IRESite_Id:615 summary record describing characteristics of TMV_UI

IRESite: The database of experimentally verified IRES structures

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:

GTATTTTTAC AACAATTACC AACAACAACA AACAACAAAC AACATTACAA TTACTATTTA CAATTACAAT GGCATACACA CAGACAGCTA CCACATCAGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTTGCTGGAC ACTGTCCGAG GAAACAACTC CTTGGTCAAT GATCTAGCAA AGCGTCGTCT TTACGACACA GCGGTTGAAG AGTTTAACGC TCGTGACCGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGGCCCAAGG TGAACTTTTC AAAAGTAATA AGCGAGGAGC AGACGCTTAT TGCTACCCGG GCGTATCCAG AATTCCAAAT TACATTTTAT AACACGCAAA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATGCCGTGCA TTCGCTTGCA GGTGGATTGC GATCTTTAGA ACTGGAATAT CTGATGATGC AAATTCCCTA CGGATCATTG ACTTATGACA TAGGCGGGAA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TTTTGCATCG CATCTGTTCA AGGGACGAGC ATATGTACAC TGCTGCATGC CCAACCTGGA CGTTCGAGAC ATCATGCGGC ACGAAGGCCA GAAAGACAGT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ATTGAACTAT ACCTTTCTAG GCTAGAGAGA GGGGGGAAAA CAGTCCCCAA CTTCCAAAAG GAAGCATTTG ACAGATACGC AGAAATTCCT GAAGACGCTG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCTGTCACAA TACTTTCCAG ACAATGCGAC ATCAGCCGAT GCAGCAATCA GGCAGAGTGT ATGCCATTGC GCTACACAGC ATATATGACA TACCAGCCGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGAGTTCGGG GCGGCACTCT TGAGGAAAAA TGTCCATACG TGCTATGCCG CTTTCCACTT CTCTGAGAAC CTGCTTCTTG AAGATTCATA CGTCAATTTG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GACGAAATCA ACGCGTGTTT TTCGCGCGAT GGAGACAAGT TGACCTTTTC TTTTGCATCA GAGAGTACTC TTAATTATTG TCATAGTTAT TCTAATATTC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTAAGTATGT GTGCAAAACT TACTTCCCGG CCTCTAATAG AGAGGTTTAC ATGAAGGAGT TTTTAGTCAC CAGAGTTAAT ACCTGGTTTT GTAAGTTTTC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TAGAATAGAT ACTTTTCTTT TGTACAAAGG TGTGGCCCAT AAAAGTGTAG ATAGTGAGCA GTTTTATACT GCAATGGAAG ACGCATGGCA TTACAAAAAG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACTCTTGCAA TGTGCAACAG CGAGAGAATC CTCCTTGAGG ATTCATCATC AGTCAATTAC TGGTTTCCCA AAATGAGGGA TATGGTCATC GTACCATTAT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TCGACATTTC TTTGGAGACT AGTAAGAGGA CGCGCAAGGA AGTCTTAGTG TCCAAGGATT TCGTGTTTAC AGTGCTTAAC CACATTCGAA CATACCAGGC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GAAAGCTCTT ACATACGCAA ATGTTTTGTC CTTTGTCGAA TCGATTCGAT CGAGGGTAAT CATTAACGGT GTGACAGCGA GGTCCGAATG GGATGTGGAC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAATCTTTGT TACAATCCTT GTCCATGACG TTTTACCTGC ATACTAAGCT TGCCGTTCTA AAGGATGACT TACTGATTAG CAAGTTTAGT CTCGGTTCGA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AAACGGTGTG CCAGCATGTG TGGGATGAGA TTTCGCTGGC GTTTGGGAAC GCATTTCCCT CCGTGAAAGA GAGGCTCTTG