The nucleic acid data:
IRESite Id: 244 Version: 5
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš Last change: 2009-09-01 18:54:49
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/XIAP/CAT which
comprises beta galactosidase and chloramphenicol acetyltransferase as the first and the second cistron
respectively and the whole part of human XIAP 5' UTR (nt from -993 to nt -1 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/XIAP/CAT
The name of the promoter used to express this mRNA:
  CMV
Aliases of the plasmid name:
Alias: pbetaGAL/hUTR/CAT
Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing the whole part of human XIAP 5' UTR (nt from -993 to nt -1 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?):
  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:
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:
Mus musculus C2C12
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
XIAP
The origin of IRES in the plasmid:
  nuclear
The donor organism of the IRES segment:
Homo sapiens fetal liver
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/XIAP/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:
  no
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 acetyl transferase
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):
  4668-5327
Citations:
Holcik M., Lefebvre C., Yeh C., Chow T., Korneluk R. G. (1999) A new internal-ribosome-entry-site motif potentiates XIAP-mediated cytoprotection. Nat. Cell. Biol. 1(3):190-192
IRESs:
IRES:
Version: 3 Last change: 2009-09-02 09:43:01
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The IRES name:
  XIAP
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  3621-4613
How IRES boundaries were determined:
guessed
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:
  1281
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -1047
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:
Whole 5'-UTR region of XIAP mRNA (from nt -993 to nt -1).
Citations:
Holcik M., Lefebvre C., Yeh C., Chow T., Korneluk R. G. (1999) A new internal-ribosome-entry-site motif potentiates XIAP-mediated cytoprotection. Nat. Cell. Biol. 1(3):190-192
The translation experiments:
Translation results:
IRESite Translation Id: 299
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:
Mus musculus C2C12
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  100.000
Name of the plasmid used as the negative control.
pbetaGAL/CAT
IRESite Id of the plasmid used as negative control.
  237
The relative translation efficiency in % of the negative control:
  0.019
The size (length) of intercistronic region in the negative control:
336
The effect of 5'-cap analogs on translation:
no
Rapamycin affects translation:
no
Type of RNA subject to translation:
  exogenous_RNA_with_GpppG_cap_with_polyA_tail
Remarks:
This plasmid was used as the positive control for experiments in article The Utrophin A 5'-Untranslated Region
Confers Internal Ribosome Entry Site-mediated Translational Control during Regeneration of Skeletal Muscle
Fibers (Miura et al., 2005; PMID:16061482).
Citations:
Miura P., Thompson J., Chakkalakal J. V., Holcik M., Jasmin B. J. (2005) The utrophin A 5'-untranslated region confers internal ribosome entry site-mediated translational control during regeneration of skeletal muscle fibers. J. Biol. Chem. 280(38):32997-33005
Translation results:
IRESite Translation Id: 660
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:
  100.000
Name of the plasmid used as the negative control.
pbetaGAL/rc_XIAP/CAT
IRESite Id of the plasmid used as negative control.
  632
The relative translation efficiency in % of the negative control:
  1.140
The size (length) of intercistronic region in the negative control:
1335
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:
Holcik M., Lefebvre C., Yeh C., Chow T., Korneluk R. G. (1999) A new internal-ribosome-entry-site motif potentiates XIAP-mediated cytoprotection. Nat. Cell. Biol. 1(3):190-192
Translation results:
IRESite Translation Id: 661
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:
  37.500
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_XIAP/CAT
IRESite Id of the plasmid used as negative control.
  632
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:
1335
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: 662
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:
  22.000
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_XIAP/CAT
IRESite Id of the plasmid used as negative control.
  632
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:
1335
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: 663
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:
  12.100
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_XIAP/CAT
IRESite Id of the plasmid used as negative control.
  632
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:
1335
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: 664
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:
  6.610
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_XIAP/CAT
IRESite Id of the plasmid used as negative control.
  632
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:
1335
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: 665
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:
  11.000
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_XIAP/CAT
IRESite Id of the plasmid used as negative control.
  632
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:
1335
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: 666
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:
  1.130
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_XIAP/CAT
IRESite Id of the plasmid used as negative control.
  632
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:
1335
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: 673
Version: 1 Last change: 2009-09-03 20:25:57
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 293T (ATCC CRL-1573)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  100.000
Name of the plasmid used as the negative control.
pbetaGAL/CAT
IRESite Id of the plasmid used as negative control.
  237
The relative translation efficiency in % of the negative control:
  0.880
The size (length) of intercistronic region in the negative control:
336
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:
Warnakulasuriyarachchi D., Ungureanu N. H., Holcik M. (2003) The translation of an antiapoptotic protein HIAP2 is regulated by an upstream open reading frame. Cell. Death. Differ. 10(8):899-904
Last change to the database: 2015-04-16 16:45:23 GMT+1