IRESite_Id:569 characteristics of Rbm3_22nt_module IRES studied in MoMLV-provirus-Rbm3-GFP plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `569`	Version: `5`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-03-16 15:57:28`
Reviewed by: Martin Mokrejš	Last change: `2009-04-08 19:29:22`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_translationally_characterized

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
our_best_guess

The mRNA/+RNA description:

Putative in vivo transcript of plasmid with chimeric MoMLV provirus driven from CMV IE promoter. The capped
and unspliced viral transcript encodes gag/gag-pol and GFP proteins separated by the putative Rbm3 IRES.

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

GCGCCAGTCC TCCGATTGAC TGAGTCGCCC GGGTACCCGT GTATCCAATA AACCCTCTTG CAGTTGCATC CGACTTGTGG TCTCGCTGTT CCTTGGGAGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GTCTCCTCTG AGTGATTGAC TACCCGTCAG CGGGGGTCTT TCATTTGGGG GCTCGTCCGG GATCGGGAGA CCCCTGCCCA GGGACCACCG ACCCACCACC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GGGAGgtaag ctggccagca acttatctgt gtctgtccga ttgtctagtg tctatgactg attttatgcg cctgcgtcgg tactagttag ctaactagct 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ctgtatctgg cggacccgtg gtggaactga cgagttcgga acacccggcc gcaaccctgg gagacgtccc agggacttcg ggggccgttt ttgtggcccg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

acctgagtcc aaaaatcccg atcgttttgg actctttggt gcacccccct tagaggaggg atatgtggtt ctggtaggag acgagaacct aaaacagttc 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ccgcctccgt ctgaattttt gctttcggtt tgggaccgaa gccgcgccgc gcgtcttgtc tgctgcagca tcgttctgtg ttgtctctgt ctgactgtgt 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ttctgtattt gtctgagaat atgggccaga ctgttaccac tcccttaagt ttgaccttag gtcactggaa agatgtcgag cggatcgctc acaaccagtc 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ggtagatgtc aagaagagac gttgggttac cttctgctct gcagaatggc caacctttaa cgtcggatgg ccgcgagacg gcacctttaa ccgagacctc 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

atcacccagg ttaagatcaa ggtcttttca cctggcccgc atggacaccc agaccaggtc ccctacatcg tgacctggga agccttggct tttgaccccc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ctccctgggt caagcccttt gtacacccta agcctccgcc tcctcttcct ccatccgccc cgtctctccc ccttgaacct cctcgttcga ccccgcctcg 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

atcctccctt tatccagccc tcactccttc tctaggcgcc aaacctaaac ctcaagttct ttctgacagt ggggggccgc tcatcgacct acttacagaa 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

gaccccccgc cttataggga cccaagacca cccccttccg acagggacgg aaatggtgga gaagcgaccc ctgcgggaga ggcaccggac ccctccccaa 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tggcatctcg cctacgtggg agacgggagc cccctgtggc cgactccact acctcgcagg cattccccct ccgcgcagga ggaaacggac agcttcaata 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ctggccgttc tcctcttctg acctttacaa ctggaaaaat aataaccctt ctttttctga agatccaggt aaactgacag ctctgatcga gtctgttctc 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

atcacccatc agcccacctg ggacgactgt cagcagctgt tggggactct gctgaccgga gaagaaaaac aacgggtgct cttagaggct agaaaggcgg 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

tgcggggcga tgatgggcgc cccactcaac tgcccaatga agtcgatgcc gcttttcccc tcgagcgccc agactgggat tacaccaccc aggcaggtag 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

gaaccaccta gtccactatc gccagttgct cctagcgggt ctccaaaacg cgggcagaag ccccaccaat ttggccaagg taaaaggaat aacacaaggg 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

cccaatgagt ctccctcggc cttcctagag agacttaagg aagcctatcg caggtacact ccttatgacc ctgaggaccc agggcaagaa actaatgtgt 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ctatgtcttt catttggcag tctgccccag acattgggag aaagttagag aggttagaag atttaaaaaa caagacgctt ggagatttgg ttagagaggc 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

agaaaagatc tttaataaac gagaaacccc ggaagaaaga gaggaacgta tcaggagaga aacagaggaa aaagaagaac gccgtaggac agaggatgag 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

cagaaagaga aagaaagaga tcgtaggaga catagagaga tgagcaagct attggccact gtcgttagtg gacagaaaca ggatagacag ggaggagaac 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gaaggaggtc ccaactcgat cgcgaccagt gtgcctactg caaagaaaag gggcactggg ctaaagattg tcccaagaaa ccacgaggac ctcggggacc 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

aagaccccag acctccctcc tgaccctaga tgactaggga ggtcagggtc aggagccccc ccctgaaccc aggataaccc tcaaagtcgg ggggcaaccc 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

gtcaccttcc tggtagatac tggggcccaa cactccgtgc tgacccaaaa tcctggaccc ctaagtgata agtctgcctg ggtccaaggg gctactggag 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

gaaagcggta tcgctggacc acggatcgca aagtacatct agctaccggt aaggtcaccc actctttcct ccatgtacca gactgtccct atcctctgtt 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

aggaagagat ttgctgacta aactaaaagc ccaaatccac tttgagggat caggagccca ggttatggga ccaatggggc agcccctgca agtgttgacc 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ctaaatatag aagatgagca tcggctacat gagacctcaa aagagccaga tgtttctcta gggtccacat ggctgtctga ttttcctcag gcctgggcgg 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

aaaccggggg catgggactg gcagttcgcc aagctcctct gatcatacct ctgaaagcaa cctctacccc cgtgtccata aaacaatacc ccatgtcaca 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

agaagccaga ctggggatca agccccacat acagagactg ttggaccagg gaatactggt accctgccag tccccctgga acacgcccct gctacccgtt 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

aagaaaccag ggactaatga ttataggcct gtccaggatc tgagagaagt caacaagcgg gtggaagaca tccaccccac cgtgcccaac ccttacaacc 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

tcttgagcgg gctcccaccg tcccaccagt ggtacactgt gcttgattta aaggatgcct ttttctgcct gagactccac cccaccagtc agcctctctt 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

