IRESite_Id:602 summary record describing characteristics of crTMV

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `602`	Version: `1`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-21 19:36:02`
Reviewed by: Martin Mokrejš	Last change: `2009-08-21 21:07:01`

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: `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:

Bicistronic, uncapped subgenomic I2 RNA (sgRNA) of crTMV. Only the movement protein (MP) is produced while
coat protein (CP) is not.

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

ttcgtttgct ttttgtagta taattaaata tttgtcagat aagagattgt ttagagattt gttctttgtt tgataATGTC GATAGTTTCG TACGAACCCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AGGTAAGTGA CTTCCTTAAT CTTTCTAAGA AGGAAGAGAT CTTGCCGAAG GCTCTAACGA GGTTAAAGAC CGTGTCTATT AGTACTAAAG ATATTATATC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGTTAAGGAG TCTGAGACTT TGTGTGATAT AGATTTGTTA ATCAATGTGC CATTAGATAA GTATAGATAT GTGGGTATCC TAGGTGCTGT TTTTACCGGA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GAGTGGCTTG TGCCAGACTT TGTTAAAGGT GGTGTGACGA TAAGTGTGAT AGATAAGCGT CTTGCGAACT CTAAGGAGTG CGTGATTGGT ACGTACAGAG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTGCAGCCAA GAGTAAGAGG TTCCAGTTCA AATTGGTTCC AAATTACTTT GTGTCCACTG TGGACGCAAA GAGGAAGCCG TGGCAGGTTC ATGTTCGTAT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCAAGACTTG AAGATCGAGG CAGGTTGGCA GCCGTTAGCT CTGGAAGTGG TTTCAGTTGC TATGGTTACC AATAACGTTG TTATGAAGGG TTTGAGGGAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AAAGTCGTCG CAATAAATGA TCCGGACGTC GAAGGTTTCG AAGGTGTGGT TGACGAATTC GTCGATTCGG TTGCAGCATT TAAAGCGGTT GACAACTTTA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AAAGAAGGAA AAAGAAGGTT GAAGAAAAGG GTGTAGTAAG TAAGTATAAG TACAGACCGG AGAAGTACGC CGGTCCTGAT TCGTTTAATT TGAAAGAAGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AAATGTCTTA CAACATTACA AACCCGAATC AGTACCAGTA TTTCGCAGCG GTGTGGGCAG AGCCCATTCC GATGCTTAAc cagtgcatat cggcattgtc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

acaatcgtac caaacacaag ctgcgagaga cactgttaga cagcaattct caaacttgtt gagtgcggtt gtggctccga gccagcggtt cccagaaaca 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

gggtcccggg tgtatgttaa ctcggctgtt ataaagccgt tgtacgaggc tcttatgaag tcctttgata ctagaaatag gatcatagag acggaagagg 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

agtcacgccc gtcagcttcc gaagtacgta acgcgacaca acgtgttgat gatgcgaccg tttccattag aagtcaaatt cagctgttgc tgagcgagct 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ttccagtgga catggttata tgaacagggc agagttcgag gctttggtgc catggactac tgctgctgct acttaggcgt ggtgcgcacg atagcgcata 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

gtgtttttct ctccacttga atcgaagaga tagacttacg gtgtaaatcc gtaggggtgg cgtaaaccaa attacgcaat gttttgggtt ccatttaaat 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

cgaaacccct tatttcctgg atcacctgtt aacgcacgtt tgacgtgtat tacagtggga ataagtaaaa gtgagaggtt cgaatcctcc ctaaccccgg 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

gtaggggccc a
^1501      ^1511

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

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:
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):

76-879

Remarks:

The 5'-UTR region was inferred from TRSIG database record 'EXPERIMENT E0074'
(http://dna01.bse.kyutech.ac.jp/jouhou/trsig/anotates.html?-page+LibInfo+-lib+TRSIG_OB).

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 10:41:07`
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):

655-802

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 
^655       ^665       ^675       ^685       ^695       ^705       ^715       ^725       ^735       ^745       

GACCGGAGAA GTACGCCGGT CCTGATTCGT TTAATTTGAA AGAAGAAA
^755       ^765       ^775       ^785       ^795

Remarks:

The IRES is not functional in this context (I2 sgRNA) although it was reported functional in in vitro assays.
More details in IRESiteId:36.

Citations:

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