IRESite_Id:214 characteristics of Kv1.4_1.2 IRES studied in pRSTF-Kv1.4

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `214`	Version: `4`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2007-09-06 00:00:00`

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:
hopefully_full-length_mRNA

The mRNA/+RNA description:

In vitro T7 transcript containing renilla_luciferase - hairpin_from_multiple_cloning_site -
Kv1.4 IRES - firefly_luciferase and terminated at XbaI site immediately after the STOP codon. An FLuc-fusion
protein should be translated from the second cistron (4 aminoacids added extra).

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

GGctagccac catGacttcg aaagtttatg atccagaaca aaggaaacgg atgataactg gtccgcagtg gtgggccaga tgtaaacaaa tgaatgttct 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tgattcattt attaattatt atgattcaga aaaacatgca gaaaatgctg ttattttttt acatggtaac gcggcctctt cttatttatg gcgacatgtt 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

gtgccacata ttgagccagt agcgcggtgt attataccag accttattgg tatgggcaaa tcaggcaaat ctggtaatgg ttcttatagg ttacttgatc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

attacaaata tcttactgca tggtttgaac ttcttaattt accaaagaag atcatttttg tcggccatga ttggggtgct tgtttggcat ttcattatag 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ctatgagcat caagataaga tcaaagcaat agttcacgct gaaagtgtag tagatgtgat tgaatcatgg gatgaatggc ctgatattga agaagatatt 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

gcgttgatca aatctgaaga aggagaaaaa atggttttgg agaataactt cttcgtggaa accatgttgc catcaaaaat catgagaaag ttagaaccag 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

aagaatttgc agcatatctt gaaccattca aagagaaagg tgaagttcgt cgtccaacat tatcatggcc tcgtgaaatc ccgttagtaa aaggtggtaa 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

acctgacgtt gtacaaattg ttaggaatta taatgcttat ctacgtgcaa gtgatgattt accaaaaatg tttattgaat cggacccagg attcttttcc 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

aatgctattg ttgaaggtgc caagaagttt cctaatactg aatttgtcaa agtaaaaggt cttcattttt cgcaagaaga tgcacctgat gaaatgggaa 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

aatatatcaa atcgttcgtt gagcgagttc tcaaaaatga acaaatGtcg aTCGACgggg gcccctaggA gatccAAGCT TATCGATTTC GAACCCGGGG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TACCGAATTC CTCGAGTCTA GAGGAgcatg cTCCTCTAGA CTCGAGGAAT TCGGTACCCC GGGTTCGAAA TCGATAAGCT TgGATCTAGC agcttAGCTA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAGAGCAAGA CTGGGATGGA TACTGTTTTA AGGAATGCAG GCTTAACAAG TGATCGCTGC TGTCTAGGAT TTTGAGTCTT TTTCGGAGAA CCTTGACTTC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CGTTCCCAGC CCATGTCTGC TGTGCCGAAC TCCAGAGGAA CCAGAAATCT CCGGGGTCTA CCTTGGGGCG TCCCCAATCT CCACCTCTGG GCTCCAGTAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CGAGGACTCT GCAATACCCC CTAGCCCCCT GGCCAAGACA ACCGAACTTG TTCCGTGGAT ATTTGGGATC CTCCACCTGC CAAACCTGAG CGATTTTTTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TGTACTGCGC CCCCACCCCC AATGATTCTG CCCCTCCTCC AGCTGTTGCA GCGTGGAAAA GGGGAAACAA ATCACCGGGG GGGATTTTTT TCGTCTATTT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTATTTTTCG CACTTGCTGG GAATGGTGAA GTGCTTCTTG TGAATGATTC TAGCCAAAGG ATGCTCTTCA TTTCCTGCTT TCTATGGAGA CCTCAGTGTT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GAGTTTGCCT CTGCTGGAAC TGCGTCTACC ACCTTCTCTA CCTTCAAGGT CTTTGCCTCT ATCTACAACC TGGCATTGCC TGTGGGTCCA TGAAGGCTTG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GATGACCTTA GAAGGAAAGG TCTGGGAGTC CACCTTCATA GACTAAGCAG CAATGGCTGG GCATATTTTA AGCCGCATTT TAACATGGGT CAAGCCATCA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTAGAAGGCA AGTGCTAAGA CTAAAGACTT ATTTGAATTT TATTTAAATT AGATGGACTG GGCCTTGGCC AATTTCCATG CAAGAAAAAG TATATTTCAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TTTCTAGGCA CAACTTCTGA GTGTCAGATA CTTGCTGTCT TTGAGTCTTG TGGCGTCATC ACCGGACAGC ATCCCAGACA GACTTCCAGA TTTGAACATC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TACCCCCCAA CACGTAGGTG TATGGGAGAC CACATCATTT CATGACTTAT GTTTGAGGAA CACTAGGCTG TTGTCTAGAC GAGGCAAGCT CTGGAAAGCA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACGCCGAGTC TCTGAGAAGA GGGAGCATAG GCTGTGCTGA TTTAAAAACA GAAAATGCAA AGTTGGACTG AAAATATCCC ACGTCTTCTA AGCAATCTGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTAAGGCTTC CAAACTTACC TTAATTTGGT AAGAAAATAA GCTGCCCTAT TTTTCTTTCT TCTTCTCTTA CAACTGGAAG CAGCCATTTC CCCAAACCAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CAccatgGCT GGATCCATGG aagacgccaa aaacataaag aaaggcccgg cgccattcta tccgctggaa gatggaaccg ctggagagca actgcataag 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

