IRESite_Id:560 characteristics of NRF_-163_-1 IRES studied in pGLuc-NRF-GFP plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `560`	Version: `0`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-03-13 17:37:44`
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:
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 the putative NRF IRES.

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 CGCGTATTTT AGGGCCGATT CTTTGGTTTT ATAGCCAAGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TACCCTGTTG ATAAAGTCTT GTGGGAGCAA TTATAAGACT GGCTTATTTT GAAGCTTTTT AAAAAAGACA TCCTTACCTG TTTTAACTGT AGATTATATT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AACTTAAATA GGTACAGCCC ACGCTTGAGT ATGGTGAGCA AGGGCGAGGA GCTGTTCACC GGGGTGGTGC CCATCCTGGT CGAGCTGGAC GGCGACGTAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ACGGCCACAA GTTCAGCGTG TCCGGCGAGG GCGAGGGCGA TGCCACCTAC GGCAAGCTGA CCCTGAAGTT CATCTGCACC ACCGGCAAGC TGCCCGTGCC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CTGGCCCACC CTCGTGACCA CCTTGACCTA CGGCGTGCAG TGCTTCGCCC GCTACCCCGA CCACATGAAG CAGCACGACT TCTTCAAGTC CGCCATGCCC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAAGGCTACG TCCAGGAGCG CACCATCTTC TTCAAGGACG ACGGCAACTA CAAGACCCGC GCCGAGGTGA AGTTCGAGGG CGACACCCTG GTGAACCGCA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TCGAGCTGAA GGGCATCGAC TTCAAGGAGG ACGGCAACAT CCTGGGGCAC AAGCTGGAGT ACAACTACAA CAGCCACAAG GTCTATATCA CCGCCGACAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GCAGAAGAAC GGCATCAAGG TGAACTTCAA GACCCGCCAC AACATCGAGG ACGGCAGCGT GCAGCTCGCC GACCACTACC AGCAGAACAC CCCCATCGGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GACGGCCCCG TGCTGCTGCC CGACAACCAC TACCTGAGCA CCCAGTCCGC CCTGAGCAAA GACCCCAACG AGAAGCGCGA TCACATGGTC CTGCTGGAGT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCGTGACCGC CGCCGGGATC ACTCTCGGCA TGGACGAGCT GTACAAGTAG CGGCCCAATC TAGAGTCGGG GCGGCCGGCC GCTTCGAGCA GACATGATAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GATACATTGA TGAGTTTGGA CAAACCACAA CTAGAATGCA GTGAAAAAAA TGCTTTATTT GTGAAATTTG TGATGCTATT GCTTTATTTG TAACCATTAT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AAGCTGCAAT AAACAAGTTA ACAACAACAA TTGCATTCAT TTTATGTTTC AGGTTCAGGG GGAGGTGTGG GAGGTTTTTT AAAGCAAGTA AAACCTCTAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AAATGTGGTA
^1801

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pGLuc-NRF-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?):

