IRESite_Id:386 characteristics of EMCV-R_260-845 IRES studied in pIREShyg plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `386`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-06-12 16:04:34`

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:
possibly_wrong

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
1899166

The mRNA/+RNA description:

Putative in vivo spliced transcript of pIREShyg plasmid from CLONTECH with synthetic intron spliced out. The
intron boundaries do not conform the GT-AG consensus.

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

agaacccact gcttactggc ttatcgaaat TAATACGACT CACTATAGGg agacccaagc ttggtaccga gctcggatcc actagtaacg gccgccagtg 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tgctgatcga gcatgcatct agggcggccg cactagagga attcgcccct ctccctcccc cccccctaac gttactggcc gaagccgctt ggaataaggc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

cggtgtgtgt ttgtctatat gtgattttcc accatattgc cgtcttttgg caatgtgagg gcccggaaac ctggccctgt cttcttgacg agcattccta 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ggggtctttc ccctctcgcc aaaggaatgc aaggtctgtt gaatgtcgtg aaggaagcag ttcctctgga agcttcttga agacaaacaa cgtctgtagc 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

gaccctttgc aggcagcgga accccccacc tggcgacagg tgcctctgcg gccaaaagcc acgtgtataa gatacacctg caaaggcggc acaaccccag 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

tgccacgttg tgagttggat agttgtggaa agagtcaaat ggctctcctc aagcgtagtc aacaaggggc tgaaggatgc ccagaaggta ccccattgta 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

tgggaatctg atctggggcc tcggtgcaca tgctttacat gtgtttagtc gaggttaaaa aagctctagg ccccccgaac cacggggacg tggttttcct 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ttgaaaaaca cgatgataag cttgccacaa ccccgtacca aagatggata gatccggaaa gcctgaactc accgcgacgt ctgtcgagaa gtttctgatc 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gaaaagttcg acagcgtctc cgacctgatg cagctctcgg agggcgaaga atctcgtgct ttcagcttcg atgtaggagg gcgtggatat gtcctgcggg 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

taaatagctg cgccgatggt ttctacaaag atcgttatgt ttatcggcac tttgcatcgg ccgcgctccc gattccggaa gtgcttgaca ttggggaatt 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

cagcgagagc ctgacctatt gcatctcccg ccgtgcacag ggtgtcacgt tgcaagacct gcctgaaacc gaactgcccg ctgttctgca gccggtcgcg 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

gaggccatgg atgcgatcgc tgcggccgat cttagccaga cgagcgggtt cggcccattc ggaccgcaag gaatcggtca atacactaca tggcgtgatt 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tcatatgcgc gattgctgat ccccatgtgt atcactggca aactgtgatg gacgacaccg tcagtgcgtc cgtcgcgcag gctctcgatg agctgatgct 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ttgggccgag gactgccccg aagtccggca cctcgtgcac gcggatttcg gctccaacaa tgtcctgacg gacaatggcc gcataacagc ggtcattgac 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

tggagcgagg cgatgttcgg ggattcccaa tacgaggtcg ccaacatctt cttctggagg ccgtggttgg cttgtatgga gcagcagacg cgctacttcg 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

agcggaggca tccggagctt gcaggatcgc cgcggctccg ggcgtatatg ctccgcattg gtcttgacca actctatcag agcttggttg acggcaattt 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

cgatgatgca gcttgggcgc agggtcgatg cgacgcaatc gtccgatccg gagccgggac tgtcgggcgt acacaaatcg cccgcagaag cgcggccgtc 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

tggaccgatg gctgtgtaga agtactcgcc gatagtggaa accgacgccc cagcactcgt ccgagggcaa aggaatagag tagatgccga ccgaacaaga 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

gctgatttcg agaacgcctc agccagcaac tcgcgcgagc ctagcaaggc aaatgcgaga gaacggcctt acgcttggtg gcacagttct cgtccacagt 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

tcgctaagct cgctcggctg ggtcgcggga gggccggtcg cagtgattca ggcccttctg gattgtgttg gtccccaggg cacgattgtc atgcccacgc 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

actcgggtga tctgactgat cccgcagatt ggagatcgcc gcccgtgcct gccgattggg tgcagatcta gagctcgctg atcagcctcg actgtgcctc 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

tagTTGCCAG CCATCTGTTG TTTGCCCCTC CCCCGTGCCT TCCTTGACCC TGGAAGGTGC CACTCCCACT GTCCTTTCCT AATAAAATGA GGAAATTGCA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TCGC
^2201

Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

The name of the plasmid:
pIREShyg The name of the promoter used to express this mRNA:
CMV_IE

Aliases of the plasmid name:

Alias: pIRES1hyg

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:

gacggatcgg gagatctccc gatcccctat ggtcgactct cagtacaatc tgctctgatg ccgcatagtt aagccagtat ctgctccctg cttgtgtgtt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ggaggtcgct gagtagtgcg cgagcaaaat ttaagctaca acaaggcaag gcttgaccga caattgcatg aagaatctgc ttagggttag gcgttttgcg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ctgcttcgcg atgtacgggc cagatatacg cgttgacatt gattattgac tagttattaa tagtaatcaa ttacggggtc attagttcat agcccatata 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

tggagttccg cgttacataa cttacggtaa atggcccgcc tggctgaccg cccaacgacc cccgcccatt gacgtcaata atgacgtatg ttcccatagt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

aacgccaata gggactttcc attgacgtca atgggtggac tatttacggt aaactgccca cttggcagta catcaagtgt atcatatgcc aagtacgccc 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

cctattgacg tcaatgacgg taaatggccc gcctggcatt atgcccagta catgacctta tgggactttc ctacttggca gtacatctac gtattagtca 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

tcgctattac catggtgatg cggttttggc agtacatcaa tgggcgtgga tagcggtttg actcacgggg atttccaagt ctccacccca ttgacgtcaa 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

tgggagtttg ttttggcacc aaaatcaacg ggactttcca aaatgtcgta acaactccgc cccattgacg caaatgggcg gtaggcgtgt acggtgggag 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gtctatataa gcagagctct ctggctaact agagaaccca ctgcttactg gcttatcgaa atTAATACGA CTCACTATAG Ggagacccaa gcttggtacc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

gagctcggat ccactagtaa cggccgccag tgtgctggaa ttaattcgct gtctgcgagg gccagctgtt ggggtgagta ctccctctca aaagcgggca 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

tgacttctgc gctaagattg tcagtttcca aaaacgagga ggatttgata ttcacctggc ccgcggtgat gcctttgagg gtggccgcgt ccatctggtc 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

agaaaagaca atctttttgt tgtcaagctt gaggtgtggc aggcttgaga tctggccata cacttgagtg acaatgacat ccactttgcc tttctctcca 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

caggtgtcca ctcccaggtc caactgcagg tcgatcgagc atgcatctag ggcggccgca ctagaggaat tcgcccctct ccctcccccc cccctaacgt 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tactggccga agccgcttgg aataaggccg gtgtgtgttt gtctatatgt gattttccac catattgccg tcttttggca atgtgagggc ccggaaacct 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ggccctgtct tcttgacgag cattcctagg ggtctttccc ctctcgccaa aggaatgcaa ggtctgttga atgtcgtgaa ggaagcagtt cctctggaag 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

cttcttgaag acaaacaacg tctgtagcga ccctttgcag gcagcggaac cccccacctg gcgacaggtg cctctgcggc caaaagccac gtgtataaga 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

tacacctgca aaggcggcac aaccccagtg ccacgttgtg agttggatag ttgtggaaag agtcaaatgg ctctcctcaa gcgtagtcaa caaggggctg 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

aaggatgccc agaaggtacc ccattgtatg ggaatctgat ctggggcctc ggtgcacatg ctttacatgt gtttagtcga ggttaaaaaa gctctaggcc 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ccccgaacca cggggacgtg gttttccttt gaaaaacacg atgataagct tgccacaacc ccgtaccaaa gatggataga tccggaaagc ctgaactcac 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

cgcgacgtct gtcgagaagt ttctgatcga aaagttcgac agcgtctccg acctgatgca gctctcggag ggcgaagaat ctcgtgcttt cagcttcgat 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

gtaggagggc gtggatatgt cctgcgggta aatagctgcg ccgatggttt ctacaaagat cgttatgttt atcggcactt tgcatcggcc gcgctcccga 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ttccggaagt gcttgacatt ggggaattca gcgagagcct gacctattgc atctcccgcc gtgcacaggg tgtcacgttg caagacctgc ctgaaaccga 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

actgcccgct gttctgcagc cggtcgcgga ggccatggat gcgatcgctg cggccgatct tagccagacg agcgggttcg gcccattcgg accgcaagga 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

