IRESite_Id:379 characteristics of EMCV-R_260-845 IRES studied in pLXRN plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `379`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-06-12 03:58:17`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_without_translational_characterization

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

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
13621323

The mRNA/+RNA description:

Putative in vivo transcript of cloning vector pLXRN from Mo-MuLV down to the end of R in right LTR.

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

agttctgaac acccggccgc aaccctggga gacgtcccag ggactttggg ggccgttttt gtggcccgac ctgaggaagg gagtcgatgt ggaatccgac 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

cccgtcagga tatgtggttc tggtaggaga cgagaaccta aaacagttcc cgcctccgtc tgaatttttg ctttcggttt ggaaccgaag ccgcgcgtct 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

tgtctgctgc agcgctgcag catcgttctg tgttgtctct gtctgactgt gtttctgtat ttgtctgaaa attagggcca gactgttacc actcccttaa 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gtttgacctt aggtcactgg aaagatgtcg agcggatcgc tcacaaccag tcggtagatg tcaagaagag acgttgggtt accttctgct ctgcagaatg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

gccaaccttt aacgtcggat ggccgcgaga cggcaccttt aaccgagacc tcatcaccca ggttaagatc aaggtctttt cacctggccc gcatggacac 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ccagaccagg tcccctacat cgtgacctgg gaagccttgg cttttgaccc ccctccctgg gtcaagccct ttgtacaccc taagcctccg cctcctcttc 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ctccatccgc cccgtctctc ccccttgaac ctcctcgttc gaccccgcct cgatcctccc tttatccagc cctcactcct tctctaggcg ccggaattcg 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ttaactcgag gatccgcccc tctccctccc ccccccctaa cgttactggc cgaagccgct tggaataagg ccggtgtgtg tttgtctata tgtgattttc 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

caccatattg ccgtcttttg gcaatgtgag ggcccggaaa cctggccctg tcttcttgac gagcattcct aggggtcttt cccctctcgc caaaggaatg 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

caaggtctgt tgaatgtcgt gaaggaagca gttcctctgg aagcttcttg aagacaaaca acgtctgtag cgaccctttg caggcagcgg aaccccccac 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ctggcgacag gtgcctctgc ggccaaaagc cacgtgtata agatacacct gcaaaggcgg cacaacccca gtgccacgtt gtgagttgga tagttgtgga 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

aagagtcaaa tggctctcct caagcgtagt caacaagggg ctgaaggatg cccagaaggt accccattgt atgggaatct gatctggggc ctcggtgcac 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

atgctttaca tgtgtttagt cgaggttaaa aaagctctag gccccccgaa ccacggggac gtggttttcc tttgaaaaac acgatgataa gcttgccaca 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

accccgggat aattcctgca gccaatatgg gatcggccat tgaacaagat ggattgcacg caggttctcc ggccgcttgg gtggagaggc tattcggcta 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

tgactgggca caacagacaa tcggctgctc tgatgccgcc gtgttccggc tgtcagcgca ggggcgcccg gttctttttg tcaagaccga cctgtccggt 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

gccctgaatg aactgcagga cgaggcagcg cggctatcgt ggctggccac gacgggcgtt ccttgcgcag ctgtgctcga cgttgtcact gaagcgggaa 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

gggactggct gctattgggc gaagtgccgg ggcaggatct cctgtcatct caccttgctc ctgccgagaa agtatccatc atggctgatg caatgcggcg 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

gctgcatacg cttgatccgg ctacctgccc attcgaccac caagcgaaac atcgcatcga gcgagcacgt actcggatgg aagccggtct tgtcgatcag 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

gatgatctgg acgaagagca tcaggggctc gcgccagccg aactgttcgc caggctcaag gcgcgcatgc ccgacggcga ggatctcgtc gtgacccatg 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

gcgatgcctg cttgccgaat atcatggtgg aaaatggccg cttttctgga ttcatcgact gtggccggct gggtgtggcg gaccgctatc aggacatagc 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

