The nucleic acid data:
IRESite Id: 631 Version: 1
Originaly submitted by: Václav Vopálenský Submission date: 2009-09-01 17:07:04
Reviewed by: Martin Mokrejš Last change: 2009-09-01 17:28:36
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:
  hopefully_full-length_mRNA
The mRNA/+RNA description: 
Putative in vivo CMV promoter-derived transcript produced from bicistronic plasmid pbetaGAL/Apaf1/CAT which
comprises beta galactosidase and chloramphenicol acetyltransferase as the first and the second cistron
respectively and the whole part of human Apaf-1 5' UTR (nt from -577 to nt +3 of the original sequence) mRNA
cloned between them.
The sequence ends at its 3'-end right after the poly(A) signal from BGH mRNA and thus the 3'-UTR might be
slightly wrong.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_reverse_engineered_and_should_match_experiment
The name of the plasmid:
pbetaGAL/Apaf1/CAT
The name of the promoter used to express this mRNA:
  CMV
Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing the whole part of human Apaf-1 5' UTR (nt from -577 to nt +3 of the original sequence) inserted between beta galactosidase and chloramphenicol acetyltransferase reporter genes.
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:
Apaf-1
The origin of IRES in the plasmid:
  nuclear
The donor organism of the IRES segment:
Homo sapiens Burkitts lymphoma cell line (BJAB)
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:
pbetaGAL/Apaf1/CAT.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: Martin Mokrejš
The abbreviated name of this ORF/gene:
LacZ
The description of the protein encoded in this ORF:
beta galactosidase
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):
  189-3332
ORF
ORF position:   2
Version: 0
Originaly submitted by: Václav Vopálenský 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):
  4255-4914
Citations:
Nevins T. A., Harder Z. M., Korneluk R. G., Holcik M. (2003) Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97/DAP5/NAT1. J. Biol. Chem. 278(6):3572-3579
IRESs:
IRES:
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The IRES name:
  Apaf-1
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  3621-4200
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  289
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  868
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -634
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -55
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Apaf-1 IRES represents whole part of the human Apaf-1 5' UTR (nt from -577 to nt +3).
Citations:
Nevins T. A., Harder Z. M., Korneluk R. G., Holcik M. (2003) Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97/DAP5/NAT1. J. Biol. Chem. 278(6):3572-3579
The translation experiments:
Translation results:
IRESite Translation Id: 654
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens HEK 293T/17 (ATCC CRL-11268)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  4.370
Name of IRES used as the positive control:
  EMCV
Name of the plasmid used as the positive control.
pbetaGAL/EMCV/CAT
Name of the plasmid used as the negative control.
pbetaGAL/rc_Apaf1/CAT
IRESite Id of the plasmid used as negative control.
  595
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  1.250
The size (length) of intercistronic region in the negative control:
922
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
Citations:
Nevins T. A., Harder Z. M., Korneluk R. G., Holcik M. (2003) Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97/DAP5/NAT1. J. Biol. Chem. 278(6):3572-3579
Translation results:
IRESite Translation Id: 655
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
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:
  2.100
Name of IRES used as the positive control:
  EMCV
Name of the plasmid used as the positive control.
pbetaGAL/EMCV/CAT
Name of the plasmid used as the negative control.
pbetaGAL/rc_Apaf1/CAT
IRESite Id of the plasmid used as negative control.
  595
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  1.000
The size (length) of intercistronic region in the negative control:
922
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
Citations:
Nevins T. A., Harder Z. M., Korneluk R. G., Holcik M. (2003) Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97/DAP5/NAT1. J. Biol. Chem. 278(6):3572-3579
Translation results:
IRESite Translation Id: 656
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The translation method used to study IRES function:
in vivo
The organism used for translation:
Cricetulus griseus CHO-K1 (ATCC CCL-61)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  0.730
Name of IRES used as the positive control:
  EMCV
Name of the plasmid used as the positive control.
pbetaGAL/EMCV/CAT
Name of the plasmid used as the negative control.
pbetaGAL/rc_Apaf1/CAT
IRESite Id of the plasmid used as negative control.
  595
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  0.770
The size (length) of intercistronic region in the negative control:
922
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
Citations:
Nevins T. A., Harder Z. M., Korneluk R. G., Holcik M. (2003) Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97/DAP5/NAT1. J. Biol. Chem. 278(6):3572-3579
Translation results:
IRESite Translation Id: 657
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens human glioblastoma (SF539)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  0.230
Name of IRES used as the positive control:
  EMCV
Name of the plasmid used as the positive control.
pbetaGAL/EMCV/CAT
Name of the plasmid used as the negative control.
pbetaGAL/rc_Apaf1/CAT
IRESite Id of the plasmid used as negative control.
  595
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  0.350
The size (length) of intercistronic region in the negative control:
922
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
Citations:
Nevins T. A., Harder Z. M., Korneluk R. G., Holcik M. (2003) Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97/DAP5/NAT1. J. Biol. Chem. 278(6):3572-3579
Translation results:
IRESite Translation Id: 658
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens NIH/3T3 (ATCC CRL-1658)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  0.530
Name of IRES used as the positive control:
  EMCV
Name of the plasmid used as the positive control.
pbetaGAL/EMCV/CAT
Name of the plasmid used as the negative control.
pbetaGAL/rc_Apaf1/CAT
IRESite Id of the plasmid used as negative control.
  595
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  0.350
The size (length) of intercistronic region in the negative control:
922
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
Citations:
Nevins T. A., Harder Z. M., Korneluk R. G., Holcik M. (2003) Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97/DAP5/NAT1. J. Biol. Chem. 278(6):3572-3579
Translation results:
IRESite Translation Id: 659
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens T24 (ATCC HTB-4)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  0.070
Name of IRES used as the positive control:
  EMCV
Name of the plasmid used as the positive control.
pbetaGAL/EMCV/CAT
Name of the plasmid used as the negative control.
pbetaGAL/rc_Apaf1/CAT
IRESite Id of the plasmid used as negative control.
  595
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  0.290
The size (length) of intercistronic region in the negative control:
922
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
Citations:
Nevins T. A., Harder Z. M., Korneluk R. G., Holcik M. (2003) Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97/DAP5/NAT1. J. Biol. Chem. 278(6):3572-3579
Last change to the database: 2015-04-16 16:45:23 GMT+1