gctatgaaga gatacgccct ggttcctgga acaattgctt ttacagatgc acatatcgag gtggacatca cttacgctga gtacttcgaa atgtccgttc 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ggttggcaga agctatgaaa cgatatgggc tgaatacaaa tcacagaatc gtcgtatgca gtgaaaactc tcttcaattc tttatgccgg tgttgggcgc 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

gttatttatc ggagttgcag ttgcgcccgc gaacgacatt tataatgaac gtgaattgct caacagtatg ggcatttcgc agcctaccgt ggtgttcgtt 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

tccaaaaagg ggttgcaaaa aattttgaac gtgcaaaaaa agctcccaat catccaaaaa attattatca tggattctaa aacggattac cagggatttc 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

agtcgatgta cacgttcgtc acatctcatc tacctcccgg ttttaatgaa tacgattttg tgccagagtc cttcgatagg gacaagacaa ttgcactgat 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

catgaactcc tctggatcta ctggtctgcc taaaggtgtc gctctgcctc atagaactgc ctgcgtgaga ttctcgcatg ccagagatcc tatttttggc 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

aatcaaatca ttccggatac tgcgatttta agtgttgttc cattccatca cggttttgga atgtttacta cactcggata tttgatatgt ggatttcgag 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

tcgtcttaat gtatagattt gaagaagagc tgtttctgag gagccttcag gattacaaga ttcaaagtgc gctgctggtg ccaaccctat tctccttctt 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

cgccaaaagc actctgattg acaaatacga tttatctaat ttacacgaaa ttgcttctgg tggcgctccc ctctctaagg aagtcgggga agcggttgcc 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

aagaggttcc atctgccagg tatcaggcaa ggatatgggc tcactgagac tacatcagct attctgatta cacccgaggg ggatgataaa ccgggcgcgg 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

tcggtaaagt tgttccattt tttgaagcga aggttgtgga tctggatacc gggaaaacgc tgggcgttaa tcaaagaggc gaactgtgtg tgagaggtcc 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

tatgattatg tccggttatg taaacaatcc ggaagcgacc aacgccttga ttgacaagga tggatggcta cattctggag acatagctta ctgggacgaa 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

gacgaacact tcttcatcgt tgaccgcctg aagtctctga ttaagtacaa aggctatcag gtggctcccg ctgaattgga atccatcttg ctccaacacc 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ccaacatctt cgacgcaggt gtcgcaggtc ttcccgacga tgacgccggt gaacttcccg ccgccgttgt tgttttggag cacggaaaga cgatgacgga 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

aaaagagatc gtggattacg tcgccagtca agtaacaacc gcgaaaaagt tgcgcggagg agttgtgttt gtggacgaag taccgaaagg tcttaccgga 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

aaactcgacg caagaaaaat cagagagatc ctcataaagg ccaagaaggg cggaaagatc gccgtgtaat T
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pRSTF-Kv1.4_1.2 The name of the promoter used to express this mRNA:
T7

