IRESite_Id:340 characteristics of BAG1_p36 IRES studied in pRBF

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `340`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-05-22 17:50:00`

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:

Putative spliced in vitro SV40 promoter-derived transcript of pRBdeltaF plasmid (same as pRBF but AUG mutated
to AGG).

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

TATTCCAGAA GTAGTGAGGA GGCTTTTTTG GAGGCCTAGG CTTTTGCAAA AAGCTGAAGT TGGTCGTGAG GCACTGGGCA GGTGTCCACT CCCAGTTCAA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTACAGCTCT TAAGGCTAGA GTACTTAATA CGACTCACTA TAGGCTAGGC TTGGCATTCC GGTACTGAAT TGATATCAAG CTCTAGCCAC CATGACTTCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AAAGTTTATG ATCCAGAACA AAGGAAACGG ATGATAACTG GTCCGCAGTG GTGGGCCAGA TGTAAACAAA TGAATGTTCT TGATTCATTT ATTAATTATT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATGATTCAGA AAAACATGCA GAAAATGCTG TTATTTTTTT ACATGGTAAC GCGGCCTCTT CTTATTTATG GCGACATGTT GTGCCACATA TTGAGCCAGT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AGCGCGGTGT ATTATACCAG ACCTTATTGG TATGGGCAAA TCAGGCAAAT CTGGTAATGG TTCTTATAGG TTACTTGATC ATTACAAATA TCTTACTGCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TGGTTTGAAC TTCTTAATTT ACCAAAGAAG ATCATTTTTG TCGGCCATGA TTGGGGTGCT TGTTTGGCAT TTCATTATAG CTATGAGCAT CAAGATAAGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCAAAGCAAT AGTTCACGCT GAAAGTGTAG TAGATGTGAT TGAATCATGG GATGAATGGC CTGATATTGA AGAAGATATT GCGTTGATCA AATCTGAAGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGGAGAAAAA ATGGTTTTGG AGAATAACTT CTTCGTGGAA ACCATGTTGC CATCAAAAAT CATGAGAAAG TTAGAACCAG AAGAATTTGC AGCATATCTT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GAACCATTCA AAGAGAAAGG TGAAGTTCGT CGTCCAACAT TATCATGGCC TCGTGAAATC CCGTTAGTAA AAGGTGGTAA ACCTGACGTT GTACAAATTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTAGGAATTA TAATGCTTAT CTACGTGCAA GTGATGATTT ACCAAAAATG TTTATTGAAT CGGACCCAGG ATTCTTTTCC AATGCTATTG TTGAAGGTGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CAAGAAGTTT CCTAATACTG AATTTGTCAA AGTAAAAGGT CTTCATTTTT CGCAAGAAGA TGCACCTGAT GAAATGGGAA AATATATCAA ATCGTTCGTT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAGCGAGTTC TCAAAAATGA ACAATAATTC TAGAGCTTAT CGATACCGTC GACCTCGAAT CACTAGTCAG CTGgaattct gggcggtcaa caagtgcggg 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

cctggctcag cgcggggggg cgcggagacc gcgaggcgac cgggagcggc tgggttcccg gctgcgcgcc cttcggccag gccgggagcc gcgccagtcg 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

gagcccccgg cccagcgtgg tccgcctccc tctgggcgtc cacctgcccg gagtactgcc agcgggcatg accgacccac caggggcgcc gccgccggcg 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ctcgcaggcc gcggatgaag aagaaaaccc ggcgccgctc gacccggagc gaggagttga cccggagcga ggagttgacc ctgagtgagg aagcgacctg 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

