IRESite_Id:562 characteristics of VEGF-A_-133_-1 IRES studied in pGLuc-SP163-GFP plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `562`	Version: `2`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-03-13 17:52:39`
Reviewed by: Martin Mokrejš	Last change: `2009-03-17 01:05:25`

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:
our_best_guess

The mRNA/+RNA description:

Putative in vivo transcript driven from CMV IE promoter and terminated after the SV40 late poly(A) signal
containing GLuc (Gaussia luciferase) and GFP cistrons separated by putative VEGF-A IRES from mouse.

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

GTCAGATCAC TAGAAGCTTA TCAGACGACA TCACTCGAGA CTAACTCACC GGAATTCCAA GCTGGCAACT TCCGGAAGCT GCAAGCCACC ATGGGAGTCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAGTCCTGTT CGCTCTGATC TGCATCGCTG TGGCCGAGGC CAAGCCCACC GAGAACAACG AAGACTTCAA CATCGTCGCC GTGGCCAGCA ACTTCGCAAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CACTGATCTG GACGCTGACA GAGGCAAACT GCCTGGCAAG AAGCTGCCTC TCGAAGTCCT GAAAGAGATG GAAGCCAACG CTCGGAAGGC TGGCTGCACA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGAGGCTGCC TGATCTGCCT GTCCCACATC AAATGCACAC CCAAGATGAA GAAATTCATC CCTGGACGCT GCCACACCTA CGAAGGCGAC AAAGAATCCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CACAGGGAGG CATTGGAGAA GCCATTGTCG ACATTCCCGA GATTCCTGGA TTCAAGGACC TGGAGCCTAT GGAGCAGTTC ATCGCACAAG TCGACCTCTG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGTGGACTGC ACAACTGGAT GCCTCAAAGG CCTCGCTAAT GTCCAATGCT CTGACCTGCT CAAGAAATGG CTCCCACAGC GCTGCGCTAC CTTCGCAAGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AAGATCCAGG GCCAAGTCGA TAAGATCAAG GGAGCAGGCG GAGACTAAAC CTAGTTTAAA CGCGTTTCGT ACGAGCGCAG AGGCTTGGGG CAGCCGAGCG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GCAGCCAGGC CCCGGCCCGG GCCTCGGTTC CAGAAGGGAG AGGAGCCCGC CAAGGCGCGC AAGAGAGCGG GCTGCCTCGC AGTCCGAGCC GGAGAGGGAG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CGCGAGCCGC GCCGGCCCCG GACGGCCTCC GAAACCATGA TTCGAACAAA GGGCGAGGAG CTGTTCACCG GGGTGGTGCC CATCCTGGTC GAGCTGGACG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GCGACGTAAA CGGCCACAAG TTCAGCGTGT CCGGCGAGGG CGAGGGCGAT GCCACCTACG GCAAGCTGAC CCTGAAGTTC ATCTGCACCA CCGGCAAGCT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GCCCGTGCCC TGGCCCACCC TCGTGACCAC CTTGACCTAC GGCGTGCAGT GCTTCGCCCG CTACCCCGAC CACATGAAGC AGCACGACTT CTTCAAGTCC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GCCATGCCCG AAGGCTACGT CCAGGAGCGC ACCATCTTCT TCAAGGACGA CGGCAACTAC AAGACCCGCG CCGAGGTGAA GTTCGAGGGC GACACCCTGG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGAACCGCAT CGAGCTGAAG GGCATCGACT TCAAGGAGGA CGGCAACATC CTGGGGCACA AGCTGGAGTA CAACTACAAC AGCCACAAGG TCTATATCAC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CGCCGACAAG CAGAAGAACG GCATCAAGGT GAACTTCAAG ACCCGCCACA ACATCGAGGA CGGCAGCGTG CAGCTCGCCG ACCACTACCA GCAGAACACC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CCCATCGGCG ACGGCCCCGT GCTGCTGCCC GACAACCACT ACCTGAGCAC CCAGTCCGCC CTGAGCAAAG ACCCCAACGA GAAGCGCGAT CACATGGTCC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGCTGGAGTT CGTGACCGCC GCCGGGATCA CTCTCGGCAT GGACGAGCTG TACAAGTAGC GGCCCAATCT AGAGTCGGGG CGGCCGGCCG CTTCGAGCAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACATGATAAG ATACATTGAT GAGTTTGGAC AAACCACAAC TAGAATGCAG TGAAAAAAAT GCTTTATTTG TGAAATTTGT GATGCTATTG CTTTATTTGT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AACCATTATA AGCTGCAATA AACAAGTTAA CAACAACAAT TGCATTCATT TTATGTTTCA GGTTCAGGGG GAGGTGTGGG AGGTTTTTTA AAGCAAGTAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AACCTCTACA AATGTGGTA
^1801      ^1811

