IRESite_Id:73 summary record describing characteristics of HIV-1 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `73`	Version: `8`
Originaly submitted by: Barbora Škaloudová	Submission date: `2005-12-21 00:00:00`
Reviewed by: Martin Mokrejš	Last change: `2007-01-23 00:00:00`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `our_best_guess`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `HIV-1`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
9629357

The mRNA/+RNA description:

Human immunodeficiency virus 1, complete genome. The unspliced genomic RNA codes for gag and gag-pol. The
spliced version codes for env and other minor proteins. As the encapsidation signal is spliced out the
sub-genomic mRNA cannot be encapsidated.

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

ggtctctctg gttagaccag atctgagcct gggagctctc tggctaacta gggaacccac tgcttaagcc tcaataaagc ttgccttgag tgcttcaagt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

agtgtgtgcc cgtctgttgt gtgactctgg taactagaga tccctcagac ccttttagtc agtgtggaaa atctctagca gtggcgcccg aacagggacc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

tgaaagcgaa agggaaacca gaggagctct ctcgacgcag gactcggctt gctgaagcgc gcacggcaag aggcgagggg cggcgactgg tgagtacgcc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

aaaaattttg actagcggag gctagaagga gagagatggg tgcgagagcg tcagtattaa gcgggggaga attagatcga tgggaaaaaa ttcggttaag 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

gccaggggga aagaaaaaat ataaattaaa acatatagta tgggcaagca gggagctaga acgattcgca gttaatcctg gcctgttaga aacatcagaa 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ggctgtagac aaatactggg acagctacaa ccatcccttc agacaggatc agaagaactt agatcattat ataatacagt agcaaccctc tattgtgtgc 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

atcaaaggat agagataaaa gacaccaagg aagctttaga caagatagag gaagagcaaa acaaaagtaa gaaaaaagca cagcaagcag cagctgacac 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

aggacacagc aatcaggtca gccaaaatta ccctatagtg cagaacatcc aggggcaaat ggtacatcag gccatatcac ctagaacttt aaatgcatgg 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gtaaaagtag tagaagagaa ggctttcagc ccagaagtga tacccatgtt ttcagcatta tcagaaggag ccaccccaca agatttaaac accatgctaa 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

acacagtggg gggacatcaa gcagccatgc aaatgttaaa agagaccatc aatgaggaag ctgcagaatg ggatagagtg catccagtgc atgcagggcc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

tattgcacca ggccagatga gagaaccaag gggaagtgac atagcaggaa ctactagtac ccttcaggaa caaataggat ggatgacaaa taatccacct 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

atcccagtag gagaaattta taaaagatgg ataatcctgg gattaaataa aatagtaaga atgtatagcc ctaccagcat tctggacata agacaaggac 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

caaaggaacc ctttagagac tatgtagacc ggttctataa aactctaaga gccgagcaag cttcacagga ggtaaaaaat tggatgacag aaaccttgtt 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ggtccaaaat gcgaacccag attgtaagac tattttaaaa gcattgggac cagcggctac actagaagaa atgatgacag catgtcaggg agtaggagga 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

cccggccata aggcaagagt tttggctgaa gcaatgagcc aagtaacaaa ttcagctacc ataatgatgc agagaggcaa ttttaggaac caaagaaaga 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ttgttaagtg tttcaattgt ggcaaagaag ggcacacagc cagaaattgc agggccccta ggaaaaaggg ctgttggaaa tgtggaaagg aaggacacca 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

aatgaaagat tgtactgaga gacaggctaa ttttttaggg aagatctggc cttcctacaa gggaaggcca gggaattttc ttcagagcag accagagcca 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

acagccccac cagaagagag cttcaggtct ggggtagaga caacaactcc ccctcagaag caggagccga tagacaagga actgtatcct ttaacttccc 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

tcaggtcact ctttggcaac gacccctcgt cacaataaag ataggggggc aactaaagga agctctatta gatacaggag cagatgatac agtattagaa 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

