IRESite_Id:622 summary record describing characteristics of HoCV1

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `622`	Version: `1`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-29 20:37:43`
Reviewed by: Martin Mokrejš	Last change: `2009-08-29 23:16:26`

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: `HoCV-1`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
84316420

The mRNA/+RNA description:

Homalodisca coagulata virus-1, complete genome.

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

CAAAAATTGT ACGCAGCAAA CACTGCGTAC AATGAGTAGC ATGACTAAGA TGGAGAGTTC CTAACCCGGC TCTCAAATTA GTGATGCAAT ACTTAAGTAG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TAGAAACGAA AGAGTTAGCA GATGATCGAA CAAACATCTA AGTCAAACCA AAAACCCAAC CCAACAAACA CAACCGTTAG CATATCCCAA AAGTTTTATA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GTACCAACTA GAAATAGAGA GATGATAAAA CTTTATTGCT AACACATTGA CGTTACGGAC AACCCGACAC GGACTGAACA GGAGCATGTT AGACATGTAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TATGGCTCCG GAAGATAGAA AATATGCTTA CATCCCCATG GTAGGTAAGA TTTCTATAAC TACTGGCCAC TGAAAAGTGA ATGCAGTAGG CGGCAACCCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCATCCAAAC TTCAACCAAA TGCCCAAAAC CCAACAGAGA GAGACAGTGG AAACACAAAC TCCTCAACAG CGGATTCGGA CCCCGCTTCG GACTGAACAA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACGGAAACGA CCCTTGCAAC CCCGGTGTGC TCTTCATTGA GTGGAACAGA TGCCTCACCA GCTATCACTG TTCTTAGCAC CAACATGACC AGCCTTCTCA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ACGAAATTTA TTCAAATACA TACTCTGTCA CTTTGAAAGA TTTTCGACGA GCTTTACACA GGTGGACGAA CAAGACACAA ATTCAATTTC GTCATTCACC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACCTTCAAAG GATCGAGCGG CCTTGTGTCT CTTGCAGATA TATTGGTGGC TTCAACAACA TCAAGATTCT TATTTTTCCA TATCCCTTGA ACAGTTGGCA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GATGATTGTT TTAAAGTGCT TGAATTGCAG TACCGCCCAT ATTACGACAA AGTCGTGTAT GGAAGTATTG ATAATGCACT TTGGACTGAA ATTTCATGGC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAGACCTCCT CCTCAAGGTA GTCTCACACA AATTGGAATA TTTGTCATTG TCTCAGGTTC TTGGAAACAG GATTTTGCGT CGCAAATTCA ACATTCGCTC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TCACATGTTG AGAATGTTGC TATCGGCGAT ACGCATGGAC CTGGAAAGAG AATTGAAACT TGAAGGAAAA GTGCAACAGC GAATTGATCA AGTCAAAGCA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAGAATGCAG AAGATTGGAG AGAGTATGAC AGAGGTGGAC CTGTCCCTTC ACGAGACAGA GATACCTACT GCCAGATTCT TTTGGAGAAC GAACTGGAAC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GACTCATGCA ATCCACCTGG ACACGCGACC TCTTGACAAA TGAATGGATC CAAGCAGAAG TACAAGGTCT TTTTGACATC AAAATTGTCC CCGACGAAGC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AGCCTTTATG GAAGTCTTTA CTTCAATCAA AGATTACATT TCAGAGCAAT TTGGGGCTTC ACTCCGATTT GCTAAAGATT TGCTTGTTAA CATTGTAGTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTCATCATCC TTTGGAACTT AGTATCCTTG CTATGGAACA AAGCATATGA TGTGAAATAC ATTGGAGTAG TTCTCACACT ACTCTCAGGA CTTGTAGCCG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCATTTGCGC TGCTGGAGTA GCTGCAGTGA TTGGCCGCAT CCTGATGCAA ATCTTAGATC TTTTCAAAAC TCCTCAAACC CTTCCCGCAC CCTTTGACAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTGGCGTCAA GAAGATCAAG AAAATGAAGC TTGGGCGCGT TGGCACCAAC GAAATTCCCA ACAAACTTTC ATTCACCCTT CCCTTCTCGA AAACACTGGA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AACAATCATT GGATTGAGGC GGAAGCACAG GCGGGAGAGC CTAAACAATC CAAAGTTTTA GCTCTTCTAT CCTTGGCGAC CATCTCACTG GTGACTTCAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AAATCAAAGA CAGTTGGTCT CTTGACTATT TCACAAAACA GATTGCACTC CTACCTCGCT TCACGACAGG AGTGACTTGT TTGCTTGACA GTGCTCAGGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGTTTTCAAA ATTGTCCACA AAGAAATTTT GGTTGATATC TTCGGATATG AGCCTTTGAC TGAGGAAGGA GAACACCCCA TGATTGACGA CTTCAACACT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CTTATGCAAC AGATTATTGA TGCTGACCAA CGAAACGAAA TTCAAACATC AACAATCTAT CAGTCCCTTG TTCTTCAAGC AGAACAACTT GGCTTGCGTA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TTCTTCAGAC TTCTGGTTTA GGAGAGTATC GCGCTGTTGT CTCACAACAG TATGCCATTT TGCGACGGCT TCACGACCGT CTTGGACTGA GAGGACTGAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGCCAAAGGA