IRESite_Id:240 characteristics of ELH IRES studied in pNEX3

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `240`	Version: `0`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš

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:
3UTR_possibly_incomplete

The mRNA/+RNA description:

Putative bicistronic mRNA molecule coding for eBFP and eGFP with the intercistronic region containing ELH
IRES.

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

GCCATTTGAC CATTCACCAC ATTGGTGTGC ACCTCCAAGC TTGCATGCCT GCAGTCGACC GGTCGCCACC ATGGTGAGCA AGGGCGAGGA GCTGTTCACC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GGGGTGGTGC CCATCCTGGT CGAGCTGGAC GGCGACGTAA ACGGCCACAA GTTCAGCGTG TCCGGCGAGG GCGAGGGCGA TGCCACCTAC GGCAAGCTGA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCCTGAAGTT CATCTGCACC ACCGGCAAGC TGCCCGTGCC CTGGCCCACC CTCGTGACCA CCCTGACCCA CGGCGTGCAG TGCTTCAGCC GCTACCCCGA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCACATGAAG CAGCACGACT TCTTCAAGTC CGCCATGCCC GAAGGCTACG TCCAGGAGCG CACCATCTTC TTCAAGGACG ACGGCAACTA CAAGACCCGC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCCGAGGTGA AGTTCGAGGG CGACACCCTG GTGAACCGCA TCGAGCTGAA GGGCATCGAC TTCAAGGAGG ACGGCAACAT CCTGGGGCAC AAGCTGGAGT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACAACTTCAA CAGCCACAAC GTCTATATCA TGGCCGACAA GCAGAAGAAC GGCATCAAGG TGAACTTCAA GATCCGCCAC AACATCGAGG ACGGCAGCGT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GCAGCTCGCC GACCACTACC AGCAGAACAC CCCCATCGGC GACGGCCCCG TGCTGCTGCC CGACAACCAC TACCTGAGCA CCCAGTCCGC CCTGAGCAAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GACCCCAACG AGAAGCGCGA TCACATGGTC CTGCTGGAGT TCGTGACCGC CGCCGGGATC ACTCTCGGCA TGGACGAGCT GTACAAGTAA AGCGGCCCGG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GATCttgata agatcttagc ggccgcggga CCGGTCGCCA Ccatgggggg gaatctttac cgacaacgtc cagcgtccca gtcgagaagt aagtagtccg 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

agctgtgagc ataactctac cagagaaacg cgcgctttat tggtcaagat agacggaagc cggcggttga aggcaaaggt tgactcggaa gctgagagat 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

tgttgagtaa cacgcagaag tcttgaaagt atcaaggtcc aatcgagaaa ttgaacatat ttcaaggaac ttggtttcgg tgaagtcgtc aattcctttt 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

