The nucleic acid data:
IRESite Id: 615 Version: 1
Originaly submitted by: Martin Mokrejš Submission date: 2009-08-26 13:22:51
Reviewed by: Martin Mokrejš Last change: 2009-08-26 13:25:42
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:
  TMV_type1
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
62124
The mRNA/+RNA description: 
Tobacco mosaic virus genome (variant 1).
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:
Tobacco mosaic virus
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
The total number of notable open-reading frames (ORFs):
  4
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:
RdRp
The description of the protein encoded in this ORF:
RNA polymerase (read-through protein)
The translational frameshift (ribosome slippage) involved:
  0
The ribosome read-through involved:
  yes
The alternative forms of this protein occur by the alternative initiation of translation:
  yes
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  69-4919
ORF
ORF position:   2
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
RdRp
The description of the protein encoded in this ORF:
RNA polymerase (read-through protein)
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:
  yes
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  69-3419
ORF
ORF position:   3
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
MP
The description of the protein encoded in this ORF:
movement protein
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):
  4903-5709
ORF
ORF position:   4
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
CP
The description of the protein encoded in this ORF:
coat protein
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):
  5712-6191
Remarks:
The 5'-UTR omega leader sequence of this genomic sequence GI:62124 (Goelet et al., 1982) matches exactly the
sequence published to be from TMV U1 (M24955). However, IRESite curators are not certain whether this is the
U1 strain.
Ivanov et al. (1997) who used a 148bp region upstream of TMV U1 CP gene as a negative control for experiments
defining IREScp148 of crTMV.
Citations:
Skulachev MV, Ivanov PA, Karpova OV, Korpela T, Rodionova NP, Dorokhov YL, Atabekov JG (1999) Internal initiation of translation directed by the 5'-untranslated region of the tobamovirus subgenomic RNA I(2). Virology. 1(263):139-154
Dorokhov YL, Skulachev MV, Ivanov PA, Zvereva SD, Tjulkina LG, Merits A, Gleba YY, Hohn T, Atabekov JG (2002) Polypurine (A)-rich sequences promote cross-kingdom conservation of internal ribosome entry. Proc. Natl. Acad. Sci. U.S.A. 8(99):5301-5306
Ivanov PA, Karpova OV, Skulachev MV, Tomashevskaya OL, Rodionova NP, Dorokhov YuL, Atabekov JG (1997) A tobamovirus genome that contains an internal ribosome entry site functional in vitro. Virology. 1(232):32-43
Goelet P, Lomonossoff GP, Butler PJ, Akam ME, Gait MJ, Karn J (1982) Nucleotide sequence of tobacco mosaic virus RNA. Proc. Natl. Acad. Sci. U.S.A. 19(79):5818-5822
IRESs:
IRES:
Version: 1 Last change: 2009-08-26 13:25:42
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  TMV_UI_IRESmp228
Warning: please make ires_name same as the gene_name and optionally append to it coordinates. E.g. when gene/virus name is EMCV-R use EMCV-R_-222_to_-1 or EMCV-R_1-456, etc. but not Emcv-R-... or EMCV-222_to_-1. Please keep case of letters as well. This rewards when searching through the database.
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  4670-4900
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  1251
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  1481
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -233
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -3
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Skulachev et al. (1999) reported upstream and downstream primers used to clone this region flanked by EcoRI
and NcoI sites.
Citations:
Ivanov P. A., Karpova O. V., Skulachev M. V., Tomashevskaya O. L., Rodionova N. P., Dorokhov YuL, Atabekov J. G. (1997) A tobamovirus genome that contains an internal ribosome entry site functional in vitro. Virology. 232(1):32-43
Last change to the database: 2015-04-16 16:45:23 GMT+1