Transcript summary



The table shows all splice variants for a gene and includes noncoding transcripts.

The transcript which you are viewing is highlighted in blue in the table.


Immediately below the transcript table, you will find additional information about the transcript you are viewing. This includes:

  • Statistics - Number of exons, transcript length in basepairs, and translation length (number of amino acids in the protein)
  • Type - Both the transcript status and the biotype are shown. More information about this is below.
  • Prediction method - The original source of the transcript (the VectorBase annotation pipeline or 3rd party annotations imported from ENA or other labs).
  • Alternative transcripts - Matching transcripts.
  • Frameshift introns - Frameshift introns (if shown) are introduced by the VectorBase genebuild in order to fit the cDNA sequence to the genome. They are indicated below the transcript diagram if these short introns are present. These are introns the length of 1, 2, 4, or 5 basepairs.


Boxes are exons. Lines connecting the boxes are introns. Filled boxes are coding sequence, and empty, unfilled boxes are UTR (UnTranslated Region).


Depending on factors such as cell type/ tissue type, you may need to use one or more of the transcripts not in these 'reviewed' sets. The general identifiers link at the left of the transcript tab shows matching IDs in other databases, and may help you decide on transcripts. ESTs and expression data from various projects can be turned on in the Location tab, Region in Detail view. This may be of use when determining which transcript set to use.


Non-coding transcripts are predicted using automated approaches.


A known transcript has a sequence match in a sequence repository external to VectorBase for the same species.
A novel transcript has a sequence match outside VectorBase for an alternate species. (Can be read as novel transcript for this species).


If the transcript contains a variation whose alternative allele has a population frequency of at least 10% and is causing the loss or gain of a stop codon in a HapMap population, the variation and affected populations are listed.