atcgtcaacg tttccacagc cctcagaata gaaatttcca acaagccaaa gcctacgtac CATGGTGAGC AAGGGCGAGG AGCTGTTCAC CGGGGTGGTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCCATCCTGG TCGAGCTGGA CGGCGACGTA AACGGCCACA AGTTCAGCGT GTCCGGCGAG GGCGAGGGCG ATGCCACCTA CGGCAAGCTG ACCCTGAAGT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TCATCTGCAC CACCGGCAAG CTGCCCGTGC CCTGGCCCAC CCTCGTGACC ACCCTGACCT ACGGCGTGCA GTGCTTCAGC CGCTACCCCG ACCACATGAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCAGCACGAC TTCTTCAAGT CCGCCATGCC CGAAGGCTAC GTCCAGGAGC GCACCATCTT CTTCAAGGAC GACGGCAACT ACAAGACCCG CGCCGAGGTG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AAGTTCGAGG GCGACACCCT GGTGAACCGC ATCGAGCTGA AGGGCATCGA CTTCAAGGAG GACGGCAACA TCCTGGGGCA CAAGCTGGAG TACAACTACA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACAGCCACAA CGTCTATATC ATGGCCGACA AGCAGAAGAA CGGCATCAAG GTGAACTTCA AGATCCGCCA CAACATCGAG GACGGCAGCG TGCAGCTCGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CGACCACTAC CAGCAGAACA CCCCCATCGG CGACGGCCCC GTGCTGCTGC CCGACAACCA CTACCTGAGC ACCCAGTCCG CCCTGAGCAA AGACCCCAAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GAGAAGCGCG ATCACATGGT CCTGCTGGAG TTCGTGACCG CCGCCGGGAT CACTCTCGGC ATGGACGAGC TGTACAAGTA AAGCGGCCGG GTACCGAGCT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGAATTCCAG CTGAGCGCCG GTCGCTACCA TTACCAGTTG GTCTGGTGTC AAAAATAATA ATAACCGGGC AGGCCATGTC TGCCCGTATT TCGCGTAAGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AAATCCATTA TGTACTATTT AAAAAACACA AACTTTTGGA TGTTCGGTTT ATTCTTTTTC TTTTACTTTT TTATCATGGG AGCCTACTTC CCGTTTTTCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGATTTGGCT ACATGACATC AACCATATCA GCAAAAGTGA TACGGGTATT ATTTTTGCCG CTATTTCTCT GTTCTCGCTA TTATTCCAAC CGCTGTTTGG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TCTGCTTTCT GACAAACTCG GAACTTGTTT ATTGCAGCTT ATAATGGTTA CAAATAAAGC AATAGCATCA CAAATTTCAC AAATAAAGCA TTTTTTTCAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TGCATTCTAG TTGTGGTTTG TCCAAACTCA TCAATGTATC TTATCACGTC TGG
^2301      ^2311      ^2321      ^2331      ^2341      ^2351

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_except_3UTR

The name of the plasmid:
pNEX3_based-eBFP-ELH-eGFP The name of the promoter used to express this mRNA:
RSV

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

no

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

no

A promoter reported in cDNA corresponding to IRES sequence:

no

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
not_tested

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
no_promoter_confirmed

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Aplysia californica

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

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Aplysia californica

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

AAGCTTGATT CGAATTCGCG CTGAGTCACA ATTCGCGCTG AGTCACAATT CGCGCTGAGT CACAATTGTG ACTCAGCCGC GAATTCCATC GAATTCGCGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGAGTCACAA TTCGCGCTGA GTCACAATTC GCGCTGAGTC ACAATTGTGA CTCAGCCGCG AATTCCTGCA GCCCCGAATT CCGCATTGCA GAGATAATTG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TATTTAAGTG CCTAGCTCGA TACAATAAAC GCCATTTGAC CATTCACCAC ATTGGTGTGC ACCTCCAAGC TTGCATGCCT GCAGTCGACC GGTCGCCACC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATGGTGAGCA AGGGCGAGGA GCTGTTCACC GGGGTGGTGC CCATCCTGGT CGAGCTGGAC GGCGACGTAA ACGGCCACAA GTTCAGCGTG TCCGGCGAGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCGAGGGCGA TGCCACCTAC GGCAAGCTGA CCCTGAAGTT CATCTGCACC ACCGGCAAGC TGCCCGTGCC CTGGCCCACC CTCGTGACCA CCCTGACCCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGGCGTGCAG TGCTTCAGCC GCTACCCCGA CCACATGAAG CAGCACGACT TCTTCAAGTC CGCCATGCCC GAAGGCTACG TCCAGGAGCG CACCATCTTC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTCAAGGACG ACGGCAACTA CAAGACCCGC GCCGAGGTGA AGTTCGAGGG CGACACCCTG GTGAACCGCA TCGAGCTGAA GGGCATCGAC TTCAAGGAGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACGGCAACAT CCTGGGGCAC AAGCTGGAGT ACAACTTCAA CAGCCACAAC GTCTATATCA TGGCCGACAA GCAGAAGAAC GGCATCAAGG TGAACTTCAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GATCCGCCAC AACATCGAGG ACGGCAGCGT GCAGCTCGCC GACCACTACC AGCAGAACAC CCCCATCGGC GACGGCCCCG TGCTGCTGCC CGACAACCAC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TACCTGAGCA CCCAGTCCGC CCTGAGCAAA GACCCCAACG AGAAGCGCGA TCACATGGTC CTGCTGGAGT TCGTGACCGC CGCCGGGATC ACTCTCGGCA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGGACGAGCT GTACAAGTAA AGCGGCCCGG GATCttgata agatcttagc ggccgcggga CCGGTCGCCA Ccatgggggg gaatctttac cgacaacgtc 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

