IRESite_Id:40 summary record describing characteristics of CrPV

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `40`	Version: `14`
Originaly submitted by: Tomáš Mašek	Submission date: `2005-06-26 00:00:00`
Reviewed by: Martin Pospíšek	Last change: `2009-08-29 19:20:40`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `end-to-end_full-length_mRNA`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `CrPV`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
21321708

The mRNA/+RNA description:

Cricket paralysis virus (Dicistroviridae) nonstructural polyprotein and structural polyprotein genes, complete
genome.

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

TTTAATAAGT GTTGTGCAGA TTAATCTGCA CAGCACTAGC CACAAAGTTC AGTGGTCCCA ATTATGGGAT ATAAAACTCA ATGGTCGACG GAGTGACCTG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GAAATGCTCC CCGTGAGAAA CCTTGTTTAA ACGCACTTGG ACCTTCTCCG GCCTCAGCGC CAGGCATAGC TGGATCGTCA ATCCCAAGTT TGGACTTAGA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CTTGCTCTAT GTTACAATTG GGAGGAGCGT GACTTACCAT TGGTCGTTGA TGACGTTAAT TCCAAACAAA AACAACAACA ACAACTTAGT TTAAATAATT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCGGTCTTTA AGCATCAGGG TAGACCGATG AGGAATAAAG AACCCTATAA GACTGATTCG ATACCAAGAG CTGGTGTCTG AGGGATTACG ACTCGCGTGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TCGGACAGCA CATGTTAGTC ATGTATTATG GTGTTTCCCA ACACGTATCT TTGCTCTAGT ATTGAACTTT AGTGATGAGT GTACTTGGCA TGTACACCTG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ATTAGTTAGC CCTTGTGGAT ACGCCACTGC CGCTCAGGTA CAGTAGGACA TACCCCAAAT ATTGGGTTCC ACTCGTAGAG AAGAAAATTA GTGGCGAAAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GTACGGTTTA TGTCAAAGGA GAAGGTGATT TTAATTGCAC CTGAAGCAAC CCTAGGTCTT CCCTTTGATG TGAGCTAATA AGGAGTAACC GATTCTTACA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATGTGATCAT GTCTTTTCAA CAAACAAACA ACAACGCAAC CAACAACATC AACTCCCTTG AGGAGCTTGC TGCTCAAGAA CTAATAGCAG CACAATTTGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AGGAAATCTT GATGGTTTCT TTTGCACTTT TTATGTGCAG TCCAAACCAC AACTATTGGA CTTAGAGAGT GAATGTTATT GTATGGATGA TTTTGATTGT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GGGTGTGATA GGATCAAGAG AGAAGAAGAA TTACGTAAAC TGATTTTCTT AACATCGGAC GTTTATGGAT ATAACTTTGA AGAGTGGAAA GGATTAGTTT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GGAAATTTGT TCAAAATTAT TGCCCAGAAC ATCGATATGG ATCAACTTTT GGTAATGGAT TATTAATTGT GAGTCCCCGT TTCTTTATGG ATCATCTTGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CTGGTTTCAG CAATGGAAAC TTGTTTCAAG TAATGATGAA TGCAGAGCCT TCTTGAGAAA GAGAACGCAA CTTTTGATGA GTGGTGATGT CGAATCTAAT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCTGGTCCTG TGCAATCGCG CCCCGTATAT GCTTGCGACA ACGACCCTAG AGCTATACGG TTGGAAAAGG CATTGCAACG CCGAGATGAG AAAATTTCAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCTTGATTAA GAAGTTGCGT CAGGAAATCA AAAACAACAG AATTTACACC CAAGGTTTCT TTGATGATCT CAAAGGAGCA AAAGGAGAAG TAGGACAATT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GAACGGAAAT TTAACAAGAA TTTGTGATTT TTTGGAAAAC TCTCTACCGA CACTAACAGC CCAAATTCAA ACAACAGTTT TGACAACAAC AGACAAATAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GTGAATTTGA