atcggtcaat acactacatg gcgtgatttc atatgcgcga ttgctgatcc ccatgtgtat cactggcaaa ctgtgatgga cgacaccgtc agtgcgtccg 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

tcgcgcaggc tctcgatgag ctgatgcttt gggccgagga ctgccccgaa gtccggcacc tcgtgcacgc ggatttcggc tccaacaatg tcctgacgga 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

caatggccgc ataacagcgg tcattgactg gagcgaggcg atgttcgggg attcccaata cgaggtcgcc aacatcttct tctggaggcc gtggttggct 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

tgtatggagc agcagacgcg ctacttcgag cggaggcatc cggagcttgc aggatcgccg cggctccggg cgtatatgct ccgcattggt cttgaccaac 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

tctatcagag cttggttgac ggcaatttcg atgatgcagc ttgggcgcag ggtcgatgcg acgcaatcgt ccgatccgga gccgggactg tcgggcgtac 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

acaaatcgcc cgcagaagcg cggccgtctg gaccgatggc tgtgtagaag tactcgccga tagtggaaac cgacgcccca gcactcgtcc gagggcaaag 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

gaatagagta gatgccgacc gaacaagagc tgatttcgag aacgcctcag ccagcaactc gcgcgagcct agcaaggcaa atgcgagaga acggccttac 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

gcttggtggc acagttctcg tccacagttc gctaagctcg ctcggctggg tcgcgggagg gccggtcgca gtgattcagg cccttctgga ttgtgttggt 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ccccagggca cgattgtcat gcccacgcac tcgggtgatc tgactgatcc cgcagattgg agatcgccgc ccgtgcctgc cgattgggtg cagatctaga 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

gctcgctgat cagcctcgac tgtgcctcta gTTGCCAGCC ATCTGTTGTT TGCCCCTCCC CCGTGCCTTC CTTGACCCTG GAAGGTGCCA CTCCCACTGT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CCTTTCCTAA TAAAATGAGG AAATTGCATC GCattgtctg agtaggtgtc attctattct ggggggtggg gtggggcagg acagcaaggg ggaggattgg 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

gaagacaata gcaggcatgc tggggatgcg gtgggctcta tggcttctga ggcggaaaga accagctggg gctcgagtgc attctagttg tggtttgtcc 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

aaactcatca atgtatctta tcatgtctgt ataccgtcga cctctagcta gagcttggcg taatcatggt catagctgtt tcctgtgtga aattgttatc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

cgctcacaat tccacacaac atacgagccg gaagcataaa gtgtaaagcc tggggtgcct aatgagtgag ctaactcaca ttaattgcgt tgcgctcact 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

gcccgctttc cagtcgggaa acctgtcgtg ccagctgcat taatgaatcg gccaacgcgc ggggagaggc ggtttgcgta ttgggcgctc ttccgcttcc 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

tcgctcactg actcgctgcg ctcggtcgtt cggctgcggc gagcggtatc agctcactca aaggcggtaa tacggttatc cacagaatca ggggataacg 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

caggaaagaa catgtgagca aaaggccagc aaaaggccag gaaccgtaaa aaggccgcgt tgctggcgtt tttccatagg ctccgccccc ctgacgagca 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcaatgct cacgctgtag gtatctcagt tcggtgtagg 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc cggtaagaca 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

cgacttatcg ccactggcag cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga agtggtggcc taactacggc 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

tacactagaa ggacagtatt tggtatctgc gctctgctga agccagttac cttcggaaaa agagttggta gctcttgatc cggcaaacaa accaccgctg 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

gtagcggtgg tttttttgtt tgcaagcagc agattacgcg cagaaaaaaa ggatctcaag aagatccttt gatcttttct acggggtctg acgctcagtg 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

gaacgaaaac tcacgttaag ggattttggt catgagatta tcaaaaagga tcttcaccta gatcctttta aattaaaaat gaagttttaa atcaatctaa 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

agtatatatg agtaaacttg gtctgacagt taccaatgct taatcagtga ggcacctatc tcagcgatct gtctatttcg ttcatccata gttgcctgac 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

tccccgtcgt gtagataact acgatacggg agggcttacc atctggcccc agtgctgcaa tgataccgcg agacccacgc tcaccggctc cagatttatc 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

agcaataaac cagccagccg gaagggccga gcgcagaagt ggtcctgcaa ctttatccgc ctccatccag tctattaatt gttgccggga agctagagta 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

agtagttcgc cagttaatag tttgcgcaac gttgttgcca ttgctacagg catcgtggtg tcacgctcgt cgtttggtat ggcttcattc agctccggtt 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