cgcctttgag tggagagatc cagagatggg aatctcagga caattgacct ggaccagact cccacagggt ttcaaaaaca gtcccaccct gtttgatgag 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

gcactgcaca gagacctagc agacttccgg atccagcacc cagacttgat cctgctacag tacgtggatg acttactgct ggccgccact tctgagctag 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

actgccaaca aggtactcgg gccctgttac aaaccctagg gaacctcggg tatcgggcct cggccaagaa agcccaaatt tgccagaaac aggtcaagta 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

tctggggtat cttctaaaag agggtcagag atggctgact gaggccagaa aagagactgt gatggggcag cctactccga agacccctcg acaactaagg 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

gagttcctag ggacggcagg cttctgtcgc ctctggatcc ctgggtttgc agaaatggca gcccccttgt accctctcac caaaacgggg actctgttta 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

attggggccc agaccaacaa aaggcctatc aagaaatcaa gcaagctctt ctaactgccc cagccctggg gttgccagat ttgactaagc cctttgaact 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ctttgtcgac gagaagcagg gctacgccaa aggtgtccta acgcaaaaac tgggaccttg gcgtcggccg gtggcctacc tgtccaaaaa gctagaccca 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

gtagcagctg ggtggccccc ttgcctacgg atggtagcag ccattgccgt actgacaaag gatgcaggca agctaaccat gggacagcca ctagtcattc 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

tggcccccca tgcagtagag gcactagtca aacaaccccc cgaccgctgg ctttccaacg cccggatgac tcactatcag gccttgcttt tggacacgga 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ccgggtccag ttcggaccgg tggtagccct gaacccggct acgctgctcc cactgcctga ggaagggctg caacacaact gccttgatat cctggccgaa 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

gcccacggaa cccgacccga cctaacggac cagccgctcc cagacgccga ccacacctgg tacacggatg gaagcagtct cttacaagag ggacagcgta 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

aggcgggagc tgcggtgacc accgagaccg aggtaatctg ggctaaagcc ctgccagccg ggacatccgc tcagcgggct gaactgatag cactcaccca 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ggccctaaag atggcagaag gtaagaagct aaatgtttat actgatagcc gttatgcttt tgctactgcc catatccatg gagaaatata cagaaggcgt 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

gggttgctca catcagaagg caaagagatc aaaaataaag acgagatctt ggccctacta aaagccctct ttctgcccaa aagacttagc ataatccatt 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

gtccaggaca tcaaaaggga cacagcgccg aggctagagg caaccggatg gctgaccaag cggcccgaaa ggcagccatc acagagactc cagacacctc 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

taccctcctc atagaaaatt catcacccta cacctcagaa cattttcatt acacagtgac tgatataaag gacctaacca agttgggggc catttatgat 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

aaaacaaaga agtattgggt ctaccaagga aaacctgtga tgcctgacca gtttactttt gaattattag actttcttca tcagctgact cacctcagct 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

tctcaaaaat gaaggctctc ctagagagaa gccacagtcc ctactacatg ctgaaccggg atcgaacact caaaaatatc actgagacct gcaaagcttg 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

tgcacaagtc aacgccagca agtctgccgt taaacaggga actagggtcc gcgggcatcg gcccggcact cattgggaga tcgatttcac cgagataaag 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

cccggattgt atggctataa atatcttcta gtttttatag ataccttttc tggctggata gaagccttcc caaccaagaa agaaaccgcc aaggtcgtaa 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ccaagaagct actagaggag atcttcccca ggttcggcat gcctcaggta ttgggaactg acaatgggcc tgccttcgtc tccaaggtga gtcagacagt 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ggccgatctg ttggggattg attggaaatt acattgtgca tacagacccc aaagctcagg ccaggtagaa agaatgaata gaaccatcaa ggagacttta 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

actaaattaa cgcttgcaac tggctctaga gactgggtgc tcctactccc cttagccctg taccgagccc gcaacacgcc gggcccccat ggcctcaccc 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

catatgagat cttatatggg gcacccccgc cccttgtaaa cttccctgac cctgacatga caagagttac taacagcccc tctctccaag ctcacttaca 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ggctctctac ttagtccagc acgaagtctg gagacctctg gcggcagcct accaagaaca actggaccga ccggtggtac ctcaccctta ccgagtcggc 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

gacacagtgt gggtccgccg acaccagact aagaacctag aacctcgctg gaaaggacct tacacagtcc tgctgaccac ccccaccgcc ctcaaagtag 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

acggcatcgc agcttggata cacgccgccc acgtgaaggc tgccgacccc gggggtggac catcctctag actgacatgg cgcgttcaac gctctcaaaa 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ccccctcaag ataagattaa cccgtggaag cccttaatag tcatgggagt cctgttagga gtagggatgg cagagagccc ccatcaggtc tttaatgtaa 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

cctggagagt caccaacctg atgactgggc gtaccgccaa tgccacctcc ctcctgggaa ctgtacaaga tgccttccca aaattatatt ttgatctatg 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

tgatctggtc ggagaggagt gggacccttc agaccaggaa ccgtatgtcg ggtatggctg caagtacccc gcagggagac agcggacccg gacttttgac 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ttttacgtgt gccctgggca taccgtaaag tcggggtgtg ggggaccagg agagggctac tgtggtaaat gggggtgtga aaccaccgga caggcttact 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

ggaagcccac atcatcgtgg gacctaatct cccttaagcg cggtaacacc ccctgggaca cgggatgctc taaagttgcc tgtggcccct gctacgacct 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

ctccaaagta tccaattcct tccaaggggc tactcgaggg ggcagatgca accctctagt cctagaattc actgatgcag gaaaaaaggc taactgggac 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

gggcccaaat cgtggggact gagactgtac cggacaggaa cagatcctat taccatgttc tccctgaccc ggcaggtcct taatgtggga ccccgagtcc 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

ccatagggcc caacccagta ttacccgacc aaagactccc ttcctcacca atagagattg taccggctcc acagccacct agccccctca ataccagtta 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