AACAGGAAAC TTATCAGAGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGCAGGCGAC GCATTAGAGA TCAGGGTGCC TGATCTATAT GTGACCTTCC ACGACAGATT AGTGACTGAG TACAAGGCCT CTGTGGACAT GCCTGCGCTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GACATTAGGA AGAAGATGGA AGAAACGGAA GTGATGTACA ATGCACTTTC AGAGTTATCG GTGTTAAGGG AGTCTGACAA ATTCGATGTT GATGTTTTTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CCCAGATGTG CCAATCTTTG GAAGTTGACC CAATGACGGC AGCGAAGGTT ATAGTCGCGG TCATGAGCAA TGAGAGCGGT CTGACTCTCA CATTTGAACG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ACCTACTGAG GCGAATGTTG CGCTAGCTTT ACAGGATCAA GAGAAGGCTT CAGAAGGTGC TTTGGTAGTT ACCTCAAGAG AAGTTGAAGA ACCGTCCATG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AAGGGTTCGA TGGCCAGAGG AGAGTTACAA TTAGCTGGTC TTGCTGGAGA TCATCCGGAG TCGTCCTATT CTAAGAACGA GGAGATAGAG TCTTTAGAGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AGTTTCATAT GGCAACGGCA GATTCGTTAA TTCGTAAGCA GATGAGCTCG ATTGTGTACA CGGGTCCGAT TAAAGTTCAG CAAATGAAAA ACTTTATCGA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TAGCCTGGTA GCATCACTAT CTGCTGCGGT GTCGAATCTC GTCAAGATCC TCAAAGATAC AGCTGCTATT GACCTTGAAA CCCGTCAAAA GTTTGGAGTC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTGGATGTTG CATCTAGGAA GTGGTTAATC AAACCAACGG CCAAGAGTCA TGCATGGGGT GTTGTTGAAA CCCACGCGAG GAAGTATCAT GTGGCGCTTT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGGAATATGA TGAGCAGGGT GTGGTGACAT GCGATGATTG GAGAAGAGTA GCTGTCAGCT CTGAGTCTGT TGTTTATTCC GACATGGCGA AACTCAGAAC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TCTGCGCAGA CTGCTTCGAA ACGGAGAACC GCATGTCAGT AGCGCAAAGG TTGTTCTTGT GGACGGAGTT CCGGGCTGTG GGAAAACCAA AGAAATTCTT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TCCAGGGTTA ATTTTGATGA AGATCTAATT TTAGTACCTG GGAAGCAAGC CGCGGAAATG ATCAGAAGAC GTGCGAATTC CTCAGGGATT ATTGTGGCCA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CGAAGGACAA CGTTAAAACC GTTGATTCTT TCATGATGAA TTTTGGGAAA AGCACACGCT GTCAGTTCAA GAGGTTATTC ATTGATGAAG GGTTGATGTT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GCATACTGGT TGTGTTAATT TTCTTGTGGC GATGTCATTG TGCGAAATTG CATATGTTTA CGGAGACACA CAGCAGATTC CATACATCAA TAGAGTTTCA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGATTCCCGT ACCCCGCCCA TTTTGCCAAA TTGGAAGTTG ACGAGGTGGA GACACGCAGA ACTACTCTCC GTTGTCCAGC CGATGTCACA CATTATCTGA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ACAGGAGATA TGAGGGCTTT GTCATGAGCA CTTCTTCGGT TAAAAAGTCT GTTTCGCAGG AGATGGTCGG CGGAGCCGCC GTGATCAATC CGATCTCAAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ACCCTTGCAT GGCAAGATCC TGACTTTTAC CCAATCGGAT AAAGAAGCTC TGCTTTCAAG AGGGTATTCA GATGTTCACA CTGTGCATGA AGTGCAAGGC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GAGACATACT CTGATGTTTC ACTAGTTAGG TTAACCCCTA CACCAGTCTC