IRESite_Id:286 summary record describing characteristics of ERAV

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `286`	Version: `3`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-10-19 12:24:34`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `5UTR_incomplete`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `ERAV`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
2231133

The mRNA/+RNA description:

Equine rhinitis A virus, genome incomplete at the 5'-end

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

TTAAGCTTGT ACCTGTAGCG TCAGTAAAAC GCAGAAACCA AACGCAATTG CCTGTAGCGT AAGTAAAACG CTGTAACTGC ATGATTTGCG CCTGTAGCGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CAGTAAAACG CAGAAACCAC AAGCAAAAAC CTGTAGCGTC AGTAAAACGC GCACATTCAC ATACAGAGCT TCCCGGCTTT AAGGGTTACT GCTCGTAATG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGAGCACATG ACAACTTGTC GAGATTACGG CAACTGTCAC GGGAGAGAGG AGCCCGTTTT CGGGCACTTG TCTCCTAAAC AATGTTGGCG CGCATTTGCG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CGCCCCCCCC CTTTTTCAGC CCCCTGTCAT TGACTGGTCG AAGCGTTCGC AATAAGACTG GTCGTCACTT GGCTGTTCTA TCGTTTCAGG CTTTAGCGCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCCTTGCGCG GCGGGCCGTC AAGCCCGTGC GCTGTATAGC GCCAGGTAAC CGGACAGCGG CGTGCTGGAT TTTCCCGGTG CCATTGCTCT GGATGGTGTC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACCAAGCTGA CAAATGCGGA GTGAACCTCA CAAAGCGACA CGCCTGTGGT AGCGCTGCCC AAAAGGGAGC GGAACTCCCC GCCGAGGCGG TCCTCTCTGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCAAAAGCCC AGCGTTGATA GCGCCTTTTG GGATGCAGGA ACCCCACCTG CCAGGTGTGA AGTGGAGTGA GCGGATCTCC AATTTGGTCT GTTCTGAACT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACACCATTTA CTGCTGTGAA GAATGCCCTG GAGGCAAGCT GGTTACAGCC CTGACCAGGC CCTGCCCGTG ACTCTCGACC GGCGCAGGGT CAAAAATTGT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTAAGCAGCA GCAGGAACGC GGGAGCGTTT CTTTTCCTTT TGTACTGACA TGATGGCGGC GTCTAAGGTG TATAGAGTTT GCGAGCAGAC TCTGCTGGCA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GGTGCCGTTC GCATGATGGA CAAATTCTTG CAAAAGAGAA CTGTTTTTGT CCCCCATCTT GACAAAACAA TTCGTTTGAC TGGACTCCAC AATTATGACA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ATACTTGCTG GTTGAATGCC TTGACACAAC TGACACAGAT TCTTGGAATT CGGCTTTTTG ATGAACACTT CGGCAATAGA GGTCTGTTCA CTCGGAAAAC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AATTGATTGG GTGAGTGACC AGACTGGTAT AAAAGATCTA AAATCAGGAG CACCGCCACT CGTGGTGGTG TACAAACTGT GGCAACATGG ACACTTGGAT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GTCGGTACGA TGGAGAAACC CCGGTCGATT ACTCTATGGT CTGGCCCCAA AGTGTGTCTT TCTGATTTCT GGGCCTGTGT TTCGGCAAAA CCGGGACATG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CAGTATTCTA CCTTCTCACA AGCGAGGGTT GGATCTGTGT TGATGACAAG AAAATATACC CAGAAACACC CAAAACAGAG GATGTACTTG TTTTTGCGCC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTATGACTTT GAGTCACTGG GCAAGGACCC ACCAAAGCTA CACCAGAGAT ATGAAAAAGC ATTTGAGCTC AGTGGCGGAG GTACATCCAC TCCAACAACT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GGCAACCAAA ACATGTCCGG AAACAGTGGT TCAATTGTTC AAAATTTTTA CATGCAACAG TACCAGAATT CAATTGACGC AGACCTGGGA GACAATGTGA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTAGCCCTGA AGGCCAGGGC AGCAACACTA GTAGTTCAAC CTCATCAAGC CAATCCTCTG GCTTGGGCGG GTGGTTCTCT AGTTTGCTGA ACCTTGGAAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AAAACTACTG GCTGACAAGA AGACAGAAGA GACTACAAAC ATTGAAGACA GAATTGAAAC AACAGTGGTT GGAGTCACTA TTATTAATTC ACAAGGATCT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTTGGAACAA CCTACTGTTA CTCCAAACCG GATGGTAGAC CACCATCCAC AGTGTCAGAC CCAGTTACCA GACTTGGACC CACGCTTTCC AGGCACTACA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CATTTAAGGT AGGTGAGTGG CCCCATTCTC AATCACATGG TCACGCATGG ATCTGTCCGT TGCCAGGTGA CAAACTCAAG AAGATGGGCA GTTTTCATGA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGTTGTCAAA GCCCACCACC TGGTCAAGAA CGGCTGGGAT GTGGTTGTGC AGGTGAATCC CTCATTTGCT CACTCCGGGC CGCTGTGTGT AGCAGCAGTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CCGGAGTACG AACACACACA TGAGAAAGCA CTCAAGTGGT CTGAGCTTGA GGAACCAGCT TACACATACC AACAACTTTC AGTTTTTCCC CACCAGTTGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TAAATTTGAG GACAAATTCA TCAGTGCATT TGGTGATGCC CTACATTGGG CCAGGCCAAC CAACAAATCT GACTTTGCAC AACCCGTGGA CCATTGTTAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTTAATTTTG TCTGAATTGA CAGGACCTGG CCAAACTGTG CCTGTGACCA TGTCGGTGGC TCCCATCGAT GCAATGGTTA ATGGGCCTCT TCCAAATCCA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GAGGCACCGA TTAGAGTGGT GTCTGTGCCT GAATCAGATT CTTTTATGTC TTCAGTACCT GATAATTCGA CTCCACTATA CCCCAAGGTT GTGGTCCCAC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CGCGCCAAGT TCCTGGCCGG TTTACAAATT TCATTGATGT GGCAAAACAG ACATATTCAT TTTGTTCCAT TTCTGGAAAA CCTTATTTTG AGGTTACCAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CACCTCTGGG GACGAGCCAC TGTTTCAGAT GGATGTGTCG CTCAGTGCGG CAGAGCTACA TGGCACTTAC GTAGCTAGTT TGTCATCATT TTTTGCACAG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TACAGAGGCT CACTTAATTT CAACTTTATT TTCACTGGTG CAGCAGCCAC TAAGGCAAAG TTTCTGGTTG CTTTTGTGCC TCCCCACAGT GCAGCGCCCA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AAACGCGCGA TGAAGCAATG GCGTGCATCC ATGCCGTGTG GGATGTTGGC TTGAACTCAG CTTTTTCTTT TAATGTACCT TATCCCTCCC CTGCTGACTT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CATGGCCGTT TATTCTGCGG AACGGACGGT TGTGAATGTC TCTGGATGGC TTCAAGTTTA TGCACTAACA GCTCTAACTT CAACTGACAT TGCCGTGAAC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

