The nucleic acid data:
IRESite Id: 320 Version: 2
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2009-04-15 13:38:32
IRESite record type:
  plasmid_with_promoter_and_putative_IRES_without_translational_characterization
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  our_best_guess
The mRNA/+RNA description: 
Putative spliced in vivo HSV-TK (thymidine kinase) promoter derived transcript containing CAT and FLuc genes
separated by FMDV IRES
The mRNA/+RNA sequence represented in the +DNA notation:


Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)
Credibility of mRNA sequence:
  reverse_engineered_sequence_and_should_match_experiment_except_both_UTRs
The name of the plasmid:
pBIC
The name of the promoter used to express this mRNA:
  HSV-TK
Description of the plasmid (facultative for promoter-less plasmid records):
Incomplete pBIC plasmid containing CAT and FLuc genes separated by FMDV IRES under the control of T7 and thymidine kinase promoters
The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):
  not tested
The in vivo produced heterogeneous transcripts occur due to alternative splicing:
  not tested
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
FMDV
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Foot-and-mouth disease virus C-S8c1
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:


GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:
pBIC.jpg
The total number of notable open-reading frames (ORFs):
  2
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
CAT
The description of the protein encoded in this ORF:
chloramphenicol acetyltransferase
The translational frameshift (ribosome slippage) involved:
  0
The ribosome read-through involved:
  no
The alternative forms of this protein occur by the alternative initiation of translation:
  not tested
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  9-668
ORF
ORF position:   2
Version: 1 Last change: 2008-08-27 11:51:23
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
FLuc
The description of the protein encoded in this ORF:
firefly luciferase
The translational frameshift (ribosome slippage) involved:
  0
The ribosome read-through involved:
  no
The alternative forms of this protein occur by the alternative initiation of translation:
  not tested
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  1230-2882
Remarks:
The +1 transcription site is not exactly known to IRESite curator so the 5'-UTR might be slightly wrong. It
seems transcription should terminate after the poly(A) signal from SV40 early region after removal of the SV40
small T antigen intron.

The sequence of the plasmid is not complete. The IRES sequence has been determined by E. Martinez-Salas while
the regions around HSV-TK promoter and intercistronic region were sequenced by IRESite (bp 2227-2802 and
3238-3961). Plasmid DNA was obtained from BCCM database.
Citations:
Martinez-Salas E., Saiz J. C., Davila M., Belsham G. J., Domingo E. (1993) A single nucleotide substitution in the internal ribosome entry site of foot-and-mouth disease virus leads to enhanced cap-independent translation in vivo. J. Virol. 67(7):3748-3755
Additional data: http://bccm.belspo.be/db/lmbp_plasmid_details.php?NM=pBIC
IRESs:
IRES:
Version: 1 Last change: 2008-08-27 11:51:23
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  FMDV
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  734-1194
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  66
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  526
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -496
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -36
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Martinez-Salas E., Saiz J. C., Davila M., Belsham G. J., Domingo E. (1993) A single nucleotide substitution in the internal ribosome entry site of foot-and-mouth disease virus leads to enhanced cap-independent translation in vivo. J. Virol. 67(7):3748-3755
Additional data: http://bccm.belspo.be/db/lmbp_plasmid_details.php?NM=pBIC
Last change to the database: 2015-04-16 16:45:23 GMT+1