ccccccttcc actaccagta caccctcaac ctcccctaca agtccaagtg tcccacagcc acccccagga actggagata gactactagc tctagtcaaa 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

ggagcctatc aggcgcttaa cctcaccaat cccgacaaga cccaagaatg ttggctgtgc ttagtgtcgg gacctcctta ttacgaagga gtagcggtcg 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

tgggcactta taccaatcat tccaccgctc cggccaactg tacggccact tcccaacata agcttaccct atctgaagtg acaggacagg gcctatgcat 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

gggggcagta cctaaaactc accaggcctt atgtaacacc acccaaagcg ccggctcagg atcctactac cttgcagcac ccgccggaac aatgtgggct 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

tgcagcactg gattgactcc ctgcttgtcc accacggtgc tcaatctaac cacagattat tgtgtattag ttgaactctg gcccagagta atttaccact 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

cccccgatta tatgtatggt cagcttgaac agcgtaccaa atataaaaga gagccagtat cattgaccct ggcccttcta ctaggaggat taaccatggg 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

agggattgca gctggaatag ggacggggac cactgcctta attaaaaccc agcagtttga gcagcttcat gccgctatcc agacagacct caacgaagtc 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

gaaaagtcaa ttaccaacct agaaaagtca ctgacctcgt tgtctgaagt agtcctacag aaccgcagag gcctagattt gctattccta aaggagggag 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

gtctctgcgc agccctaaaa gaagaatgtt gtttttatgc agaccacacg gggctagtga gagacagcat ggccaaatta agagaaaggc ttaatcagag 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

acaaaaacta tttgagacag gccaaggatg gttcgaaggg ctgtttaata gatccccctg gtttaccacc ttaatctcca ccatcatggg acctctaata 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

gtactcttac tgatcttact ctttggacct tgcattctca atcgattagt ccaatttgtt aaagacagga tatcagtggt ccaggctcta gttttgactc 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

aacaatatca ccagctgaag cctatagagt atgaaccgtg aacgcgttta taatttcttc ttccagAACG TACGATGGTG AGCAAGGGCG AGGAGCTGTT 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

CACCGGGGTG GTGCCCATCC TGGTCGAGCT GGACGGCGAC GTAAACGGCC ACAAGTTCAG CGTGTCCGGC GAGGGCGAGG GCGATGCCAC CTACGGCAAG 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

CTGACCCTGA AGTTCATCTG CACCACCGGC AAGCTGCCCG TGCCCTGGCC CACCCTCGTG ACCACCTTGA CCTACGGCGT GCAGTGCTTC GCCCGCTACC 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

CCGACCACAT GAAGCAGCAC GACTTCTTCA AGTCCGCCAT GCCCGAAGGC TACGTCCAGG AGCGCACCAT CTTCTTCAAG GACGACGGCA ACTACAAGAC 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

CCGCGCCGAG GTGAAGTTCG AGGGCGACAC CCTGGTGAAC CGCATCGAGC TGAAGGGCAT CGACTTCAAG GAGGACGGCA ACATCCTGGG GCACAAGCTG 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

GAGTACAACT ACAACAGCCA CAAGGTCTAT ATCACCGCCG ACAAGCAGAA GAACGGCATC AAGGTGAACT TCAAGACCCG CCACAACATC GAGGACGGCA 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

GCGTGCAGCT CGCCGACCAC TACCAGCAGA ACACCCCCAT CGGCGACGGC CCCGTGCTGC TGCCCGACAA CCACTACCTG AGCACCCAGT CCGCCCTGAG 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

CAAAGACCCC AACGAGAAGC GCGATCACAT GGTCCTGCTG GAGTTCGTGA CCGCCGCCGG GATCACTCTC GGCATGGACG AGCTGTACAA GTAGCGGCCG 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

CGCCATAGAT AAAATAAAAG ATTTTATTTA GTCTCCAGAA AAAGGGGGGA ATGAAAGACC CCACCTGTAG GTTTGGCAAG CTAGCTTAAG TAACGCCATT 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

TTGCAAGGCA TGGAAAAATA CATAACTGAG AATAGAGAAG TTCAGATCAA GGTCAGGAAC AGATGGAACA GCTGAATATG GGCCAAACAG GATATCTGTG 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

GTAAGCAGTT CCTGCCCCGG CTCAGGGCCA AGAACAGATG GAACAGCTGA ATATGGGCCA AACAGGATAT CTGTGGTAAG CAGTTCCTGC CCCGGCTCAG 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

GGCCAAGAAC AGATGGTCCC CAGATGCGGT CCAGCCCTCA GCAGTTTCTA GAGAACCATC AGATGTTTCC AGGGTGCCCC AAGGACCTGA AATGACCCTG 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

TGCCTTGTTT AAACTAACCA ATCAGTTCGC TTCTCGCTTC TGTTCGCGCG CTTCTGCTCC CCGAGCTCAA TAAAAGAGCC CACAACCCCT CACTCGGG
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
MoMLV-provirus-Rbm3-GFP The name of the promoter used to express this mRNA:
CMV_IE

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

yes

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

yes

A promoter reported in cDNA corresponding to IRES sequence:

not tested

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:
heterogeneous_population_of_molecules_found

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:
heterogeneous_population_of_molecules_found

The organism used:

Homo sapiens PC-3 (ATCC CRL 1435)

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
Rbm3

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Mus musculus

The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:

TAGTTATTAA TAGTAATCAA TTACGGGGTC ATTAGTTCAT AGCCCATATA TGGAGTTCCG CGTTACATAA CTTACGGTAA ATGGCCCGCC TGGCTGACCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCCAACGACC CCCGCCCATT GACGTCAATA ATGACGTATG TTCCCATAGT AACGCCAATA GGGACTTTCC ATTGACGTCA ATGGGTGGAG TATTTACGGT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AAACTGCCCA CTTGGCAGTA CATCAAGTGT ATCATATGCC AAGTACGCCC CCTATTGACG TCAATGACGG TAAATGGCCC GCCTGGCATT ATGCCCAGTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CATGACCTTA TGGGACTTTC CTACTTGGCA GTACATCTAC GTATTAGTCA TCGCTATTAC CATGGTGATG CGGTTTTGGC AGTACATCAA TGGGCGTGGA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TAGCGGTTTG ACTCACGGGG ATTTCCAAGT CTCCACCCCA TTGACGTCAA TGGGAGTTTG TTTTGGCACC AAAATCAACG GGACTTTCCA AAATGTCGTA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACAACTCCGC CCCATTGACG CAAATGGGCG GTAGGCGTGT ACGGTGGGAG GTCTATATAA GCAGAGCTGG TTTAGTGAAC CGGCGCCAGT CCTCCGATTG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ACTGAGTCGC CCGGGTACCC GTGTATCCAA TAAACCCTCT TGCAGTTGCA TCCGACTTGT GGTCTCGCTG TTCCTTGGGA GGGTCTCCTC TGAGTGATTG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACTACCCGTC AGCGGGGGTC TTTCATTTGG GGGCTCGTCC GGGATCGGGA GACCCCTGCC CAGGGACCAC CGACCCACCA CCGGGAGgta agctggccag 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

caacttatct gtgtctgtcc gattgtctag tgtctatgac tgattttatg cgcctgcgtc ggtactagtt agctaactag ctctgtatct ggcggacccg 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

tggtggaact gacgagttcg gaacacccgg ccgcaaccct gggagacgtc ccagggactt cgggggccgt ttttgtggcc cgacctgagt ccaaaaatcc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

cgatcgtttt ggactctttg gtgcaccccc cttagaggag ggatatgtgg ttctggtagg agacgagaac ctaaaacagt tcccgcctcc gtctgaattt 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ttgctttcgg tttgggaccg aagccgcgcc gcgcgtcttg tctgctgcag catcgttctg tgttgtctct gtctgactgt gtttctgtat ttgtctgaga 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

atatgggcca gactgttacc actcccttaa gtttgacctt aggtcactgg aaagatgtcg agcggatcgc tcacaaccag tcggtagatg tcaagaagag 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

acgttgggtt accttctgct ctgcagaatg gccaaccttt aacgtcggat ggccgcgaga cggcaccttt aaccgagacc tcatcaccca ggttaagatc 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

aaggtctttt cacctggccc gcatggacac ccagaccagg tcccctacat cgtgacctgg gaagccttgg cttttgaccc ccctccctgg gtcaagccct 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ttgtacaccc taagcctccg cctcctcttc ctccatccgc cccgtctctc ccccttgaac ctcctcgttc gaccccgcct cgatcctccc tttatccagc 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

cctcactcct tctctaggcg ccaaacctaa acctcaagtt ctttctgaca gtggggggcc gctcatcgac ctacttacag aagacccccc gccttatagg 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

gacccaagac cacccccttc cgacagggac ggaaatggtg gagaagcgac ccctgcggga gaggcaccgg acccctcccc aatggcatct cgcctacgtg 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ggagacggga gccccctgtg gccgactcca ctacctcgca ggcattcccc ctccgcgcag gaggaaacgg acagcttcaa tactggccgt tctcctcttc 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

tgacctttac aactggaaaa ataataaccc ttctttttct gaagatccag gtaaactgac agctctgatc gagtctgttc tcatcaccca tcagcccacc 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

tgggacgact gtcagcagct gttggggact ctgctgaccg gagaagaaaa acaacgggtg ctcttagagg ctagaaaggc ggtgcggggc gatgatgggc 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gccccactca actgcccaat gaagtcgatg ccgcttttcc cctcgagcgc ccagactggg attacaccac ccaggcaggt aggaaccacc tagtccacta 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

tcgccagttg ctcctagcgg gtctccaaaa cgcgggcaga agccccacca atttggccaa ggtaaaagga ataacacaag ggcccaatga gtctccctcg 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

gccttcctag agagacttaa ggaagcctat cgcaggtaca ctccttatga ccctgaggac ccagggcaag aaactaatgt gtctatgtct ttcatttggc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

agtctgcccc agacattggg agaaagttag agaggttaga agatttaaaa aacaagacgc ttggagattt ggttagagag gcagaaaaga tctttaataa 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

acgagaaacc ccggaagaaa gagaggaacg tatcaggaga gaaacagagg aaaaagaaga acgccgtagg acagaggatg agcagaaaga gaaagaaaga 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

gatcgtagga gacatagaga gatgagcaag ctattggcca ctgtcgttag tggacagaaa caggatagac agggaggaga acgaaggagg tcccaactcg 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

atcgcgacca gtgtgcctac tgcaaagaaa aggggcactg ggctaaagat tgtcccaaga aaccacgagg acctcgggga ccaagacccc agacctccct 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

cctgacccta gatgactagg gaggtcaggg tcaggagccc ccccctgaac ccaggataac cctcaaagtc ggggggcaac ccgtcacctt cctggtagat 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

actggggccc aacactccgt gctgacccaa aatcctggac ccctaagtga taagtctgcc tgggtccaag gggctactgg aggaaagcgg tatcgctgga 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ccacggatcg caaagtacat ctagctaccg gtaaggtcac ccactctttc ctccatgtac cagactgtcc ctatcctctg ttaggaagag atttgctgac 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

taaactaaaa gcccaaatcc actttgaggg atcaggagcc caggttatgg gaccaatggg gcagcccctg caagtgttga ccctaaatat agaagatgag 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

catcggctac atgagacctc aaaagagcca gatgtttctc tagggtccac atggctgtct gattttcctc aggcctgggc ggaaaccggg ggcatgggac 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

tggcagttcg ccaagctcct ctgatcatac ctctgaaagc aacctctacc cccgtgtcca taaaacaata ccccatgtca caagaagcca gactggggat 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

caagccccac atacagagac tgttggacca gggaatactg gtaccctgcc agtccccctg gaacacgccc ctgctacccg ttaagaaacc agggactaat 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

gattataggc ctgtccagga tctgagagaa gtcaacaagc gggtggaaga catccacccc accgtgccca acccttacaa cctcttgagc gggctcccac 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