gttggctacc cgtgatattg ctgaagagct tggcggcgaa tgggctgacc gcttcctcgt gctttacggt atcgccgctc ccgattcgca gcgcatcgcc 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ttctatcgcc ttcttgacga gttcttctga gcgggactct ggggttcgat aaaataaaag attttattta gtctccagaa aaagggggga atgaaagacc 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ccacctgtag gtttggcaag ctagcttaag taacgccatt ttgcaaggca tggaaaaata cataactgag aatagagaag ttcagatcaa ggtcaggaac 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

agatggaaca gctgaatatg ggccaaacag gatatctgtg gtaagcagtt cctgccccgg ctcagggcca agaacagatg gaacagctga atatgggcca 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

aacaggatat ctgtggtaag cagttcctgc cccggctcag ggccaagaac agatggtccc cagatgcggt ccagccctca gcagtttcta gagaaccatc 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

agatgtttcc agggtgcccc aaggacctga aatgaccctg tgccttattt gaactaacca atcagttcgc ttctcgcttc tgttcgcgcg cttctgctcc 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ccgagctcaa taaaagagcc cacaacccct cactcggggc gccagtcctc cgattgactg agtcgcccgg gtacccgtgt atccaataaa ccctcttgca 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

gttgca
^2701

Credibility of mRNA sequence:

reverse_engineered_fragment_and_the_rest_is_a_guess

The name of the plasmid:
pLXRN The name of the promoter used to express this mRNA:
Mo-MuLV_LTR

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

not tested

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

not tested

A promoter reported in cDNA corresponding to IRES sequence:

not tested

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

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Encephalomyocarditis virus Rueckert

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

gaattgctag caattgctag caattgctag caattcatac cagatcaccg aaaactgtcc tccaaatgtg tccccctcac actcccaaat tcgcgggctt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ctgcctctta gaccactcta ccctattccc cacactcacc ggagccaaag ccgcggccct tccgtttctt tgcttttgaa agaccccacc cgtaggtggc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

aagctagctt aagtaacgcc actttgcaag gcatggaaaa atacataact gagaatagaa aagttcagat caaggtcagg aacaaagaaa cagctgaata 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ccaaacagga tatctgtggt aagcggttcc tgccccggct cagggccaag aacagatgag acagctgagt gatgggccaa acaggatatc tgtggtaagc 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

agttcctgcc ccggctcggg gccaagaaca gatggtcccc agatgcggtc cagccctcag cagtttctag tgaatcatca gatgtttcca gggtgcccca 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

aggacctgaa aatgaccctg taccttattt gaactaacca atcagttcgc ttctcgcttc tgttcgcgcg cttccgctct ccgagctcaa taaaagagcc 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

cacaacccct cactcggcgc gccagtcttc cgatagactg cgtcgcccgg gtacccgtat tcccaataaa gcctcttgct gtttgcatcc gaatcgtggt 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ctcgctgttc cttgggaggg tctcctctga gtgattgact acccacgacg ggggtctttc atttgggggc tcgtccggga tttggagacc cctgcccagg 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gaccaccgac ccaccaccgg gaggtaagct ggccagcaac ttatctgtgt ctgtccgatt gtctagtgtc tatgtttgat gttatgcgcc tgcgtctgta 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ctagttagct aactagctct gtatctggcg gacccgtggt ggaactgacg agttctgaac acccggccgc aaccctggga gacgtcccag ggactttggg 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ggccgttttt gtggcccgac ctgaggaagg gagtcgatgt ggaatccgac cccgtcagga tatgtggttc tggtaggaga cgagaaccta aaacagttcc 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

cgcctccgtc tgaatttttg ctttcggttt ggaaccgaag ccgcgcgtct tgtctgctgc agcgctgcag catcgttctg tgttgtctct gtctgactgt 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

gtttctgtat ttgtctgaaa attagggcca gactgttacc actcccttaa gtttgacctt aggtcactgg aaagatgtcg agcggatcgc tcacaaccag 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