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:
Kv1.4

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:

agatcgatct gcgcagcacc atggcctgaa ataacctctg aaagaggaac ttggttaggt accttctgag gcggaaagaa ccagctgtgg aatgtgtgtc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

agttagggtg tggaaagtcc ccaggctccc cagcaggcag aagtatgcaa agcatgcatc tcaattagtc agcaaccagg tgtggaaagt ccccaggctc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

cccagcaggc agaagtatgc aaagcatgca tctcaattag tcagcaacca tagtcccgcc cctaactccg cccatcccgc ccctaactcc gcccagttcc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gcccattctc cgccccatgg ctgactaatt ttttttattt atgcagaggc cgaggccgcc tcggcctctg agctattcca gaagtagtga ggaggctttt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ttggaggcct aggcttttgc aaaaagcttg attcttctga cacaacagtc tcgaacttaa gctgcagaag ttggtcgtga ggcactgggc aggtaagtat 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

caaggttaca agacaggttt aaggagacca atagaaactg ggcttgtcga gacagagaag actcttgcgt ttctgatagg cacctattgg tcttactgac 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

atccactttg cctttctctc cacaggtgtc cactcccagt tcaattacag ctcttaaggc tagagtacTT AATACGACTC ACTATAGGct agccaccatG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

acttcgaaag tttatgatcc agaacaaagg aaacggatga taactggtcc gcagtggtgg gccagatgta aacaaatgaa tgttcttgat tcatttatta 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

attattatga ttcagaaaaa catgcagaaa atgctgttat ttttttacat ggtaacgcgg cctcttctta tttatggcga catgttgtgc cacatattga 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

gccagtagcg cggtgtatta taccagacct tattggtatg ggcaaatcag gcaaatctgg taatggttct tataggttac ttgatcatta caaatatctt 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

actgcatggt ttgaacttct taatttacca aagaagatca tttttgtcgg ccatgattgg ggtgcttgtt tggcatttca ttatagctat gagcatcaag 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ataagatcaa agcaatagtt cacgctgaaa gtgtagtaga tgtgattgaa tcatgggatg aatggcctga tattgaagaa gatattgcgt tgatcaaatc 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tgaagaagga gaaaaaatgg ttttggagaa taacttcttc gtggaaacca tgttgccatc aaaaatcatg agaaagttag aaccagaaga atttgcagca 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tatcttgaac cattcaaaga gaaaggtgaa gttcgtcgtc caacattatc atggcctcgt gaaatcccgt tagtaaaagg tggtaaacct gacgttgtac 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

aaattgttag gaattataat gcttatctac gtgcaagtga tgatttacca aaaatgttta ttgaatcgga cccaggattc ttttccaatg ctattgttga 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