CAGCGAATGG CACCCATCAT AATTCAGTTG TATGGAGAGA CAGGACAAGG AAAGTCAACC ATTGTRACAA CATTGGCACT CAAGCTTCTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TCAAAAATCT GTGATGCAGA AGGTATAGAC AAAGCTGTTA TCAATCCAGA CAATCTCATC TACGCCCGCA ACGTAGAACA AGAGTTTTGG GACGGATATC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ACGGACAGCT GGTTAGTGTG TTTGATGATT TCGCACAACA TCAAGATTTT GCTCAGGTTC CAAACCCTGA GCTATTTGAA ATCATTCGAG CAGGAAACAC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TTTCCCCTAT CCTTTGCATA TGGCTGACAT TGCTGACAAA AACACAACAA CTTTTCAGTC ACGCATTGTC ATTTTGACGA CCAACCAAAA GAAGCCAAAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GTGGAATCCT TAGTAGCACC AGAAGCTTTC TATCGCCGTA TTGACCAGTC CTACGAAGTA TCCTTCAAAC CAGAGGTACT TACTAGGCAG TCAAAAACGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TTGAGACAAT TGAAGAAAGT GCTCGTGGGA ATTTGACAAC CTACTCCTAC TCTCTCAAGC CCGAACATCG GCAGGAGTAT TCCCCAGAGA TCCAACAGTT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TCAGCAGTTT GACATCAATA CTGAAAGGAA GATTGGCAAC CCAATTTCAC TTGATGAATT GGTTGACAAT GCTTTTCGCC AGTACAATGC CCGGTTCAAC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TTCGAAACAA CACGCAAAAT GCATGATGAT CAATTGGCAC GTCAACTTGG GTTCATCAGA GCCCAACCCC AAATTGGATG GTTCGCTCCA CTACACTATA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TTCGCCCTGC CCAACCTCGG GARGATRTAG ATGTGGAGAG GCGCAACCTA GCACAAGAAT TTCATGCAAG TTTTCAAAAT TACAAAATCA AACTCCAACA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AATCAAGGAA AATTTGAAAC GCAAAATGGA AGAACACAAA GTTGTGTTGA AGGCTCTTGG CGTTGTTGCT ATGGCTGTTG GGGTGTATAA GATTGGTAGT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GCACTTGCTG GACTTGTTTC AAAAAGAGAC ACTCAACCTA AAGTGTCTGC AAGTGCGCAA TCACCTTATG CTCCCCGACC TGTGGCGCTG CGTCAGTCAG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CCTATCATCC GACAACACGG GCAACAAAAA CCACCATCAA CAAAATTGTG AAAGCGACAG GACAAGCAGC GGATAATAGC GCGCGTGACA TCATCACAAG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CGTTATGAAC CGAGGCATGT ACTCCTTGAG CGTCGATTCT CGCGTTCTAG GGAGTGCAAC GTTCTTAACT GGAAAAATTT TGATGTTTCC CCGACATTTC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ATTAGTTTCA TGGCCCATCA GGCAGAAGCT AATCCAAATT CAAAAGTCAC ACTCAAATCA CACAACACAC AGTATGAAAT GCTGACAAAG GACGTGCTGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TTGAAGTGGA GAACATTTTT GACGACGACA ATCTTCCCCT TGATTCTGAC GGAAATCCCG ACCAAACTTG GACTCATGAC TGTGTTGCTG TAGTCTTCAA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GACTGCAGAC AACCACAAAG ACAGAACAGA TCAATTCTTG TCGAGGGAGG AGCAATCCAA ACTTGACAAA GTTGATGTAA TTCTGGCAAA CATCCACGAA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AAAGACAACA ACATCACACA CACAACATCG TGTGTTTCAG CATCTGGTGT CCAACGAGTA ACGCCTGGGG CAGGACCACC TGTCTATGGT GAATACGAAA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TTGGAGACAC TCAATATAGA ACCTACACGC GTGACTATTG GAGATATGCC CTCAACACTA CCTACGGGGA CTGTGGAGGA CTAATCTTCT TGAACAACAA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AATGAGTCAC CGTAAGATTC TTGGAATGCA CGTTATGGGA CTTTCGCAAC TAGATTCTGG CTTTGCCCTC TCGGTTTACC GAGAGGATGT ACAAGCTTAC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GTTCGACTAG TACGACAGGA CGATCCTTCA CTGGTGACAC CCTGTGCAGA GCCCATCATA ACGACAGCAG TCCAGTGTTT GCCATTTGCT GGAGACTTCC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ACCCCTTGGG AAAAAGTCCG TTCCCTAGCA CAAATCCTGG AAAGAGTAAG ATTGAAAAGT CAGAACTCCA TCCTGACAAT TGTGCTGTGG CATGGAGGGA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ACCCGTTTCT CATCCCGCAC TGTTGAAACC CATCACAGTG AGGCCTGAGG ACGGTATTCC CTTCCCAAGT GGCACGACAT TCGACCCCCT TCATTACCGA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CTGGAAAAGT GTGGACAGCG TGCAAAATGT CTAGACCAAC AGCTTTTGGA CATTGTGCGT CGTTCATACA CCACCGAACT TCGACAAATT TTGCAGACTC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ACAAGCACCC TGAGTACAAG TCAGCCTACA CATTTGATGA AGCAGTACTA GGTTTGCCTG GTGATCCCTA TGTAAATTCG ATAAACAGAG CGTCAGCTCC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TGGTTACGGA TGGACTAAGG ACCCAGGCTT TCCTGGCAAG AAAACATGGT TTGGAAGAGA CGAAGAGTTT GATCTTAGTC GCGCTGGACC CGTGAGGGAA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

