IRESite_Id:603 summary record describing characteristics of crTMV

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `603`	Version: `1`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-21 20:18:28`
Reviewed by: Martin Mokrejš	Last change: `2009-08-21 21:07:28`

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: `crTMV`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
488713

The mRNA/+RNA description:

Monocistronic crTMV sgRNA determined by oligo(dT) primed cDNA sequencing (pG3A16 clone), encoding only CP
protein.

The mRNA/+RNA sequence represented in the +DNA notation:

cgaaggtttc gaaggtgtgg ttgacgaatt cgtcgattcg gttgcagcat ttaaagcggt tgacaacttt aaaagaagga aaaagaaggt tgaagaaaag 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ggtgtagtaa gtaagtataa gtacagaccg gagaagtacg ccggtcctga ttcgtttaat ttgaaagaag aaaATGTCTT ACAACATTAC AAACCCGAAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CAGTACCAGT ATTTCGCAGC GGTGTGGGCA GAGCCCATTC CGATGCTTAA CCAGTGCATA TCGGCATTGT CACAATCGTA CCAAACACAA GCTGCGAGAG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ACACTGTTAG ACAGCAATTC TCAAACTTGT TGAGTGCGGT TGTGGCTCCG AGCCAGCGGT TCCCAGAAAC AGGGTCCCGG GTGTATGTTA ACTCGGCTGT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TATAAAGCCG TTGTACGAGG CTCTTATGAA GTCCTTTGAT ACTAGAAATA GGATCATAGA GACGGAAGAG GAGTCACGCC CGTCAGCTTC CGAAGTACGT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AACGCGACAC AACGTGTTGA TGATGCGACC GTTTCCATTA GAAGTCAAAT TCAGCTGTTG CTGAGCGAGC TTTCCAGTGG ACATGGTTAT ATGAACAGGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CAGAGTTCGA GGCTTTGGTG CCATGGACTA CTGCTGCTGC TACTTAGgcg tggtgcgcac gatagcgcat agtgtttttc tctccacttg aatcgaagag 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

atagacttac ggtgtaaatc cgtaggggtg gcgtaaacca aattacgcaa tgttttgggt tccatttaaa tcgaaacccc ttatttcctg gatcacctgt 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

taacgcacgt ttgacgtgta ttacagtggg aataagtaaa agtgagaggt tcgaatcctc cctaaccccg ggtaggggcc ca
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881

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:

Crucifer tobamovirus

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:
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):

174-647

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

Dorokhov YuL, Ivanov PA, Novikov VK, Agranovsky AA, Morozov SYu, Efimov VA, Casper R, Atabekov JG (1994) Complete nucleotide sequence and genome organization of a tobamovirus infecting cruciferae plants. FEBS Lett. 1(350):5-8

IRESs:

IRES:

Version: `1`	Last change: `2009-08-25 10:41:30`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `crTMV_IREScp`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

26-173

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

The sequence of IRES region aligned to its secondary structure (if available):

gaattcgtcg attcggttgc agcatttaaa gcggttgaca actttaaaag aaggaaaaag aaggttgaag aaaagggtgt agtaagtaag tataagtaca 
^26        ^36        ^46        ^56        ^66        ^76        ^86        ^96        ^106       ^116       

gaccggagaa gtacgccggt cctgattcgt ttaatttgaa agaagaaa
^126       ^136       ^146       ^156       ^166

Citations:

Last change to the database: 2019-03-18 09:32:49 GMT+1