Access Method
All the three methods can be used to access to the gene profile page:
- Using the top-right search box in the website navigation bar
- Using the search box in the Homepage
- Using the URL:
https://cottonfgd.org/profiles/gene/[geneID]
Basic Information
This section lists the basic information of this gene:
- ID: the gene ID from data providers.
- Name and description: Corresponding UniProt name and description.
- Species
- Genomic location: Chromosome, start position, end position and strand
- Genomic DNA length: The full-length genomic DNA sequence could be viewed (≤ 10kb) and download in FASTA format. It is displayed using the Sequence-viewer Plugin
- Gene IDs in major assembly: Only visible in Gossypium hirsutum(None CRI assemblies). This shows the gene ID mapping relationship with the CRI assembly through genome coordinate coversion (by LiftOver).
- JBrowse links
Associated Transcripts Table
This section lists all the possible isoforms (However, multiple isoforms are available only in Gossypium raimondii, JGI. )
Genomic Context View
This section shows surrounding genes in 10kb genomic DNA region(Snapshot from JBrowse). The target gene is highlighted.
Cross-Database References
This section shows links to other databases.
| Database Name | Description | Available Genome Assemblies |
|---|---|---|
| Cotton specific databases | ||
| CottonGen | A genomics, genetics and breeding database for cotton research | G. raimondii (JGI & BGI), G. arboreum (BGI), G. hirsutum (NAU & BGI) |
| GraP | Platform of Functional Genomics Analysis in Gossypium raimondii | G. raimondii (JGI) |
| ccNet | Database of co-expression networks for diploid and polyploid Gossypium | G. arboreum (BGI) G. hirsutum (NAU) |
| CGP | Cotton Genome Project from BGI-Shenzhen (Registration Required) | G. raimondii (BGI), G. arboreum (BGI), G. hirsutum (BGI) |
| General plant databases | ||
| Phytozome | A comparative platform for green plant genomics | G. raimondii (JGI) |
| GreeNC | A Wiki-database of plant lncRNAs | G. raimondii (JGI) |
| PGDD | Plant Genome Duplication Database | G. raimondii (JGI) |
| PIECE | Plant gene structure comparison and evolution database | G. raimondii (JGI) |
| Planteome | Plant Ontology database | G. raimondii (JGI) |
| PlantTFDB | Plant Transcription Factor Database | G. raimondii (JGI) G. arboreum (BGI) G. hirsutum (NAU) |
| PLAZA | An access point for plant comparative genomics | G. raimondii (JGI) |