The nucleic acid data:
IRESite Id: 437 Version: 4
Originaly submitted by: Martin Mokrejš
Reviewed by: Václav Vopálenský Last change: 2009-09-02 03:02:20
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  hopefully_full-length_mRNA
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  RhPV
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
2911298
The mRNA/+RNA description: 
Rhopalosiphum padi virus, complete genome.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_reverse_engineered_and_should_match_experiment
The organism containing this mRNA with IRES segment in its genome:
Rhopalosiphum padi virus
A promoter reported in cDNA corresponding to IRES sequence:
  yes
The total number of notable open-reading frames (ORFs):
  2
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:
weak_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:
Spodoptera frugiperda Sf-21
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: Václav Vopálenský
The abbreviated name of this ORF/gene:
polyprotein
The description of the protein encoded in this ORF:
non-structural polyprotein
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):
  580-6576
ORF
ORF position:   2
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
The abbreviated name of this ORF/gene:
polyprotein
The description of the protein encoded in this ORF:
structural polyprotein
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):
  7107-9560
Remarks:
The second ORF is not initiated by a +1 frameshift as proposed originally but the first two aminoacid residues
come from 'CCTGCA' in Domier et al. (2000), Figure 6.

The cryptic promoter activity in Spodoptera frugiperda Sf21 cells was shown by Wu et al. (2008), and
postulated already in Wu et al. (2007).

Please refer also to patent no. WO 02/12522.
Citations:
Woolaway K. E., Lazaridis K., Belsham G. J., Carter M. J., Roberts L. O. (2001) The 5' untranslated region of Rhopalosiphum padi virus contains an internal ribosome entry site which functions efficiently in mammalian, plant, and insect translation systems. J. Virol. 75(21):10244-10249
Domier L. L., McCoppin N. K., D'Arcy C. J. (2000) Sequence requirements for translation initiation of Rhopalosiphum padi virus ORF2. Virology. 268(2):264-271
Wu YJ, Teng CY, Chen YJ, Chen SC, Chen YJ, Lin YT, Wu TY (2008) Internal ribosome entry site of Rhopalosiphum padi virus is functional in mammalian cells and has cryptic promoter activity in baculovirus-infected Sf21 cells. Acta Pharmacol. Sin. 8(29):965-974
Wu TY, Wu CY, Chen YJ, Chen CY, Wang CH (2007) The 5' untranslated region of Perina nuda virus (PnV) possesses a strong internal translation activity in baculovirus-infected insect cells. FEBS Lett. 581(16):3120-3126
IRESs:
IRES:
Version: 5 Last change: 2009-09-02 02:48:02
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
The IRES name:
  RhPV_5NCR
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-579
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Sequence 1 from Patent WO0212522. The IRES is also functional in wheat-germ lysates (Woolaway et al., (2001),
Figure 2), also in Drosophila SL2 cell extracts (Woolaway et al., (2001), Figure 3), in Spodoptera frugiperda
Sf21 cells (Royall et al., (2004)). In contrast, EMCV IRES is functional only in mammalian cells or cell
extracts.

Robert and Groppeli (2009) reported that the 5'-UTR IRES is largely unstructured.