gaaatgagtt tgccaggaag atggaaacca aaaatgatag ggggaattgg aggttttatc aaagtaagac agtatgatca gatactcata gaaatctgtg 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

gacataaagc tataggtaca gtattagtag gacctacacc tgtcaacata attggaagaa atctgttgac tcagattggt tgcactttaa attttcccat 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

tagccctatt gagactgtac cagtaaaatt aaagccagga atggatggcc caaaagttaa acaatggcca ttgacagaag aaaaaataaa agcattagta 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

gaaatttgta cagagatgga aaaggaaggg aaaatttcaa aaattgggcc tgaaaatcca tacaatactc cagtatttgc cataaagaaa aaagacagta 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ctaaatggag aaaattagta gatttcagag aacttaataa gagaactcaa gacttctggg aagttcaatt aggaatacca catcccgcag ggttaaaaaa 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

gaaaaaatca gtaacagtac tggatgtggg tgatgcatat ttttcagttc ccttagatga agacttcagg aagtatactg catttaccat acctagtata 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

aacaatgaga caccagggat tagatatcag tacaatgtgc ttccacaggg atggaaagga tcaccagcaa tattccaaag tagcatgaca aaaatcttag 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

agccttttag aaaacaaaat ccagacatag ttatctatca atacatggat gatttgtatg taggatctga cttagaaata gggcagcata gaacaaaaat 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

agaggagctg agacaacatc tgttgaggtg gggacttacc acaccagaca aaaaacatca gaaagaacct ccattccttt ggatgggtta tgaactccat 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

cctgataaat ggacagtaca gcctatagtg ctgccagaaa aagacagctg gactgtcaat gacatacaga agttagtggg gaaattgaat tgggcaagtc 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

agatttaccc agggattaaa gtaaggcaat tatgtaaact ccttagagga accaaagcac taacagaagt aataccacta acagaagaag cagagctaga 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

actggcagaa aacagagaga ttctaaaaga accagtacat ggagtgtatt atgacccatc aaaagactta atagcagaaa tacagaagca ggggcaaggc 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

caatggacat atcaaattta tcaagagcca tttaaaaatc tgaaaacagg aaaatatgca agaatgaggg gtgcccacac taatgatgta aaacaattaa 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

cagaggcagt gcaaaaaata accacagaaa gcatagtaat atggggaaag actcctaaat ttaaactgcc catacaaaag gaaacatggg aaacatggtg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

gacagagtat tggcaagcca cctggattcc tgagtgggag tttgttaata cccctccctt agtgaaatta tggtaccagt tagagaaaga acccatagta 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ggagcagaaa ccttctatgt agatggggca gctaacaggg agactaaatt aggaaaagca ggatatgtta ctaatagagg aagacaaaaa gttgtcaccc 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

taactgacac aacaaatcag aagactgagt tacaagcaat ttatctagct ttgcaggatt cgggattaga agtaaacata gtaacagact cacaatatgc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

attaggaatc attcaagcac aaccagatca aagtgaatca gagttagtca atcaaataat agagcagtta ataaaaaagg aaaaggtcta tctggcatgg 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

gtaccagcac acaaaggaat tggaggaaat gaacaagtag ataaattagt cagtgctgga atcaggaaag tactattttt agatggaata gataaggccc 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

aagatgaaca tgagaaatat cacagtaatt ggagagcaat ggctagtgat tttaacctgc cacctgtagt agcaaaagaa atagtagcca gctgtgataa 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

atgtcagcta aaaggagaag ccatgcatgg acaagtagac tgtagtccag gaatatggca actagattgt acacatttag aaggaaaagt tatcctggta 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

gcagttcatg tagccagtgg atatatagaa gcagaagtta ttccagcaga aacagggcag gaaacagcat attttctttt aaaattagca ggaagatggc 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