AAGAAGACTT GCTAAAGGTT GCCATTCTAC TTGTCCTAGT CCGTCTTTTG ATGGTCTGGA AGAAGTATCG TGCCGCCTTG ATTGTAATTA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TCCTCTTTGT AATGCACTTT TATGGCTTTG ACAAACAGAT TTTGGATATC GTGCTGGATT TAAAAGACAA AATTTTGCAG ACAACAACCC AAGCAGGAAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AGAAACACTG GAAGAGGTAG TATACCACCC TTGGTTCGAT ACATGTGGAA AATTAATCTT CGCTGTTTTG GCTTTCTTTG CAATCAAGAA GATTCCTGGA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AAACAGGATT GGGATAATTA CATATCTCGA CTAGACCGTA TTCCAAAAGC AATTGAAGGA TCAAAGAAAA TTGTTGATTA TTGTTCTGAA TATTTCAACC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TCTCTGTGGA TGAAGTGAAG AAAGTTGTGC TCGGAAAAGA ACTTAAAGGA ACACAAGGAT TGTATGACGA AATTCATGTT TGGGCAAAGG AAATAAGACA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CTATTTGGAC CTTGATGAGA GAAATAAAAT CACTTTGGAT ACTGAGACAG CCGCAAAAGT TGAGGATTTA TACAAAAGAG GATTGAAATA CTCTGAAGAA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AAGATCCCGG ACCGAGACAT TGCTCGCTTC ATAACAACTA TGTTATTCCC AGCAAAATCT CTGTATGAGC AAGTTCTCCT CTCTCCTGTC AAAGGAGGTG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GACCAAAGAT GCGGCCCATT ACAGTATGGT TGACCGGAGA ATCTGGCATA GGTAAGACTC AAATGATTTA CCCACTGTGT ATTGATATAT TACGAGAGAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GGGTATTGTC AAACCCGACG CTTACAAACA CCAAGCATAT GCCAGACAAG TGGAGACAGA GTATTGGGAC GGATATAATG GACAAAAAAT TGTGATTTAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GATGATGCTT TTCAACTTAA GGATGACAAA ACTAAACCAA ATCCCGAGAT TTTTGAGGTC ATTAGAACTT GCAATACCTT TCCCCAACAC TTGCACATGG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CTGCTTTACA AGACAAAAAC ATGTATTCTC AGGCCGAAGT ACTCCTGTAC ACTACAAACC AATTTCAAGT ACAACTGGAG AGTATTACTT TCCCAGACGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTTCTATAAT CGAATGAAGA CTCACGCATA CCGCGTGCAG ATAAAACAAG AAAAATCTAT ATGGGTTAGA AATGCGAGGG GAGAGGAATA CAATGCCCTT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GATGTGACAA AACTAAATAA AGATGAAGCT ATAGATTTGA GTGTTTATGA GTTTCAAAAG ATGCGTTTTG ACGACGAGAG TGCCACTAAA TGGATAGATG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ATGGAGAACC GATTTCGTAT GACGAGTTTG CGCGAACAAT TTGTAAAGCG TGGAAAGAAG AAAAAGAGAA GACATTCCAC CAACTTCAAT GGTTGGAGGC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CTATGCCAGT AGAACAGTGG CGCAAGGAGG TAGCGAAACA AGTGAATATT ACGATGTGTG GGATGAAACA TACTTTTCAA ACTTACTTTC ACAAGGCTTT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ATGGCAGGAA AATCTCTGAT AGAAATGGAA GCTGAATTTG CTAGTGATGC TGAAACGTTC AACGCATATA TTGAGTACAA AAAGAATATT CCCAAAGAAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCAAATGGAG CAAGTGGATG ACCATTTTGG ACGAGCAAAT TAGTGCTTTG TCGACCAAAA TCAGAGAACT TAAGAACAAA GCTTACAAAT TTATTAGTGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ACATCCCTAT TTAACAGCCT TAGGATTCAT TGGAGTAATG ATCTCCGCTT TTGCCATGTA TTCATTTTTT GAACGCACAT TGACAGATGA TACCATAACT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TCAGAAGTTG GTTCGTCTGG CGATAATAAA ACTCAGAAAA TTAGTAAACG AGTGGTGGAA GTTGGAGGTT CAGGAGATGT GAAGACAACC AAACCCGCGA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