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pGLuc-SP163-GFP The name of the promoter used to express this mRNA:
CMV_IE

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:
homogeneous_population_of_molecules_confirmed

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:
not_tested

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:
homogeneous_population_of_molecules_confirmed

The organism used:

Homo sapiens HeLa (ATCC CCL-2)

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

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:

TCAATATTGG CCATTAGCCA TATTATTCAT TGGTTATATA GCATAAATCA ATATTGGCTA TTGGCCATTG CATACGTTGT ATCTATATCA TAATATGTAC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ATTTATATTG GCTCATGTCC AATATGACCG CCATGTTGGC ATTGATTATT GACTAGTTAT TAATAGTAAT CAATTACGGG GTCATTAGTT CATAGCCCAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ATATGGAGTT CCGCGTTACA TAACTTACGG TAAATGGCCC GCCTGGCTGA CCGCCCAACG ACCCCCGCCC ATTGACGTCA ATAATGACGT ATGTTCCCAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGTAACGCCA ATAGGGACTT TCCATTGACG TCAATGGGTG GAGTATTTAC GGTAAACTGC CCACTTGGCA GTACATCAAG TGTATCATAT GCCAAGTCCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCCCCTATTG ACGTCAATGA CGGTAAATGG CCCGCCTGGC ATTATGCCCA GTACATGACC TTACGGGACT TTCCTACTTG GCAGTACATC TACGTATTAG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCATCGCTAT TACCATGGTG ATGCGGTTTT GGCAGTACAC CAATGGGCGT GGATAGCGGT TTGACTCACG GGGATTTCCA AGTCTCCACC CCATTGACGT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CAATGGGAGT TTGTTTTGGC ACCAAAATCA ACGGGACTTT CCAAAATGTC GTAATAACCC CGCCCCGTTG ACGCAAATGG GCGGTAGGCG TGTACGGTGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GAGGTCTATA TAAGCAGAGC TCGTTTAGTG AACCGTCAGA TCACTAGAAG CTTATCAGAC GACATCACTC GAGACTAACT CACCGGAATT CCAAGCTGGC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AACTTCCGGA AGCTGCAAGC CACCATGGGA GTCAAAGTCC TGTTCGCTCT GATCTGCATC GCTGTGGCCG AGGCCAAGCC CACCGAGAAC AACGAAGACT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCAACATCGT CGCCGTGGCC AGCAACTTCG CAACCACTGA TCTGGACGCT GACAGAGGCA AACTGCCTGG CAAGAAGCTG CCTCTCGAAG TCCTGAAAGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GATGGAAGCC AACGCTCGGA AGGCTGGCTG CACAAGAGGC TGCCTGATCT GCCTGTCCCA CATCAAATGC ACACCCAAGA TGAAGAAATT CATCCCTGGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CGCTGCCACA CCTACGAAGG CGACAAAGAA TCCGCACAGG GAGGCATTGG AGAAGCCATT GTCGACATTC CCGAGATTCC TGGATTCAAG GACCTGGAGC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CTATGGAGCA GTTCATCGCA CAAGTCGACC TCTGCGTGGA CTGCACAACT GGATGCCTCA AAGGCCTCGC TAATGTCCAA TGCTCTGACC TGCTCAAGAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ATGGCTCCCA CAGCGCTGCG CTACCTTCGC AAGCAAGATC CAGGGCCAAG TCGATAAGAT CAAGGGAGCA GGCGGAGACT AAACCTAGTT TAAACGCGTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCGTACGAGC GCAGAGGCTT GGGGCAGCCG AGCGGCAGCC AGGCCCCGGC CCGGGCCTCG GTTCCAGAAG GGAGAGGAGC CCGCCAAGGC GCGCAAGAGA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GCGGGCTGCC TCGCAGTCCG AGCCGGAGAG GGAGCGCGAG CCGCGCCGGC CCCGGACGGC CTCCGAAACC ATGATTCGAA CAAAGGGCGA GGAGCTGTTC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACCGGGGTGG TGCCCATCCT GGTCGAGCTG GACGGCGACG TAAACGGCCA CAAGTTCAGC GTGTCCGGCG AGGGCGAGGG CGATGCCACC TACGGCAAGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGACCCTGAA GTTCATCTGC ACCACCGGCA AGCTGCCCGT GCCCTGGCCC ACCCTCGTGA CCACCTTGAC CTACGGCGTG CAGTGCTTCG CCCGCTACCC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CGACCACATG AAGCAGCACG ACTTCTTCAA GTCCGCCATG CCCGAAGGCT ACGTCCAGGA GCGCACCATC TTCTTCAAGG ACGACGGCAA CTACAAGACC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGCGCCGAGG TGAAGTTCGA GGGCGACACC CTGGTGAACC GCATCGAGCT GAAGGGCATC GACTTCAAGG AGGACGGCAA CATCCTGGGG CACAAGCTGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGTACAACTA CAACAGCCAC AAGGTCTATA TCACCGCCGA CAAGCAGAAG AACGGCATCA AGGTGAACTT CAAGACCCGC CACAACATCG AGGACGGCAG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGTGCAGCTC GCCGACCACT ACCAGCAGAA CACCCCCATC GGCGACGGCC CCGTGCTGCT GCCCGACAAC CACTACCTGA GCACCCAGTC CGCCCTGAGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AAAGACCCCA ACGAGAAGCG CGATCACATG GTCCTGCTGG AGTTCGTGAC