cagtaaaaac aatacatact gacaatggca gcaatttcac cggtgctacg gttagggccg cctgttggtg ggcgggaatc aagcaggaat ttggaattcc 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ctacaatccc caaagtcaag gagtagtaga atctatgaat aaagaattaa agaaaattat aggacaggta agagatcagg ctgaacatct taagacagca 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

gtacaaatgg cagtattcat ccacaatttt aaaagaaaag gggggattgg ggggtacagt gcaggggaaa gaatagtaga cataatagca acagacatac 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

aaactaaaga attacaaaaa caaattacaa aaattcaaaa ttttcgggtt tattacaggg acagcagaaa tccactttgg aaaggaccag caaagctcct 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ctggaaaggt gaaggggcag tagtaataca agataatagt gacataaaag tagtgccaag aagaaaagca aagatcatta gggattatgg aaaacagatg 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

gcaggtgatg attgtgtggc aagtagacag gatgaggatt agaacatgga aaagtttagt aaaacaccat atgtatgttt cagggaaagc taggggatgg 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ttttatagac atcactatga aagccctcat ccaagaataa gttcagaagt acacatccca ctaggggatg ctagattggt aataacaaca tattggggtc 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

tgcatacagg agaaagagac tggcatttgg gtcagggagt ctccatagaa tggaggaaaa agagatatag cacacaagta gaccctgaac tagcagacca 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

actaattcat ctgtattact ttgactgttt ttcagactct gctataagaa aggccttatt aggacacata gttagcccta ggtgtgaata tcaagcagga 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

cataacaagg taggatctct acaatacttg gcactagcag cattaataac accaaaaaag ataaagccac ctttgcctag tgttacgaaa ctgacagagg 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

atagatggaa caagccccag aagaccaagg gccacagagg gagccacaca atgaatggac actagagctt ttagaggagc ttaagaatga agctgttaga 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

cattttccta ggatttggct ccatggctta gggcaacata tctatgaaac ttatggggat acttgggcag gagtggaagc cataataaga attctgcaac 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

aactgctgtt tatccatttt cagaattggg tgtcgacata gcagaatagg cgttactcga cagaggagag caagaaatgg agccagtaga tcctagacta 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

gagccctgga agcatccagg aagtcagcct aaaactgctt gtaccaattg ctattgtaaa aagtgttgct ttcattgcca agtttgtttc ataacaaaag 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ccttaggcat ctcctatggc aggaagaagc ggagacagcg acgaagagct catcagaaca gtcagactca tcaagcttct ctatcaaagc agtaagtagt 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

acatgtaatg caacctatac caatagtagc aatagtagca ttagtagtag caataataat agcaatagtt gtgtggtcca tagtaatcat agaatatagg 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

aaaatattaa gacaaagaaa aatagacagg ttaattgata gactaataga aagagcagaa gacagtggca atgagagtga aggagaaata tcagcacttg 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

tggagatggg ggtggagatg gggcaccatg ctccttggga tgttgatgat ctgtagtgct acagaaaaat tgtgggtcac agtctattat ggggtacctg 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

tgtggaagga agcaaccacc actctatttt gtgcatcaga tgctaaagca tatgatacag aggtacataa tgtttgggcc acacatgcct gtgtacccac 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

agaccccaac ccacaagaag tagtattggt aaatgtgaca gaaaatttta acatgtggaa aaatgacatg gtagaacaga tgcatgagga tataatcagt 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ttatgggatc aaagcctaaa gccatgtgta aaattaaccc cactctgtgt tagtttaaag tgcactgatt tgaagaatga tactaatacc aatagtagta 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

gcgggagaat gataatggag aaaggagaga taaaaaactg ctctttcaat atcagcacaa gcataagagg taaggtgcag aaagaatatg cattttttta 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

taaacttgat ataataccaa tagataatga tactaccagc tataagttga caagttgtaa cacctcagtc attacacagg cctgtccaaa ggtatccttt 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

gagccaattc ccatacatta ttgtgccccg gctggttttg cgattctaaa atgtaataat aagacgttca atggaacagg accatgtaca aatgtcagca 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