CATCATTGCA GGAGACAGCC CACATGTTTT GGTCGCATTG TCAAGGCACA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CCTGTTCGCT CAAGTACTAC ACTGTTGTTA TGGATCCTTT AGTTAGTATC ATTAGAGATC TAGAGAAACT TAGCTCGTAC TTGTTAGATA TGTATAAGGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CGATGCAGGA ACACAATAGC AATTACAGAT TGACTCGGTG TTCAAAGGTT CCAATCTTTT TGTTGCAGCG CCAAAGACTG GTGATATTTC TGATATGCAG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TTTTACTATG ATAAGTGTCT CCCAGGCAAC AGCACCATGA TGAATAATTT TGATGCTGTT ACCATGAGGT TGACTGACAT TTCATTGAAT GTCAAAGATT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GCATATTGGA TATGTCTAAG TCTGTTGCTG CGCCTAAGGA TCAAATCAAA CCACTAATAC CTATGGTACG AACGGCGGCA GAAATGCCAC GCCAGACTGG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ACTATTGGAA AATTTAGTGG CGATGATTAA AAGGAACTTT AACGCACCCG AGTTGTCTGG CATCATTGAT ATTGAAAATA CTGCATCTTT AGTTGTAGAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AAGTTTTTTG ATAGTTATTT GCTTAAAGAA AAAAGAAAAC CAAATAAAAA TGTTTCTTTG TTCAGTAGAG AGTCTCTCAA TAGATGGTTA GAAAAGCAGG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AACAGGTAAC AATAGGCCAG CTCGCAGATT TTGATTTTGT AGATTTGCCA GCAGTTGATC AGTACAGACA CATGATTAAA GCACAACCCA AGCAAAAATT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GGACACTTCA ATCCAAACGG AGTACCCGGC TTTGCAGACG ATTGTGTACC ATTCAAAAAA GATCAATGCA ATATTTGGCC CGTTGTTTAG TGAGCTTACT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AGGCAATTAC TGGACAGTGT TGATTCGAGC AGATTTTTGT TTTTCACAAG AAAGACACCA GCGCAGATTG AGGATTTCTT CGGAGATCTC GACAGTCATG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TGCCGATGGA TGTCTTGGAG CTGGATATAT CAAAATACGA CAAATCTCAG AATGAATTCC ACTGTGCAGT AGAATACGAG ATCTGGCGAA GATTGGGTTT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TGAAGACTTC TTGGGAGAAG TTTGGAAACA AGGGCATAGA AAGACCACCC TCAAGGATTA TACCGCAGGT ATAAAAACTT GCATCTGGTA TCAAAGAAAG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AGCGGGGACG TCACGACGTT CATTGGAAAC ACTGTGATCA TTGCTGCATG TTTGGCCTCG ATGCTTCCGA TGGAGAAAAT AATCAAAGGA GCCTTTTGCG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GTGACGATAG TCTGCTGTAC TTTCCAAAGG GTTGTGAGTT TCCGGATGTG CAACACTCCG CGAATCTTAT GTGGAATTTT GAAGCAAAAC TGTTTAAAAA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ACAGTATGGA TACTTTTGCG GAAGATATGT AATACATCAC GACAGAGGAT GCATTGTGTA TTACGATCCC CTAAAGTTGA TCTCGAAACT TGGTGCTAAA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CACATCAAGG ATTGGGAACA CTTGGAGGAG TTCAGAAGGT CTCTTTGTGA TGTTGCTGTT TCGTTGAACA ATTGTGCGTA TTACACACAG TTGGACGACG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CTGTATGGGA GGTTCATAAG ACCGCCCCTC CAGGTTCGTT TGTTTATAAA AGTCTGGTGA AGTATTTGTC TGATAAAGTT CTTTTTAGAA GTTTGTTTAT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