AGTAAAGGCC GTGTGCTGGT TGCTGTTTCC GCCGGCCCAG ACTTCTCCCT TCGTCACCCG GCGGACCTGC CCGACAAGCA GGTTACCAAT GTGGGAGAGG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ATGGTGAACC CGGTGAGACA GAGCCTCGTC ATGCTTTGTC ACCCGTGGAC ATGCACGTGC ACACAGATGT CAGTTTCTTG CTTGACCGGT TCTTTGATGT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGAGACACTT GAGCTTTCAA ATTTGACAGG TTCTCCTGCC ACACATGTTC TGGATCCGTT TGGCTCGACT GCCCAACTGG CTTGGGCACG TCTGCTAAAC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ACTTGCACCT ACTTCTTTTC TGATTTGGAA TTGTCAATCC AGTTTAAATT TACCACCACT CCGTCCTCTG TTGGAGAGGG CTTTGTGTGG GTGAAGTGGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TCCCTGTTGG AGCACCAACC AAGACCACAG ATGCTTGGCA GTTAGAAGGA GGTGGAAATT CAGTTAGAAT TCAAAAATTG GCCGTTGCAG GGATGTGCCC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CACTGTTGTG TTCAAGATTG CAGGCTCCCG TTCACAAGCC TGTGCTTCAG CGTTGCCATA TACATCAATG TGGCGTGTTG TGCCAGTCTT TTACAATGGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TGGGGTGCAC CTACCAAAGA AAAGGCAACC TACAATTGGC TTCCTGGTGC ACACTTTGGT TCCATCTTGC TGACTTCTGA TGCGCATGAT AAAGGAGGGT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GCTACTTGCG GTATGCTTTC CGCGCGCCAG CGATGTATTG CCCTCGACCC ATTCCGCCGG CTTTTACGCG TCCAGCGGAC AAAACCAGAC ATAAATTTCC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CACTAACATC AACAAACAGT GTACTAATTA CTCTCTCCTC AAATTGGCTG GAGATGTTGA GAGCAACCCT GGCCCCACTA TTTTTTCCAA AGCATCAGCA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GACCTGAATG CCTTGTCAAC GTCGCTAGGT GAATTGACTG GCATGCTAAA AGATCTTAAA GCCAAGGCAG AAACTTATTC CCCGTTTTAC AAAATGGCCA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AAATGCTTTT CAAACTTGCA ACACTAGCTG TGGCAGCTAT GAGGACAAAG GACCCAGTAG TGGTGGTTAT GTTGATTGCT GATTTCGGAT TGGAGGTCTT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TGACACTGGG TTTTTCTTTT CCTACTTTCA AGAGAAGTTG CAGCCTTATA TGAAAACTAT TCCTGGTAAG ATTTCTGATT TGGTCACTGA TGCGGCTACG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GCTGCCGCCC AAATTCCAAA GGGAGTGTAT TCTTTTGTGT CGTCATTTTT CGAAACGCCT GAAGGAGTGG TTGAGAAGCA GGTGTCTCTT CGGACAGTGA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ATGACATATT TGCTTTGCTT AAAAATTCTG ATTGGTTCAT AAAGACTCTT GTTGCCCTCA AGAAATGGCT GACATCCTGG TTTGCTCAAG AACAACAGGC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AGATGATGCG CTCTATTCAG AATTGGAAAA ATATCCCTTG TACAAGTTAA AATTGAAGGA ACCTGATACT CAAGAGGAAG CGCGCCAGTG GTTTAAAGAC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ATGCAGCAGC GTGCTCTCGC TGTGAAGGAC AAAGGTCTCT TTTCCCTCCT GCAAATTCCA TTAGTTAACT TGCCCCAGAG CCGTCCAGAG CCCGTTGTAT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GCGTCCTTCG GGGCGCATCA GGGCAAGGCA AATCTTATTT GGCAAATCTG ATGGCTCAAG CAATTTCGCT TCTCTTGGTT GGCAAGCAGG ACAGTGTGTG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