cagcgtccca gtcgagaagt aagtagtccg agctgtgagc ataactctac cagagaaacg cgcgctttat tggtcaagat agacggaagc cggcggttga 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

aggcaaaggt tgactcggaa gctgagagat tgttgagtaa cacgcagaag tcttgaaagt atcaaggtcc aatcgagaaa ttgaacatat ttcaaggaac 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ttggtttcgg tgaagtcgtc aattcctttt atcgtcaacg tttccacagc cctcagaata gaaatttcca acaagccaaa gcctacgtac CATGGTGAGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAGGGCGAGG AGCTGTTCAC CGGGGTGGTG CCCATCCTGG TCGAGCTGGA CGGCGACGTA AACGGCCACA AGTTCAGCGT GTCCGGCGAG GGCGAGGGCG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ATGCCACCTA CGGCAAGCTG ACCCTGAAGT TCATCTGCAC CACCGGCAAG CTGCCCGTGC CCTGGCCCAC CCTCGTGACC ACCCTGACCT ACGGCGTGCA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GTGCTTCAGC CGCTACCCCG ACCACATGAA GCAGCACGAC TTCTTCAAGT CCGCCATGCC CGAAGGCTAC GTCCAGGAGC GCACCATCTT CTTCAAGGAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GACGGCAACT ACAAGACCCG CGCCGAGGTG AAGTTCGAGG GCGACACCCT GGTGAACCGC ATCGAGCTGA AGGGCATCGA CTTCAAGGAG GACGGCAACA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TCCTGGGGCA CAAGCTGGAG TACAACTACA ACAGCCACAA CGTCTATATC ATGGCCGACA AGCAGAAGAA CGGCATCAAG GTGAACTTCA AGATCCGCCA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CAACATCGAG GACGGCAGCG TGCAGCTCGC CGACCACTAC CAGCAGAACA CCCCCATCGG CGACGGCCCC GTGCTGCTGC CCGACAACCA CTACCTGAGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACCCAGTCCG CCCTGAGCAA AGACCCCAAC GAGAAGCGCG ATCACATGGT CCTGCTGGAG TTCGTGACCG CCGCCGGGAT CACTCTCGGC ATGGACGAGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGTACAAGTA AAGCGGCCGG GTACCGAGCT CGAATTCCAG CTGAGCGCCG GTCGCTACCA TTACCAGTTG GTCTGGTGTC AAAAATAATA ATAACCGGGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AGGCCATGTC TGCCCGTATT TCGCGTAAGG AAATCCATTA TGTACTATTT AAAAAACACA AACTTTTGGA TGTTCGGTTT ATTCTTTTTC TTTTACTTTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTATCATGGG AGCCTACTTC CCGTTTTTCC CGATTTGGCT ACATGACATC AACCATATCA GCAAAAGTGA TACGGGTATT ATTTTTGCCG CTATTTCTCT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GTTCTCGCTA TTATTCCAAC CGCTGTTTGG TCTGCTTTCT GACAAACTCG GAACTTGTTT ATTGCAGCTT ATAATGGTTA CAAATAAAGC AATAGCATCA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CAAATTTCAC AAATAAAGCA TTTTTTTCAC TGCATTCTAG TTGTGGTTTG TCCAAACTCA TCAATGTATC TTATCACGTC TGGGCGAACG TGGCGAGAAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GGAAGGGAAG AAAGCGAAAG GAGCGGGCGC TAGGGCGCTG GCAAGTGTAG CGGTCACGCT GCGCGTAACC ACCACACCCG CCGCGCTTAA TGCGCCGCTA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CAGGGCGTCA GGTGGCACTT TTCGGGGAAA TGTGCGCGGA ACCCCTATTT GTTTATTTTT CTAAATACAT TCAAATATGT ATCCGCTCAT GAGACAATAA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CCCTGATAAA TGCTTCAATA ATATTGAAAA AGGAAGAGTA TGAGTATTCA ACATTTCCGT GTCGCCCTTA TTCCCTTTTT TGCGGCATTT TGCCTTCCTG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TTTTTGCTCA CCCAGAAACG CTGGTGAAAG TAAAAGATGC TGAAGATCAG TTGGGTGCAC GAGTGGGTTA CATCGAACTG GATCTCAACA GCGGTAAGAT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CCTTGAGAGT