CGCCGCCGGG ATCACTCTCG GCATGGACGA GCTGTACAAG TAGCGGCCCA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ATCTAGAGTC GGGGCGGCCG GCCGCTTCGA GCAGACATGA TAAGATACAT TGATGAGTTT GGACAAACCA CAACTAGAAT GCAGTGAAAA AAATGCTTTA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTTGTGAAAT TTGTGATGCT ATTGCTTTAT TTGTAACCAT TATAAGCTGC AATAAACAAG TTAACAACAA CAATTGCATT CATTTTATGT TTCAGGTTCA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GGGGGAGGTG TGGGAGGTTT TTTAAAGCAA GTAAAACCTC TACAAATGTG GTAAAATCGA TAAGGATCCG TCGACCGATG CCCTTGAGAG CCTTCAACCC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AGTCAGCTCC TTCCGGTGGG CGCGGGGCAT GACTATCGTC GCCGCACTTA TGACTGTCTT CTTTATCATG CAACTCGTAG GACAGGTGCC GGCAGCGCTC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TTCCGCTTCC TCGCTCACTG ACTCGCTGCG CTCGGTCGTT CGGCTGCGGC GAGCGGTATC AGCTCACTCA AAGGCGGTAA TACGGTTATC CACAGAATCA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GGGGATAACG CAGGAAAGAA CATGTGAGCA AAAGGCCAGC AAAAGGCCAG GAACCGTAAA AAGGCCGCGT TGCTGGCGTT TTTCCATAGG CTCCGCCCCC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CTGACGAGCA TCACAAAAAT CGACGCTCAA GTCAGAGGTG GCGAAACCCG ACAGGACTAT AAAGATACCA GGCGTTTCCC CCTGGAAGCT CCCTCGTGCG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CTCTCCTGTT CCGACCCTGC CGCTTACCGG ATACCTGTCC GCCTTTCTCC CTTCGGGAAG CGTGGCGCTT TCTCATAGCT CACGCTGTAG GTATCTCAGT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TCGGTGTAGG TCGTTCGCTC CAAGCTGGGC TGTGTGCACG AACCCCCCGT TCAGCCCGAC CGCTGCGCCT TATCCGGTAA CTATCGTCTT GAGTCCAACC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CGGTAAGACA CGACTTATCG CCACTGGCAG CAGCCACTGG TAACAGGATT AGCAGAGCGA GGTATGTAGG CGGTGCTACA GAGTTCTTGA AGTGGTGGCC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TAACTACGGC TACACTAGAA GAACAGTATT TGGTATCTGC GCTCTGCTGA AGCCAGTTAC CTTCGGAAAA AGAGTTGGTA GCTCTTGATC CGGCAAACAA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ACCACCGCTG GTAGCGGTGG TTTTTTTGTT TGCAAGCAGC AGATTACGCG CAGAAAAAAA GGATCTCAAG AAGATCCTTT GATCTTTTCT ACGGGGTCTG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ACGCTCAGTG GAACGAAAAC TCACGTTAAG GGATTTTGGT CATGAGATTA TCAAAAAGGA TCTTCACCTA GATCCTTTTA AATTAAAAAT GAAGTTTTAA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ATCAATCTAA AGTATATATG AGTAAACTTG GTCTGACAGC GGCCGCAAAT GCTAAACCAC TGCAGTGGTT ACCAGTGCTT GATCAGTGAG GCACCGATCT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CAGCGATCTG CCTATTTCGT TCGTCCATAG TGGCCTGACT CCCCGTCGTG TAGATCACTA CGATTCGTGA GGGCTTACCA TCAGGCCCCA GCGCAGCAAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GATGCCGCGA GAGCCGCGTT CACCGGCCCC CGATTTGTCA GCAATGAACC AGCCAGCAGG GAGGGCCGAG CGAAGAAGTG GTCCTGCTAC TTTGTCCGCC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TCCATCCAGT CTATGAGCTG CTGTCGTGAT GCTAGAGTAA GAAGTTCGCC AGTGAGTAGT TTCCGAAGAG TTGTGGCCAT TGCTACTGGC ATCGTGGTAT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CACGCTCGTC GTTCGGTATG GCTTCGTTCA ACTCTGGTTC CCAGCGGTCA AGCCGGGTCA CATGATCACC CATATTATGA AGAAATGCAG TCAGCTCCTT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AGGGCCTCCG ATCGTTGTCA GAAGTAAGTT GGCCGCGGTG TTGTCGCTCA TGGTAATGGC AGCACTACAC AATTCTCTTA CCGTCATGCC ATCCGTAAGA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TGCTTTTCCG TGACCGGCGA GTACTCAACC AAGTCGTTTT GTGAGTAGTG TATACGGCGA CCAAGCTGCT CTTGCCCGGC GTCTATACGG GACAACACCG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CGCCACATAG CAGTACTTTG AAAGTGCTCA TCATCGGGAA TCGTTCTTCG GGGCGGAAAG ACTCAAGGAT CTTGCCGCTA TTGAGATCCA GTTCGATATA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GCCCACTCTT GCACCCAGTT GATCTTCAGC ATCTTTTACT TTCACCAGCG TTTCGGGGTG TGCAAAAACA GGCAAGCAAA ATGCCGCAAA GAAGGGAATG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AGTGCGACAC GAAAATGTTG GATGCTCATA CTCGTCCTTT TTCAATATTA TTGAAGCATT TATCAGGGTT ACTAGTACGT CTCTCAAGGA TAAGTAAGTA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ATATTAAGGT ACGGGAGGTA TTGGACAGGC CGCAATAAAA TATCTTTATT TTCATTACAT CTGTGTGTTG GTTTTTTGTG TGAATCGATA GTACTAACAT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ACGCTCTCCA TCAAAACAAA ACGAAACAAA ACAAACTAGC AAAATAGGCT GTCCCCAGTG CAAGTGCAGG TGCCAGAACA TTTCTCTGGC CTAACTGGCC
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791

