Example and Figure reference sequences

For a coding DNA reference sequence the basic recommendation is that it should represent the major and largest transcript of the gene. Alternatively spliced exons (5'-first, internal or 3'-terminal) derived from within the gene can be numbered as for intronic sequences. Variants in transcripts initiating or terminating outside this region can be described as upstream / downstream sequences. 

Examples

• alternative promoter
  • 5' of the major transcript; example DMD promoter brain-specific transcript
  • inside gene; example DMD promoter retina-specific transcript  (in intron 29)
• introns in 5' untranslated region (UTR)
      for details see RefSeq numbering with introns 5' of the ATG
      example FKRP coding DNA reference sequence  (three 5' UTR introns)
• alternatively spliced exon
  • exon larger at 3' end;  example
  • entirely in intron;  example
  • exon larger at 5' end;  example
• alternative 3' terminal exon
  • inside gene
    • directly 3' of exon; example LMNA coding DNA reference sequence  (exon/intron 10)
    • completely in intron; example TTN coding DNA reference sequence  (in intron 47)
  • after gene (in gene downstream sequence);  example