cagtacaatg tacacatgga attaggccag tagtatcaac tcaactgctg ttaaatggca gtctagcaga agaagaggta gtaattagat ctgtcaattt 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

cacggacaat gctaaaacca taatagtaca gctgaacaca tctgtagaaa ttaattgtac aagacccaac aacaatacaa gaaaaagaat ccgtatccag 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

agaggaccag ggagagcatt tgttacaata ggaaaaatag gaaatatgag acaagcacat tgtaacatta gtagagcaaa atggaataac actttaaaac 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

agatagctag caaattaaga gaacaatttg gaaataataa aacaataatc tttaagcaat cctcaggagg ggacccagaa attgtaacgc acagttttaa 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

ttgtggaggg gaatttttct actgtaattc aacacaactg tttaatagta cttggtttaa tagtacttgg agtactgaag ggtcaaataa cactgaagga 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

agtgacacaa tcaccctccc atgcagaata aaacaaatta taaacatgtg gcagaaagta ggaaaagcaa tgtatgcccc tcccatcagt ggacaaatta 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

gatgttcatc aaatattaca gggctgctat taacaagaga tggtggtaat agcaacaatg agtccgagat cttcagacct ggaggaggag atatgaggga 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

caattggaga agtgaattat ataaatataa agtagtaaaa attgaaccat taggagtagc acccaccaag gcaaagagaa gagtggtgca gagagaaaaa 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

agagcagtgg gaataggagc tttgttcctt gggttcttgg gagcagcagg aagcactatg ggcgcagcct caatgacgct gacggtacag gccagacaat 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

tattgtctgg tatagtgcag cagcagaaca atttgctgag ggctattgag gcgcaacagc atctgttgca actcacagtc tggggcatca agcagctcca 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

ggcaagaatc ctggctgtgg aaagatacct aaaggatcaa cagctcctgg ggatttgggg ttgctctgga aaactcattt gcaccactgc tgtgccttgg 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

aatgctagtt ggagtaataa atctctggaa cagatttgga atcacacgac ctggatggag tgggacagag aaattaacaa ttacacaagc ttaatacact 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

ccttaattga agaatcgcaa aaccagcaag aaaagaatga acaagaatta ttggaattag ataaatgggc aagtttgtgg aattggttta acataacaaa 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

ttggctgtgg tatataaaat tattcataat gatagtagga ggcttggtag gtttaagaat agtttttgct gtactttcta tagtgaatag agttaggcag 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

ggatattcac cattatcgtt tcagacccac ctcccaaccc cgaggggacc cgacaggccc gaaggaatag aagaagaagg tggagagaga gacagagaca 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

gatccattcg attagtgaac ggatccttgg cacttatctg ggacgatctg cggagcctgt gcctcttcag ctaccaccgc ttgagagact tactcttgat 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

tgtaacgagg attgtggaac ttctgggacg cagggggtgg gaagccctca aatattggtg gaatctccta cagtattgga gtcaggaact aaagaatagt 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

gctgttagct tgctcaatgc cacagccata gcagtagctg aggggacaga tagggttata gaagtagtac aaggagcttg tagagctatt cgccacatac 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

ctagaagaat aagacagggc ttggaaagga ttttgctata agatgggtgg caagtggtca aaaagtagtg tgattggatg gcctactgta agggaaagaa 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

tgagacgagc tgagccagca gcagataggg tgggagcagc atctcgagac ctggaaaaac atggagcaat cacaagtagc aatacagcag ctaccaatgc 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

tgcttgtgcc tggctagaag cacaagagga ggaggaggtg ggttttccag tcacacctca ggtaccttta agaccaatga cttacaaggc agctgtagat 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

cttagccact ttttaaaaga aaagggggga ctggaagggc taattcactc ccaaagaaga caagatatcc ttgatctgtg gatctaccac acacaaggct 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