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

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

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

cgatcctccc tttatccagc cctcactcct tctctaggcg ccggaattcg ttaactcgag gatccgcccc tctccctccc ccccccctaa cgttactggc 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

cgaagccgct tggaataagg ccggtgtgtg tttgtctata tgtgattttc caccatattg ccgtcttttg gcaatgtgag ggcccggaaa cctggccctg 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

tcttcttgac gagcattcct aggggtcttt cccctctcgc caaaggaatg caaggtctgt tgaatgtcgt gaaggaagca gttcctctgg aagcttcttg 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

aagacaaaca acgtctgtag cgaccctttg caggcagcgg aaccccccac ctggcgacag gtgcctctgc ggccaaaagc cacgtgtata agatacacct 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

gcaaaggcgg cacaacccca gtgccacgtt gtgagttgga tagttgtgga aagagtcaaa tggctctcct caagcgtagt caacaagggg ctgaaggatg 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

cccagaaggt accccattgt atgggaatct gatctggggc ctcggtgcac atgctttaca tgtgtttagt cgaggttaaa aaagctctag gccccccgaa 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ccacggggac gtggttttcc tttgaaaaac acgatgataa gcttgccaca accccgggat aattcctgca gccaatatgg gatcggccat tgaacaagat 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ggattgcacg caggttctcc ggccgcttgg gtggagaggc tattcggcta tgactgggca caacagacaa tcggctgctc tgatgccgcc gtgttccggc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

tgtcagcgca ggggcgcccg gttctttttg tcaagaccga cctgtccggt gccctgaatg aactgcagga cgaggcagcg cggctatcgt ggctggccac 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

gacgggcgtt ccttgcgcag ctgtgctcga cgttgtcact gaagcgggaa gggactggct gctattgggc gaagtgccgg ggcaggatct cctgtcatct 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

caccttgctc ctgccgagaa agtatccatc atggctgatg caatgcggcg gctgcatacg cttgatccgg ctacctgccc attcgaccac caagcgaaac 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

atcgcatcga gcgagcacgt actcggatgg aagccggtct tgtcgatcag gatgatctgg acgaagagca tcaggggctc gcgccagccg aactgttcgc 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

caggctcaag gcgcgcatgc ccgacggcga ggatctcgtc gtgacccatg gcgatgcctg cttgccgaat atcatggtgg aaaatggccg cttttctgga 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ttcatcgact gtggccggct gggtgtggcg gaccgctatc aggacatagc gttggctacc cgtgatattg ctgaagagct tggcggcgaa tgggctgacc 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

gcttcctcgt gctttacggt atcgccgctc ccgattcgca gcgcatcgcc ttctatcgcc ttcttgacga gttcttctga gcgggactct ggggttcgat 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

aaaataaaag attttattta gtctccagaa aaagggggga atgaaagacc ccacctgtag gtttggcaag ctagcttaag taacgccatt ttgcaaggca 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

tggaaaaata cataactgag aatagagaag ttcagatcaa ggtcaggaac agatggaaca gctgaatatg ggccaaacag gatatctgtg gtaagcagtt 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

cctgccccgg ctcagggcca agaacagatg gaacagctga atatgggcca aacaggatat ctgtggtaag cagttcctgc cccggctcag ggccaagaac 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

agatggtccc cagatgcggt ccagccctca gcagtttcta gagaaccatc agatgtttcc agggtgcccc aaggacctga aatgaccctg tgccttattt 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

gaactaacca atcagttcgc ttctcgcttc tgttcgcgcg cttctgctcc ccgagctcaa taaaagagcc cacaacccct cactcggggc gccagtcctc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

cgattgactg agtcgcccgg gtacccgtgt atccaataaa ccctcttgca gttgcatccg acttgtggtc tcgctgttcc ttgggagggt ctcctctgag 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

tgattgacta cccgtcagcg ggggtctttc atttgggggc tcgtccggga tcgggagacc cctgcccagg gaccaccgac ccaccaccgg gaggtaagct 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ggctgcctcg cgcgtttcgg tgatgacggt gaaaacctct gacacatgca gctcccggag acggtcacag cttgtctgta agcggatgcc gggagcagac 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

aagcccgtca gggcgcgtca gcgggtgttg gcgggtgtcg gggcgcagcc atgacccagt cacgtagcga tagcggagtg tatactggct taactatgcg 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

