IRESite_Id:382 characteristics of EMCV-R_260-845 IRES studied in pNBioSec plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `382`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-06-12 15:25:07`

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:
our_best_guess

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
158534336

The mRNA/+RNA description:

One of the two putative in vivo transcripts of mammalian expression vector pNBioSec: this one is from minimal
CMV promoter down to beta-globin poly(A) signal from rabbit.

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

tcagatcgcc tggagacgcc atccacgctg ttttgacctc catagaagac accgggaccg atccagcctc cgcggccccg aattcgagct cggtacccgg 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ggatctgccg ccaccatgcc gtcttctgtc tcgtggggca tcctcctgct ggcaggcctg tgctgcctgg tccctgtctc cctggctgag cgtggatctt 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

tgaacgacat ttttgaagcg caaaaaattg aatggcatgg atccgatatc gcggccgctt gaacgacatt tttgaagcgc aaaaaattga atggcattaa 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ggccgcgcta gcctcgagaa ttcacgcgtc gagcatgcat ctagggcggc caattccgcc cctctccctc ccccccccct aacgttactg gccgaagccg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

cttggaataa ggccggtgtg cgtttgtcta tatgtgattt tccaccatat tgccgtcttt tggcaatgtg agggcccgga aacctggccc tgtcttcttg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

acgagcattc ctaggggtct ttcccctctc gccaaaggaa tgcaaggtct gttgaatgtc gtgaaggaag cagttcctct ggaagcttct tgaagacaaa 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

caacgtctgt agcgaccctt tgcaggcagc ggaacccccc acctggcgac aggtgcctct gcggccaaaa gccacgtgta taagatacac ctgcaaaggc 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ggcacaaccc cagtgccacg ttgtgagttg gatagttgtg gaaagagtca aatggctctc ctcaagcgta ttcaacaagg ggctgaagga tgcccagaag 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gtaccccatt gtatgggatc tgatctgggg cctcggtgca catgctttac atgtgtttag tcgaggttaa aaaaacgtct aggccccccg aaccacgggg 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

acgtggtttt cctttgaaaa acacgatgat aagcttgcca caacccaaac ttaaggccgc caccatggac agcaaaggtt cgtcgcagaa agggtcccgc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ctgctcctgc tgctggtggt gtcaaatcta ctcttgtgcc agggtgtggt ctccgattat aaggatgatg atgataagct taagatgaag gataacaccg 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

tgccactgaa attgattgcc ctgttagcga acggtgaatt tcactctggc gagcagttgg gtgaaacgct gggaatgagc cgggcggcta ttaataaaca 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

cattcagaca ctgcgtgact ggggcgttga tgtctttacc gttccgggta aaggatacag cctgcctgag cctatccagt tacttaatgc taaacagata 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ttgggtcagc tggatggcgg tagtgtagcc gtgctgccag tgattgactc cacgaatcag taccttcttg atcgtatcgg agagcttaaa tcgggcgatg 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

cttgcattgc agaataccag caggctggcc gtggtcgccg gggtcggaaa tggttttcgc cttttggcgc aaacttatat ttgtcgatgt tctggcgtct 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ggaacaaggc ccggcggcgg cgattggttt aagtctggtt atcggtatcg tgatggcgga agtattacgc aagctgggtg cagataaagt tcgtgttaaa 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

tggcctaatg acctctatct gcaggatcgc aagctggcag gcattctggt ggagctgact ggcaaaactg gcgatgcggc gcaaatagtc attggagccg 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ggatcaacat ggcaatgcgc cgtgttgaag agagtgtcgt taatcagggg tggatcacgc tgcaggaagc ggggatcaat ctcgatcgta atacgttggc 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ggccatgcta atacgtgaat tacgtgctgc gttggaactc ttcgaacaag aaggattggc accttatctg tcgcgctggg aaaagctgga taattttatt 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

aatcgcccag tgaaacttat cattggtgat aaagaaatat ttggcatttc acgcggaata gacaaacagg gggctttatt acttgagcag gatggaataa 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

taaaaccctg gatgggcggt gaaatatccc tgcgtagtgc agaaaaataa gaattcagat ctctgcagct cgagtctaga gggcccgttt atctctagag 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ctgagaactt cagggtgagt ttggggaccc ttgattgttc tttctttttc gctattgtaa aattcatgtt atatggaggg ggcaaagttt tcagggtgtt 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