AGATGGCTCT AGTTGTTAAA GGAAAAGTGA ATATCAATGA GTTTATCGAC CTGACAAAAA TGGAGAAGAT CTTACCGTCG ATGTTTACCC CTGTAAAGAG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TGTTATGTGT TCCAAAGTTG ATAAAATAAT GGTTCATGAG AATGAGTCAT TGTCAGAGGT GAACCTTCTT AAAGGAGTTA AGCTTATTGA TAGTGGATAC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GTCTGTTTAG CCGGTTTGGT CGTCACGGGC GAGTGGAACT TGCCTGACAA TTGCAGAGGA GGTGTGAGCG TGTGTCTGGT GGACAAAAGG ATGGAAAGAG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CCGACGAGGC CACTCTCGGA TCTTACTACA CAGCAGCTGC AAAGAAAAGA TTTCAGTTCA AGGTCGTTCC CAATTATGCT ATAACCACCC AGGACGCGAT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GAAAAACGTC TGGCAAGTTT TAGTTAATAT TAGAAATGTG AAGATGTCAG CGGGTTTCTG TCCGCTTTCT CTGGAGTTTG TGTCGGTGTG TATTGTTTAT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

AGAAATAATA TAAAATTAGG TTTGAGAGAG AAGATTACAA ACGTGAGAGA CGGAGGGCCC ATGGAACTTA CAGAAGAAGT CGTTGATGAG TTCATGGAAG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ATGTCCCTAT GTCGATCAGG CTTGCAAAGT TTCGATCTCG AACCGGAAAA AAGAGTGATG TCCGCAAAGG GAAAAATAGT AGTAATGATC GGTCAGTGCC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

GAACAAGAAC TATAGAAATG TTAAGGATTT TGGAGGAATG AGTTTTAAAA AGAATAATTT AATCGATGAT GATTCGGAGG CTACTGTCGC CGAATCGGAT 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TCGTTTTAAA TATGTCTTAC AGTATCACTA CTCCATCTCA GTTCGTGTTC TTGTCATCAG CGTGGGCCGA CCCAATAGAG TTAATTAATT TATGTACTAA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TGCCTTAGGA AATCAGTTTC AAACACAACA AGCTCGAACT GTCGTTCAAA GACAATTCAG TGAGGTGTGG AAACCTTCAC CACAAGTAAC TGTTAGGTTC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CCTGACAGTG ACTTTAAGGT GTACAGGTAC AATGCGGTAT TAGACCCGCT AGTCACAGCA CTGTTAGGTG CATTCGACAC TAGAAATAGA ATAATAGAAG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

TTGAAAATCA GGCGAACCCC ACGACTGCCG AAACGTTAGA TGCTACTCGT AGAGTAGACG ACGCAACGGT GGCCATAAGG AGCGCGATAA ATAATTTAAT 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

AGTAGAATTG ATCAGAGGAA CCGGATCTTA TAATCGGAGC TCTTTCGAGA GCTCTTCTGG TTTGGTTTGG ACCTCTGGTC CTGCAACTTG AGGTAGTCAA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

GATGCATAAT AAATAACGGA TTGTGTCCGT AATCACACGT GGTGCGTACG ATAACGCATA GTGTTTTTCC CTCCACTTAA ATCGAAGGGT TGTGTCTTGG 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

ATCGCGCGGG TCAAATGTAT ATGGTTCATA TACATCCGCA GGCACGTAAT AAAGCGAGGG GTTCGAATCC CCCCGTTACC CCCGGTAGGG GCCCA
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391

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):

CCTAAAGTTG ATCTCGAAAC TTGGTGCTAA ACACATCAAG GATTGGGAAC ACTTGGAGGA GTTCAGAAGG TCTCTTTGTG ATGTTGCTGT TTCGTTGAAC 
^4670      ^4680      ^4690      ^4700      ^4710      ^4720      ^4730      ^4740      ^4750      ^4760      

AATTGTGCGT ATTACACACA GTTGGACGAC GCTGTATGGG AGGTTCATAA GACCGCCCCT CCAGGTTCGT TTGTTTATAA AAGTCTGGTG AAGTATTTGT 
^4770      ^4780      ^4790      ^4800      ^4810      ^4820      ^4830      ^4840      ^4850      ^4860      

CTGATAAAGT TCTTTTTAGA AGTTTGTTTA T
^4870      ^4880      ^4890      ^4900

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: 2019-03-18 09:32:49 GMT+1