cgtcccacca gtggtacact gtgcttgatt taaaggatgc ctttttctgc ctgagactcc accccaccag tcagcctctc ttcgcctttg agtggagaga 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

tccagagatg ggaatctcag gacaattgac ctggaccaga ctcccacagg gtttcaaaaa cagtcccacc ctgtttgatg aggcactgca cagagaccta 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

gcagacttcc ggatccagca cccagacttg atcctgctac agtacgtgga tgacttactg ctggccgcca cttctgagct agactgccaa caaggtactc 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

gggccctgtt acaaacccta gggaacctcg ggtatcgggc ctcggccaag aaagcccaaa tttgccagaa acaggtcaag tatctggggt atcttctaaa 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

agagggtcag agatggctga ctgaggccag aaaagagact gtgatggggc agcctactcc gaagacccct cgacaactaa gggagttcct agggacggca 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ggcttctgtc gcctctggat ccctgggttt gcagaaatgg cagccccctt gtaccctctc accaaaacgg ggactctgtt taattggggc ccagaccaac 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

aaaaggccta tcaagaaatc aagcaagctc ttctaactgc cccagccctg gggttgccag atttgactaa gccctttgaa ctctttgtcg acgagaagca 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

gggctacgcc aaaggtgtcc taacgcaaaa actgggacct tggcgtcggc cggtggccta cctgtccaaa aagctagacc cagtagcagc tgggtggccc 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ccttgcctac ggatggtagc agccattgcc gtactgacaa aggatgcagg caagctaacc atgggacagc cactagtcat tctggccccc catgcagtag 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

aggcactagt caaacaaccc cccgaccgct ggctttccaa cgcccggatg actcactatc aggccttgct tttggacacg gaccgggtcc agttcggacc 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ggtggtagcc ctgaacccgg ctacgctgct cccactgcct gaggaagggc tgcaacacaa ctgccttgat atcctggccg aagcccacgg aacccgaccc 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

gacctaacgg accagccgct cccagacgcc gaccacacct ggtacacgga tggaagcagt ctcttacaag agggacagcg taaggcggga gctgcggtga 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ccaccgagac cgaggtaatc tgggctaaag ccctgccagc cgggacatcc gctcagcggg ctgaactgat agcactcacc caggccctaa agatggcaga 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

aggtaagaag ctaaatgttt atactgatag ccgttatgct tttgctactg cccatatcca tggagaaata tacagaaggc gtgggttgct cacatcagaa 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

ggcaaagaga tcaaaaataa agacgagatc ttggccctac taaaagccct ctttctgccc aaaagactta gcataatcca ttgtccagga catcaaaagg 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

gacacagcgc cgaggctaga ggcaaccgga tggctgacca agcggcccga aaggcagcca tcacagagac tccagacacc tctaccctcc tcatagaaaa 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ttcatcaccc tacacctcag aacattttca ttacacagtg actgatataa aggacctaac caagttgggg gccatttatg ataaaacaaa gaagtattgg 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

gtctaccaag gaaaacctgt gatgcctgac cagtttactt ttgaattatt agactttctt catcagctga ctcacctcag cttctcaaaa atgaaggctc 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

tcctagagag aagccacagt ccctactaca tgctgaaccg ggatcgaaca ctcaaaaata tcactgagac ctgcaaagct tgtgcacaag tcaacgccag 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

caagtctgcc gttaaacagg gaactagggt ccgcgggcat cggcccggca ctcattggga gatcgatttc accgagataa agcccggatt gtatggctat 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

aaatatcttc tagtttttat agataccttt tctggctgga tagaagcctt cccaaccaag aaagaaaccg ccaaggtcgt aaccaagaag ctactagagg 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

agatcttccc caggttcggc atgcctcagg tattgggaac tgacaatggg cctgccttcg tctccaaggt gagtcagaca gtggccgatc tgttggggat 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

tgattggaaa ttacattgtg catacagacc ccaaagctca ggccaggtag aaagaatgaa tagaaccatc aaggagactt taactaaatt aacgcttgca 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

actggctcta gagactgggt gctcctactc cccttagccc tgtaccgagc ccgcaacacg ccgggccccc atggcctcac cccatatgag atcttatatg 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

gggcaccccc gccccttgta aacttccctg accctgacat gacaagagtt actaacagcc cctctctcca agctcactta caggctctct acttagtcca 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

gcacgaagtc tggagacctc tggcggcagc ctaccaagaa caactggacc gaccggtggt acctcaccct taccgagtcg gcgacacagt gtgggtccgc 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

cgacaccaga ctaagaacct agaacctcgc tggaaaggac cttacacagt cctgctgacc acccccaccg ccctcaaagt agacggcatc gcagcttgga 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

tacacgccgc ccacgtgaag gctgccgacc ccgggggtgg accatcctct agactgacat ggcgcgttca acgctctcaa aaccccctca agataagatt 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

aacccgtgga agcccttaat agtcatggga gtcctgttag gagtagggat ggcagagagc ccccatcagg tctttaatgt aacctggaga gtcaccaacc 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

tgatgactgg gcgtaccgcc aatgccacct ccctcctggg aactgtacaa gatgccttcc caaaattata ttttgatcta tgtgatctgg tcggagagga 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

gtgggaccct tcagaccagg aaccgtatgt cgggtatggc tgcaagtacc ccgcagggag acagcggacc cggacttttg acttttacgt gtgccctggg 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

cataccgtaa agtcggggtg tgggggacca ggagagggct actgtggtaa atgggggtgt gaaaccaccg gacaggctta ctggaagccc acatcatcgt 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

gggacctaat ctcccttaag cgcggtaaca ccccctggga cacgggatgc tctaaagttg cctgtggccc ctgctacgac ctctccaaag tatccaattc 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

cttccaaggg gctactcgag ggggcagatg caaccctcta gtcctagaat tcactgatgc aggaaaaaag gctaactggg acgggcccaa atcgtgggga 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

ctgagactgt accggacagg aacagatcct attaccatgt tctccctgac ccggcaggtc cttaatgtgg gaccccgagt ccccataggg cccaacccag 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