aggtgccaag aagtttccta atactgaatt tgtcaaagta aaaggtcttc atttttcgca agaagatgca cctgatgaaa tgggaaaata tatcaaatcg 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ttcgttgagc gagttctcaa aaatgaacaa atGtcgaTCG ACgggggccc ctaggAgatc cAAGCTTATC GATTTCGAAC CCGGGGTACC GAATTCCTCG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AGTCTAGAGG AgcatgcTCC TCTAGACTCG AGGAATTCGG TACCCCGGGT TCGAAATCGA TAAGCTTgGA TCTAGCagct tAGCTAGAGA GCAAGACTGG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GATGGATACT GTTTTAAGGA ATGCAGGCTT AACAAGTGAT CGCTGCTGTC TAGGATTTTG AGTCTTTTTC GGAGAACCTT GACTTCCGTT CCCAGCCCAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GTCTGCTGTG CCGAACTCCA GAGGAACCAG AAATCTCCGG GGTCTACCTT GGGGCGTCCC CAATCTCCAC CTCTGGGCTC CAGTAACGAG GACTCTGCAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TACCCCCTAG CCCCCTGGCC AAGACAACCG AACTTGTTCC GTGGATATTT GGGATCCTCC ACCTGCCAAA CCTGAGCGAT TTTTTTTGTA CTGCGCCCCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACCCCCAATG ATTCTGCCCC TCCTCCAGCT GTTGCAGCGT GGAAAAGGGG AAACAAATCA CCGGGGGGGA TTTTTTTCGT CTATTTTTAT TTTTCGCACT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGCTGGGAAT GGTGAAGTGC TTCTTGTGAA TGATTCTAGC CAAAGGATGC TCTTCATTTC CTGCTTTCTA TGGAGACCTC AGTGTTGAGT TTGCCTCTGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TGGAACTGCG TCTACCACCT TCTCTACCTT CAAGGTCTTT GCCTCTATCT ACAACCTGGC ATTGCCTGTG GGTCCATGAA GGCTTGGATG ACCTTAGAAG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GAAAGGTCTG GGAGTCCACC TTCATAGACT AAGCAGCAAT GGCTGGGCAT ATTTTAAGCC GCATTTTAAC ATGGGTCAAG CCATCAGTAG AAGGCAAGTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CTAAGACTAA AGACTTATTT GAATTTTATT TAAATTAGAT GGACTGGGCC TTGGCCAATT TCCATGCAAG AAAAAGTATA TTTCATTTTC TAGGCACAAC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTCTGAGTGT CAGATACTTG CTGTCTTTGA GTCTTGTGGC GTCATCACCG GACAGCATCC CAGACAGACT TCCAGATTTG AACATCTACC CCCCAACACG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TAGGTGTATG GGAGACCACA TCATTTCATG ACTTATGTTT GAGGAACACT AGGCTGTTGT CTAGACGAGG CAAGCTCTGG AAAGCAACGC CGAGTCTCTG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AGAAGAGGGA GCATAGGCTG TGCTGATTTA AAAACAGAAA ATGCAAAGTT GGACTGAAAA TATCCCACGT CTTCTAAGCA ATCTGCTTAA GGCTTCCAAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CTTACCTTAA TTTGGTAAGA AAATAAGCTG CCCTATTTTT CTTTCTTCTT CTCTTACAAC TGGAAGCAGC CATTTCCCCA AACCACCAcc atgGCTGGAT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CCATGGaaga cgccaaaaac ataaagaaag gcccggcgcc attctatccg ctggaagatg gaaccgctgg agagcaactg cataaggcta tgaagagata 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

cgccctggtt cctggaacaa ttgcttttac agatgcacat atcgaggtgg acatcactta cgctgagtac ttcgaaatgt ccgttcggtt ggcagaagct 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

atgaaacgat atgggctgaa tacaaatcac agaatcgtcg tatgcagtga aaactctctt caattcttta tgccggtgtt gggcgcgtta tttatcggag 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ttgcagttgc gcccgcgaac gacatttata atgaacgtga attgctcaac agtatgggca tttcgcagcc taccgtggtg ttcgtttcca aaaaggggtt 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

gcaaaaaatt ttgaacgtgc aaaaaaagct cccaatcatc caaaaaatta ttatcatgga ttctaaaacg gattaccagg gatttcagtc gatgtacacg 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ttcgtcacat ctcatctacc tcccggtttt aatgaatacg attttgtgcc agagtccttc gatagggaca agacaattgc actgatcatg aactcctctg 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

gatctactgg tctgcctaaa ggtgtcgctc tgcctcatag aactgcctgc gtgagattct cgcatgccag agatcctatt tttggcaatc aaatcattcc 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ggatactgcg attttaagtg ttgttccatt ccatcacggt tttggaatgt ttactacact cggatatttg atatgtggat ttcgagtcgt cttaatgtat 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

agatttgaag aagagctgtt tctgaggagc cttcaggatt acaagattca aagtgcgctg ctggtgccaa ccctattctc cttcttcgcc aaaagcactc 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

tgattgacaa atacgattta tctaatttac acgaaattgc ttctggtggc gctcccctct ctaaggaagt cggggaagcg gttgccaaga ggttccatct 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

gccaggtatc aggcaaggat atgggctcac tgagactaca tcagctattc tgattacacc cgagggggat gataaaccgg gcgcggtcgg taaagttgtt 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ccattttttg aagcgaaggt tgtggatctg gataccggga aaacgctggg cgttaatcaa agaggcgaac tgtgtgtgag aggtcctatg attatgtccg 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

gttatgtaaa caatccggaa gcgaccaacg ccttgattga caaggatgga tggctacatt ctggagacat agcttactgg gacgaagacg aacacttctt 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

catcgttgac cgcctgaagt ctctgattaa gtacaaaggc tatcaggtgg ctcccgctga attggaatcc atcttgctcc aacaccccaa catcttcgac 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