GAGTTGTCCT CCTGACCCCA CATATTTTGA TGGCTATAAC GGACAGGCTG TGGTGATTAT GGATGCATTG GGCCAGGATC CGAATGGTGC TGACTTTAAA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TATTTTTGCC AGATGGTCTC TACAACAGCT TTTGTACCAC CTATGGCCCA TTTGGATGAT AAAGGCATTC CATTTACTTC TCCTGTTGTT ATTTGTACTA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CAAATTTGCA TTCATCTTTT ACCCCTATTA CTGTTTCTTG TCCTGAAGCT CTTAAGAGGA GGTTTCGGTT TGATGTGACG GTGTCCGCTA AACCGGGCTT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TGTGCGCACT GTTGGTTCAA ACCAGCTTTT GAATCTCCCA CTTGCTCTTA AGCCAGCTGG TCTTCCCCCA CACCCTATCT TTGAAAATGA CATGCCCATT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ATAAATGGGC AGGCTGTTAA ATTGGCTCTT TCTGGTGGAG AAGTGACAGC TTTTGAGCTT ATTGAGATGA TACTGTCAGA AGTTCAAAAC AGACAAGACA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CACACAAAAT GCCCATTTTT AAACAATCAT GGTCTGATTT GTTCAGAAAG TGTACAACTG ATGAGGAACA GAAAATGTTG CAGTTTTTAA TTGACAATAA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

