Promoters & UTRs

Information on the elements that regulate SCN1A expression such as the promoter and the 5'-untranslated region (5'-UTR).

Reference: Long, J Neurosci Res (2008)


Using RACE, Long and co-workers found three untranslated exons (h1u-h3u) within a stretch of 75 kb upstream of Exon 1. Transcription begins with the first base of h1u. The open reading frame begins immediately after h3u.

[h1u] ---------- (71 kb intronic) ---------- [h2u] ---------- (4 kb intronic) ---------- [h3u] > ATG... (EXON1)

Click on the links above for the individual sequence information via GenBank.

Presence of these untranslated exons more than tripled luciferase expression in a control experiment using human neuroblastoma SH-SY5Y cells. Because this enhancing effect could not be reproduced in human embryonic kidney cells (HEK-293), the authors suggest neuronal specificity of the promoter region.

Transcriptional elements

Six candidates for transcriptional elements were predicted in a 2.5-kb stretch upstream of h1u (in silico approach, sequence-based). In order of appearance; position based on the first base of h1u being "+1":

  • ETF binding site (-1869 > - 1880): GTGCTAGGGGC
  • TATA box (-1058 > -1067): TTTATATATA
  • CAAT box (-114 > -103): CTGCCAATACTT
  • Initiator (-1 > +5): GGAAAC
  • EBF binding site (+32 > +42, i.e., within h1u): ACTTCAGGGGT
  • C/EBP binding site (within h2u): GGCAATT