Generating a transcript

The Generate Transcript dialog box lets you assemble a transcription sequence from segments defined by exon, intron, CDS or RNA features.

An entire sequence of DNA in the sequence window can be transcribed with a single touch of the Sequence Type button.

However, if you want to transcribe one or more features in the sequence, use the Generate Transcript dialog box.

NOTE: MacVector detects these features by their feature table entries. It does not predict exons, so you must first ensure that the appropriate features have been defined.

SPECIFYING A CDS feature

This is the initial default method. When you choose the Single CDS method and select a range of the current DNA sequence, MacVector lists all CDSs found within the range. The CDS features for both strands are listed together; those on the minus (complementary) strand are marked with a blue 'C'. Each CDS may contain several exons; these are listed on successive lines within the CDS feature entry. Only one CDS feature can be selected for transcription, because only a single CDS can contribute to a mRNA molecule.

Note that a CDS feature may or may not include the terminal stop codon, depending on the preference of the submitting author.

SPECIFYING EXONS

When you choose Specify exons, and select a strand and a range of the current DNA sequence, MacVector lists all exons found on that strand within the range. Initially all exons are checked, so they will be included in the transcription. However, you can deselect exons to prevent them from being transcribed. This is useful where a gene has alternate splice sites.

The default assembly order is from 5' to 3' on the selected strand. Therefore the exons are listed in ascending order of residue numbering on the plus strand, and in descending order on the minus strand. You can change the order of assembly by moving items in the list.

TIP: Rearranging the order of exons may be useful if the gene has been cloned into circular DNA, and the origin of the circular DNA is inside the gene.

SPECIFYING INTRONS

When you choose the Specify introns method, and select a strand and a range of the current DNA sequence, MacVector lists all introns found on that strand within the range. In contrast to MacVector's treatment of exons, all introns are initially unchecked, so they will be excluded from the transcription. If you select any introns, they will be transcribed.

SPECIFYING RNA features

When you choose the Specify RNA features method, and select a strand and a range of the current DNA sequence, MacVector lists all RNA features found on that strand within the range. Initially all features are unchecked, so they will be excluded from the transcription. If you select any RNA features, they will be transcribed. You can also change the order of assembly, by moving items in the list.

PRESERVING FEATURES

When the mRNA window is created, the relevant features from the DNA sequence's feature table can be copied into it. Where a feature lies partially within a selected range, it will be split and copied as a feature fragment. If several segments have been transcribed, there can be many such feature fragments in the resulting mRNA sequence. MacVector lets you choose how much feature information to include in the transcribed sequence: all the features, just the features that define the selected segments, or no features at all. The default is to include only the defining features. If no features are copied, the mRNA window will contain only the residues.

TO TRANSCRIBE DNA features into mRNA

Choose Analyze | Generate Transcript.
From the Method drop-down menu, choose one of the following methods for selecting segments to transcribe. Single CDS
1. Specify exons
2. Specify introns
3. Specify RNA sequences.
The appropriate features are displayed in a list. To enter a range in the sequence, type the appropriate sequence numbers in the From and to text boxes.
From the Strand menu, select plus or minus. If you have selected the Single CDS method, CDS features of both strands are listed and this menu is not available.
Do one of the following, depending on the transcription method you chose in step 2.
- Specify exons : To deselect any listed features that you do not want transcribed, click in their check boxes.
- Single CDS: Select a CDS feature for transcription from the list. The selected feature is highlighted.
- Specify introns or Specify RNA sequences:To select any listed introns that you want transcribed, click in their check boxes.
If you chose Specify exons or Specify RNA features, you can change the order of assembly of the listed features. To move a feature, click on the double arrow at the left of the line. Holding down the mouse button, drag the feature to its new position in the list, and then release the mouse button.
As the line is dragged, a dashed outline follows the cursor, and an arrow at the left of the list shows where the insertion position will be if the mouse is released.
From the mRNA Feature Table drop-down menu, choose which features should be copied into the transcribed sequence: Copy all features, Default, or Do not copy features.
Type a name for the transcribed sequence in the mRNA Sequence Name text box.
Select OK to perform the transcription and display the resulting mRNA sequence.