AGATTCAGAA ATTCTCAGGG CGTTTGTTTC AGAACGCTCC ATTTTACTAC ATGAAGAGTA TCTTAAATGG GAGTCATATA TGACCAGGAG AGCCAAGTTT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CACCGCCTGG CTGCTGATTT TGCTATGTTT CTATCCATTC TTACTTCACT GATTGTTATT TTTTGTTTAG TTTATTCTAT GTATCAACTT TTTAAGACCC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

CTGACGAGGG TTCAGCTTAT GATCCTTCAA CTAAGCCAAA ACCAAAGACC CAGGAAGTGA AAACACTGAA GATTAGGACT GAGACTGGTG TACCAGCAAC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TGACTTGCAA CAATCCATCA TGAAAAATGT TCAGCCAATT GAGCTTTACC TTGACAATGA ATTGGTTACT GACTGCTCTG CCTTGGGTGT TTATGACAAT 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TCATATTTGG TGCCCCTTCA TTTGTTTGAA TTTGATTTTG ATACCATTGT GCTTGGTGGA CGTCATTACA AGAAAGCTGA GTGTGAGAAG GTAGAGTTTG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

AGCTTGAAGT GAATGGAGAC GTGGTGTCAT CAGATGCGTG TCTACTTCGA GTGTCATCGG GGCCTAAAGT TAGAAATATT GTTCATCTTT TTACAAATGA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

AATTGAATTG AAGAAAATGA CCCAAGTGAC AGGAATCATG AATTCACCAC ACCAGGCACG CACTGTGTTT TTTGGCAGTT TTTTGACAGT GAGGAAGTCC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ATCTTAACAT CGGATGGGAC TGTAATGCCC AATGTTTTGT CCTATGCCGC TCAGACCTCG CGTGGGTATT GTGGCGCTGC AATTGTTGCT GGCTCACCTG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CCCGCATAAT TGGTATCCAT TCAGCTGGCA CTGGATCTGT TGCATTTTGC TCCCTGGTGT CCAGAGACGC GCTGGAGCAA CTCTGGCCCC AGAAACAGGG 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

CAACGTTAGT CGCCTTGATG ACGATGTGAG GGTGTCTGTT CCGCGCCGCT CCAAATTGGT GAAATCATTG GCTTACCCCA TTTTCAAACC TGACTATGGC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

CCAGCGCCAC TCTCTCAATT TGACAAGCGC CTGTCAGACG GCGTGAAGCT GGATGAAGTG GTTTTTGCTA AACATACTGG AGACAAGGAG ATTTCCGCAC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AGGACCAGAA ATGGCTCTTG CGTGCGGCGC ATGTATACGC CCAGAAGGTT TTCTCCCGGA TTGGATTTGA CAACCAGGCT TTGACTGAAA AAGAGGCCAT 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TTGTGGCATT CCTGGCCTTG ACAAGATGGA GCAGGACACC GCTCCCGGGC TGCCCTATGC TCAGCAAAAT AAGAGAAGGA AAGACATCTG TGATTTTGAA 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