AGACAGCAGT TGAAGTCGGT TCATCGGGAG ATTCAAAAAC AATGAAAAAC AAAATTACAA AAGTTGAAGT AGGTTCATCC GGAGACAGTA AAACGCAAAA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ACAGCGAAAC ACAAAAGTAG AAGTTGGCAA AGAACTTGAA AAAGAAGCTG AAACTCAAGG TTGCAGCGAC CCAGCAGCTC ATGCTTTGGT GCTTGATGTG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TTGCAGAAGA ATACGTACTG TTTATATTAT GAGCGAATGG TGAAAGGAGA AATGAAACGC TATCGATTGG CAACAGCAAC GTTTTTGCGT GGATGGGTTT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GTATGATGCC TTATCATTTT ATTGAAACTT TATATGCAAG AAAAGTTGCA CCATCAACCA ATATTTATTT TAGCCAGCCA AATTGTGACG ACGTAATTGT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TGTTCCAGTG TCTCATTTCA TTGCCCCAAA TGCAGAAAGA GTCGAATTGA CGACAGCTTG CACTCGTATT CATTATAAGG ATGAAACACC AAGAGATTGT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GTACTGGTGA ATTTACATCG CCGTATGTGC CATCCACATC GAGACATTTT GAAACACTTC GTTAAAAAGA GTGATCAAGG AAATTTGCGA GGAGTATTCC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AAGGAACGTT GGCAACATTT CATCAGAGTG CTAATGAACT GTGTCGTGCA TATCAGTGGC TACAAGCCAT CCGTCCTTTG GACCAAGAAA TTACCATTTA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TCATGAAGAT ACCGACATGT TTGATTACGA GAGTGAAAGC TATACACAGC GGGATTGCTA TGAATACAAT GCGCCTACTC AAACAGGAAA TTGTGGATCT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ATAGTAGGTC TTTACAATAA ACGCATGGAG AGAAAACTCA TTGGTATGCA TATACCTGGT AATGTAAGTG AATGTCACGG ATATGCTTGC CCCTTAACCC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AGGAAGCCAT AATGGATGGT CTTAATCGAT TGGAAAAATT GGACCCAGTA AATAACATTA CAGTGCAATG CTGCTTTGAA CCACCATCAG ATATCAAAGA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TACCATGAGT GGAGAAACGC CTGAAGGAAA ATTTTGCGCT ATCGGAAAGA GTAATATCAA GGTTGGTCAG GCGGTAAAAA CAACTTTACT AAAATCTTGT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ATCTATGGAA TGTTGAGCAA ACCAATAACG AAACCAGCAC ATCTTACACG AACTAGACTC CCCAATGGAG AGATTGTAGA TCCCCTCATG AAAGGATTGA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

AGAAGTGTGG CGTAGACACC GCAGTGTTAG ACGCAGAAAT TGTTGAATCG GCTGCTCTGG ATGTAAAACA AGTTGTGTTA ACTCAGTACA ACTCGATGTT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

AGATGTAAAC AAATATAGGA GATTTCTCAC TTACGAGGAA GCAACTCAAG GAACCGGCGA CGATGACTTT ATGAAAGGAA TTGCTCGACA AACTTCACCC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GGTTACAGAT ATTTTCAAAT GCCTCGAAAA TTACCAGGAA AACAGGATTG GATGGGTTCA GGCGAGCAAT ATGACTTTAC ATCTCAGCGG GCTCAGGAGT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TGCGACGTGA CGTGGAAGAG TTAATTGACA ACTGCGCGAA AGGCATTATT AAGGATGTAG TATTTGTTGA CACACTTAAA GATGAAAGGC GACCCATTGA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GAAGGTAGAT GCTGGAAAGA CAAGAGTTTT CTCAGCGGGA CCTCAACACT TTGTAGTAGC ATTTCGAAAA TATTTCTTGC CCTTTGCTGC TTATTTGATG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

