The nucleic acid data:
IRESite Id: 216 Version: 5
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2007-01-23 00:00:00
IRESite record type:
  promoter-less_plasmid_with_putative_IRES
The name of the plasmid:
(deltaSV40)RSTF-LEF1-1.2
Description of the plasmid (facultative for promoter-less plasmid records):
The promoter-less plasmid was created by insertion of PCR-based product of 1.178kb of the LEF1 5'-UTR blunt-end ligated into (deltaSV40)pRSTF plasmid backbone linearized in the AfeI (Eco47III) site AGC^GCT.
The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):
  no
The in vivo produced heterogeneous transcripts occur due to alternative splicing:
  no
A promoter reported in cDNA corresponding to IRES sequence:
  no
Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:
Summary of experiments studying integrity of the in vivo transcripts in a particular host:
Integrity (uniformity) of mRNA tested using Northern-blot:
homogeneous_population_of_molecules_confirmed
Integrity (uniformity) of mRNA tested using RNase protection:
not_tested
Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested
Integrity (uniformity) of mRNA tested using primer extension :
not_tested
Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested
Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested
Integrity (uniformity) of mRNA tested using RNAi:
not_tested
Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested
Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
no_promoter_confirmed
Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested
Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested
The organism used:
Cercopithecus aethiops COS-1 (ATCC CRL-1650)
The origin of IRES in the plasmid:
  nuclear
The donor organism of the IRES segment:
Homo sapiens
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
LEF1
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:
(deltaSV40)RSTF-LEF1-1.2.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:
RLuc
The description of the protein encoded in this ORF:
Renilla 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):
  33-989
ORF
ORF position:   2
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
FLuc-fusion
The description of the protein encoded in this ORF:
Firefly-luciferase protein with one additional amoniacid residues at its N-terminus
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):
  2299-3951
Remarks:
Authentic RNA pol II promoter was confirmed between bases +280 and +640 relative to the main start site of
transcription. Comment from J. Jimenez: Our original studies of the LEF1 5'UTR were based on characterizing
a third promoter in the 5'UTR that is responsible for generating a 3.0 kb transcript. Because we had evidence
of an authentic promoter, we performed N. blot analysis. We did also attempt RT-PCR, but had technical
problems due to the high GC content of the 5'UTR.
Citations:
Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399
IRESs:
IRES:
Version: 1 Last change: 2007-01-06 00:00:00
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  LEF1
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1112-2289
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  123
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  1300
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -1187
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -10
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399
Last change to the database: 2015-04-16 16:45:23 GMT+1