The nucleic acid data:
IRESite Id: 148 Version: 1
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2006-06-29 00:00:00
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  our_best_guess
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  CSFV
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
1220145
The mRNA/+RNA description: 
Hog cholera virus (Classical swine fever virus) 'Chinese' strain (C-strain; EP 0 351 901 B1) encoding
polyprotein.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_completely_same_as_in_the_experiment
The organism containing this mRNA with IRES segment in its genome:
Classical swine fever virus - C Chinese strain (C-strain, EP 0 351 901 B1)
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:
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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  374-12070
Citations:
Moormann R. J., van Gennip H. G., Miedema G. K., Hulst M. M., van Rijn P. A. (1996) Infectious RNA transcribed from an engineered full-length cDNA template of the genome of a pestivirus. J. Virol. 70(2):763-770
IRESs:
IRES:
Version: 2 Last change: 2009-08-30 04:48:09
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  CSFV
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-373
Conclusion:
  strongly_supported_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Rijnbrand R., Bredenbeek P. J., Haasnoot P. C., Kieft J. S., Spaan W. J., Lemon S. M. (2001) The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAs. RNA. 7(4):585-597
RNA:protein interactions:
The RNA:protein interaction:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The description of the protein interacting with the RNA:
eIF3
The interacting RNA base range: 182-234
The organism where this RNA:protein interaction occurs:
Remarks:
The interaction was studied in vitro with isolated ribosomes from rabbit reticulocyte lysates.
Citations:
Sizova D. V., Kolupaeva V. G., Pestova T. V., Shatsky I. N., Hellen C. U. (1998) Specific interaction of eukaryotic translation initiation factor 3 with the 5' nontranslated regions of hepatitis C virus and classical swine fever virus RNAs. J. Virol. 72(6):4775-4782
The RNA:protein interaction:
Version: 2 Last change: 2009-08-29 13:01:59
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Abbreviated name of the protein interacting with the RNA:
RPS9
Full name of the protein interacting with the RNA:
ribosomal protein S9
The description of the protein interacting with the RNA:
ribosomal protein S9
The organism where this RNA:protein interaction occurs:
Oryctolagus cuniculus RRL
Remarks:
The interaction with RPS9 was shown in RRL-based toe-printing assay (Pestova et al., 1998). It could be that
the RPS9 protein was misplaced instead of RPS5 (Fukushi et al., 2001).
Citations:
Pestova TV, Shatsky IN, Fletcher SP, Jackson RJ, Hellen CU (1998) A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes Dev. 1(12):67-83
Fukushi S, Okada M, Stahl J, Kageyama T, Hoshino FB, Katayama K (2001) Ribosomal protein S5 interacts with the internal ribosomal entry site of hepatitis C virus. J. Biol. Chem. 24(276):20824-20826
Last change to the database: 2015-04-16 16:45:23 GMT+1