tattacccga ccaaagactc ccttcctcac caatagagat tgtaccggct ccacagccac ctagccccct caataccagt tacccccctt ccactaccag 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

tacaccctca acctccccta caagtccaag tgtcccacag ccacccccag gaactggaga tagactacta gctctagtca aaggagccta tcaggcgctt 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

aacctcacca atcccgacaa gacccaagaa tgttggctgt gcttagtgtc gggacctcct tattacgaag gagtagcggt cgtgggcact tataccaatc 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

attccaccgc tccggccaac tgtacggcca cttcccaaca taagcttacc ctatctgaag tgacaggaca gggcctatgc atgggggcag tacctaaaac 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

tcaccaggcc ttatgtaaca ccacccaaag cgccggctca ggatcctact accttgcagc acccgccgga acaatgtggg cttgcagcac tggattgact 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

ccctgcttgt ccaccacggt gctcaatcta accacagatt attgtgtatt agttgaactc tggcccagag taatttacca ctcccccgat tatatgtatg 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

gtcagcttga acagcgtacc aaatataaaa gagagccagt atcattgacc ctggcccttc tactaggagg attaaccatg ggagggattg cagctggaat 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

agggacgggg accactgcct taattaaaac ccagcagttt gagcagcttc atgccgctat ccagacagac ctcaacgaag tcgaaaagtc aattaccaac 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

ctagaaaagt cactgacctc gttgtctgaa gtagtcctac agaaccgcag aggcctagat ttgctattcc taaaggaggg aggtctctgc gcagccctaa 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

aagaagaatg ttgtttttat gcagaccaca cggggctagt gagagacagc atggccaaat taagagaaag gcttaatcag agacaaaaac tatttgagac 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

aggccaagga tggttcgaag ggctgtttaa tagatccccc tggtttacca ccttaatctc caccatcatg ggacctctaa tagtactctt actgatctta 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

ctctttggac cttgcattct caatcgatta gtccaatttg ttaaagacag gatatcagtg gtccaggctc tagttttgac tcaacaatat caccagctga 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

agcctataga gtatgaaccg tgaacgcgtt tataatttct tcttccagAA CGTACGATGG TGAGCAAGGG CGAGGAGCTG TTCACCGGGG TGGTGCCCAT 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

CCTGGTCGAG CTGGACGGCG ACGTAAACGG CCACAAGTTC AGCGTGTCCG GCGAGGGCGA GGGCGATGCC ACCTACGGCA AGCTGACCCT GAAGTTCATC 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

TGCACCACCG GCAAGCTGCC CGTGCCCTGG CCCACCCTCG TGACCACCTT GACCTACGGC GTGCAGTGCT TCGCCCGCTA CCCCGACCAC ATGAAGCAGC 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

ACGACTTCTT CAAGTCCGCC ATGCCCGAAG GCTACGTCCA GGAGCGCACC ATCTTCTTCA AGGACGACGG CAACTACAAG ACCCGCGCCG AGGTGAAGTT 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

CGAGGGCGAC ACCCTGGTGA ACCGCATCGA GCTGAAGGGC ATCGACTTCA AGGAGGACGG CAACATCCTG GGGCACAAGC TGGAGTACAA CTACAACAGC 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

CACAAGGTCT ATATCACCGC CGACAAGCAG AAGAACGGCA TCAAGGTGAA CTTCAAGACC CGCCACAACA TCGAGGACGG CAGCGTGCAG CTCGCCGACC 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

ACTACCAGCA GAACACCCCC ATCGGCGACG GCCCCGTGCT GCTGCCCGAC AACCACTACC TGAGCACCCA GTCCGCCCTG AGCAAAGACC CCAACGAGAA 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

GCGCGATCAC ATGGTCCTGC TGGAGTTCGT GACCGCCGCC GGGATCACTC TCGGCATGGA CGAGCTGTAC AAGTAGCGGC CGCGCCATAG ATAAAATAAA 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

AGATTTTATT TAGTCTCCAG AAAAAGGGGG GAATGAAAGA CCCCACCTGT AGGTTTGGCA AGCTAGCTTA AGTAACGCCA TTTTGCAAGG CATGGAAAAA 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

TACATAACTG AGAATAGAGA AGTTCAGATC AAGGTCAGGA ACAGATGGAA CAGCTGAATA TGGGCCAAAC AGGATATCTG TGGTAAGCAG TTCCTGCCCC 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

GGCTCAGGGC CAAGAACAGA TGGAACAGCT GAATATGGGC CAAACAGGAT ATCTGTGGTA AGCAGTTCCT GCCCCGGCTC AGGGCCAAGA ACAGATGGTC 
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391      

CCCAGATGCG GTCCAGCCCT CAGCAGTTTC TAGAGAACCA TCAGATGTTT CCAGGGTGCC CCAAGGACCT GAAATGACCC TGTGCCTTGT TTAAACTAAC 
^9401      ^9411      ^9421      ^9431      ^9441      ^9451      ^9461      ^9471      ^9481      ^9491      

CAATCAGTTC GCTTCTCGCT TCTGTTCGCG CGCTTCTGCT CCCCGAGCTC AATAAAAGAG CCCACAACCC CTCACTCGGG GCGCCAGTCC TCCGATTGAC 
^9501      ^9511      ^9521      ^9531      ^9541      ^9551      ^9561      ^9571      ^9581      ^9591      

TGAGTCGCCC GGGTACCCGT GTATCCAATA AACCCTCTTG CAGTTGCATC CGACTTGTGG TCTCGCTGTT CCTTGGGAGG GTCTCCTCTG AGTGATTGAC 
^9601      ^9611      ^9621      ^9631      ^9641      ^9651      ^9661      ^9671      ^9681      ^9691      

TACCCGTCAG CGGGGGTCTT TCATTTGGGG GCTCGTCCGG GATCGGGAGA CCCCTGCCCA GGGACCACCG ACCCACCACC GGGAGGTAAG CTGGCTGCCT 
^9701      ^9711      ^9721      ^9731      ^9741      ^9751      ^9761      ^9771      ^9781      ^9791      