AGGTGTGCAA AGATCATTGA CCTTGCACGA AACAATGAAA GGTACCCTCA TGTCTTCATT GACACCCTGA AGGATGAGAG GAAGCCCATT GCAAAGTGGT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GGAAGACGCG TGTGTTTTCT GCATGTAGCC AGGATTACTA CATTGCATGT AAGCAATACT ATCAAGGTAT CGTCGGTCTA CTGACACGGC ATCGTATTGA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TACTGGGATT TGTGTCGGCA TTAATGTCTA CTCTCACGAG TGGGACTTAA TTGTTCGGCA TTTGCACCAG TGCAATGATC GAGTTGTAGC AGGAGATTTT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GAGAACTTTG ATGCCAGCTT GCTGACTCAA GTTCTCGATG CAGCCAGAAT TGTTTTGAAT GATCTCGCCG GTGATCTTCC AGACCATCAA CGAGAACATG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ATGATATTCG TTCTGTGCTG TTCCTCGACC TTGTACATTC CACCCACCTT GCTCGGGATG TCCTCTATTC ATGGACACAT TCACTCCCAA GTGGTCATTT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TCTCACAGCA ATTGTAAATT CTTTGTACGT AAATCTGATC TTCAGATATC TTCTTGCAAA ATCTTCAAAA TTGACTTCAC ACATCCAAAT TGACCAGCTG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TGTCGTCGGA TGAAACTTGT TTCATACGGC GATGACCACA TTGTCTCTAT CCCTTCTGGA TACGAGAAAA TTTTCAACCA ATCCACTCTT CCAACCTTGT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TTTCTGAAAT AGGTATGACC TACACAGACG AGACAAAATC CGACAGAGAA GTACCTGAAA CAAGACGCAT CGAGGACGTA ACTTTCTTGA AACGTGGGTT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TCGATGGGAA AAAGAACTTA ATCGCTATGT CGCACCGCTA TCTTTAGACA CAGTGCTTGA AACGCCATTT TGGCGCTCAA AATCCCTCAA CCCGCGCTCT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ATCACAGAGA GTAGCGTAGA GTGGGCTTGC CATGAGCTAG CCCTCCACGA TGAGTCAACA TTTCAGGAGT GGACGAAAAA GATTGGGTTA GTCTGCAAAG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ATGCAATTAA TTTTGTGCCT AATCTGTCTG CGCAACGCGT GGAATATATC CGCTATTTGG AAACTTCTTG GGACTCACTT GATGAGTCTC GCGATGACGA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GGACTAAGTG TGAACTTGCC TCTCTCAACA AAAAGCCACC GACATTAAGA GAGAGAGTAT TGCTGCTTAG TTAACTGCAG GCCCTATTTA GGGTTACCGC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CCAGGATCTG CAACAGCATT CCTGTATCAT CCAGGGCACC GGTGGACTTG GTGAGGATTG AGTTGACCTC ATCATTAGAG ACCAGACTCG CAACATCACA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ACAAATACAC GACACCATGG AAACTCATTC ACATGAGCCC ATAAACACCA ACATAGATGG AGAAACTTCT GAGAACACGT TCGAAGAGAA GCGCGAAATC 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ACCCACTTCA CAGAGGATGA CCGCGTACTC ACCGACGCAG TGACAGAAAT TACTTCATTA CCCCTCTCTT TACTACAGTA TGGAGACGAG CCACGAGAAC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