gtttagaatg ggaagatgtc ccttgtatca ccatggaccc tcatgataat tttgtttctt tcactttcta ctctgttgac aaccattgtc tcctcttatt 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ttcttttcat tttctgtaac ttttttcgtt aaactttagc ttgcatttgt aacgaatttt taaattcact ttcgtttatt tgtcagattg taagtacttt 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ctctaatcac ttttttttca aggcaatcag ggtaattata ttgtacttca gcacagtttt agagaacaat tgttataatt aaatgataag gtagaatatt 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

tctgcatata aattctggct ggcgtggaaa tattcttatt ggtagaaaca actacatcct ggtaatcatc ctgcctttct ctttatggtt acaatgatat 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

acactgtttg agatgaggat aaaatactct gagtccaaac cgggcccctc tgctaaccat gttcatgcct tcttcttttt cctacagctc ctgggcaacg 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

tgctggttgt tgtgctgtct catcattttg gcaaagaatt cactcctcag gtgcaggctg cctatcagaa ggtggtggct ggtgtggcca atgccctggc 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

tcacaaatac cactgagatc tttttccctc tgccaaaaat tatggggaca tcatgaagcc ccttgagcat ctgacttctg ggtaataaag gaaatttatt 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ttcattgc
^2901

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pNBioSec The name of the promoter used to express this mRNA:
CMV

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:

ctcgagttta ccactcccta tcagtgatag agaaaagtga aagtcgagtt taccactccc tatcagtgat agagaaaagt gaaagtcgag tttaccactc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

cctatcagtg atagagaaaa gtgaaagtcg agtttaccac tccctatcag tgatagagaa aagtgaaagt cgagtttacc actccctatc agtgatagag 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

aaaagtgaaa gtcgagttta ccactcccta tcagtgatag agaaaagtga aagtcgagtt taccactccc tatcagtgat agagaaaagt gaaagtcgag 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ctcggtaccc gggtcgaggt aggcgtgtac ggtgggaggc ctatataagc agagctcgtt tagtgaaccg tcagatcgcc tggagacgcc atccacgctg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ttttgacctc catagaagac accgggaccg atccagcctc cgcggccccg aattcgagct cggtacccgg ggatctgccg ccaccatgcc gtcttctgtc 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

tcgtggggca tcctcctgct ggcaggcctg tgctgcctgg tccctgtctc cctggctgag cgtggatctt tgaacgacat ttttgaagcg caaaaaattg 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

aatggcatgg atccgatatc gcggccgctt gaacgacatt tttgaagcgc aaaaaattga atggcattaa ggccgcgcta gcctcgagaa ttcacgcgtc 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

gagcatgcat ctagggcggc caattccgcc cctctccctc ccccccccct aacgttactg gccgaagccg cttggaataa ggccggtgtg cgtttgtcta 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

tatgtgattt tccaccatat tgccgtcttt tggcaatgtg agggcccgga aacctggccc tgtcttcttg acgagcattc ctaggggtct ttcccctctc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

gccaaaggaa tgcaaggtct gttgaatgtc gtgaaggaag cagttcctct ggaagcttct tgaagacaaa caacgtctgt agcgaccctt tgcaggcagc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ggaacccccc acctggcgac aggtgcctct gcggccaaaa gccacgtgta taagatacac ctgcaaaggc ggcacaaccc cagtgccacg ttgtgagttg 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

gatagttgtg gaaagagtca aatggctctc ctcaagcgta ttcaacaagg ggctgaagga tgcccagaag gtaccccatt gtatgggatc tgatctgggg 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

cctcggtgca catgctttac atgtgtttag tcgaggttaa aaaaacgtct aggccccccg aaccacgggg acgtggtttt cctttgaaaa acacgatgat 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

aagcttgcca caacccaaac ttaaggccgc caccatggac agcaaaggtt cgtcgcagaa agggtcccgc ctgctcctgc tgctggtggt gtcaaatcta 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ctcttgtgcc agggtgtggt ctccgattat aaggatgatg atgataagct taagatgaag gataacaccg tgccactgaa attgattgcc ctgttagcga 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

acggtgaatt tcactctggc gagcagttgg gtgaaacgct gggaatgagc cgggcggcta ttaataaaca cattcagaca ctgcgtgact ggggcgttga 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