AATAACCGAA TTGACAACGA AATTGCTGTA GGAACTAATG TTTATTCAAC TGATTGGGAG CGAATTGCAA AAAGATTAAA GAAGCACGGA AACAAGGTGA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TTGCAGGAGA TTTCGGAAAT TTTGATGGTT CCCTAGTTGC TCAGTTCTTT GGGCAATCTT GTGGGAAGTC CTTTTATCCT TGGTTTAAAA CTTTCAACGA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TGTAAATACT GAAGATGGAA AACGAAACTT AATGATCTGC ATTGGACTCT GGACACACAT TGTACATTCA GTTCACTCAT ATGGAGACAA CGTGTATATG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TGGACGCACT CCCAACCTTC AGGAAACCCC TTCACTGTAA TTATTAACTG CTTGTACAAT TCCATGATTA TGCGTATTGT TTGGATTTTA TTGGCTAGAA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AATTGGCTCC CGAAATGCAA TCCATGAAGA AATTTAGAGA GAATGTGTCG ATGATAAGCT ACGGAGATGA CAATTGCCTA AATATTTCAG ACCGCGTTGT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

AGAATGGTTT AACCAAATCA CCATCAGTGA ACAGATGAAA GAAATTAAAC ATGAGTACAC CGATGAAGGA AAGACTGGAG ATATGGTTAA GTTCCCATCA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CTTTCCGAAA TACACTTTTT GAAAAAAAGA TTCGTTTTTA GCCACCAACT ACAACGAACT GTCGCACCTT TGCAAAAAGA TGTTATTTAC GAAATGCTAA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ACTGGACACG GAACACTATT GACCCAAACG AAATTCTAAT GATGAACATA AACACAGCTT TTAGAGAAAT AGTATACCAT GGAAAGAGTG AGTACCAGAA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

GTTGCGTAGC GGAATTGAAG ATCTGGCTAT GAAAGGTATA CTACCACAAC AACCCCAAAT TCTCACTTTT AAAGCGTATC TCTGGGATGC CACTATGTTG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GCTGATGAGG TTTACGACTT CTAAAAAGCA AAAATGTGAT CTTGCTTGTA AATACAATTT TGAGAGGTTA ATAAATTACA AGTAGTGCTA TTTTTGTATT 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

TAGGTTAGCT ATTTAGCTTT ACGTTCCAGG ATGCCTAGTG GCAGCCCCAC AATATCCAGG AAGCCCTCTC TGCGGTTTTT CAGATTAGGT AGTCGAAAAA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

CCTAAGAAAT TTACCTGCTA CATTTCAAGA TAAACAAGAA AATTCACACA TTGAAAATGA AGATAAAAGA CTTATGTCCG AACAGAAAGA AATTGTACAT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TTTGTTAGCG AAGGAATTAC CCCTAGTACT ACTGCGCTCC CTGATATCGT TAATCTTTCA ACTAATTATC TGGACATGAC TACGAGAGAA GATAGAATTC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

ATTCAATTAA AGACTTTCTT AGTGGACCTA TTATTATTGC AACTAACCTT TGGTCATCTA GTGACCCTGT AGAAAAACAA TTGTATACAG CCAATTTCCC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

AGAAGTTCTA ATTTCTAATG CTATGTACCA AGACAAATTG AAAGGTTTCG TAGGACTTCG CGCCACACTT GTTGTCAAAG TACAGGTTAA TTCCCAACCC 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

TTCCAGCAAG GTAGATTGAT GTTACAGTAT ATTCCATATG CTCAATATAT GCCAAATAGA GTGACCCTAA TAAATGAAAC TCTGCAAGGT AGATCAGGAT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GTCCCACAAC AGATTTGGAA TTGAGTGTAG GAACAGAAGT GGAAATGAGA ATTCCCTATG TTTCACCCCA TTTGTATTAT AATTTAATTA CTGGACAAGG 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

