Overview

This interface allows the extraction of gene regulatory regions (promoters and terminators) using a gene identifier or a gene name. Users can adjust several parameters to precisely configure the extraction.

Detailed Features

1.1 Gene ID

• Description: Enter the gene name or Gene ID in this section.
  • *PRKN, 351, NM_003130.4*
  • Allowed : gene name, Gene ID, transcript (NM_, XM, NR_, XR_,)
  • Exemple
• "Check genes availability" option: Allows users to verify whether the entered gene is available for extraction in the species (Human, Mouse, Rat, Drosophila, Zebrafish).

1.2 Genome version, species of Gene Names and Sliced Variants

• Genome Version: Select the genome version to be used (e.g., Current (GrCh38)).
• Species: Specify the species corresponding to the gene. A dropdown menu allows selection from the available species (e.g., Human, Mouse, Rat, Drosophila, Zebrafish).
• "All variants" option:
  • Enabled: Includes all available variants for the gene (NM_, XM_, NR_, XR_).
  • Disabled: Limits the search to a specific variant (by default: transcript variant 1).

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Note: You can use any Gene ID or transcript even if the species in question is not listed in TFinder. Species is only important for Gene Name.

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1.3 Regulatory Region

• Choose the type of region:
  • Promoter: Region upstream of the gene start (Transcription Start Site, TSS).
  • Terminator: Region downstream of the gene end.
• Help