The nucleic acid data:
IRESite Id: 76 Version: 2
Originaly submitted by: Václav Vopálenský Submission date: 2005-10-06 00:00:00
Reviewed by: Václav Vopálenský Last change: 2008-07-01 13:32:32
IRESite record type:
  plasmid_with_promoter_and_putative_IRES_translationally_characterized
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 SV40 promoter-derived transcript produced from bicistronic plasmid pRL which
comprises renilla and firefly luciferases as the first and the second cistron, respectively and the part of 5'
UTR (from nt -207 to nt +27 of the original sequence) from human n-myc mRNA.
The sequence ends at its 3'-end right after the poly(A) signal from SV40 mRNA and thus the 3'-UTR might be
slightly wrong.
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:
  guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail
The name of the plasmid:
-234/1
The name of the promoter used to express this mRNA:
  SV40
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:
not_tested
Integrity (uniformity) of mRNA tested using RNase protection:
homogeneous_population_of_molecules_confirmed
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:
not_tested
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:
Homo sapiens HeLa (ATCC CCL-2)
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
n-myc
The origin of IRES in the plasmid:
  nuclear
The donor organism of the IRES segment:
Homo sapiens SH-SY5Y (ATCC CRL-2266)
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:
-234/1.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: Václav Vopálenský Reviewed by: Václav Vopálenský
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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  1-936
ORF
ORF position:   2
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The abbreviated name of this ORF/gene:
FFluc
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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  1220-2872
Citations:
Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670
IRESs:
IRES:
Version: 2 Last change: 2008-07-01 13:32:32
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The IRES name:
  n-myc_delta1-93
The functional status of IRES:
  defective
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  989-1222
How IRES boundaries were determined:
guessed
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  53
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  286
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -231
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  2
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
5' end of mRNA (from nt -207 to nt +27) coding for human n-myc mRNA (in this construct the first 93 bp of  5'
UTR were removed).
Citations:
Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670
The translation experiments:
Translation results:
IRESite Translation Id: 67
Version: 3 Last change: 2007-07-24 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens HeLa (ATCC CCL-2)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  53.000
Name of IRES used as the positive control:
  n-myc
Name of the plasmid used as the positive control.
pRNF
Name of the plasmid used as the negative control.
pRF
IRESite Id of the plasmid used as positive control.
  72
IRESite Id of the plasmid used as negative control.
  184
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  2.500
The size (length) of intercistronic region in the positive control:
446
The size (length) of intercistronic region in the negative control:
67
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  endogenous_nuclear_RNA_Pol_II_transcript
Remarks:
As a positive control was used HeLa cell line transfected by pRNF vector which contains major part of the 5'
UTR (nt 8 to nt 300) plus first 27 bp from human n-myc mRNA cloned between renilla and firefly luciferase (see
IRESite Id 72).
As a negative control was used HeLa cell line transfected by control vector pRF (formerly
pGL3R, vector without insert).
ATCC number of used cell line - CCL-2
Citations:
Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670
Translation results:
IRESite Translation Id: 68
Version: 2 Last change: 2007-07-24 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The translation method used to study IRES function:
in vivo
The organism used for translation:
Mus musculus Neuro-2a [N2a] (ATCC CCL-131)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  49.000
Name of IRES used as the positive control:
  n-myc
Name of the plasmid used as the positive control.
pRNF
IRESite Id of the plasmid used as positive control.
  72
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
446
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  endogenous_nuclear_RNA_Pol_II_transcript
Remarks:
As a positive control was used NB2a cell line transfected by pRNF vector which contains major part of the 5'
UTR (nt 8 to nt 300) plus first 27 bp from human n-myc mRNA cloned between renilla and firefly luciferase (see
IRESite Id #72).
ATCC number of used cell line - CCL-131; Designation - N2a; Neuro-2a
Citations:
Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670
Translation results:
IRESite Translation Id: 69
Version: 2 Last change: 2007-07-24 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens NTERA-2 cl.D1 [NT2/D1] (ATCC CRL-1973)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  40.000
Name of IRES used as the positive control:
  n-myc
Name of the plasmid used as the positive control.
pRNF
IRESite Id of the plasmid used as positive control.
  72
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
446
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  endogenous_nuclear_RNA_Pol_II_transcript
Remarks:
As a positive control was used NT2 cell line transfected by pRNF vector which contains major part of the 5'
UTR (nt 8 to nt 300) plus first 27 bp from human n-myc mRNA cloned between renilla and firefly luciferase (see
IRESite Id #72).
ATCC number of used cell line - CRL-1973; Designation - NTERA-2 cl.D1, NT2/D1
Citations:
Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670
Last change to the database: 2015-04-16 16:45:23 GMT+1