tgtctttacc gttccgggta aaggatacag cctgcctgag cctatccagt tacttaatgc taaacagata ttgggtcagc tggatggcgg tagtgtagcc 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

gtgctgccag tgattgactc cacgaatcag taccttcttg atcgtatcgg agagcttaaa tcgggcgatg cttgcattgc agaataccag caggctggcc 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

gtggtcgccg gggtcggaaa tggttttcgc cttttggcgc aaacttatat ttgtcgatgt tctggcgtct ggaacaaggc ccggcggcgg cgattggttt 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

aagtctggtt atcggtatcg tgatggcgga agtattacgc aagctgggtg cagataaagt tcgtgttaaa tggcctaatg acctctatct gcaggatcgc 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

aagctggcag gcattctggt ggagctgact ggcaaaactg gcgatgcggc gcaaatagtc attggagccg ggatcaacat ggcaatgcgc cgtgttgaag 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

agagtgtcgt taatcagggg tggatcacgc tgcaggaagc ggggatcaat ctcgatcgta atacgttggc ggccatgcta atacgtgaat tacgtgctgc 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

gttggaactc ttcgaacaag aaggattggc accttatctg tcgcgctggg aaaagctgga taattttatt aatcgcccag tgaaacttat cattggtgat 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

aaagaaatat ttggcatttc acgcggaata gacaaacagg gggctttatt acttgagcag gatggaataa taaaaccctg gatgggcggt gaaatatccc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

tgcgtagtgc agaaaaataa gaattcagat ctctgcagct cgagtctaga gggcccgttt atctctagag ctgagaactt cagggtgagt ttggggaccc 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ttgattgttc tttctttttc gctattgtaa aattcatgtt atatggaggg ggcaaagttt tcagggtgtt gtttagaatg ggaagatgtc ccttgtatca 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ccatggaccc tcatgataat tttgtttctt tcactttcta ctctgttgac aaccattgtc tcctcttatt ttcttttcat tttctgtaac ttttttcgtt 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

aaactttagc ttgcatttgt aacgaatttt taaattcact ttcgtttatt tgtcagattg taagtacttt ctctaatcac ttttttttca aggcaatcag 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ggtaattata ttgtacttca gcacagtttt agagaacaat tgttataatt aaatgataag gtagaatatt tctgcatata aattctggct ggcgtggaaa 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tattcttatt ggtagaaaca actacatcct ggtaatcatc ctgcctttct ctttatggtt acaatgatat acactgtttg agatgaggat aaaatactct 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

gagtccaaac cgggcccctc tgctaaccat gttcatgcct tcttcttttt cctacagctc ctgggcaacg tgctggttgt tgtgctgtct catcattttg 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

gcaaagaatt cactcctcag gtgcaggctg cctatcagaa ggtggtggct ggtgtggcca atgccctggc tcacaaatac cactgagatc tttttccctc 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

tgccaaaaat tatggggaca tcatgaagcc ccttgagcat ctgacttctg ggtaataaag gaaatttatt ttcattgcaa tagtgtgtgg gaattttttg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

tgtctctcac tcggaaggac atatgggagg gcaaatcatt taaaacatca gaatgagtat ttggtttaga gtttggcaac atatgccata tgctggctgc 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

catgaacaaa ggtggctata aagaggtcat cagtatatga aacagccccc tgctgtccat tccttattcc atagaaaagc cttgacttga ggttagattt 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

tttttatatt ttgttttgtg ttattttttt ctttaacatc cctaaaattt tccttacatg ttttactagc cagatttttc ctcctctcct gactactccc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

agtcatagct gtccctcttc tcttatgaac tcgactgcat taatgaatcg gccaacgcgc ggggagaggc ggtttgcgta ttgggcgctc ttccgcttcc 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

tcgctcactg actcgctgcg ctcggtcgtt cggctgcggc gagcggtatc agctcactca aaggcggtaa tacggttatc cacagaatca ggggataacg 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

caggaaagaa catgtgagca aaaggccagc aaaaggccag gaaccgtaaa aaggccgcgt tgctggcgtt tttccatagg ctccgccccc ctgacgagca 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcaatgct cacgctgtag gtatctcagt tcggtgtagg 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc cggtaagaca 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