ATAGTGTAAT ATCCTTTCTT CAAAGACCGG AGAAAATCGC TACAGTGACG TGGACTACGG CTCAAACAAA GACGACTAAC TTGGTATCCT TGCCAATTCC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

ATCGTCTGTG TTGACGACTA TGTACAGAGA GAAGCTGAGA GGCTTTGGCC TGCTTCGCGC AGACATTGTC TTTAAGCTGC AATTCAACTC ACAGCCCTTC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

CAAGCTGGGA GATTGATTGC GACATACATT CCAGTTCCTG CCTATCTTTT ACAAAGAACG CGTATGGCTC GAGCAAGTCT CACAAGACTG ACCTCGTTAC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CTAACGTGAT TATTGACATT AGTAAGCAGA CTGAATGTAA TATCACATTA CCCTACGTAA GCTCGTTTAC CCACTATGAT TTAACAAGTG GCGGAGGAGA 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

TTGGGGCTTG TTCGACCTTT GGGTCTATAG TCCCCTCAGT AGTGCGTCTT CTCAGACAAT CAACATCTCA ATACGAGCCT ACCTCGACAA TGTACGCTTG 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GGTGCGCCCA CGCAACAATC GTTAGTCACA GCGGAAAAGA TGCTAAAAGC AAACGTACAG ACACGGGATT TATCCCGGGG TACATCTAGT TGTGGCTCGA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

TCTCAGCGCG CGCCCAAGGA GGAAAGCAGA CAGCCGGCTC GGGCGATGGA TCCTTCGGAT CTCTCCTGAA TAAGGGCACA AAAAGTGTCA CTATGCAGGA 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