gcatcagagc agattgtact gagagtgcac catatgcggt gtgaaatacc gcacagatgc gtaaggagaa aataccgcat caggcgctct tccgcttcct 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

cgctcactga ctcgctgcgc tcggtcgttc ggctgcggcg agcggtatca gctcactcaa aggcggtaat acggttatcc acagaatcag gggataacgc 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

aggaaagaac atgtgagcaa aaggccagca aaaggccagg aaccgtaaaa aggccgcgtt gctggcgttt ttccataggc tccgcccccc tgacgagcat 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgtagg tatctcagtt cggtgtaggt 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

gacttatcgc cactggcagc agccactggt aacaggatta gcagagcgag gtatgtaggc ggtgctacag agttcttgaa gtggtggcct aactacggct 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

acactagaag gacagtattt ggtatctgcg ctctgctgaa gccagttacc ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga agatcctttg atcttttcta cggggtctga cgctcagtgg 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

aacgaaaact cacgttaagg gattttggtc atgagattat caaaaaggat cttcacctag atccttttaa attaaaaatg aagttttaaa tcaatctaaa 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

gtatatatga gtaaacttgg tctgacagtt accaatgctt aatcagtgag gcacctatct cagcgatctg tctatttcgt tcatccatag ttgcctgact 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ccccgtcgtg tagataacta cgatacggga gggcttacca tctggcccca gtgctgcaat gataccgcga gacccacgct caccggctcc agatttatca 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

gcaataaacc agccagccgg aagggccgag cgcagaagtg gtcctgcaac tttatccgcc tccatccagt ctattaattg ttgccgggaa gctagagtaa 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

gtagttcgcc agttaatagt ttgcgcaacg ttgttgccat tgctgcaggc atcgtggtgt cacgctcgtc gtttggtatg gcttcattca gctccggttc 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ccaacgatca aggcgagtta catgatcccc catgttgtgc aaaaaagcgg ttagctcctt cggtcctccg atcgttgtca gaagtaagtt ggccgcagtg 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ttatcactca tggttatggc agcactgcat aattctctta ctgtcatgcc atccgtaaga tgcttttctg tgactggtga gtactcaacc aagtcattct 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

gagaatagtg tatgcggcga ccgagttgct cttgcccggc gtcaacacgg gataataccg cgccacatag cagaacttta aaagtgctca tcattggaaa 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

acgttcttcg gggcgaaaac tctcaaggat cttaccgctg ttgagatcca gttcgatgta acccactcgt gcacccaact gatcttcagc atcttttact 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa atgccgcaaa aaagggaata agggcgacac ggaaatgttg aatactcata ctcttccttt 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ttcaatatta ttgaagcatt tatcagggtt attgtctcat gagcggatac atatttgaat gtatttagaa aaataaacaa ataggggttc cgcgcacatt 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

tccccgaaaa gtgccacctg acgtctaaga aaccattatt atcatgacat taacctataa aaataggcgt atcacgaggc cctttcgtct tcaa
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091

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

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

1

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:
aph

The description of the protein encoded in this ORF:
aminoglycoside-3'-O-phosphotransferase

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):

1327-2130

Citations:

Miller A. D., Rosman G. J. (1989) Improved retroviral vectors for gene transfer and expression. Biotechniques. 7(9):980-2, 984-6, 989-90

IRESs:

IRES:

Version: `1`	Last change: `2011-04-08 22:26:36`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `EMCV-R_260-845`	The functional status of IRES: `functional`

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

717-1303

How IRES boundaries were determined:
experimentally_determined

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

cccctctccc tccccccccc ctaacgttac tggccgaagc cgcttggaat aaggccggtg tgtgtttgtc tatatgtgat tttccaccat attgccgtct 
^717       ^727       ^737       ^747       ^757       ^767       ^777       ^787       ^797       ^807       

tttggcaatg tgagggcccg gaaacctggc cctgtcttct tgacgagcat tcctaggggt ctttcccctc tcgccaaagg aatgcaaggt ctgttgaatg 
^817       ^827       ^837       ^847       ^857       ^867       ^877       ^887       ^897       ^907       

