IRESite_Id:401 characteristics of BiP IRES studied in pBL-p(A) plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `401`	Version: `1`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-06-20 12:56:22`

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:
end-to-end_full-length_mRNA

The mRNA/+RNA description:

In vitro T3 run-off transcript containing 5' UTR of human BiP (nt from -219 to -3) mRNA cloned upstream of the
luciferase reporter RNA bearing a poly(A) tail.

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

GGGAACAAAA GCTGGGTACC GGGCCCCCCC TCGAGGTCGA CGGTATCGAT AAGCTTGATA TCGAATTCCT GCAGCCCGGG GGATCCAGGT CGACGCCGGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CAAGACAGCA CAGACAGATT GACCTATTGG GGTGTTTCGC GAGTGTGAGA GGGAAGCGCC GCGGCCTGTA TTTCTAGACC TGCCCTTCGC CTGGTTCGTG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCGCCTTGTG ACCCCGGGCC CCTGCCGCCT GCAAGTCGGA AATTGCGCTG TGCTCCTGTG CTACGGCCTG TGGCTGGACT GCCTGCTGCT GCCCAACTGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CTGGCACCAT GGCCGAAGAC GCCAAAAACA TAAAGAAAGG CCCGGCGCCA TTCTATCCTC TAGAGGATGG AACCGCTGGA GAGCAACTGC ATAAGGCTAT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GAAGAGATAC GCCCTGGTTC CTGGAACAAT TGCTTTTACA GATGCACATA TCGAGGTGAA CATCACGTAC GCGGAATACT TCGAAATGTC CGTTCGGTTG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GCAGAAGCTA TGAAACGATA TGGGCTGAAT ACAAATCACA GAATCGTCGT ATGCAGTGAA AACTCTCTTC AATTCTTTAT GCCGGTGTTG GGCGCGTTAT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTATCGGAGT TGCAGTTGCG CCCGCGAACG ACATTTATAA TGAACGTGAA TTGCTCAACA GTATGAACAT TTCGCAGCCT ACCGTAGTGT TTGTTTCCAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AAAGGGGTTG CAAAAAATTT TGAACGTGCA AAAAAAATTA CCAATAATCC AGAAAATTAT TATCATGGAT TCTAAAACGG ATTACCAGGG ATTTCAGTCG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATGTACACGT TCGTCACATC TCATCTACCT CCCGGTTTTA ATGAATACGA TTTTGTACCA GAGTCCTTTG ATCGTGACAA AACAATTGCA CTGATAATGA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATTCCTCTGG ATCTACTGGG TTACCTAAGG GTGTGGCCCT TCCGCATAGA ACTGCCTGCG TCAGATTCTC GCATGCCAGA GATCCTATTT TTGGCAATCA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AATCATTCCG GATACTGCGA TTTTAAGTGT TGTTCCATTC CATCACGGTT TTGGAATGTT TACTACACTC GGATATTTGA TATGTGGATT TCGAGTCGTC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TTAATGTATA GATTTGAAGA AGAGCTGTTT TTACGATCCC TTCAGGATTA CAAAATTCAA AGTGCGTTGC TAGTACCAAC CCTATTTTCA TTCTTCGCCA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AAAGCACTCT GATTGACAAA TACGATTTAT CTAATTTACA CGAAATTGCT TCTGGGGGCG CACCTCTTTC GAAAGAAGTC GGGGAAGCGG TTGCAAAACG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CTTCCATCTT CCAGGGATAC GACAAGGATA TGGGCTCACT GAGACTACAT CAGCTATTCT GATTACACCC GAGGGGGATG ATAAACCGGG CGCGGTCGGT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAAGTTGTTC CATTTTTTGA AGCGAAGGTT GTGGATCTGG ATACCGGGAA AACGCTGGGC GTTAATCAGA GAGGCGAATT ATGTGTCAGA GGACCTATGA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTATGTCCGG TTATGTAAAC AATCCGGAAG CGACCAACGC CTTGATTGAC AAGGATGGAT GGCTACATTC TGGAGACATA GCTTACTGGG ACGAAGACGA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACACTTCTTC ATAGTTGACC GCTTGAAGTC TTTAATTAAA TACAAAGGAT ATCAGGTGGC CCCCGCTGAA TTGGAATCGA TATTGTTACA ACACCCCAAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ATCTTCGACG CGGGCGTGGC AGGTCTTCCC GACGATGACG CCGGTGAACT TCCCGCCGCC GTTGTTGTTT TGGAGCACGG AAAGACGATG ACGGAAAAAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGATCGTGGA TTACGTCGCC AGTCAAGTAA CAACCGCGAA AAAGTTGCGC GGAGGAGTTG TGTTTGTGGA CGAAGTACCG AAAGGTCTTA CCGGAAAACT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGACGCAAGA AAAATCAGAG AGATCCTCAT AAAGGCCAAG AAGGGCGGAA AGTCCAAATT GTAATAGATC CACTAGTTCT AGAGCGGCCG CCACCGCGGT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGAGGGGTAC AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAGTACCGAG
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The name of the plasmid:
pBL-p(A) The name of the promoter used to express this mRNA:
T3

Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing 5' UTR of human BiP (nt from -219 to -3) and firefly luciferase coding region (luc version of the luciferase gene) with the poly(A)tract.

