The nucleic acid data:
IRESite Id: 637 Version: 0
Originaly submitted by: Martin Mokrejš Submission date: 2009-09-17 03:48:52
Reviewed by: Martin Mokrejš
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  end-to-end_full-length_mRNA
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  EV71
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
66967945
The mRNA/+RNA description: 
Human enterovirus 71 strain pinf7-54A from Taiwan, 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:
Human enterovirus 71 pinf7-54A
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
The total number of notable open-reading frames (ORFs):
  1
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:
polyprotein
The description of the protein encoded in this ORF:
viral 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):
  746-7327
Citations:
Lin JY, Shih SR, Pan M, Li C, Lue CF, Stollar V, Li ML (2009) hnRNP A1 interacts with the 5' untranslated regions of enterovirus 71 and Sindbis virus RNA and is required for viral replication. J. Virol. 83(12):6106-6114
IRESs:
IRES:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  EV71_1-748
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-748
Conclusion:
  strongly_supported_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Lin JY, Shih SR, Pan M, Li C, Lue CF, Stollar V, Li ML (2009) hnRNP A1 interacts with the 5' untranslated regions of enterovirus 71 and Sindbis virus RNA and is required for viral replication. J. Virol. 83(12):6106-6114
IRES trans-acting factor (ITAFS):
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
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: Martin Mokrejš
ITAF abbreviated name:
PTB
ITAF fullname:
polypyrimidine-tract binding protein (unspecified isoform)
ITAF description (long):
polypyrimidine-tract binding protein
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:
unknown
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
SF268 cell lysate (human glioblastoma)
Citations:
Lin JY, Shih SR, Pan M, Li C, Lue CF, Stollar V, Li ML (2009) hnRNP A1 interacts with the 5' untranslated regions of enterovirus 71 and Sindbis virus RNA and is required for viral replication. J. Virol. 83(12):6106-6114
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
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:
Unr
ITAF fullname:
upstream of N-ras
ITAF description (long):
Unr protein is known to bind to gaagaaguaa
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:
unknown
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
SF268 cell lysate (human glioblastoma)
Citations:
Lin JY, Shih SR, Pan M, Li C, Lue CF, Stollar V, Li ML (2009) hnRNP A1 interacts with the 5' untranslated regions of enterovirus 71 and Sindbis virus RNA and is required for viral replication. J. Virol. 83(12):6106-6114
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
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: Martin Mokrejš
ITAF abbreviated name:
PCBP-1
ITAF fullname:
poly(rC)-binding protein 1
ITAF description (long):
Binds EV71 IRES (Lin et al., 2009)
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:
unknown
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
SF268 cell lysate (human glioblastoma)
Citations:
Lin JY, Shih SR, Pan M, Li C, Lue CF, Stollar V, Li ML (2009) hnRNP A1 interacts with the 5' untranslated regions of enterovirus 71 and Sindbis virus RNA and is required for viral replication. J. Virol. 83(12):6106-6114
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 3 Last change: 2009-08-30 14:16:52
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
PCBP-2
ITAF fullname:
poly(rC)-binding protein 2 (39 kDa)
ITAF description (long):
Required for poliovirus IRES activity (Blyn et al. 1996 and 1997) and replication (Toyoda et al., 2007). Its amount is not limiting in rabbit reticulocyte lysates (RRL) (Hunt and Jackson 1999).
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:
unknown
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
SF268 cell lysate (human glioblastoma)
Citations:
Lin JY, Shih SR, Pan M, Li C, Lue CF, Stollar V, Li ML (2009) hnRNP A1 interacts with the 5' untranslated regions of enterovirus 71 and Sindbis virus RNA and is required for viral replication. J. Virol. 83(12):6106-6114
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
OPTIONAL: The interacting RNA base range (if any):
91-167,561-745
ITAF protein characteristics:
Version: 1 Last change: 2008-06-27 20:14:51
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
hnRNP_A1
ITAF fullname:
heterogeneous nuclear ribonucleoprotein A1
ITAF description (long):
heterogeneous nuclear ribonucleoprotein A1 (p37), 37 kDa
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:
unknown
Method used to demonstrate ITAF effect:
in_vivo
The organism where action of this ITAF was studied:
Homo sapiens HeLa (ATCC CCL-2)
Remarks:
It interacts with loops II and VI of the EV71 5'-UTR. It seems to be necessary for efficient viral replication
and stimulates IRES-activity (Figure 3C).
Citations:
Lin JY, Shih SR, Pan M, Li C, Lue CF, Stollar V, Li ML (2009) hnRNP A1 interacts with the 5' untranslated regions of enterovirus 71 and Sindbis virus RNA and is required for viral replication. J. Virol. 83(12):6106-6114
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
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: Martin Mokrejš
ITAF abbreviated name:
FBP2
ITAF fullname:
far upstream element (FUSE) binding protein 2
ITAF description (long):
far upstream element (FUSE) binding protein 2
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:
inhibitory
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
SF268 cell lysate (human glioblastoma)
Citations:
Lin JY, Li ML, Shih SR (2009) Far upstream element binding protein 2 interacts with enterovirus 71 internal ribosomal entry site and negatively regulates viral translation. Nucleic Acids Res. 37(1):47-59
Last change to the database: 2015-04-16 16:45:23 GMT+1