gcaggtgtcg caggtcttcc cgacgatgac gccggtgaac ttcccgccgc cgttgttgtt ttggagcacg gaaagacgat gacggaaaaa gagatcgtgg 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

attacgtcgc cagtcaagta acaaccgcga aaaagttgcg cggaggagtt gtgtttgtgg acgaagtacc gaaaggtctt accggaaaac tcgacgcaag 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

aaaaatcaga gagatcctca taaaggccaa gaagggcgga aagatcgccg tgtaatTCTA GAgcggccgc ttcgagcaga catgataaga tacattgatg 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

agtttggaca aaccacaact agaatgcagt gaaaaaaatg ctttatttgt gaaatttgtg atgctattgc tttatttgta accattataa gctgcaataa 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

acaagttaac aacaacaatt gcattcattt tatgtttcag gttcaggggg aggtgtggga ggttttttaa agcaagtaaa acctctacaa atgtggtaaa 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

atcgataagt ttaaacagat ccaggtggca cttttcgggg aaatgtgcgc ggaaccccta tttgtttatt tttctaaata cattcaaata tgtatccgct 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

catgagacaa taaccctgat aaatgcttca ataatattga aaaaggaaga gtatgagtat tcaacatttc cgtgtcgccc ttattccctt ttttgcggca 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ttttgccttc ctgtttttgc tcacccagaa acgctggtga aagtaaaaga tgctgaagat cagttgggtg cacgagtggg ttacatcgaa ctggatctca 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

acagcggtaa gatccttgag agttttcgcc ccgaagaacg ttttccaatg atgagcactt ttaaagttct gctatgtggc gcggtattat cccgtattga 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

cgccgggcaa gagcaactcg gtcgccgcat acactattct cagaatgact tggttgagta ctcaccagtc acagaaaagc atcttacgga tggcatgaca 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

gtaagagaat tatgcagtgc tgccataacc atgagtgata acactgcggc caacttactt ctgacaacga tcggaggacc gaaggagcta accgcttttt 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

tgcacaacat gggggatcat gtaactcgcc ttgatcgttg ggaaccggag ctgaatgaag ccataccaaa cgacgagcgt gacaccacga tgcctgtagc 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

aatggcaaca acgttgcgca aactattaac tggcgaacta cttactctag cttcccggca acaattaata gactggatgg aggcggataa agttgcagga 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ccacttctgc gctcggccct tccggctggc tggtttattg ctgataaatc tggagccggt gagcgtgggt ctcgcggtat cattgcagca ctggggccag 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

atggtaagcc ctcccgtatc gtagttatct acacgacggg gagtcaggca actatggatg aacgaaatag acagatcgct gagataggtg cctcactgat 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

taagcattgg taactgtcag accaagttta ctcatatata ctttagattg atttaaaact tcatttttaa tttaaaagga tctaggtgaa gatccttttt 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

gataatctca tgaccaaaat cccttaacgt gagttttcgt tccactgagc gtcagacccc gtagaaaaga tcaaaggatc ttcttgagat cctttttttc 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

tgcgcgtaat ctgctgcttg caaacaaaaa aaccaccgct accagcggtg gtttgtttgc cggatcaaga gctaccaact ctttttccga aggtaactgg 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

cttcagcaga gcgcagatac caaatactgt ccttctagtg tagccgtagt taggccacca cttcaagaac tctgtagcac cgcctacata cctcgctctg 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

ctaatcctgt taccagtggc tgctgccagt ggcgataagt cgtgtcttac cgggttggac tcaagacgat agttaccgga taaggcgcag cggtcgggct 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

gaacgggggg ttcgtgcaca cagcccagct tggagcgaac gacctacacc gaactgagat acctacagcg tgagctatga gaaagcgcca cgcttcccga 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

agggagaaag gcggacaggt atccggtaag cggcagggtc ggaacaggag agcgcacgag ggagcttcca gggggaaacg cctggtatct ttatagtcct 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

gtcgggtttc gccacctctg acttgagcgt cgatttttgt gatgctcgtc aggggggcgg agcctatgga aaaacgccag caacgcggcc tttttacggt 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

tcctggcctt ttgctggcct tttgctcaca tggctcgac
^6701      ^6711      ^6721      ^6731