tcgtgaagga agcagttcct ctggaagctt cttgaagaca aacaacgtct gtagcgaccc tttgcaggca gcggaacccc ccacctggcg acaggtgcct 
^917       ^927       ^937       ^947       ^957       ^967       ^977       ^987       ^997       ^1007      

ctgcggccaa aagccacgtg tataagatac acctgcaaag gcggcacaac cccagtgcca cgttgtgagt tggatagttg tggaaagagt caaatggctc 
^1017      ^1027      ^1037      ^1047      ^1057      ^1067      ^1077      ^1087      ^1097      ^1107      

tcctcaagcg tagtcaacaa ggggctgaag gatgcccaga aggtacccca ttgtatggga atctgatctg gggcctcggt gcacatgctt tacatgtgtt 
^1117      ^1127      ^1137      ^1147      ^1157      ^1167      ^1177      ^1187      ^1197      ^1207      

tagtcgaggt taaaaaagct ctaggccccc cgaaccacgg ggacgtggtt ttcctttgaa aaacacgatg ataagcttgc cacaacc
^1217      ^1227      ^1237      ^1247      ^1257      ^1267      ^1277      ^1287      ^1297

Remarks:

There are several differences compared to the reference EMCV-R IRES region sequence:

>IRESite_Id:140 EMCV-R virus
          Length = 7835

 Score =  975 bits (558), Expect = 0.0
 Identities = 580/590 (98%), Gaps = 7/590 (1%)
 Strand = Plus / Plus


Query: 1   cccctctccctcccccccccctaacgttactggccgaagccgcttggaataaggccggtg 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 260 cccctctccctcccccccccctaacgttactggccgaagccgcttggaataaggccggtg 319


Query: 61  tgtgtttgtctatatgtgattttccaccatattgccgtcttttggcaatgtgagggcccg 120
           || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 320 tgcgtttgtctatatgttattttccaccatattgccgtcttttggcaatgtgagggcccg 379


Query: 121 gaaacctggccctgtcttcttgacgagcattcctaggggtctttcccctctcgccaaagg 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 380 gaaacctggccctgtcttcttgacgagcattcctaggggtctttcccctctcgccaaagg 439


Query: 181 aatgcaaggtctgttgaatgtcgtgaaggaagcagttcctctggaagcttcttgaagaca 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 440 aatgcaaggtctgttgaatgtcgtgaaggaagcagttcctctggaagcttcttgaagaca 499


Query: 241 aacaacgtctgtagcgaccctttgcaggcagcggaaccccccacctggcgacaggtgcct 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 500 aacaacgtctgtagcgaccctttgcaggcagcggaaccccccacctggcgacaggtgcct 559


Query: 301 ctgcggccaaaagccacgtgtataagatacacctgcaaaggcggcacaaccccagtgcca 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 560 ctgcggccaaaagccacgtgtataagatacacctgcaaaggcggcacaaccccagtgcca 619


Query: 361 cgttgtgagttggatagttgtggaaagagtcaaatggctctcctcaagcgtagtcaacaa 420
           |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Sbjct: 620 cgttgtgagttggatagttgtggaaagagtcaaatggctctcctcaagcgtattcaacaa 679


Query: 421 ggggctgaaggatgcccagaaggtaccccattgtatgggaatctgatctggggcctcggt 480
           ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
Sbjct: 680 ggggctgaaggatgcccagaaggtaccccattgtatggg-atctgatctggggcctcggt 738


Query: 481 gcacatgctttacatgtgtttagtcgaggttaaaaaa-gctctaggccccccgaaccacg 539
           ||||||||||||||||||||||||||||||||||||| | ||||||||||||||||||||
Sbjct: 739 gcacatgctttacatgtgtttagtcgaggttaaaaaacg-tctaggccccccgaaccacg 797


Query: 540 gggacgtggttttcctttgaaaaacacgatgataagct-t-gccacaacc 587
           |||||||||||||||||||||||||||||||||||  | | |||||||||
Sbjct: 798 gggacgtggttttcctttgaaaaacacgatgataa--tatggccacaacc 845

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