TTCATTTGGT TCTATTTATG TTGTAGTTTA TAGTCAACTG CATGATCAAG TTTCAGGAAC AGGTAGTATC GAGTATACTG TCTGGGCACA TTTAGAAGAT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

GTGGATGTTC AATACCCAAC TGGCGCTAAC ATTTTTACCG GGAATAGTCC AAATTATCTT TCTATTGCTG AGCGCATTGC CACAGGCGAT TTTACAGAGA 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

CAGAGATGCG CAAATTGTGG ATACATAAAA CGTACTTAAA GAGACCTGCC CGTATTTATG CACAAGCAGC TAAAGAATTG AAACAACTTG AAACTAACAA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

CTCACCATCA ACAGCATTAG GACAAATTTC TGAAGGTTTA ACCACACTAA GTCATATCCC CGTTTTAGGA AATATTTTTA GTACTCCAGC TTGGATCTCA 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

GCGAAAGCAG CGGATTTAGC CAAACTGTTT GGCTTTTCTA AACCAACAGT TCAAGGAAAG ATTGGAGAGT GTAAACTGCG TGGTCAAGGA AGAATGGCGA 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

ATTTTGACGG TATGGACATG TCACACAAGA TGGCATTGTC TTCGACGAAT GAAATTGAGA CGAAAGAAGG CTTAGCTGGA ACGTCATTGG ATGAAATGGA 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

TCTTTCCCGA GTATTATCTA TCCCAAATTA TTGGGATCGC TTTACTTGGA AAACTTCAGA TGTAACTAAC ACCGTTTTAT GGGATAATTA TGTATCACCT 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

TTTAAAGTAA AACCATATTC AGCAACCATC ACTGATAGAT TTAGATGCAC ACACATGGGT TACGTGGCTA ATGCTTTCAC TTATTGGAGA GGTTCTATTG 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

TATATACTTT TAAATTTGTA AAAACACAAT ATCATTCAGG TAGGTTAAGA ATATCTTTTA TCCCCTATTA TTATAACACA ACTATATCTA CAGGGACCCC 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

GGACGTTTCT AGAACTCAAA AGATTGTAGT AGATTTAAGG ACATCAACAG AAGTTAGTTT TACAGTGCCT TACATTGCCA GTAGACCTTG GTTATATTGC 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

ATACGCCCTG AATCATCTTG GTTGAGTAAA GATAACAAGG ATGGGGCTTT GATGTATAAT TGTGTTAGTG GAATAGTGCG AGTAGAAGTT TTAAATCAAC 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

TTGTGGCTGC TCAGAACGTT TTCTCTGAAA TCGACGTGAT TTGCGAAGTG AGCGGAGGAC CAGATTTAGA GTTTGCAGGA CCGACCTGCC CCAGCTATGT 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

ACCATACGCC GGTGATTTAA CACTGGCTGA TACCAGAAAG ATTGAAGCAG AGAGAACGCA AGAGTATTCC AATAATGAAG ACAATAGAAT AACAACTCAG 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

TGTAGCAGAA TCGTCGCACA GGTTATGGGA GAAGATCAGC AAATTCCACG AAATGAAGCA CAGCACGGCG TTCACCCTAT ATCTATTGAT ACACACCGAA 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

TTAGTAATAA TTGGAGTCCT CAAGCCATGT GTATAGGAGA GAAAATTGTA TCGATTCGAC AACTGATTAA GCGCTTTGGA ATTTTTGGAG ACGCAAACAC 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

TCTTCAGGCT GATGGCAGCT CTTTTGTAGT TGCCCCCTTC ACAGTAACCT CCCCCACTAA GACACTTACC TCAACACGAA ATTATACACA ATTTGATTAT 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

TACTATTATT TGTATGCTTT TTGGCGTGGT AGTATGCGTA TTAAGATGGT AGCCGAGACG CAGGACGGAA CAGGAACTCC CCGGAAGAAA ACAAACTTTA 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

CTTGGTTTGT GCGTATGTTT AATTCTTTAC AAGACTCTTT TAATTCCCTT ATTTCAACGA GTTCTTCTGC AGTGACGACC ACAGTTTTAC CATCCGGCAC 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