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

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

2

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
RLuc

The description of the protein encoded in this ORF:
Renilla luciferase

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):

12-968

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
FLuc-fusion

The description of the protein encoded in this ORF:
Firefly luciferase protein with additional 4 aminoacid residues at its N-terminus

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):

2305-3969

Citations:

Jang G. M., Leong L. E., Hoang L. T., Wang P. H., Gutman G. A., Semler B. L. (2004) Structurally distinct elements mediate internal ribosome entry within the 5'-noncoding region of a voltage-gated potassium channel mRNA. J. Biol. Chem. 279(46):47419-47430

IRESs:

IRES:

Version: `3`	Last change: `2007-01-23 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `Kv1.4_1.2`	The functional status of IRES: `defective`

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

1107-2304

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `139`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `1336`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-1198`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-1`

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

AAGACTGGGA TGGATACTGT TTTAAGGAAT GCAGGCTTAA CAAGTGATCG CTGCTGTCTA GGATTTTGAG TCTTTTTCGG AGAACCTTGA CTTCCGTTCC 
^1107      ^1117      ^1127      ^1137      ^1147      ^1157      ^1167      ^1177      ^1187      ^1197      

CAGCCCATGT CTGCTGTGCC GAACTCCAGA GGAACCAGAA ATCTCCGGGG TCTACCTTGG GGCGTCCCCA ATCTCCACCT CTGGGCTCCA GTAACGAGGA 
^1207      ^1217      ^1227      ^1237      ^1247      ^1257      ^1267      ^1277      ^1287      ^1297      

CTCTGCAATA CCCCCTAGCC CCCTGGCCAA GACAACCGAA CTTGTTCCGT GGATATTTGG GATCCTCCAC CTGCCAAACC TGAGCGATTT TTTTTGTACT 
^1307      ^1317      ^1327      ^1337      ^1347      ^1357      ^1367      ^1377      ^1387      ^1397      

GCGCCCCCAC CCCCAATGAT TCTGCCCCTC CTCCAGCTGT TGCAGCGTGG AAAAGGGGAA ACAAATCACC GGGGGGGATT TTTTTCGTCT ATTTTTATTT 
^1407      ^1417      ^1427      ^1437      ^1447      ^1457      ^1467      ^1477      ^1487      ^1497      

TTCGCACTTG CTGGGAATGG TGAAGTGCTT CTTGTGAATG ATTCTAGCCA AAGGATGCTC TTCATTTCCT GCTTTCTATG GAGACCTCAG TGTTGAGTTT 
^1507      ^1517      ^1527      ^1537      ^1547      ^1557      ^1567      ^1577      ^1587      ^1597      

GCCTCTGCTG GAACTGCGTC TACCACCTTC TCTACCTTCA AGGTCTTTGC CTCTATCTAC AACCTGGCAT TGCCTGTGGG TCCATGAAGG CTTGGATGAC 
^1607      ^1617      ^1627      ^1637      ^1647      ^1657      ^1667      ^1677      ^1687      ^1697      

CTTAGAAGGA AAGGTCTGGG AGTCCACCTT CATAGACTAA GCAGCAATGG CTGGGCATAT TTTAAGCCGC ATTTTAACAT GGGTCAAGCC ATCAGTAGAA 
^1707      ^1717      ^1727      ^1737      ^1747      ^1757      ^1767      ^1777      ^1787      ^1797      

GGCAAGTGCT AAGACTAAAG ACTTATTTGA ATTTTATTTA AATTAGATGG ACTGGGCCTT GGCCAATTTC CATGCAAGAA AAAGTATATT TCATTTTCTA 
^1807      ^1817      ^1827      ^1837      ^1847      ^1857      ^1867      ^1877      ^1887      ^1897      

GGCACAACTT CTGAGTGTCA GATACTTGCT GTCTTTGAGT CTTGTGGCGT CATCACCGGA CAGCATCCCA GACAGACTTC CAGATTTGAA CATCTACCCC 
^1907      ^1917      ^1927      ^1937      ^1947      ^1957      ^1967      ^1977      ^1987      ^1997      

CCAACACGTA GGTGTATGGG AGACCACATC ATTTCATGAC TTATGTTTGA GGAACACTAG GCTGTTGTCT AGACGAGGCA AGCTCTGGAA AGCAACGCCG 
^2007      ^2017      ^2027      ^2037      ^2047      ^2057      ^2067      ^2077      ^2087      ^2097      

