The nucleic acid data:
IRESite Id: 77 Version: 3
Originaly submitted by: Václav Vopálenský Submission date: 2005-10-12 00:00:00
Reviewed by: Václav Vopálenský Last change: 2009-08-29 17:55:55
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:
  TSV
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
14701764
The mRNA/+RNA description: 
Taura syndrome virus, Dicistroviridae, 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:
Taura syndrome virus
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
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: Václav Vopálenský
The abbreviated name of this ORF/gene:
ORF1
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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  417-6740
OPTIONAL: The function of the encoded protein
encodes putative helicase, protease and RNA-dependent RNA polymerase
ORF
ORF position:   2
Version: 2 Last change: 2009-08-29 17:55:55
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The abbreviated name of this ORF/gene:
ORF2
The description of the protein encoded in this ORF:
capsid protein precursor
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):
  6953-9982
OPTIONAL: The function of the encoded protein
capsid protein
Remarks:
The CP protein probably starts at 6953 instead. [Hatakeyama et al., 2004, actually Mari et al., 2002
referenced therein]
Citations:
Hatakeyama Y., Shibuya N., Nishiyama T., Nakashima N. (2004) Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts. RNA. 10(5):779-786
Cevallos R. C., Sarnow P. (2005) Factor-independent assembly of elongation-competent ribosomes by an internal ribosome entry site located in an RNA virus that infects penaeid shrimp. J. Virol. 79(2):677-683
Mari J, Poulos BT, Lightner DV, Bonami JR (2002) Shrimp Taura syndrome virus: genomic characterization and similarity with members of the genus Cricket paralysis-like viruses. J. Gen. Virol. 4(83):915-926
IRESs:
IRES:
Version: 7 Last change: 2009-08-30 04:46:27
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The IRES name:
  TSV_IGR
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  6741-6990
Conclusion:
  weakly_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:
  1
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  250
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -212
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  37
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Entire intergenic region of TSV (from nt 6741 to nt 6946) and 44 bases of CP. The bicistronic capped and
uncapped constructs were tested in wheat germ lysates.

The region 6719-7005 was studied in rabbit reticulocyte lysates.

Nakashima and Uchiumi (2009) in Table 1 annotated as the IRES region 6761–6952.
Citations:
Hatakeyama Y., Shibuya N., Nishiyama T., Nakashima N. (2004) Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts. RNA. 10(5):779-786
Cevallos R. C., Sarnow P. (2005) Factor-independent assembly of elongation-competent ribosomes by an internal ribosome entry site located in an RNA virus that infects penaeid shrimp. J. Virol. 79(2):677-683
Nakashima N, Uchiumi T (2009) Functional analysis of structural motifs in dicistroviruses. Virus Res. 139(2):137-147
Last change to the database: 2015-04-16 16:45:23 GMT+1