acttccctga ttagcagaac tacacaccag ggccaggggt cagatatcca ctgacctttg gatggtgcta caagctagta ccagttgagc cagataagat 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

agaagaggcc aataaaggag agaacaccag cttgttacac cctgtgagcc tgcatgggat ggatgacccg gagagagaag tgttagagtg gaggtttgac 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

agccgcctag catttcatca cgtggcccga gagctgcatc cggagtactt caagaactgc tgacatcgag cttgctacaa gggactttcc gctggggact 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

ttccagggag gcgtggcctg ggcgggactg gggagtggcg agccctcaga tcctgcatat aagcagctgc tttttgcctg tactgggtct ctctggttag 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

accagatctg agcctgggag ctctctggct aactagggaa cccactgctt aagcctcaat aaagcttgcc ttgagtgctt c
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181

Credibility of mRNA sequence:

guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail

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

Human Immunodeficiency Virus type 1 NY5/BRU (LAV-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: `2`
Originaly submitted by: Barbora Škaloudová	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
gag

The description of the protein encoded in this ORF:
Pr55 is further cleaved by a protease into final mature peptides

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):

336-1838

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
gag-pol

The description of the protein encoded in this ORF:
Gag-Pol is further cleaved by a protease into final mature peptides

The translational frameshift (ribosome slippage) involved:
-1 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):

336-4642

OPTIONAL: The function of the encoded protein

viral structural protein, important for virus infectivity, protein processing, and genomic RNA dimer
stability, important for incorporation of Vpr into assembling HIV-1 virions; helps mediate efficient virus
particle release from infected cells

Citations:

Brasey A., Lopez-Lastra M., Ohlmann T., Beerens N., Berkhout B., Darlix J. L., Sonenberg N. (2003) The leader of human immunodeficiency virus type 1 genomic RNA harbors an internal ribosome entry segment that is active during the G2/M phase of the cell cycle. J. Virol. 77(7):3939-3949

Berkhout B. (1996) Structure and function of the human immunodeficiency virus leader RNA. Prog. Nucleic. Acid Res. Mol. Biol. 54:1-34

IRESs:

IRES:

Version: `7`	Last change: `2009-08-18 17:28:34`
Originaly submitted by: Barbora Škaloudová	Reviewed by: Martin Mokrejš
The IRES name: `HIV-1`

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

104-336

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccct tttagtcagt gtggaaaatc tctagcagtg gcgcccgaac agggacctga 
).......(( ((..(((((. .(((((((.. ((((((((.. (((((((... ....)))..) ).))...))) )))))..... .......... .......... 
^104       ^114       ^124       ^134       ^144       ^154       ^164       ^174       ^184       ^194       

aagcgaaagg gaaaccagag gagctctctc gacgcaggac tcggcttgct gaagcgcgca cggcaagagg cgaggggcgg cgactggtga gtacgccaaa 
.......... ...))))))) (((....))) .))))))))) ....(((((( (......... )))))))... ........(( (((((....) )).))))... 
^204       ^214       ^224       ^234       ^244       ^254       ^264       ^274       ^284       ^294       

aattttgact agcggaggct agaaggagag aga
........(( (((....))) ))........ .((
^304       ^314       ^324       ^334

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:

).......((((..(((((..(((((((..((((((((..(((((((.......)))..)).))...))))))))......................................)))))))(((....))).)))))))))....(((((((.........)))))))...........(((((((....))).))))...........(((((....))))).........((
ERROR: unbalanced brackets in make_pair_table

STDOUT was:

Remarks:

Mono- and bicistronic (capped and uncapped) T7 transcripts were tested in rabbit reticulocyte lysates. Also
transiently transfected cells were used to show IRES activity. The intercistronic region contained impaired
EMCV IRES followed by the tested HIV-1 fragment. The impaired EMCV IRES should inhibit the potential ribosome
read-through.

With further deletions of the HIV-1 UTR, region 243-336 has very low IRES activity in in vitro
bicistronic assay using capped/uncapped mRNAs. Highest IRES activity was observed with 1-336 region.