TTTCGCCCCG AAGAACGTTT TCCAATGATG AGCACTTTTA AAGTTCTGCT ATGTGGCGCG GTATTATCCC GTATTGACGC CGGGCAAGAG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CAACTCGGTC GCCGCATACA CTATTCTCAG AATGACTTGG TTGAGTACTC ACCAGTCACA GAAAAGCATC TTACGGATGG CATGACAGTA AGAGAATTAT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GCAGTGCTGC CATAACCATG AGTGATAACA CTGCGGCCAA CTTACTTCTG ACAACGATCG GAGGACCGAA GGAGCTAACC GCTTTTTTGC ACAACATGGG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GGATCATGTA ACTCGCCTTG ATCGTTGGGA ACCGGAGCTG AATGAAGCCA TACCAAACGA CGAGCGTGAC ACCACGATGC CTGTAGCAAT GGCAACAACG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TTGCGCAAAC TATTAACTGG CGAACTACTT ACTCTAGCTT CCCGGCAACA ATTAATAGAC TGGATGGAGG CGGATAAAGT TGCAGGACCA CTTCTGCGCT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CGGCCCTTCC GGCTGGCTGG TTTATTGCTG ATAAATCTGG AGCCGGTGAG CGTGGGTCTC GCGGTATCAT TGCAGCACTG GGGCCAGATG GTAAGCCCTC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CCGTATCGTA GTTATCTACA CGACGGGGAG TCAGGCAACT ATGGATGAAC GAAATAGACA GATCGCTGAG ATAGGTGCCT CACTGATTAA GCATTGGTAA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CTGTCAGACC AAGTTTACTC ATATATACTT TAGATTGATT TAAAACTTCA TTTTTAATTT AAAAGGATCT AGGTGAAGAT CCTTTTTGAT AATCTCATGA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CCAAAATCCC TTAACGTGAG TTTTCGTTCC ACTGAGCGTC AGACCCCGTA GAAAAGATCA AAGGATCTTC TTGAGATCCT TTTTTTCTGC GCGTAATCTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CTGCTTGCAA ACAAAAAAAC CACCGCTACC AGCGGTGGTT TGTTTGCCGG ATCAAGAGCT ACCAACTCTT TTTCCGAAGG TAACTGGCTT CAGCAGAGCG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CAGATACCAA ATACTGTCCT TCTAGTGTAG CCGTAGTTAG GCCACCACTT CAAGAACTCT GTAGCACCGC CTACATACCT CGCTCTGCTA ATCCTGTTAC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CAGTGGCTGC TGCCAGTGGC GATAAGTCGT GTCTTACCGG GTTGGACTCA AGACGATAGT TACCGGATAA GGCGCAGCGG TCGGGCTGAA CGGGGGGTTC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GTGCACACAG CCCAGCTTGG AGCGAACGAC CTACACCGAA CTGAGATACC TACAGCGTGA GCATTGAGAA AGCGCCACGC TTCCCGAAGG GAGAAAGGCG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GACAGGTATC CGGTAAGCGG CAGGGTCGGA ACAGGAGAGC GCACGAGGGA GCTTCCAGGG GGAAACGCCT GGTATCTTTC TCGTCCTGTC GGGTTTCGCC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ACCTCTGACT TGAGCGTCGA TTTTTGTGAT GCTCGTCAGG GGGGCGGAGC CTATGGAAAA ACGCCAGCAA CGCGGCCTTT TTACGGTTCC TGGCCTTTTG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CTGGCCTTTT GCTCACATGT TCTTTCCTGC GTTATCCCCT GATTCTGTGG ATAACCGTAT TACCGCCTTT GAGTGAGCTG ATACCGCTCG CCGCAGCCGA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ACGACCGAGC GCAGCGAGTC AGTGAGCGAG GAAGCGGAAG AGCGCCCAAT ACGCAAACCG CCTCTCCCCG CGCGTTGGCC GATTCATTAA TGCAGCTGGC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ACGACAGGTT TCCCGACTGG AAAGCGGGCA GTGAGCGCAA CGCAATTAAT GTGAGTTAGC TCACTCATTA GGCACCCCAG GCTTTACACT TTATGCTTCC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GGCTCGTATG TTGTGTGGAA TTGTGAGCGG ATAACAATTT CACACAGGAA ACAGCTATGA CCATGATTAC GCC
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871

