Query text

You may choose to search by U12 database intron id or intron cluster id or by Ensembl gene ids, names, or descriptions using the fields:

  • Intron ID
  • Intron Cluster ID
  • Ensembl Gene ID
  • Gene Name
  • Gene Description

Pattern matching

You may specify whether to return exact matches to your query or to return records that either begin with or merely contain the query text using the drop down list. Queries are always case insensitive.

If the single wildcard character ( * ) is typed in the text field, the corresponding database field will not be queried and results will only be limited by the other criteria given. However, the wildcard ( * ) can also be used to match any string, and the question mark ( ? ) matches any single character in conjuction with the "begins with" or "contains" options. The SQL wildcards ('%' and '_') are also recognized and may or may not cause unexpected results with certain queries such as "NP_*", which would not only retrieve the expected RefSeq entries starting with NP, but would also retrieve introns in the genes TNPO1, TNPO2, Rnpc3, etc.

Other options

Results can be limited by species and/or intron type or subtype.

If the "intron cluster" radio button is selected, all members of the orthologous cluster of introns to which an intron matching the original query criteria belongs will be returned.

"Lost" or "absent" introns are essentially dummy intron records that belong to orthologous genes where either there was no match to the U12-intron-flanking exons or where an alignment was obtained by exonerate without insertion of an intron. These introns may be displayed by checking the '"lost" or absent' checkbox.

Results may also be limited to introns for which there is evidence of involvement in an alternative splicing event by checking the 'altsplice' checkbox. To be considered in this category, the intron must be present in the AltSplice Human Release 2 intron database, present in an alternatively spliced gene, present in at least one splice form, and either modified or absent in another transcript which spans the coordinates of the original intron.

Format

If GFF or FASTA text output may be obtained by checking the corresponding checkbox.