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:
BiP

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens HeLa (ATCC CCL-2)

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

GTGGCACTTT TCGGGGAAAT GTGCGCGGAA CCCCTATTTG TTTATTTTTC TAAATACATT CAAATATGTA TCCGCTCATG AGACAATAAC CCTGATAAAT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCTTCAATAA TATTGAAAAA GGAAGAGTAT GAGTATTCAA CATTTCCGTG TCGCCCTTAT TCCCTTTTTT GCGGCATTTT GCCTTCCTGT TTTTGCTCAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCAGAAACGC TGGTGAAAGT AAAAGATGCT GAAGATCAGT TGGGTGCACG AGTGGGTTAC ATCGAACTGG ATCTCAACAG CGGTAAGATC CTTGAGAGTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTCGCCCCGA AGAACGTTTT CCAATGATGA GCACTTTTAA AGTTCTGCTA TGTGGCGCGG TATTATCCCG TATTGACGCC GGGCAAGAGC AACTCGGTCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCGCATACAC TATTCTCAGA ATGACTTGGT TGAGTACTCA CCAGTCACAG AAAAGCATCT TACGGATGGC ATGACAGTAA GAGAATTATG CAGTGCTGCC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ATAACCATGA GTGATAACAC TGCGGCCAAC TTACTTCTGA CAACGATCGG AGGACCGAAG GAGCTAACCG CTTTTTTGCA CAACATGGGG GATCATGTAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CTCGCCTTGA TCGTTGGGAA CCGGAGCTGA ATGAAGCCAT ACCAAACGAC GAGCGTGACA CCACGATGCC TGTAGCAATG GCAACAACGT TGCGCAAACT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATTAACTGGC GAACTACTTA CTCTAGCTTC CCGGCAACAA TTAATAGACT GGATGGAGGC GGATAAAGTT GCAGGACCAC TTCTGCGCTC GGCCCTTCCG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GCTGGCTGGT TTATTGCTGA TAAATCTGGA GCCGGTGAGC GTGGGTCTCG CGGTATCATT GCAGCACTGG GGCCAGATGG TAAGCCCTCC CGTATCGTAG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTATCTACAC GACGGGGAGT CAGGCAACTA TGGATGAACG AAATAGACAG ATCGCTGAGA TAGGTGCCTC ACTGATTAAG CATTGGTAAC TGTCAGACCA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGTTTACTCA TATATACTTT AGATTGATTT AAAACTTCAT TTTTAATTTA AAAGGATCTA GGTGAAGATC CTTTTTGATA ATCTCATGAC CAAAATCCCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TAACGTGAGT TTTCGTTCCA CTGAGCGTCA GACCCCGTAG AAAAGATCAA AGGATCTTCT TGAGATCCTT TTTTTCTGCG CGTAATCTGC TGCTTGCAAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CAAAAAAACC ACCGCTACCA GCGGTGGTTT GTTTGCCGGA TCAAGAGCTA CCAACTCTTT TTCCGAAGGT AACTGGCTTC AGCAGAGCGC AGATACCAAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TACTGTCCTT CTAGTGTAGC CGTAGTTAGG CCACCACTTC AAGAACTCTG TAGCACCGCC TACATACCTC GCTCTGCTAA TCCTGTTACC AGTGGCTGCT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCCAGTGGCG ATAAGTCGTG TCTTACCGGG TTGGACTCAA GACGATAGTT ACCGGATAAG GCGCAGCGGT CGGGCTGAAC GGGGGGTTCG TGCACACAGC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CCAGCTTGGA GCGAACGACC TACACCGAAC TGAGATACCT ACAGCGTGAG CTATGAGAAA GCGCCACGCT TCCCGAAGGG AGAAAGGCGG ACAGGTATCC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGTAAGCGGC AGGGTCGGAA CAGGAGAGCG CACGAGGGAG CTTCCAGGGG GAAACGCCTG GTATCTTTAT AGTCCTGTCG GGTTTCGCCA CCTCTGACTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GAGCGTCGAT TTTTGTGATG CTCGTCAGGG GGGCGGAGCC TATGGAAAAA CGCCAGCAAC GCGGCCTTTT TACGGTTCCT GGCCTTTTGC TGGCCTTTTG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTCACATGTT CTTTCCTGCG TTATCCCCTG ATTCTGTGGA TAACCGTATT ACCGCCTTTG AGTGAGCTGA TACCGCTCGC CGCAGCCGAA CGACCGAGCG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CAGCGAGTCA GTGAGCGAGG AAGCGGAAGA GCGCCCAATA CGCAAACCGC CTCTCCCCGC GCGTTGGCCG ATTCATTAAT GCAGCTGGCA CGACAGGTTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCCGACTGGA AAGCGGGCAG TGAGCGCAAC GCAATTAATG TGAGTTAGCT CACTCATTAG GCACCCCAGG CTTTACACTT TATGCTTCCG GCTCGTATGT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGTGTGGAAT TGTGAGCGGA TAACAATTTC ACACAGGAAA CAGCTATGAC CATGATTACG CCAAGCGCGC AATTAACCCT CACTAAAGGG AACAAAAGCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GGGTACCGGG CCCCCCCTCG AGGTCGACGG TATCGATAAG CTTGATATCG AATTCCTGCA GCCCGGGGGA TCCAGGTCGA CGCCGGCCAA GACAGCACAG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ACAGATTGAC CTATTGGGGT GTTTCGCGAG TGTGAGAGGG AAGCGCCGCG GCCTGTATTT CTAGACCTGC CCTTCGCCTG GTTCGTGGCG