Wu et al. (2007) reported that the 5NTR IRES was functional in in baculovirus-infected Sf21 cells.
Citations:
Woolaway K. E., Lazaridis K., Belsham G. J., Carter M. J., Roberts L. O. (2001) The 5' untranslated region of Rhopalosiphum padi virus contains an internal ribosome entry site which functions efficiently in mammalian, plant, and insect translation systems. J. Virol. 75(21):10244-10249
Domier L. L., McCoppin N. K., D'Arcy C. J. (2000) Sequence requirements for translation initiation of Rhopalosiphum padi virus ORF2. Virology. 268(2):264-271
Royall E., Woolaway K. E., Schacherl J., Kubick S., Belsham G. J., Roberts L. O. (2004) The Rhopalosiphum padi virus 5' internal ribosome entry site is functional in Spodoptera frugiperda 21 cells and in their cell-free lysates: implications for the baculovirus expression system. J. Gen. Virol. 85(Pt 6):1565-1569
Roberts LO, Groppelli E (2009) An atypical IRES within the 5' UTR of a dicistrovirus genome. Virus Res. 139(2):157-165
Wu TY, Wu CY, Chen YJ, Chen CY, Wang CH (2007) The 5' untranslated region of Perina nuda virus (PnV) possesses a strong internal translation activity in baculovirus-infected insect cells. FEBS Lett. 581(16):3120-3126
IRES:
Version: 1 Last change: 2009-08-29 18:26:08
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
The IRES name:
  RhPV_IGR
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  6875-7106
Conclusion:
  strongly_supported_IRES
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  299
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  530
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -232
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -1
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
The IRES is followed by CCU translation initiation codon. Localization of RhPV_IGR IRES containing RNA in
80S ribosomal fraction was shown in Domier et al. (2003), Figure 3.
Citations:
Domier L. L., McCoppin N. K., D'Arcy C. J. (2000) Sequence requirements for translation initiation of Rhopalosiphum padi virus ORF2. Virology. 268(2):264-271
Groppelli E, Belsham GJ, Roberts LO (2007) Identification of minimal sequences of the Rhopalosiphum padi virus 5' untranslated region required for internal initiation of protein synthesis in mammalian, plant and insect translation systems. J. Gen. Virol. 5(88):1583-1588
IRES trans-acting factor (ITAFS):
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
ITAF abbreviated name:
eIF1
ITAF fullname:
eukaryotic translation initiation factor 1
ITAF description (long):
eukaryotic translation initiation factor 1
3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
other
Citations:
Terenin I. M., Dmitriev S. E., Andreev D. E., Royall E., Belsham G. J., Roberts L. O., Shatsky I. N. (2005) A cross-kingdom internal ribosome entry site reveals a simplified mode of internal ribosome entry. Mol. Cell. Biol. 25(17):7879-7888
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
ITAF abbreviated name:
eIF2
ITAF fullname:
eukaryotic translation initiation factor 2
ITAF description (long):
eukaryotic translation initiation factor 2
3.2.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
other
Citations:
Terenin I. M., Dmitriev S. E., Andreev D. E., Royall E., Belsham G. J., Roberts L. O., Shatsky I. N. (2005) A cross-kingdom internal ribosome entry site reveals a simplified mode of internal ribosome entry. Mol. Cell. Biol. 25(17):7879-7888
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
ITAF abbreviated name:
eIF3
ITAF fullname:
eukaryotic translation initiation factor 3
ITAF description (long):
eukaryotic translation initiation factor 3
3.3.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
other
Citations:
Terenin I. M., Dmitriev S. E., Andreev D. E., Royall E., Belsham G. J., Roberts L. O., Shatsky I. N. (2005) A cross-kingdom internal ribosome entry site reveals a simplified mode of internal ribosome entry. Mol. Cell. Biol. 25(17):7879-7888
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
ITAF abbreviated name:
eIF1A
ITAF fullname:
eukaryotic translation initiation factor 1A
ITAF description (long):
eukaryotic translation initiation factor 1A
3.4.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
stimulatory
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
other
Citations:
Terenin I. M., Dmitriev S. E., Andreev D. E., Royall E., Belsham G. J., Roberts L. O., Shatsky I. N. (2005) A cross-kingdom internal ribosome entry site reveals a simplified mode of internal ribosome entry. Mol. Cell. Biol. 25(17):7879-7888
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 1 Last change: 2009-08-18 16:32:07
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
eIF4G
ITAF fullname:
eukaryotic translation initiation factor 4G
ITAF description (long):
eIF4G is the scaffolding protein bridging together the cap-binding protein eIF4E with other proteins of the initiating ribosome
3.5.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
stimulatory
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
other
Citations:
Terenin I. M., Dmitriev S. E., Andreev D. E., Royall E., Belsham G. J., Roberts L. O., Shatsky I. N. (2005) A cross-kingdom internal ribosome entry site reveals a simplified mode of internal ribosome entry. Mol. Cell. Biol. 25(17):7879-7888
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
ITAF abbreviated name:
eIF4A
ITAF fullname:
eukaryotic translation initiation factor 4A
ITAF description (long):
eukaryotic translation initiation factor 4A
3.6.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
stimulatory
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
other
Citations:
Terenin I. M., Dmitriev S. E., Andreev D. E., Royall E., Belsham G. J., Roberts L. O., Shatsky I. N. (2005) A cross-kingdom internal ribosome entry site reveals a simplified mode of internal ribosome entry. Mol. Cell. Biol. 25(17):7879-7888
Last change to the database: 2015-04-16 16:45:23 GMT+1