AGTCTCTGAG AAGAGGGAGC ATAGGCTGTG CTGATTTAAA AACAGAAAAT GCAAAGTTGG ACTGAAAATA TCCCACGTCT TCTAAGCAAT CTGCTTAAGG 
^2107      ^2117      ^2127      ^2137      ^2147      ^2157      ^2167      ^2177      ^2187      ^2197      

CTTCCAAACT TACCTTAATT TGGTAAGAAA ATAAGCTGCC CTATTTTTCT TTCTTCTTCT CTTACAACTG GAAGCAGCCA TTTCCCCAAA CCACCAcc
^2207      ^2217      ^2227      ^2237      ^2247      ^2257      ^2267      ^2277      ^2287      ^2297

Remarks:

The results of Jang et al (2004) and of Jimenez et al (2005) disproved the former report of IRES
activity in KCNA4/Kv1.4 1.2, 1.0 and 0.2 kb segments by Negulescu et al. (1998).

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 194

Version: `2`	Last change: `2007-09-09 00:00:00`
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:

9.100

Name of IRES used as the positive control:

CVB3

Name of the plasmid used as the positive control. `pRSTF-CVB3`	Name of the plasmid used as the negative control. `pRSTF`
`IRESite Id` of the plasmid used as positive control. `210`	`IRESite Id` of the plasmid used as negative control. `212`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0.500`
The size (length) of intercistronic region in the positive control: `819`	The size (length) of intercistronic region in the negative control: `133`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_without_cap_without_polyA_tail

Remarks:

The data are from Fig. 2B. Although Jang et al. (2004) did not state it explicitly the in vitro
transcripts used in the direct RNA transfection were most probably uncapped (this artificially increases the
yields from the second cistron and thus makes the IRES appear stronger and also increases the risk of degraded
RNA). In comparison with CVB3 IRES the Kv1.4 1.2kb fragment seriously underperforms. The transcripts should
have also been capped in yet another experiment. In the legend they mentioned measuring firefly
luciferase/beta-galactosidase measurements in these cells but that does not make sense as beta-galactosidase
was only measured in experiment shown in Fig. 2A.

Citations:

Translation results:

IRESite Translation Id: 200

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Cercopithecus aethiops COS-1 (ATCC CRL-1650)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

1.440

Name of IRES used as the positive control:

CVB3

Name of the plasmid used as the positive control. `pRSTF-CVB3`	Name of the plasmid used as the negative control. `pRSTF`
`IRESite Id` of the plasmid used as positive control. `210`	`IRESite Id` of the plasmid used as negative control. `212`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0.210`
The size (length) of intercistronic region in the positive control: `819`	The size (length) of intercistronic region in the negative control: `131`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_without_cap_with_polyA_tail

Remarks:

Fig. 4A

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

Translation results:

IRESite Translation Id: 201

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Cercopithecus aethiops COS-1 (ATCC CRL-1650)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

2.270

Name of IRES used as the positive control:

CVB3

Name of the plasmid used as the positive control. `pRSTF-CVB3`	Name of the plasmid used as the negative control. `pRSTF`
`IRESite Id` of the plasmid used as positive control. `210`	`IRESite Id` of the plasmid used as negative control. `212`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0.390`
The size (length) of intercistronic region in the positive control: `819`	The size (length) of intercistronic region in the negative control: `131`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_without_cap_without_polyA_tail

Remarks:

Fig. 4B, measured values provided by J. Jimenez.

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

Translation results:

IRESite Translation Id: 202

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Cercopithecus aethiops COS-1 (ATCC CRL-1650)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

2.600

Name of IRES used as the positive control:

CVB3

Name of the plasmid used as the positive control. `pRSTF-CVB3`	Name of the plasmid used as the negative control. `pRSTF`
`IRESite Id` of the plasmid used as positive control. `210`	`IRESite Id` of the plasmid used as negative control. `212`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `6.060`
The size (length) of intercistronic region in the positive control: `819`	The size (length) of intercistronic region in the negative control: `131`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_GpppG_cap_without_polyA_tail

Remarks:

Fig. 4B, measured values provided by J. Jimenez.

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

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