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:
eBFP

The description of the protein encoded in this ORF:
Enhanced blue fluorescent protein

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

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

not tested

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

71-790

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
eGFP

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

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

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

not tested

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

1162-1881

Remarks:

The transcription initiation site has been annotated based on the knowledge from GenBank records AF052428 and
X77629.

Citations:

Dyer J. R., Michel S., Lee W., Castellucci V. F., Wayne N. L., Sossin W. S. (2003) An activity-dependent switch to cap-independent translation triggered by eIF4E dephosphorylation. Nat. Neurosci. 6(3):219-220

IRESs:

IRES:

Version: `2`	Last change: `2007-01-23 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `ELH`	The functional status of IRES: `functional`

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

842-1160

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `52`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `370`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-320`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-2`

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

catggggggg aatctttacc gacaacgtcc agcgtcccag tcgagaagta agtagtccga gctgtgagca taactctacc agagaaacgc gcgctttatt 
^842       ^852       ^862       ^872       ^882       ^892       ^902       ^912       ^922       ^932       

ggtcaagata gacggaagcc ggcggttgaa ggcaaaggtt gactcggaag ctgagagatt gttgagtaac acgcagaagt cttgaaagta tcaaggtcca 
^942       ^952       ^962       ^972       ^982       ^992       ^1002      ^1012      ^1022      ^1032      

atcgagaaat tgaacatatt tcaaggaact tggtttcggt gaagtcgtca attcctttta tcgtcaacgt ttccacagcc ctcagaatag aaatttccaa 
^1042      ^1052      ^1062      ^1072      ^1082      ^1092      ^1102      ^1112      ^1122      ^1132      

caagccaaag cctacgtac
^1142      ^1152

Remarks:

Although the article states the 5'-UTR of ELH (bases 1-313) have been cloned into the vector W. Sossin who
provided us with the sequence annotated 319nt as the ELH 5'-UTR insert. We preferred the later annotation.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 298

Version: `2`	Last change: `2007-05-15 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:

Aplysia californica

The temperature (in degrees of Celsia):
20

The relative translation efficiency in % of this IRES:

100.000

	Name of the plasmid used as the negative control. `LR`
	The relative translation efficiency in % of the negative control: `17.800`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

The exact experimental temperature has not been stated in the article. However, it seems A. californica
lays eggs in the temperature around 20 oC, while about 15 oC does not. The egg-laying activity switch is
attributed to the presence of the egg-laying hormone. The sequence of the negative control plasmid with
reverse-oriented ELH insert is not available. Data from Suppl. Fig. 1.

Citations:

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