cgacttatcg ccactggcag cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga agtggtggcc taactacggc 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

tacactagaa ggacagtatt tggtatctgc gctctgctga agccagttac cttcggaaaa agagttggta gctcttgatc cggcaaacaa accaccgctg 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

gtagcggtgg tttttttgtt tgcaagcagc agattacgcg cagaaaaaaa ggatctcaag aagatccttt gatcttttct acggggtctg acgctcagtg 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

gaacgaaaac tcacgttaag ggattttggt catgagatta tcaaaaagga tcttcaccta gatcctttta aattaaaaat gaagttttaa atcaatctaa 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

agtatatatg agtaaacttg gtctgacagt taccaatgct taatcagtga ggcacctatc tcagcgatct gtctatttcg ttcatccata gttgcctgac 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

tccccgtcgt gtagataact acgatacggg agggcttacc atctggcccc agtgctgcaa tgataccgcg agacccacgc tcaccggctc cagatttatc 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

agcaataaac cagccagccg gaagggccga gcgcagaagt ggtcctgcaa ctttatccgc ctccatccag tctattaatt gttgccggga agctagagta 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

agtagttcgc cagttaatag tttgcgcaac gttgttgcca ttgctacagg catcgtggtg tcacgctcgt cgtttggtat ggcttcattc agctccggtt 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

cccaacgatc aaggcgagtt acatgatccc ccatgttgtg caaaaaagcg gttagctcct tcggtcctcc gatcgttgtc agaagtaagt tggccgcagt 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

gttatcactc atggttatgg cagcactgca taattctctt actgtcatgc catccgtaag atgcttttct gtgactggtg agtactcaac caagtcattc 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

tgagaatagt gtatgcggcg accgagttgc tcttgcccgg cgtcaatacg ggataatacc gcgccacata gcagaacttt aaaagtgctc atcattggaa 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

aacgttcttc ggggcgaaaa ctctcaagga tcttaccgct gttgagatcc agttcgatgt aacccactcg tgcacccaac tgatcttcag catcttttac 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

tttcaccagc gtttctgggt gagcaaaaac aggaaggcaa aatgccgcaa aaaagggaat aagggcgaca cggaaatgtt gaatactcat actcttcctt 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

tttcaatatt attgaagcat ttatcagggt tattgtctca tgagcggata catatttgaa tgtatttaga aaaataaaca aataggggtt ccgcgcacat 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ttccccgaaa agtgccacct gacgtctaag aaaccattat tatcatgaca ttaacctata aaaataggcg tatcacgagg ccctttcgtc ttcactcgag 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

tgtgtcagtt agggtgtgga aagtccccag gctccccagc aggcagaagt atgcaaagca tgcatctcaa ttagtcagca accaggtgtg gaaagtcccc 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

aggctcccca gcaggcagaa gtatgcaaag catgcatctc aattagtcag caaccatagt cccgccccta actccgccca tcccgcccct aactccgccc 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

agttccgccc attctccgcc ccatggctga CTAATTTTTT TTATTTATGC AGAGGCCGAG GCCGCCTCGG CCTCTGAGCT ATTCCAGAAG TAGTGAGGAG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GCTTTTTTGG AGGCCTAGGC TTTTGCAAAA AGCTtgcatg cctgcaggtc ggccgccacg accggtgccg ccaccatccc ctgacccacg cccctgaccc 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ctcacaagga gacgaccttc catgaccgag tacaagccca cggtgcgcct cgccacccgc gacgacgtcc cccgggccgt acgcaccctc gccgccgcgt 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

tcgccgacta ccccgccacg cgccacaccg tcgacccgga ccgccacatc gagcgggtca ccgagctgca agaactcttc ctcacgcgcg tcgggctcga 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

catcggcaag gtgtgggtcg cggacgacgg cgccgcggtg gcggtctgga ccacgccgga gagcgtcgaa gcgggggcgg tgttcgccga gatcggcccg 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

cgcatggccg agttgagcgg ttcccggctg gccgcgcagc aacagatgga aggcctcctg gcgccgcacc ggcccaagga gcccgcgtgg ttcctggcca 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

ccgtcggcgt ctcgcccgac caccagggca agggtctggg cagcgccgtc gtgctccccg gagtggaggc ggccgagcgc gccggggtgc ccgccttcct 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