TATTAATATG GGTCCATCCA CACAAGTAAT TGACCCAACT GTAGAAGGCT TGATAGAGGT AGAAGTTCCC TATTACAATA TTTCACATAT TACACCTGCT 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

GTGACCATTG ACGATGGAAC TCCATCTATG GAGGATTATC TCAAGGGTCA TAGCCCACCC TGTCTCTTAA CCTTTTCGCC CAGAGATAGT ATTTCAGCCA 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

CAAACCACCA CATCACCGCC AGTTTTATGC GTGCGCCTGG AGATGATTTT AGCTTTATGT ATTTGCTTGA AGTTCCACCT TTAGTAAATG TAGCACGCGC 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

CTAACTAACT ATTTGCTTTG TATTTTAAGA TTTTGTAAAT AGAAAAATAT ATAACCCCAC TCGTAGGTAA GGATTTATTG TATATTTTAT TTAGTTAGTT 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

ATTCGGTACT TACGGCCCTA TTACCAACGG GTATTAATCA CAAACACTTT ATCCCCATAG GATTCTTTTA AATTTAAAAT TTTAAATAAT TAACGTCAGA 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

GTCCCATCGG GGCTAACAGG TTTTTCGCAC TTTTCCTGCT AACTGACAGA AGTGCAATTT GGTTTTTGAT TAATAGTTGT TTTCT
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The organism containing this mRNA with IRES segment in its genome:

Cricket paralysis virus

A promoter reported in cDNA corresponding to IRES sequence:
no The total number of notable open-reading frames (ORFs):
2

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
not_tested

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
not_tested

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
homogeneous_population_of_molecules_confirmed

The organism used:

Drosophila melanogaster SL2

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
homogeneous_population_of_molecules_confirmed

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
no_promoter_confirmed

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Mus musculus

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `2`	Last change: `2006-01-13 00:00:00`
Originaly submitted by: Tomáš Mašek	Reviewed by: Martin Pospíšek

The abbreviated name of this ORF/gene:
CrPVgp1

The description of the protein encoded in this ORF:
nonstructural 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):

709-6024

OPTIONAL: The function of the encoded protein

nonstructural polyprotein contains sequence motifs for RNA helicase, 3C-like proteinase and RNA-dependent RNA
polymerase

ORF

ORF position:

2

Version: `1`
Originaly submitted by: Tomáš Mašek	Reviewed by: Martin Pospíšek

The abbreviated name of this ORF/gene:
CrPVgp2

The description of the protein encoded in this ORF:
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):

6214-8904

Remarks:

Translation of the second cistron is modulated by IGR (intragenic region) long 192 bp (6025-6216). Regions
1-708 and 6025-6232 were tested in two different bicistronic constructs for IRES activity. The IGR putative
IGR region was also point mutated and revealed that CCU start codon is used for the second ORF (candidate
sites were suggested by N-terminal protein "sequencing" showing Ala as the first aminoacid).

Dicistronic mRNA transcripts from pRF based plasmid were tested by direct RNA transfection of Drosophila SL2
cells. T7 in vitro transcripts were tested in rabbit reticulocyte lysates and both IRESs were functional. In
wheat germ extract only CrPV IGR IRES was functional (5'-NCR IRES not) while no positive control was shown. An
inverted repeat which includes the CCU codon 6187-6191:6212-6216 was confirmed by biochemical studies and
utilization of compensatory mutations.

Wilson et al. (2000) do not show any positive control IRES used in the intercistronic region except the
defective EMCV IRES (Figs. 3 and 7). The functional EMCV and defective EMCV IRESs were used in front of the
first cistron to affect cap-dependent translation (Figs. 5 and 6). From similar luciferase activities of DNA
(Fig. 3) versus RNA (Fig. 4) transfected cells one can conclude that there is no promoter activity
contributing the observed IRES activity.