RNA:protein interactions:

The RNA:protein interaction:

Version: `1`
Originaly submitted by: Barbora Škaloudová	Reviewed by: Martin Mokrejš

The description of the protein interacting with the RNA:
tat protein, the trans-activator protein

The interacting RNA base range: 22-24,29-33

The function of the protein interaction:

essential for viral replication

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

protein binds TAR hairpin of HIV 5' untranslated region, the functional TAR hairpin must maintain a
base-paired stem although the actual sequence of 29-CUGGG-33 pentanucleotide is not important for Tat
responsiveness

Citations:

Dingwall C., Ernberg I., Gait M. J., Green S. M., Heaphy S., Karn J., Lowe A. D., Singh M., Skinner M. A., Valerio R. (1989) Human immunodeficiency virus 1 tat protein binds trans-activation-responsive region (TAR) RNA in vitro. Proc. Natl. Acad. Sci. U. S. A. 86(18):6925-6929

Berkhout B., Jeang K. T. (1989) trans activation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and loop of the trans-acting-responsive hairpin: a quantitative analysis. J. Virol. 63(12):5501-5504

The RNA:protein interaction:

Version: `5`	Last change: `2006-04-28 00:00:00`
Originaly submitted by: Barbora Škaloudová	Reviewed by: Martin Mokrejš

The description of the protein interacting with the RNA:
nucleocapsid protein (NC protein)

The function of the protein interaction:

virus replication (increase the efficiency of strand transfer by HIV-1 reverse transcriptase), packaging of
genomic RNA

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

binding is not sequence-specific, the NC protein binds 5 untranslated region, TAR stem-loop

Citations:

Rein A., Henderson L. E., Levin J. G. (1998) Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: significance for viral replication. Trends. Biochem. Sci. 23(8):297-301

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 34

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

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
232-369

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

tcgacgcagg actcggcttg ctgaagcgcg cacggcaaga ggcgaggggc ggcgactggt gagtacgcca aaaattttga ctagcggagg ctagaaggag 
.......... .((((.(((( (((....... ..))))))). ..)))).... (((((((... .))).)))). .......... (((((....) ))))...... 
^232       ^242       ^252       ^262       ^272       ^282       ^292       ^302       ^312       ^322       

agagatgggt gcgagagcgt cagtattaag cgggggag
.......((( ((....)))) )......... ........
^332       ^342       ^352       ^362

Rendering structure of HIV-1 mRNA 138 nt long with energy of -32.20 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 reaction mixtures were treated with
0.02 to 0.1 U of RNase T1 (Pharmacia) at 08C for 20 min,
0.15 to 0.7 U of RNase CV or V1 (Pharmacia) at 08C for 20 min,
0.5 to 1.0% dimethylsulfate (Aldrich) at 08C for 20 min,
1.5 to 3.0% diethylpyrocarbonate (Sigma) at 08C for 30 min,
20 mg of carbodiimide (Sigma) per ml at 258C for 30 min
   or 4 to 8 mg of kethoxal (U.S. Biochemical) per ml at 08C for 1 h.

4.1.1. Enzymes used to characterize at least partially the 2D structure.

Enzyme or a combination of enzymes used in a single experiment with respective buffer:

ss_experiment_with_enzyme_id: 66

The temperature (in degrees of Celsia):
0 The enzymatic method used to determine the 2D structure:
ribonuclease T1/V1 mix

Enzyme or a combination of enzymes used in a single experiment with respective buffer:

Version: 0

pH `7.50`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `50.00`	Mg²⁺ [mM] `0`	Ca²⁺ [mM] `0`
Cl^- [mM] `50.00`	Tris [mM] `0`	BSA [mM] `0`	HEPES [mM] `30.00`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

Other buffer components and their relative concentrations:

10 mM ZnCl2
2 mM dithiothreitol

4.1.2. Chemicals used to characterize at least partially the 2D structure.