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:
NRF

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens

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 TAAACGCGTA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TTTTAGGGCC GATTCTTTGG TTTTATAGCC AAGATACCCT GTTGATAAAG TCTTGTGGGA GCAATTATAA GACTGGCTTA TTTTGAAGCT TTTTAAAAAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GACATCCTTA CCTGTTTTAA CTGTAGATTA TATTAACTTA AATAGGTACA GCCCACGCTT GAGTATGGTG AGCAAGGGCG AGGAGCTGTT CACCGGGGTG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GTGCCCATCC TGGTCGAGCT GGACGGCGAC GTAAACGGCC ACAAGTTCAG CGTGTCCGGC GAGGGCGAGG GCGATGCCAC CTACGGCAAG CTGACCCTGA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AGTTCATCTG CACCACCGGC AAGCTGCCCG TGCCCTGGCC CACCCTCGTG ACCACCTTGA CCTACGGCGT GCAGTGCTTC GCCCGCTACC CCGACCACAT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GAAGCAGCAC GACTTCTTCA AGTCCGCCAT GCCCGAAGGC TACGTCCAGG AGCGCACCAT CTTCTTCAAG GACGACGGCA ACTACAAGAC CCGCGCCGAG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GTGAAGTTCG AGGGCGACAC CCTGGTGAAC CGCATCGAGC TGAAGGGCAT CGACTTCAAG GAGGACGGCA ACATCCTGGG GCACAAGCTG GAGTACAACT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACAACAGCCA CAAGGTCTAT ATCACCGCCG ACAAGCAGAA GAACGGCATC AAGGTGAACT TCAAGACCCG CCACAACATC GAGGACGGCA GCGTGCAGCT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGCCGACCAC TACCAGCAGA ACACCCCCAT CGGCGACGGC CCCGTGCTGC TGCCCGACAA CCACTACCTG AGCACCCAGT CCGCCCTGAG CAAAGACCCC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AACGAGAAGC GCGATCACAT GGTCCTGCTG GAGTTCGTGA CCGCCGCCGG GATCACTCTC GGCATGGACG AGCTGTACAA GTAGCGGCCC AATCTAGAGT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CGGGGCGGCC GGCCGCTTCG AGCAGACATG ATAAGATACA TTGATGAGTT TGGACAAACC ACAACTAGAA TGCAGTGAAA AAAATGCTTT ATTTGTGAAA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTTGTGATGC TATTGCTTTA TTTGTAACCA TTATAAGCTG CAATAAACAA GTTAACAACA ACAATTGCAT TCATTTTATG TTTCAGGTTC AGGGGGAGGT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTGGGAGGTT TTTTAAAGCA AGTAAAACCT CTACAAATGT GGTAAAATCG ATAAGGATCC GTCGACCGAT GCCCTTGAGA GCCTTCAACC CAGTCAGCTC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CTTCCGGTGG GCGCGGGGCA TGACTATCGT CGCCGCACTT ATGACTGTCT TCTTTATCAT GCAACTCGTA GGACAGGTGC CGGCAGCGCT CTTCCGCTTC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CTCGCTCACT GACTCGCTGC GCTCGGTCGT TCGGCTGCGG CGAGCGGTAT CAGCTCACTC AAAGGCGGTA ATACGGTTAT CCACAGAATC AGGGGATAAC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GCAGGAAAGA ACATGTGAGC AAAAGGCCAG CAAAAGGCCA GGAACCGTAA AAAGGCCGCG TTGCTGGCGT TTTTCCATAG GCTCCGCCCC CCTGACGAGC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ATCACAAAAA TCGACGCTCA AGTCAGAGGT GGCGAAACCC GACAGGACTA TAAAGATACC AGGCGTTTCC CCCTGGAAGC TCCCTCGTGC GCTCTCCTGT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TCCGACCCTG CCGCTTACCG GATACCTGTC CGCCTTTCTC CCTTCGGGAA GCGTGGCGCT TTCTCATAGC TCACGCTGTA GGTATCTCAG TTCGGTGTAG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GTCGTTCGCT CCAAGCTGGG CTGTGTGCAC GAACCCCCCG TTCAGCCCGA CCGCTGCGCC TTATCCGGTA ACTATCGTCT TGAGTCCAAC CCGGTAAGAC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ACGACTTATC GCCACTGGCA GCAGCCACTG GTAACAGGAT TAGCAGAGCG AGGTATGTAG GCGGTGCTAC AGAGTTCTTG AAGTGGTGGC CTAACTACGG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CTACACTAGA AGAACAGTAT TTGGTATCTG CGCTCTGCTG AAGCCAGTTA CCTTCGGAAA AAGAGTTGGT AGCTCTTGAT CCGGCAAACA AACCACCGCT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GGTAGCGGTG