From the work of Li et al. (2006), Fig. 3B it can be concluded there is no cryptic promoter in CrPV IRES,
although it is not clear into what plasmid context they re-cloned the CrPV IRES sequence and in which cells
they performed the test. Moreover, from direct transfection of ARCA capped (mMESSAGE mMACHINE® T7 ULTRA Kit,
Ambion) RNA it can be seen (Fig. 4) that CrPV IRES is about 3x above the negative control (empty pRF vector).
Unfortunately it is not clear which CrPV IRES was tested and whether the pRF plasmid contained in that moment
the defective EMCV IRES or not.

Citations:

Wilson J. E., Powell M. J., Hoover S. E., Sarnow P. (2000) Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol. Cell. Biol. 20(14):4990-4999

Li P. W., Li J., Timmerman S. L., Krushel L. A., Martin S. L. (2006) The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition. Nucleic. Acids Res. 34(3):853-864

IRESs:

IRES:

Version: `4`	Last change: `2009-09-13 22:14:20`
Originaly submitted by: Tomáš Mašek	Reviewed by: Martin Pospíšek
The IRES name: `CrPV_5NCR`

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

1-708

Conclusion:
putative_IRES

How IRES boundaries were determined:
unknown

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

TTTAATAAGT GTTGTGCAGA TTAATCTGCA CAGCACTAGC CACAAAGTTC AGTGGTCCCA ATTATGGGAT ATAAAACTCA ATGGTCGACG GAGTGACCTG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GAAATGCTCC CCGTGAGAAA CCTTGTTTAA ACGCACTTGG ACCTTCTCCG GCCTCAGCGC CAGGCATAGC TGGATCGTCA ATCCCAAGTT TGGACTTAGA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CTTGCTCTAT GTTACAATTG GGAGGAGCGT GACTTACCAT TGGTCGTTGA TGACGTTAAT TCCAAACAAA AACAACAACA ACAACTTAGT TTAAATAATT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCGGTCTTTA AGCATCAGGG TAGACCGATG AGGAATAAAG AACCCTATAA GACTGATTCG ATACCAAGAG CTGGTGTCTG AGGGATTACG ACTCGCGTGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TCGGACAGCA CATGTTAGTC ATGTATTATG GTGTTTCCCA ACACGTATCT TTGCTCTAGT ATTGAACTTT AGTGATGAGT GTACTTGGCA TGTACACCTG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ATTAGTTAGC CCTTGTGGAT ACGCCACTGC CGCTCAGGTA CAGTAGGACA TACCCCAAAT ATTGGGTTCC ACTCGTAGAG AAGAAAATTA GTGGCGAAAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GTACGGTTTA TGTCAAAGGA GAAGGTGATT TTAATTGCAC CTGAAGCAAC CCTAGGTCTT CCCTTTGATG TGAGCTAATA AGGAGTAACC GATTCTTACA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATGTGATC
^701

Remarks:

Wu et al. (2007) reported that their 5NTR IRES (247bp) was not functional in baculovirus-infected Sf21 cells.

Citations:

Wu TY, Wu CY, Chen YJ, Chen CY, Wang CH (2007) The 5' untranslated region of Perina nuda virus (PnV) possesses a strong internal translation activity in baculovirus-infected insect cells. FEBS Lett. 581(16):3120-3126

IRES:

Version: `11`	Last change: `2009-09-13 22:14:20`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `CrPV_IGR`

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

6025-6216

Conclusion:
strongly_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: `192`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-189`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `2`

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

AAAGCAAAAA TGTGATCTTG CTTGTAAATA CAATTTTGAG AGGTTAATAA ATTACAAGTA GTGCTATTTT TGTATTTAGG TTAGCTATTT AGCTTTACGT 
^6025      ^6035      ^6045      ^6055      ^6065      ^6075      ^6085      ^6095      ^6105      ^6115      

TCCAGGATGC CTAGTGGCAG CCCCACAATA TCCAGGAAGC CCTCTCTGCG GTTTTTCAGA TTAGGTAGTC GAAAAACCTA AGAAATTTAC CT
^6125      ^6135      ^6145      ^6155      ^6165      ^6175      ^6185      ^6195      ^6205      ^6215

Remarks:

Entire intergenic region of CrPV (6025-6213) and 3 bases of CrPVgp2. Inverted-repeat element, which is
predicted for bases 6187-6191 and 6212-6216 and in which is included initiator CCU codon, is necessary for
IRES activity.