cccaacgatc aaggcgagtt acatgatccc ccatgttgtg caaaaaagcg gttagctcct tcggtcctcc gatcgttgtc agaagtaagt tggccgcagt 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

gttatcactc atggttatgg cagcactgca taattctctt actgtcatgc catccgtaag atgcttttct gtgactggtg agtactcaac caagtcattc 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

tgagaatagt gtatgcggcg accgagttgc tcttgcccgg cgtcaatacg ggataatacc gcgccacata gcagaacttt aaaagtgctc atcattggaa 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

aacgttcttc ggggcgaaaa ctctcaagga tcttaccgct gttgagatcc agttcgatgt aacccactcg tgcacccaac tgatcttcag catcttttac 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

tttcaccagc gtttctgggt gagcaaaaac aggaaggcaa aatgccgcaa aaaagggaat aagggcgaca cggaaatgtt gaatactcat actcttcctt 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

tttcaatatt attgaagcat ttatcagggt tattgtctca tgagcggata catatttgaa tgtatttaga aaaataaaca aataggggtt ccgcgcacat 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ttccccgaaa agtgccacct gacgtc
^5701      ^5711      ^5721

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:
hph

The description of the protein encoded in this ORF:
hygromycin B 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):

744-1778

Remarks:

The mRNA sequence considered here is probably partly wrong due to the mis-annotated intron region by Clontech
and starts from the putative CMV immediate early promoter transcription start site and continues up to the
very end of BGH poly(A) signal.

Citations:

Rees S., Coote J., Stables J., Goodson S., Harris S., Lee M. G. (1996) Bicistronic vector for the creation of stable mammalian cell lines that predisposes all antibiotic-resistant cells to express recombinant protein. Biotechniques. 20(1):102-4, 106, 108-10

Jackson R. J., Howell M. T., Kaminski A. (1990) The novel mechanism of initiation of picornavirus RNA translation. Trends Biochem. Sci. 15(12):477-483

Jang S. K., Krausslich H. G., Nicklin M. J., Duke G. M., Palmenberg A. C., Wimmer E. (1988) A segment of the 5' nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation. J. Virol. 62(8):2636-2643

Huang M. T., Gorman C. M. (1990) Intervening sequences increase efficiency of RNA 3' processing and accumulation of cytoplasmic RNA. Nucleic Acids Res. 18(4):937-947

IRESs:

IRES:

Version: `1`	Last change: `2011-04-08 22:24:46`
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):

146-732

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 
^146       ^156       ^166       ^176       ^186       ^196       ^206       ^216       ^226       ^236       

tttggcaatg tgagggcccg gaaacctggc cctgtcttct tgacgagcat tcctaggggt ctttcccctc tcgccaaagg aatgcaaggt ctgttgaatg 
^246       ^256       ^266       ^276       ^286       ^296       ^306       ^316       ^326       ^336       

tcgtgaagga agcagttcct ctggaagctt cttgaagaca aacaacgtct gtagcgaccc tttgcaggca gcggaacccc ccacctggcg acaggtgcct 
^346       ^356       ^366       ^376       ^386       ^396       ^406       ^416       ^426       ^436       

ctgcggccaa aagccacgtg tataagatac acctgcaaag gcggcacaac cccagtgcca cgttgtgagt tggatagttg tggaaagagt caaatggctc 
^446       ^456       ^466       ^476       ^486       ^496       ^506       ^516       ^526       ^536       

tcctcaagcg tagtcaacaa ggggctgaag gatgcccaga aggtacccca ttgtatggga atctgatctg gggcctcggt gcacatgctt tacatgtgtt 
^546       ^556       ^566       ^576       ^586       ^596       ^606       ^616       ^626       ^636       

tagtcgaggt taaaaaagct ctaggccccc cgaaccacgg ggacgtggtt ttcctttgaa aaacacgatg ataagcttgc cacaacc
^646       ^656       ^666       ^676       ^686       ^696       ^706       ^716       ^726

Remarks:

There are several differences 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

Citations:

Jackson R. J., Howell M. T., Kaminski A. (1990) The novel mechanism of initiation of picornavirus RNA translation. Trends Biochem. Sci. 15(12):477-483

Huang M. T., Gorman C. M. (1990) Intervening sequences increase efficiency of RNA 3' processing and accumulation of cytoplasmic RNA. Nucleic Acids Res. 18(4):937-947

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