(November 2024) Pangene ver-3 integration, custom GCV, expression

Posted on 20 November 2024

Custom Arachis version of GCV, Pan3 integration, Gene expression in gene report page

Custom Arachis Genome Context Viewer
A custom version of GCV(Genome Context Version) for Arachis is now available at PeanutBase. It shows micro-syntenic view of the genomic region with adjacent genes and the gene families they belong to. Start with a full query gene ID like, arahy.Tifrunner.gnm2.ann2.Ah02g344500,arahy.Tifrunner.gnm2.ann1.H916D0, arahy.BaileyII.gnm1.ann1.mikado.chr02G4069,aradu.V14167.gnm1.ann1.Aradu.32WCY in the search box to get their genomic context.

Pangene set version-3 has been integrated into GCV(Genome Context Viewer)
The updated pangene version pan3 has also been integrated into the custom GCV version.
An example with
i. a pangene: https://www.peanutbase.org/tools/gcv_pangenes/gene;arachis_pangenes=Arachis.pan3.pan18851
ii. a Tifrunner gene: https://www.peanutbase.org/tools/gcv_pangenes/gene;arachis_pangenes=arahy.Tifrunner.gnm2.ann2.Ah02g344500

Now Gene Report Page shows gene expression view
The ArachisMine gene report page now shows the expression chart below the gene structure.
An example link with a starch synthase gene