to them shows the current zoom level
• The fit button resets the view so that the whole tree and alignment fit into the panel
• The info button show the legend of the coloring scheme
• Drag the handle in the bottom right corner of the panel to make the viewer taller or wider

TIP

For phylogenetic trees of whole samples rather than of a single gene family, see the Tree Window.

Gene Expression

If expression data is available for the project, the passport offers a View Expression action that opens the Gene Expression view for the selected gene. There you can explore per-tissue expression on an anatomical diagram, filter tissues by mean TPM, and compare expression across treatments, tissues, and cultivars as violin plots or heatmaps.