Transcript Structure and Domain Display

1. For IE users, enable ActiveX; Please pay attention to your browser's hint or notification on top-right or bottom-right when accessing the page.

2. Data can be entered by GFF/GFF3 file, BED file, or by selecting an organism from the pull-down menu.
To enter data in GFF/GFF3 format, select "Custom GFF3 file", then paste your data into the text box or load data from a local file by clicking the "Load Data File..." button. The file must have the extension ".gff" or ".gff3". The GFF file must be in the same format as the example GFF file below.
To enter data in BED format, select "Custom BED file", then paste your data into the text box or load data from a local file by clicking the "Load Data File..." button. The file must have the extension ".bed". The BED file must be in the same format as the example BED file below.
To enter data for an organism, select an organism, then paste your list of locus IDs into the text box or load data from a local text file by clicking the "Load Data File..." button. The file containing the list of locus IDs must have the extension ".txt".
A "Demo Data" button was provided to demonstrate example data for all types of data files and organisms.

3. Adjust the parameters until the demo preview is satisfactory. The parameters can be adjusted by keyboard entry, mouse wheel, or by clicking on the arrows by the prompt. Avoid setting all the colors to same value so that genomic features can be easily distinguished.

4. To submit, click the [View Gene Structures] button or press Ctrl+Enter when the data input box is in focus for some browsers. Some browsers will require you to allow popup windows to view the transcript structures.

5. The [View Gene Structures] button is disabled while the data input box empty. If the [View Gene Structures] button is disabled and data is in the input box, click on the input box to set the focus and the button will enable.

6. If you have loaded data into the input box, but the domain table below has not updated, please click the input box to update the domain table.

7. To download your results to your PC, click the [Download Results] button after submission and result has been return. All your temporary data in the server will be totally cleared once you have downloaded it.

8. You may save your settings by clicking the [Save Parameters...] buttons to local file, and can load it again in the future.

9. If you have no data to use this tool, please click the [Demo Data] buttons to load demo data for your experience. Then click [View Gene Structures] to see the demo.

10. Default values for the HEIGHTs, SPACE and FONTSIZE parameters are recommended.

11. please mouse over the each element to view its hint and usage if available.

12. Below is an example of a standard GFF3 data format supported by this tool (mouse over cells to view the hints if available.):
Chr Source Feature Start Position End Position Score Strand Frame Attributes
chr01 MSU_osa1r7 mRNA 4340849 4356383 . - . ID=LOC_Os01g08710.1;Name=LOC_Os01g08710.1;Parent=LOC_Os01g08710
chr01 MSU_osa1r7 exon 4356223 4356383 . - . ID=LOC_Os01g08710.1_exon_1;Parent=LOC_Os01g08710.1
... ... ... ... ... . - . ...
chr01 MSU_osa1r7 five_prime_UTR 4356369 4356383 . - . ID=LOC_Os01g08710.1_utr_2;Parent=LOC_Os01g08710.1
chr01 MSU_osa1r7 CDS 4356223 4356368 . - . ID=LOC_Os01g08710.1_cds_1;Parent=LOC_Os01g08710.1
... ... ... ... ... . - . ...
chr01 MSU_osa1r7 WRKY 4343688 4343993 . - . ID=LOC_Os01g08710.1_cds_6;Parent=LOC_Os01g08710.1
... ... ... ... ... . - . ...
chr01 MSU_osa1r7 three_prime_UTR 4340849 4341016 . - . ID=LOC_Os01g08710.1_utr_1;Parent=LOC_Os01g08710.1
... ... ... ... ... . - . ...
Note:Your GFF3 data file must meet this format in order for this tool to function properly.
  • Each transcript in the GFF3 file must contain the feature "mRNA" or "transcript" as its first row.
  • If your GFF3 file containes the feature "utr" or "UTR", the feature names must be converted to "five_prime_UTR" or "three_prime_UTR".
  • The "exon" feature is ignored since the same information is contained in the CDSs and UTRs.
  • Each Attribute MUST contain the gend ID.
  • All feature names are case-sensative.
    •  13. Below is an example of a standard BED data format supported by this tool (mouse over cells to view the hints if available.):
    Chrom Start Position End Position name Score Strand
    AT5G64810.1 25908412 25909803 mRNA 255 +
    AT5G64810.1 25908414 25909687 protein 255 +
    AT5G64810.1 25908412 25908656 exon 255 +
    AT5G64810.1 25908412 25908414 five_prime_UR 255 +
    AT5G64810.1 25908414 25908656 CDS 255 +
    AT5G64810.1 25908812 25908824 WRKY 255 +
    AT5G64810.1 25909687 25909803 three_prime_UTR 255 +
    ...... ...... ...... ...... ...... ......
    AT5G46350.1 18803901 18804043 five_prime_UTR 255 -
    AT5G46350.1 18803434 18803901 CDS 255 -
    AT5G46350.1 18801217 18801402 three_prime_UTR 255 -
    ...... ...... ...... ...... ...... ......
    Note:Your BED data file must meet this format in order for this tool to function properly.
  • The "exon" "protein" "mRNA" feature are ignored since the same information is contained in the CDSs and UTRs.
  • All feature names are case-sensative.
    •