GAGGGCCGGC TGAAGGGCGC CGAACTCCAA AAGGACAGAT TTATGGCTGG TGACTACTCT AATTTGGTCT ATCAATCATT TTTGAAAGAT GAGATCCGCC 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

CACTTGAGAA AGTTAGGGCT GGAAAGACCC GCCTGATTGA CGTGCCGCCG ATGCCCCATG TGGTGGTTGG TAGGCAGCTC TTGGGCCGGT TTGTGGCAAA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ATTTCATGAA GCAAATGGAT TTGACATTGG CTCAGCCATT GGATGTGACC CAGATGTGGA CTGGACTCGG TTTGGCCTCG AGTTGGAGCG TTTCAGGTAT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

GTATATGCCT GTGACTACTC ACGGTTCGAT GCCAACCATG CAGCTGATGC AATGAGAGTT GTGCTTAACT ACTTTTTCTC TGAGGACCAC GGTTTCGACC 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

CTGGTGTGCC TGCTTTTATT GAGTCACTGG TTGATTCAGT GCATGCCTAT GAAGAGAAAA GGTATAACAT CTACGGTGGC TTGCCATCCG GGTGTTCCTG 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

CACATCAATT TTGAATACCA TCTTGAACAA TGTTTACATT CTTGCAGCTA TGATGAAGGC TTATGAGAAT TTTGAGCCAG ATGACATTCA GGTCATTTGC 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TATGGGGACG ACTGCCTCAT TGCTTCTGAT TTTGAAATTG ATTTCCAACA ACTGGTGCCT GTCTTTTCTA GTTTTGGACA GGTAATAACT ACAGCTGACA 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

AGACTGATTT TTTTAAACTG ACAACGCTTT CGGAGGTGAC CTTCCTTAAG CGCGCTTTTG TTCTGACGGC CTTTTACAAG CCAGTGATGG ATGTGAAGAC 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

CCTTGAAGCA ATCTTAAGCT TTGTTCGCCC AGGCACACAG GCTGAAAAGC TCCTGTCCGT GGCGCAGTTG GCAGGCCACT GCGAACCGGA GCAGTATGAG 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

CGCCTGTTTG AGCCCTTTGC TGGGATGTAT TTCGTCCCTA CTTGGCGACT TGCGCCTGCA GTGGTTGATG AAGCTTGGAT GCTAAATTCT TTTTGACTTT 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

GTTTTTCTTT GTTTTCTTTT AGGCTTTTAA GGTGTTAAGT TTAAAGGTTA AGAGTTTTTA GAAGTTAAGA TAGAGTTTAG TTTTTAGTTT TGAGC
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691

Credibility of mRNA sequence:

reverse_engineered_fragment_and_the_rest_is_a_guess

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

Equine rhinitis A virus 1 393/76

A promoter reported in cDNA corresponding to IRES sequence:
not tested The total number of notable open-reading frames (ORFs):
5

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:
Lab

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

yes

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

850-7596

ORF

ORF position:

2

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
Lab

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

yes

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

853-7596

ORF

ORF position:

3

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
Lb

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

yes

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

913-7596

ORF

ORF position:

4

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
Lb

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

yes

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

916-7596

ORF

ORF position:

5

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
polyprotein

The description of the protein encoded in this ORF:
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:

yes

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

1210-7596

Remarks:

The genomic sequence was in silico assembled by IRESite curator as a merge of sequences provided by T. Hinton
and merged with GI:2231133 from the same lab. The sequences mostly overlap, so in summary 59bp sequence
'TTAAGCTTGTACCTGTAGCGTCAGTAAAACGCAGAAACCAAACGCAATTGCCTGTAGCG' was prepended to the original GenBank record.
According to the article by Hinton et al. (2000) they studied only the 5'-UTR region downstream the poly(C)
tract and thus their base position +1 was actually the one downstream poly(C) tract. Thus, the sequence
reconstructed here is still an incomplete genome at the 5'-end at least.