CCTTGTGACC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCGGGCCCCT GCCGCCTGCA AGTCGGAAAT TGCGCTGTGC TCCTGTGCTA CGGCCTGTGG CTGGACTGCC TGCTGCTGCC CAACTGGCTG GCACCATGGC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CGAAGACGCC AAAAACATAA AGAAAGGCCC GGCGCCATTC TATCCTCTAG AGGATGGAAC CGCTGGAGAG CAACTGCATA AGGCTATGAA GAGATACGCC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CTGGTTCCTG GAACAATTGC TTTTACAGAT GCACATATCG AGGTGAACAT CACGTACGCG GAATACTTCG AAATGTCCGT TCGGTTGGCA GAAGCTATGA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AACGATATGG GCTGAATACA AATCACAGAA TCGTCGTATG CAGTGAAAAC TCTCTTCAAT TCTTTATGCC GGTGTTGGGC GCGTTATTTA TCGGAGTTGC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AGTTGCGCCC GCGAACGACA TTTATAATGA ACGTGAATTG CTCAACAGTA TGAACATTTC GCAGCCTACC GTAGTGTTTG TTTCCAAAAA GGGGTTGCAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AAAATTTTGA ACGTGCAAAA AAAATTACCA ATAATCCAGA AAATTATTAT CATGGATTCT AAAACGGATT ACCAGGGATT TCAGTCGATG TACACGTTCG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TCACATCTCA TCTACCTCCC GGTTTTAATG AATACGATTT TGTACCAGAG TCCTTTGATC GTGACAAAAC AATTGCACTG ATAATGAATT CCTCTGGATC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TACTGGGTTA CCTAAGGGTG TGGCCCTTCC GCATAGAACT GCCTGCGTCA GATTCTCGCA TGCCAGAGAT CCTATTTTTG GCAATCAAAT CATTCCGGAT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ACTGCGATTT TAAGTGTTGT TCCATTCCAT CACGGTTTTG GAATGTTTAC TACACTCGGA TATTTGATAT GTGGATTTCG AGTCGTCTTA ATGTATAGAT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TTGAAGAAGA GCTGTTTTTA CGATCCCTTC AGGATTACAA AATTCAAAGT GCGTTGCTAG TACCAACCCT ATTTTCATTC TTCGCCAAAA GCACTCTGAT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TGACAAATAC GATTTATCTA ATTTACACGA AATTGCTTCT GGGGGCGCAC CTCTTTCGAA AGAAGTCGGG GAAGCGGTTG CAAAACGCTT CCATCTTCCA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GGGATACGAC AAGGATATGG GCTCACTGAG ACTACATCAG CTATTCTGAT TACACCCGAG GGGGATGATA AACCGGGCGC GGTCGGTAAA GTTGTTCCAT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TTTTTGAAGC GAAGGTTGTG GATCTGGATA CCGGGAAAAC GCTGGGCGTT AATCAGAGAG GCGAATTATG TGTCAGAGGA CCTATGATTA TGTCCGGTTA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TGTAAACAAT CCGGAAGCGA CCAACGCCTT GATTGACAAG GATGGATGGC TACATTCTGG AGACATAGCT TACTGGGACG AAGACGAACA CTTCTTCATA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GTTGACCGCT TGAAGTCTTT AATTAAATAC AAAGGATATC AGGTGGCCCC CGCTGAATTG GAATCGATAT TGTTACAACA CCCCAACATC TTCGACGCGG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GCGTGGCAGG TCTTCCCGAC GATGACGCCG GTGAACTTCC CGCCGCCGTT GTTGTTTTGG AGCACGGAAA GACGATGACG GAAAAAGAGA TCGTGGATTA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CGTCGCCAGT CAAGTAACAA CCGCGAAAAA GTTGCGCGGA GGAGTTGTGT TTGTGGACGA AGTACCGAAA GGTCTTACCG GAAAACTCGA CGCAAGAAAA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ATCAGAGAGA TCCTCATAAA GGCCAAGAAG GGCGGAAAGT CCAAATTGTA ATAGATCCAC TAGTTCTAGA GCGGCCGCCA CCGCGGTGGA GGGGTACAAA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAG TACCGAGCTC GAATTCTAGT TCTAGAGCGG CCGCCACCGC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GGTGGAGCTC CAATTCGCCC TATAGTGAGT CGTATTACGC GCGCTCACTG GCCGTCGTTT TACAACGTCG TGACTGGGAA AACCCTGGCG TTACCCAACT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TAATCGCCTT GCAGCACATC CCCCTTTCGC CAGCTGGCGT AATAGCGAAG AGGCCCGCAC CGATCGCCCT TCCCAACAGT TGCGCAGCCT GAATGGCGAA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TGGGACGCGC CCTGTAGCGG CGCATTAAGC GCGGCGGGTG TGGTGGTTAC GCGCAGCGTG ACCGCTACAC TTGCCAGCGC CCTAGCGCCC GCTCCTTTCG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CTTTCTTCCC TTCCTTTCTC GCCACGTTCG CCGGCTTTCC CCGTCAAGCT CTAAATCGGG GGCTCCCTTT AGGGTTCCGA TTTAGTGCTT TACGGCACCT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CGACCCCAAA AAACTTGATT AGGGTGATGG TTCACGTAGT GGGCCATCGC CCTGATAGAC GGTTTTTCGC CCTTTGACGT TGGAGTCCAC GTTCTTTAAT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AGTGGACTCT TGTTCCAAAC TGGAACAACA CTCAACCCTA TCTCGGTCTA TTCTTTTGAT TTATAAGGGA TTTTGCCGAT TTCGGCCTAT TGGTTAAAAA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