Masoumi et al. (2003) tested IRES activity (Figure 2) and effect on viral yields of both NCR and IGR IRESs in
several insect cell lines using the original pRF plasmids containing the defective EMCV IRES. Only in one
cell line there were high yields of the FLuc protein.

Citations:

Masoumi A, Hanzlik TN, Christian PD (2003) Functionality of the 5'- and intergenic IRES elements of cricket paralysis virus in a range of insect cell lines, and its relationship with viral activities. Virus Res. 2(94):113-120

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

Version: `1`	Last change: `2008-07-15 16:41:33`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Type of the interaction between ITAF and the RNA subject to translation:
unknown

ITAF protein characteristics:

Version: `1`	Last change: `2009-08-18 16:32:07`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
eIF4G

ITAF fullname:
eukaryotic translation initiation factor 4G

ITAF description (long):
eIF4G is the scaffolding protein bridging together the cap-binding protein eIF4E with other proteins of the initiating ribosome

3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
no_effect_on_translation

Method used to demonstrate ITAF effect:
in_vivo

The organism where action of this ITAF was studied:

Saccharomyces cerevisiae

Remarks:

Depletion of eIF4G to 37% reduced CrPV IGR IRES to 75%. Further, over-expression of eIF4G does not increase
CrPV IRES activity. Data from Figure 2A,B.

Citations:

Gilbert W. V., Zhou K., Butler T. K., Doudna J. A. (2007) Cap-independent translation is required for starvation-induced differentiation in yeast. Science. 317(5842):1224-1227

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 44

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `unknown`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
6030-6219

The underlying nucleic acid sequence and structure of the mapped region:

AAAAATGTGA TCTTGCTTGT AAATACAATT TTGAGAGGTT AATAAATTAC AAGTAGTGCT ATTTTTGTAT TTAGGTTAGC TATTTAGCTT TACGTTCCAG 
(((((..... ...((((((( ((((...... .......... ....)))))) )))))..... .))))).... .......((( (....)))). ....(((((( 
^6030      ^6040      ^6050      ^6060      ^6070      ^6080      ^6090      ^6100      ^6110      ^6120      

GATGCCTAGT GGCAGCCCCA CAATATCCAG GAAGCCCTCT CTGCGGTTTT TCAGATTAGG TAGTCGAAAA ACCTAAGAAA TTTACCTGCT
(((.....(( ((.....))) )...)))))) )))....... ....(((((( ((........ .....))))) )))....... ..........
^6130      ^6140      ^6150      ^6160      ^6170      ^6180      ^6190      ^6200      ^6210

There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:

WARNING: bases 23 and 46 (AA) can't pair!
WARNING: bases 99 and 129 (AA) can't pair!

STDOUT was:

AAAAAUGUGAUCUUGCUUGUAAAUACAAUUUUGAGAGGUUAAUAAAUUACAAGUAGUGCUAUUUUUGUAUUUAGGUUAGCUAUUUAGCUUUACGUUCCAGGAUGCCUAGUGGCAGCCCCACAAUAUCCAGGAAGCCCUCUCUGCGGUUUUUCAGAUUAGGUAGUCGAAAAACCUAAGAAAUUUACCUGCU
(((((........(((((((((((....................)))))))))))......)))))...........((((....)))).....(((((((((.....((((.....))))...)))))))))...........((((((((.............))))))))................. (-30.50)

Rendering structure of CrPV mRNA 190 nt long with energy of -30.50 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

Remarks:

The pseudoknot interactions were omitted from the CryoEM structure (PDB:2NOQ).

Citations:

Schüler M, Connell SR, Lescoute A, Giesebrecht J, Dabrowski M, Schroeer B, Mielke T, Penczek PA, Westhof E, Spahn CM (2006) Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat. Struct. Mol. Biol. 12(13):1092-1096

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