There are two AUGAUG regions: 852-857 and 915-920. Results indicate that translation predominantly occurs from
the first pair of AUG codons and that the latter 855-AUG-857 appears to be the major initiator. Translation in
ERAV also appears to initiate from the second pair of AUG codons, probably 918-AUG-920, but this occurs at
only about 1/10 of the level of initiation from 850-AUG-857. Full IRES activity requires nt 245 to 961
downstream of the poly(C) tract. Bicistronic T7 transcripts were transcribed in vivo in recombinant vaccinia
virus infected human cells BHK21.

Citations:

Hinton T. M., Li F., Crabb B. S. (2000) Internal ribosomal entry site-mediated translation initiation in equine rhinitis A virus: similarities to and differences from that of foot-and-mouth disease virus. J. Virol. 74(24):11708-11716

Hinton T. M., Ross-Smith N., Warner S., Belsham G. J., Crabb B. S. (2002) Conservation of L and 3C proteinase activities across distantly related aphthoviruses. J. Gen. Virol. 83(Pt 12):3111-3121

IRESs:

IRES:

Version: `1`	Last change: `2007-04-16 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `ERAV_245-961`

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

245-956

Conclusion:
strongly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

GAGAGGAGCC CGTTTTCGGG CACTTGTCTC CTAAACAATG TTGGCGCGCA TTTGCGCGCC CCCCCCCTTT TTCAGCCCCC TGTCATTGAC TGGTCGAAGC 
^245       ^255       ^265       ^275       ^285       ^295       ^305       ^315       ^325       ^335       

GTTCGCAATA AGACTGGTCG TCACTTGGCT GTTCTATCGT TTCAGGCTTT AGCGCGCCCT TGCGCGGCGG GCCGTCAAGC CCGTGCGCTG TATAGCGCCA 
^345       ^355       ^365       ^375       ^385       ^395       ^405       ^415       ^425       ^435       

GGTAACCGGA CAGCGGCGTG CTGGATTTTC CCGGTGCCAT TGCTCTGGAT GGTGTCACCA AGCTGACAAA TGCGGAGTGA ACCTCACAAA GCGACACGCC 
^445       ^455       ^465       ^475       ^485       ^495       ^505       ^515       ^525       ^535       

TGTGGTAGCG CTGCCCAAAA GGGAGCGGAA CTCCCCGCCG AGGCGGTCCT CTCTGGCCAA AAGCCCAGCG TTGATAGCGC CTTTTGGGAT GCAGGAACCC 
^545       ^555       ^565       ^575       ^585       ^595       ^605       ^615       ^625       ^635       

CACCTGCCAG GTGTGAAGTG GAGTGAGCGG ATCTCCAATT TGGTCTGTTC TGAACTACAC CATTTACTGC TGTGAAGAAT GCCCTGGAGG CAAGCTGGTT 
^645       ^655       ^665       ^675       ^685       ^695       ^705       ^715       ^725       ^735       

ACAGCCCTGA CCAGGCCCTG CCCGTGACTC TCGACCGGCG CAGGGTCAAA AATTGTCTAA GCAGCAGCAG GAACGCGGGA GCGTTTCTTT TCCTTTTGTA 
^745       ^755       ^765       ^775       ^785       ^795       ^805       ^815       ^825       ^835       

CTGACATGAT GGCGGCGTCT AAGGTGTATA GAGTTTGCGA GCAGACTCTG CTGGCAGGTG CCGTTCGCAT GATGGACAAA TTCTTGCAAA AGAGAACTGT 
^845       ^855       ^865       ^875       ^885       ^895       ^905       ^915       ^925       ^935       

TTTTGTCCCC CA
^945       ^955

Remarks:

Deletion of the 5' end to nt 245 had no apparent effect on the IRES activity. A further 5' truncation to nt
338 caused a substantial decrease in the IRES activity. Truncation of the 3' end of the IRES to nt 921 also
led to reduction in IRES activity.

Citations:

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