CGCGCGTTTC GGTGATGACG GTGAAAACCT CTGACATGTG AGCAAAAGGC CAGCAAAAGG CCAGGAACCG TAAAAAGGCC GCGTTGCTGG CGTTTTTCCA 
^9801      ^9811      ^9821      ^9831      ^9841      ^9851      ^9861      ^9871      ^9881      ^9891      

TAGGCTCCGC CCCCCTGACG AGCATCACAA AAATCGACGC TCAAGTCAGA GGTGGCGAAA CCCGACAGGA CTATAAAGAT ACCAGGCGTT TCCCCCTGGA 
^9901      ^9911      ^9921      ^9931      ^9941      ^9951      ^9961      ^9971      ^9981      ^9991      

AGCTCCCTCG TGCGCTCTCC TGTTCCGACC CTGCCGCTTA CCGGATACCT GTCCGCCTTT CTCCCTTCGG GAAGCGTGGC GCTTTCTCAA TGCTCACGCT 
^10001     ^10011     ^10021     ^10031     ^10041     ^10051     ^10061     ^10071     ^10081     ^10091     

GTAGGTATCT CAGTTCGGTG TAGGTCGTTC GCTCCAAGCT GGGCTGTGTG CACGAACCCC CCGTTCAGCC CGACCGCTGC GCCTTATCCG GTAACTATCG 
^10101     ^10111     ^10121     ^10131     ^10141     ^10151     ^10161     ^10171     ^10181     ^10191     

TCTTGAGTCC AACCCGGTAA GACACGACTT ATCGCCACTG GCAGCAGCCA CTGGTAACAG GATTAGCAGA GCGAGGTATG TAGGCGGTGC TACAGAGTTC 
^10201     ^10211     ^10221     ^10231     ^10241     ^10251     ^10261     ^10271     ^10281     ^10291     

TTGAAGTGGT GGCCTAACTA CGGCTACACT AGAAGGACAG TATTTGGTAT CTGCGCTCTG CTGAAGCCAG TTACCTTCGG AAAAAGAGTT GGTAGCTCTT 
^10301     ^10311     ^10321     ^10331     ^10341     ^10351     ^10361     ^10371     ^10381     ^10391     

GATCCGGCAA ACAAACCACC GCTGGTAGCG GTGGTTTTTT TGTTTGCAAG CAGCAGATTA CGCGCAGAAA AAAAGGATCT CAAGAAGATC CTTTGATCTT 
^10401     ^10411     ^10421     ^10431     ^10441     ^10451     ^10461     ^10471     ^10481     ^10491     

TTCTACGGGG TCTGACGCTC AGTGGAACGA AAACTCACGT TAAGGGATTT TGGTCATGAG ATTATCAAAA AGGATCTTCA CCTAGATCCT TTTAAATTAA 
^10501     ^10511     ^10521     ^10531     ^10541     ^10551     ^10561     ^10571     ^10581     ^10591     

AAATGAAGTT TTAAATCAAT CTAAAGTATA TATGAGTAAA CTTGGTCTGA CAGTTACCAA TGCTTAATCA GTGAGGCACC TATCTCAGCG ATCTGTCTAT 
^10601     ^10611     ^10621     ^10631     ^10641     ^10651     ^10661     ^10671     ^10681     ^10691     

TTCGTTCATC CATAGTTGCC TGACTCCCCG TCGTGTAGAT AACTACGATA CGGGAGGGCT TACCATCTGG CCCCAGTGCT GCAATGATAC CGCGAGACCC 
^10701     ^10711     ^10721     ^10731     ^10741     ^10751     ^10761     ^10771     ^10781     ^10791     

ACGCTCACCG GCTCCAGATT TATCAGCAAT AAACCAGCCA GCCGGAAGGG CCGAGCGCAG AAGTGGTCCT GCAACTTTAT CCGCCTCCAT CCAGTCTATT 
^10801     ^10811     ^10821     ^10831     ^10841     ^10851     ^10861     ^10871     ^10881     ^10891     

AATTGTTGCC GGGAAGCTAG AGTAAGTAGT TCGCCAGTTA ATAGTTTGCG CAACGTTGTT GCCATTGCTG CAGGCATCGT GGTGTCACGC TCGTCGTTTG 
^10901     ^10911     ^10921     ^10931     ^10941     ^10951     ^10961     ^10971     ^10981     ^10991     

GTATGGCTTC ATTCAGCTCC GGTTCCCAAC GATCAAGGCG AGTTACATGA TCCCCCATGT TGTGCAAAAA AGCGGTTAGC TCCTTCGGTC CTCCGATCGT 
^11001     ^11011     ^11021     ^11031     ^11041     ^11051     ^11061     ^11071     ^11081     ^11091     

TGTCAGAAGT AAGTTGGCCG CAGTGTTATC ACTCATGGTT ATGGCAGCAC TGCATAATTC TCTTACTGTC ATGCCATCCG TAAGATGCTT TTCTGTGACT 
^11101     ^11111     ^11121     ^11131     ^11141     ^11151     ^11161     ^11171     ^11181     ^11191     

GGTGAGTACT CAACCAAGTC ATTCTGAGAA TAGTGTATGC GGCGACCGAG TTGCTCTTGC CCGGCGTCAA CACGGGATAA TACCGCGCCA CATAGCAGAA 
^11201     ^11211     ^11221     ^11231     ^11241     ^11251     ^11261     ^11271     ^11281     ^11291     

CTTTAAAAGT GCTCATCATT GGAAAACGTT CTTCGGGGCG AAAACTCTCA AGGATCTTAC CGCTGTTGAG ATCCAGTTCG ATGTAACCCA CTCGTGCACC 
^11301     ^11311     ^11321     ^11331     ^11341     ^11351     ^11361     ^11371     ^11381     ^11391     

CAACTGATCT TCAGCATCTT TTACTTTCAC CAGCGTTTCT GGGTGAGCAA AAACAGGAAG GCAAAATGCC GCAAAAAAGG GAATAAGGGC GACACGGAAA 
^11401     ^11411     ^11421     ^11431     ^11441     ^11451     ^11461     ^11471     ^11481     ^11491     