ggagacctcc gcgccccgca acctcccctt ctacgagcgg ctcggcttca ccgtcaccgc cgacgtcgag gtgcccgaag gaccgcgcac ctggtgcatg 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

acccgcaagc ccggtgcctg acgcccgccc cacgacccgc agcgcccgac cgaaaggagc gcacgacccc atggctccga ccgaagccga cccgggcggc 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

cccgccgacc ccgcacccgc ccccgaggcc caccgactct agaggatcat aatcagccat accacatttg tagaggtttt acttgcttta aaaaacctcc 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

cacacctccc cctgaacctg aaacataaaa tgaatgcaat tgttgttgtt aacttgttta ttgcagctta taatggttac aaataaagca atagcatcac 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

aaatttcaca aataaagcat ttttttcact gc
^7001      ^7011      ^7021      ^7031

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:
birA

The description of the protein encoded in this ORF:
biotin ligase, holocarboxylase synthetase

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):

965-2050

Citations:

Kulman J. D., Satake M., Harris J. E. (2007) A versatile system for site-specific enzymatic biotinylation and regulated expression of proteins in cultured mammalian cells. Protein Expr. Purif. 52(2):320-328

IRESs:

IRES:

Version: `1`	Last change: `2011-04-08 22:29:43`
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):

359-945

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 tgcgtttgtc tatatgtgat tttccaccat attgccgtct 
^359       ^369       ^379       ^389       ^399       ^409       ^419       ^429       ^439       ^449       

tttggcaatg tgagggcccg gaaacctggc cctgtcttct tgacgagcat tcctaggggt ctttcccctc tcgccaaagg aatgcaaggt ctgttgaatg 
^459       ^469       ^479       ^489       ^499       ^509       ^519       ^529       ^539       ^549       

tcgtgaagga agcagttcct ctggaagctt cttgaagaca aacaacgtct gtagcgaccc tttgcaggca gcggaacccc ccacctggcg acaggtgcct 
^559       ^569       ^579       ^589       ^599       ^609       ^619       ^629       ^639       ^649       

ctgcggccaa aagccacgtg tataagatac acctgcaaag gcggcacaac cccagtgcca cgttgtgagt tggatagttg tggaaagagt caaatggctc 
^659       ^669       ^679       ^689       ^699       ^709       ^719       ^729       ^739       ^749       

tcctcaagcg tattcaacaa ggggctgaag gatgcccaga aggtacccca ttgtatggga tctgatctgg ggcctcggtg cacatgcttt acatgtgttt 
^759       ^769       ^779       ^789       ^799       ^809       ^819       ^829       ^839       ^849       

agtcgaggtt aaaaaaacgt ctaggccccc cgaaccacgg ggacgtggtt ttcctttgaa aaacacgatg ataagcttgc cacaacc
^859       ^869       ^879       ^889       ^899       ^909       ^919       ^929       ^939

Remarks:

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

>IRESite_Id:140 EMCV-R virus
          Length = 7835

 Score =  998 bits (571), Expect = 0.0
 Identities = 583/589 (98%), Gaps = 5/589 (0%)
 Strand = Plus / Plus


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


Query: 61  tgcgtttgtctatatgtgattttccaccatattgccgtcttttggcaatgtgagggcccg 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 cgttgtgagttggatagttgtggaaagagtcaaatggctctcctcaagcgtattcaacaa 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 620 cgttgtgagttggatagttgtggaaagagtcaaatggctctcctcaagcgtattcaacaa 679


Query: 421 ggggctgaaggatgcccagaaggtaccccattgtatgggatctgatctggggcctcggtg 480
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 680 ggggctgaaggatgcccagaaggtaccccattgtatgggatctgatctggggcctcggtg 739


Query: 481 cacatgctttacatgtgtttagtcgaggttaaaaaaacgtctaggccccccgaaccacgg 540
           |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct: 740 cacatgctttacatgtgtttagtcgaggtt-aaaaaacgtctaggccccccgaaccacgg 798


Query: 541 ggacgtggttttcctttgaaaaacacgatgataagct-t-gccacaacc 587
           ||||||||||||||||||||||||||||||||||  | | |||||||||
Sbjct: 799 ggacgtggttttcctttgaaaaacacgatgataa--tatggccacaacc 845

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