GCGATCCGCA GGGACTATCT CCCGAGTTGG ACATAGTATA CGTGAGGGCC TTGTCAGGGG ACTCAATGTC GTCGGCGAAT TTATTCCCGG CCTCAGTGAG 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

ATCACTGACA CCGCCAACAG TGTTGCTATG GGAGTTTTAA ACACTCTTGC TGCTTTCGGC CTTGGAAAGC CCAAGAACCT CGACAAAATT GCACCTAGGA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

CGCTGCATGC GTTTTCTGAT TTTGCTCAGG CCACTGGTGT GGACAATGGT CACATTTTGT CTCTTCACGG AGACAACAAG GTGACCGTGC TCCCCGGCTT 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TGCTGGTTCA AACACCGATG AACTGTCAAT GACGTATCTC ATGCAGACCC TACAGTACTA CGACACTCAC ACGATTTCAA CAACTACAGC TGTTGGCACG 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

CAGATCGCTG CTTATCGTGT AACTCCGTTT CGTTTTGACT TAGACCTTGC AAAGACTGCA CAGTCTTTTG TTAGTGGTAG CCCACTCATC AACTTTGGGC 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

AACCCAACCT TCAATGGTAC ATAGGTTCTA ATTTCAAATA CTGGCGGGGC GACATAATAA TGCATCTCGC TCTCGTGAAA ACTGACTATC ATAGCGTAAG 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

GTTAAAGATC GTCTACGATC CAATGGCGCA GTCCGCTGCT GCCGTGACGT ATGATGCATC CGAATACTGC TACTCAATAG TTGTAGATTT CCGTGACAAG 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

ACTGACATAT ATGTGCGTTT ACCATTCATT TCCGCAACAC CTTGGAAATT GGTACCACCA TCAACTTACA CCGGATACAC TCCTCCGCCT GTGAACCAAC 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

AGGAAGGCCT TTCCACTTAT AGTGGTTATG TGGCTGTGTT CGTTGATAAT ATTCTGCAAG CTTCCTCAGC GGTAGTTAGT CAGAGTATAG AAATGGTGAG 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

TGAGTTTTGC GCAGCTTCAA ACCTGGACAT GGGTTTCCCC CATGGCGGAC AAAATTGGAT CCCGATTAGT ACCGTTCTTA ATCCCGGTGA CCCTATACAA 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

GCAGACGTAC AATCTGCGTT CGCAGCTGAT GGCATACTCA AAACACGCAC TAATATGCAA GAAAATACCC TGGACATCAA AAACATTACA GGAATGGCTC 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

CGAGACCTCT ATACGATAAC ATCACGAGTT ACACGACTGG TGAAGAAGTT TATTCCCTTA GAATGTTAAT GAAACGCTTC AATTGGATAG CGTCTGTCCC 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

TTCTGGACAG GCGTCAATAG CACTCCCAAA CACAGTCAAG ACCATAGATG CTGCTGCTCC TGTGTCAAAT CCTAACCAGA TTGTCGACAT TCGAACAGGG 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

CCTCCCTATG CCAACAACAC AGTCTCAGAT TGCGCTTTGG TGGATGTTGT AGGAGCATTG TTTGCCTTTA GAGCGGGCGG GTTTCGATGG AAAGCCTGGG 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

ACTCCGGTTC TGAGCTCATA TCAGCCTATC TCGTTCCTTT TGGACCATAC AATACCTATG GCATCCCTCC TTCTACATTT ACAAACTTGA TTAGTAATAC 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

TTCCGTTTAC GAGTTAGATT CAAGACAGGT TAAAGGCTCC GCAGAGTTTG CAACCCCTTT TTATCATCCT TGTTACACCC AAGTAAATTC AAATTTTTCA 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

TATTTTACAG AAGGAGGAGA ACCAGATTTG TATTTTCACT TTACTCAACC CCAAACAGTA ACAGTAGTCA GTCGTAGTAA CCCCGGATCA GAGATGAATA 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