ATGAGCTGAT TTAACAAAAA TTTAACGCGA ATTTTAACAA AATATTAACG CTTACAATTT AG
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961

Plasmid sequence verified (partially/completely) by IRESite (more details in Remarks):

plasmid sequence confirmed by IRESite curators by restriction analysis + parts by PCR + sequencing

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

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

1

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

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
FFluc

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

309-1964

Remarks:

IRESite notes about verification of plasmid sequence:
The complete sequence of IRES element was determined by sequencing using Fluc_seq_reverse
(AGGAACCAGGGCGTATCTC) primer.

For detailed verification of whole plasmid sequence see item IRESite Id: 413.

Citations:

Thoma C., Bergamini G., Galy B., Hundsdoerfer P., Hentze M. W. (2004) Enhancement of IRES-mediated translation of the c-myc and BiP mRNAs by the poly(A) tail is independent of intact eIF4G and PABP. Mol. Cell. 15(6):925-935

IRESs:

IRES:

Version: `0`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `BiP`	The functional status of IRES: `functional`

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

87-306

How IRES boundaries were determined:
experimentally_determined

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

AGGTCGACGC CGGCCAAGAC AGCACAGACA GATTGACCTA TTGGGGTGTT TCGCGAGTGT GAGAGGGAAG CGCCGCGGCC TGTATTTCTA GACCTGCCCT 
^87        ^97        ^107       ^117       ^127       ^137       ^147       ^157       ^167       ^177       

TCGCCTGGTT CGTGGCGCCT TGTGACCCCG GGCCCCTGCC GCCTGCAAGT CGGAAATTGC GCTGTGCTCC TGTGCTACGG CCTGTGGCTG GACTGCCTGC 
^187       ^197       ^207       ^217       ^227       ^237       ^247       ^257       ^267       ^277       

TGCTGCCCAA CTGGCTGGCA
^287       ^297

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 457

Version: `4`	Last change: `2008-07-08 09:09:13`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vitro The in vitro translation system:
HeLa cell lysate

The organism used for translation:

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

100.000

	Name of the plasmid used as the negative control. `pBiL-p(A)`
	`IRESite Id` of the plasmid used as negative control. `397`
	The relative translation efficiency in % of the negative control: `7.100`

The effect of 5'-cap analogs on translation:
no

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_ApppG_cap_with_polyA_tail

Remarks:

The translation of BiP.IRES-pA RNA is about 6-fold more efficient than the translation of the
non-polyadenylated counterpart BiP.IRES RNA (IRESite ID: 397).

Translational data are derived from Fig 1A.

Citations:

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