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:
GLuc

The description of the protein encoded in this ORF:
Gaussia 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):

91-648

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
GFP

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

837-1559

Remarks:

The IRES sequence is a part of mouse VEGF-A 5'-UTR (while considering the AUG codon as the translation START
site). The alternative CUG codon is -534bp usptream. The "IRES" region is -133 to -1 upstream of the AUG
codon.

Citations:

Baranick B. T., Lemp N. A., Nagashima J., Hiraoka K., Kasahara N., Logg C. R. (2008) Splicing mediates the activity of four putative cellular internal ribosome entry sites. Proc. Natl. Acad. Sci. U. S. A. 105(12):4733-4738

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `VEGF-A_-133_-1`	The functional status of IRES: `functional`

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

705-836

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `57`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `188`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-132`	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):

CCAGGCCCCG GCCCGGGCCT CGGTTCCAGA AGGGAGAGGA GCCCGCCAAG GCGCGCAAGA GAGCGGGCTG CCTCGCAGTC CGAGCCGGAG AGGGAGCGCG 
^705       ^715       ^725       ^735       ^745       ^755       ^765       ^775       ^785       ^795       

AGCCGCGCCG GCCCCGGACG GCCTCCGAAA CC
^805       ^815       ^825       ^835

Remarks:

The IRES "activity" was about 20% of EMCV and in general, close to BiP, eIF4G, NRF, Rbm3, see Figures 1B and
1C. There were no splice donor nor acceptor sites unleashed in the sequence (nor by RT-PCR nor by functional
assay using MoMLV sensitive to altered levels of spliced messages of its own transcripts followed by the
putative IRES and GFP CDS.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 611

Version: `2`	Last change: `2009-07-16 14:45:15`
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:

17.000

Name of IRES used as the positive control:

EMCV-R_-541_-7

Name of the plasmid used as the positive control. `pGLuc-EMCV-GFP`	Name of the plasmid used as the negative control. `pGLuc-GFP`
`IRESite Id` of the plasmid used as positive control. `557`	`IRESite Id` of the plasmid used as negative control. `556`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `10.800`
The size (length) of intercistronic region in the positive control: `565`	The size (length) of intercistronic region in the negative control: `17`

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:

Data from Figure 1B.

Citations:

Translation results:

IRESite Translation Id: 612

Version: `2`	Last change: `2009-07-16 14:45:15`
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 NIH/3T3 (ATCC CRL-1658)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

14.100

Name of IRES used as the positive control:

EMCV-R_-541_-7

Name of the plasmid used as the positive control. `pGLuc-EMCV-GFP`	Name of the plasmid used as the negative control. `pGLuc-GFP`
`IRESite Id` of the plasmid used as positive control. `557`	`IRESite Id` of the plasmid used as negative control. `556`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `10.900`
The size (length) of intercistronic region in the positive control: `565`	The size (length) of intercistronic region in the negative control: `17`

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:

Data from Figure 1B.

Citations:

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