TCGCGAAATC TGCTGGCGAC GATCTCAATT TTGGCTTTCT CTTAGGAGTT CCAGATTGTT TGCCGTCTCA GATAGTAGCA GGACTTCTCT CACGTCCGAG 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

TTCTCAGCCA AACTTACCCA ATTCGACACC AATCTCATAG AACCGCTGAC CCGAGAAACA GGTCCCGGGC GCCTCTGTGA GAGAACCTTT CAGAATCGCT 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

GACCCGAGAA ACAGGTCCCG GGCGCCTCTG GAAGTCATTT TCTTCTTTAC TTAGTTTTAG AGCGAAGGAT CAGTCTCTTC CCTTTGGTAT GTATCCTAGA 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

TACAGTCACT ATTGGGGGGC AGCCCTTAGC TAACTTAGAT TTAAGGCAGA TTAGTTTATA GTCAAATTAG GCAGAGCGAA GCAACTTTCT TGAGGTAAGT 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

GGTCATCCAC TGTCACTTCG AGGGGGCTTG CCGACACTCT AGATAAGTAC ACGTGGTCGC AGGTTTCTGT AGGGTTTCCC TGTGATGTAA CTAGAATTAG 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

CACGTGAAGA GCAATACCAA CCTCATTTCG ATATGCCGTA TGTCCCAATA AACCGCACGG TTTCCCTAGG GAAGTAACCG GATGAGTCTT GAGTTTTGGT 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

TTTGCTGTGG CTTCACCACC CCCTACATTT GTTTATTCTT TTGGCAATTT AGGATATCCA CGGATTAAAC TCCCGTGAGG TGCTTGTGTG CAGCTTCACT 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

GCGCACGAGA GTTTTCTTAG CAAAAAAAAA AAAAAAAAAA AAAAA
^9301      ^9311      ^9321      ^9331      ^9341

Credibility of mRNA sequence:

unknown

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

Homalodisca coagulata virus-1

A promoter reported in cDNA corresponding to IRES sequence:
not tested The total number of notable open-reading frames (ORFs):
2

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:
NS

The description of the protein encoded in this ORF:
non-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:

not tested

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

420-5807

ORF

ORF position:

2

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:
capsid 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):

5990-8740

Citations:

Hunnicutt LE, Hunter WB, Cave RD, Powell CA, Mozoruk JJ (2006) Genome sequence and molecular characterization of Homalodisca coagulata virus-1, a novel virus discovered in the glassy-winged sharpshooter (Hemiptera: Cicadellidae). Virology. 350(1):67-78

Hunter WB, Katsar CS, Chaparro JX (2006) Molecular analysis of capsid protein of Homalodisca coagulata Virus-1, a new leafhopper-infecting virus from the glassy-winged sharpshooter, Homalodisca coagulata. J. Insect Sci. 6:1-10

IRESs:

IRES:

Version: `1`	Last change: `2009-08-29 21:28:20`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `HoCV1_IGRpred` 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):

5802-5989

Conclusion:
putative_IRES

How IRES boundaries were determined:
guessed

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

GACTAAGTGT GAACTTGCCT CTCTCAACAA AAAGCCACCG ACATTAAGAG AGAGAGTATT GCTGCTTAGT TAACTGCAGG CCCTATTTAG GGTTACCGCC 
^5802      ^5812      ^5822      ^5832      ^5842      ^5852      ^5862      ^5872      ^5882      ^5892      

CAGGATCTGC AACAGCATTC CTGTATCATC CAGGGCACCG GTGGACTTGG TGAGGATTGA GTTGACCTCA TCATTAGAGA CCAGACTC
^5902      ^5912      ^5922      ^5932      ^5942      ^5952      ^5962      ^5972      ^5982

Remarks:

The IRES was NOT characterized experimentally. The presumed IRES region was taken over from Nakashima and
Uchiumi (2009) from Table 1.

Citations:

Nakashima N, Uchiumi T (2009) Functional analysis of structural motifs in dicistroviruses. Virus Res. 2(139):137-147

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