TGTTGAATAC TCATACTCTT CCTTTTTCAA TATTATTGAA GCATTTATCA GGGTTATTGT CTCATGAGCG GATACATATT TGAATGTATT TAGAAAAATA 
^11501     ^11511     ^11521     ^11531     ^11541     ^11551     ^11561     ^11571     ^11581     ^11591     

AACAAATAGG GGTTCCGCGC ACATTTCCCC GAAAAGTGCC ACCTGACGTC TAAGAAACCA TTATTATCAT GACATTAACC TATAAAAATA GGCGTATCAC 
^11601     ^11611     ^11621     ^11631     ^11641     ^11651     ^11661     ^11671     ^11681     ^11691     

GAGGCCCTTT CGTCTTCAAG AATTCCAT
^11701     ^11711     ^11721

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

The total number of notable open-reading frames (ORFs):

3

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:
gag

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

621-2237

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 polyprotein

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
yes

The alternative forms of this protein occur by the alternative initiation of translation:

no

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

621-5837

ORF

ORF position:

3

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

The abbreviated name of this ORF/gene:
GFP

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

7775-8494

Remarks:

Presence of alternative splice products was monitored functionally by evaluation of efficiency of the virus
to replicate, produce reverse-transcriptase which activity in the media was measured, and infectious virions.
In this case alternatively spliced monocistronic products were found by RT-PCR containing only the GFP ORF
intact. It is presumed that these messages contributed the most to the observed GFP activity.

The splice acceptor site located in the putative IRES region was (-267bp upstream of the cellular initiator
AUG codon): tataatttcttcttccagAA.

The 5'-splice donors were located:
  - in the non-coding region after U5 and well before gag CDS (788-GT-789 of this proviral plasmid, actually
    206-gt-207 of the putative non-spliced mRNA)
  - in env gene GTATGTCGGgtatggctg (6634-GT-6635 of this proviral plasmid, actually 6052-gt-6053 of the
    putative non-spliced mRNA)

The plasmid flatfile attached to this entry has the largest intron in lowercase letters although shorter
splice variants existed as well (also the cryptic 5'-splice donor within env gene was used). More details
in Figure 3 and Supplementary Information 12 of the article by Baranick et al. (2008). They report that the
sequence reported originally as Rbm3 IRES comes actually from Thoc1 mRNA (AY052560) and not from Rbm3 (Suppl.
Image 11).




From: C. Logg
Date: Mar 5 2009

The provirus sequence is almost all derived from a clone of Moloney MLV (NC_001501). We switched the ecotropic
env gene with the amphotropic env gene from MLV 4070A (M33469), so it's a hybrid of those two MLV strains. In
MoMLV, there is a stop codon at the end of gag, which is sometimes bypassed. In these cases, a gag-pol
polyprotein is produced, and this is how pol is translated. Pol doesn't have a separate start codon. I believe
all of the sequences are correct. We've sequenced the entire virus-derived portions of the original provirus
plasmids from which all of the other provirus plasmids were constructed. For each of these individual later
plasmids, we've at least verified the IRES/UTR/control-GFP insert sequence. I am assuming that no mutations
outside that region were acquired during the cloning. Each of the provirus plasmids has either a BsiWI or MluI
at the 5' side of the IRES (just after the env stop codon) and a NotI at the 3' side of GFP (just before the
MLV 3' UTR). These are the sites we used to transfer the IRES-GFP cassettes.


When the acceptor site was destroyed by mutation the activity of the reverse transcriptase produced into the
cultivation media by the virus was rescued as expected (mutant 2 in Supplementary Figure 10). However, the
mutations in mutants 1 and 3 in regions elsewhere should have not rescued the viral production but did quite
well in case of mutant 3. Thus, the results are a bit puzzling. Maybe due to additional mutations outside
the region sequenced?

However, the GFP results based on these mutants shown in Figure 4 reflect as stated by the authors that the
type I splicing case (shown in black in Figure 4A) is proportional to the GFP values shown in Figure 4B.

Citations:

Baranick B. T., Lemp N. A., Nagashima J., Hiraoka K., Kasahara N., Logg C. R. (2008) Splicing mediates the activity of four putative cellular internal ribosome entry sites. Proc. Natl. Acad. Sci. U. S. A. 105(12):4733-4738

IRESs:

IRES:

Version: `2`	Last change: `2009-03-16 16:37:38`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `Rbm3_22nt_module`	The functional status of IRES: `functional`

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

7747-7768

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `1910`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `1931`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-28`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-7`

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

tttataattt cttcttccag AA
^7747      ^7757      ^7767

Remarks:

Baranick et al. postulate that the "IRES" activity observed so far was due to the splice artifacts.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 609

Version: `1`	Last change: `2009-07-16 15:13:35`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HeLa (ATCC CCL-2)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

302.000

Name of IRES used as the positive control:

EMCV-R_-541_-7

Name of the plasmid used as the positive control. `MoMLV-provirus-EMCV-GFP`	Name of the plasmid used as the negative control. `MoMLV-provirus-GFP`
`IRESite Id` of the plasmid used as positive control. `550`	`IRESite Id` of the plasmid used as negative control. `549`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `9.000`
The size (length) of intercistronic region in the positive control: `2458`	The size (length) of intercistronic region in the negative control: `1914`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

Data from Figure 2B.

Citations:

Translation results:

IRESite Translation Id: 610

Version: `1`	Last change: `2009-07-16 15:13:35`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens PC-3 (ATCC CRL 1435)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

394.000

Name of IRES used as the positive control:

EMCV-R_-541_-7

Name of the plasmid used as the positive control. `MoMLV-provirus-EMCV-GFP`	Name of the plasmid used as the negative control. `MoMLV-provirus-GFP`
`IRESite Id` of the plasmid used as positive control. `550`	`IRESite Id` of the plasmid used as negative control. `549`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `9.000`
The size (length) of intercistronic region in the positive control: `2458`	The size (length) of intercistronic region in the negative control: `1914`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

Data from Figure 2B.

Citations:

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