GTTTTTTTGT TTGCAAGCAG CAGATTACGC GCAGAAAAAA AGGATCTCAA GAAGATCCTT TGATCTTTTC TACGGGGTCT GACGCTCAGT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GGAACGAAAA CTCACGTTAA GGGATTTTGG TCATGAGATT ATCAAAAAGG ATCTTCACCT AGATCCTTTT AAATTAAAAA TGAAGTTTTA AATCAATCTA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AAGTATATAT GAGTAAACTT GGTCTGACAG CGGCCGCAAA TGCTAAACCA CTGCAGTGGT TACCAGTGCT TGATCAGTGA GGCACCGATC TCAGCGATCT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GCCTATTTCG TTCGTCCATA GTGGCCTGAC TCCCCGTCGT GTAGATCACT ACGATTCGTG AGGGCTTACC ATCAGGCCCC AGCGCAGCAA TGATGCCGCG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AGAGCCGCGT TCACCGGCCC CCGATTTGTC AGCAATGAAC CAGCCAGCAG GGAGGGCCGA GCGAAGAAGT GGTCCTGCTA CTTTGTCCGC CTCCATCCAG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TCTATGAGCT GCTGTCGTGA TGCTAGAGTA AGAAGTTCGC CAGTGAGTAG TTTCCGAAGA GTTGTGGCCA TTGCTACTGG CATCGTGGTA TCACGCTCGT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CGTTCGGTAT GGCTTCGTTC AACTCTGGTT CCCAGCGGTC AAGCCGGGTC ACATGATCAC CCATATTATG AAGAAATGCA GTCAGCTCCT TAGGGCCTCC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GATCGTTGTC AGAAGTAAGT TGGCCGCGGT GTTGTCGCTC ATGGTAATGG CAGCACTACA CAATTCTCTT ACCGTCATGC CATCCGTAAG ATGCTTTTCC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GTGACCGGCG AGTACTCAAC CAAGTCGTTT TGTGAGTAGT GTATACGGCG ACCAAGCTGC TCTTGCCCGG CGTCTATACG GGACAACACC GCGCCACATA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GCAGTACTTT GAAAGTGCTC ATCATCGGGA ATCGTTCTTC GGGGCGGAAA GACTCAAGGA TCTTGCCGCT ATTGAGATCC AGTTCGATAT AGCCCACTCT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TGCACCCAGT TGATCTTCAG CATCTTTTAC TTTCACCAGC GTTTCGGGGT GTGCAAAAAC AGGCAAGCAA AATGCCGCAA AGAAGGGAAT GAGTGCGACA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CGAAAATGTT GGATGCTCAT ACTCGTCCTT TTTCAATATT ATTGAAGCAT TTATCAGGGT TACTAGTACG TCTCTCAAGG ATAAGTAAGT AATATTAAGG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TACGGGAGGT ATTGGACAGG CCGCAATAAA ATATCTTTAT TTTCATTACA TCTGTGTGTT GGTTTTTTGT GTGAATCGAT AGTACTAACA TACGCTCTCC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ATCAAAACAA AACGAAACAA AACAAACTAG CAAAATAGGC TGTCCCCAGT GCAAGTGCAG GTGCCAGAAC ATTTCTCTGG CCTAACTGGC C
^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):

831-1550

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: `NRF_-163_-1`	The functional status of IRES: `functional`

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

665-827

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `17`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `179`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-166`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-4`

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

TATTTTAGGG CCGATTCTTT GGTTTTATAG CCAAGATACC CTGTTGATAA AGTCTTGTGG GAGCAATTAT AAGACTGGCT TATTTTGAAG CTTTTTAAAA 
^665       ^675       ^685       ^695       ^705       ^715       ^725       ^735       ^745       ^755       

AAGACATCCT TACCTGTTTT AACTGTAGAT TATATTAACT TAAATAGGTA CAGCCCACGC TTG
^765       ^775       ^785       ^795       ^805       ^815       ^825

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 603

Version: `1`	Last change: `2009-07-16 14:39:41`
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:

21.800

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: 604

Version: `1`	Last change: `2009-07-16 14:39:41`
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:

25.700

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