gagtgaagag gcgacccaga gtgaggaggc gacccagggc gaagccAgTG GAAGACGCCA AAAACATAAA GAAAGGCCCG GCGCCATTCT ATCCGCTGGA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AGATGGAACC GCTGGAGAGC AACTGCATAA GGCTATGAAG AGATACGCCC TGGTTCCTGG AACAATTGCT TTTACAGATG CACATATCGA GGTGGACATC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ACTTACGCTG AGTACTTCGA AATGTCCGTT CGGTTGGCAG AAGCTATGAA ACGATATGGG CTGAATACAA ATCACAGAAT CGTCGTATGC AGTGAAAACT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTCTTCAATT CTTTATGCCG GTGTTGGGCG CGTTATTTAT CGGAGTTGCA GTTGCGCCCG CGAACGACAT TTATAATGAA CGTGAATTGC TCAACAGTAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GGGCATTTCG CAGCCTACCG TGGTGTTCGT TTCCAAAAAG GGGTTGCAAA AAATTTTGAA CGTGCAAAAA AAGCTCCCAA TCATCCAAAA AATTATTATC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ATGGATTCTA AAACGGATTA CCAGGGATTT CAGTCGATGT ACACGTTCGT CACATCTCAT CTACCTCCCG GTTTTAATGA ATACGATTTT GTGCCAGAGT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CCTTCGATAG GGACAAGACA ATTGCACTGA TCATGAACTC CTCTGGATCT ACTGGTCTGC CTAAAGGTGT CGCTCTGCCT CATAGAACTG CCTGCGTGAG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATTCTCGCAT GCCAGAGATC CTATTTTTGG CAATCAAATC ATTCCGGATA CTGCGATTTT AAGTGTTGTT CCATTCCATC ACGGTTTTGG AATGTTTACT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ACACTCGGAT ATTTGATATG TGGATTTCGA GTCGTCTTAA TGTATAGATT TGAAGAAGAG CTGTTTCTGA GGAGCCTTCA GGATTACAAG ATTCAAAGTG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CGCTGCTGGT GCCAACCCTA TTCTCCTTCT TCGCCAAAAG CACTCTGATT GACAAATACG ATTTATCTAA TTTACACGAA ATTGCTTCTG GTGGCGCTCC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CCTCTCTAAG GAAGTCGGGG AAGCGGTTGC CAAGAGGTTC CATCTGCCAG GTATCAGGCA AGGATATGGG CTCACTGAGA CTACATCAGC TATTCTGATT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ACACCCGAGG GGGATGATAA ACCGGGCGCG GTCGGTAAAG TTGTTCCATT TTTTGAAGCG AAGGTTGTGG ATCTGGATAC CGGGAAAACG CTGGGCGTTA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ATCAAAGAGG CGAACTGTGT GTGAGAGGTC CTATGATTAT GTCCGGTTAT GTAAACAATC CGGAAGCGAC CAACGCCTTG ATTGACAAGG ATGGATGGCT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ACATTCTGGA GACATAGCTT ACTGGGACGA AGACGAACAC TTCTTCATCG TTGACCGCCT GAAGTCTCTG ATTAAGTACA AAGGCTATCA GGTGGCTCCC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GCTGAATTGG AATCCATCTT GCTCCAACAC CCCAACATCT TCGACGCAGG TGTCGCAGGT CTTCCCGACG ATGACGCCGG TGAACTTCCC GCCGCCGTTG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TTGTTTTGGA GCACGGAAAG ACGATGACGG AAAAAGAGAT CGTGGATTAC GTCGCCAGTC AAGTAACAAC CGCGAAAAAG TTGCGCGGAG GAGTTGTGTT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TGTGGACGAA GTACCGAAAG GTCTTACCGG AAAACTCGAC GCAAGAAAAA TCAGAGAGAT CCTCATAAAG GCCAAGAAGG GCGGAAAGAT CGCCGTGTAA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TTCTAGAGTC GGGGCGGCCG GCCGCTTCGA GCAGACATGA TAAGATACAT TGATGAGTTT GGACAAACCA CAACTAGAAT GCAGTGAAAA AAATGCTTTA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TTTGTGAAAT TTGTGATGCT ATTGCTTTAT TTGTAACCAT TATAAGCTGC AATAAACAAG TTAACAACAA CAATTGCATT CATTTTATGT TTCAGGTTCA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GGGGGAGGTG TGGGAGGTTT TTTAAAGCAA GTAAAACCTC TACAAATGTG GTA
^3401      ^3411      ^3421      ^3431      ^3441      ^3451

Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)

Credibility of mRNA sequence:

guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail

The name of the plasmid:
pRBF_AUG-to-AGG The name of the promoter used to express this mRNA:
SV40

Aliases of the plasmid name:

Alias: pRBdeltaF

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:
Bag-1

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:

GGTACCGAGC TCTTACGCGT GCTAGCCCGG GCTCGAGATC TGCGATCTGC ATCTCAATTA GTCAGCAACC ATAGTCCCGC CCCTAACTCC GCCCATCCCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCCCTAACTC CGCCCAGTTC CGCCCATTCT CCGCCCCATC GCTGACTAAT TTTTTTTATT TATGCAGAGG CCGAGGCCGC CTCGGCCTCT GAGCTATTCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGAAGTAGTG AGGAGGCTTT TTTGGAGGCC TAGGCTTTTG CAAAAAGCTG AAGTTGGTCG TGAGGCACTG GGCAGGTAAG TATCAAGGTT ACAAGACAGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTTAAGGAGA CCAATAGAAA CTGGGCTTGT CGAGACAGAG AAGACTCTTG CGTTTCTGAT AGGCACCTAT TGGTCTTACT GACATCCACT TTGCCTTTCT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTCCACAGGT GTCCACTCCC AGTTCAATTA CAGCTCTTAA GGCTAGAGTA CTTAATACGA CTCACTATAG GCTAGGCTTG GCATTCCGGT ACTGAATTGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TATCAAGCTC TAGCCACCAT GACTTCGAAA GTTTATGATC CAGAACAAAG GAAACGGATG ATAACTGGTC CGCAGTGGTG GGCCAGATGT AAACAAATGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATGTTCTTGA TTCATTTATT AATTATTATG ATTCAGAAAA ACATGCAGAA AATGCTGTTA TTTTTTTACA TGGTAACGCG GCCTCTTCTT ATTTATGGCG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACATGTTGTG CCACATATTG AGCCAGTAGC GCGGTGTATT ATACCAGACC TTATTGGTAT GGGCAAATCA GGCAAATCTG GTAATGGTTC TTATAGGTTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTTGATCATT ACAAATATCT TACTGCATGG TTTGAACTTC TTAATTTACC AAAGAAGATC ATTTTTGTCG GCCATGATTG GGGTGCTTGT TTGGCATTTC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATTATAGCTA TGAGCATCAA GATAAGATCA AAGCAATAGT TCACGCTGAA AGTGTAGTAG ATGTGATTGA ATCATGGGAT GAATGGCCTG ATATTGAAGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGATATTGCG TTGATCAAAT CTGAAGAAGG AGAAAAAATG GTTTTGGAGA ATAACTTCTT CGTGGAAACC ATGTTGCCAT CAAAAATCAT GAGAAAGTTA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAACCAGAAG AATTTGCAGC ATATCTTGAA CCATTCAAAG AGAAAGGTGA AGTTCGTCGT CCAACATTAT CATGGCCTCG TGAAATCCCG TTAGTAAAAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GTGGTAAACC TGACGTTGTA CAAATTGTTA GGAATTATAA TGCTTATCTA CGTGCAAGTG ATGATTTACC AAAAATGTTT ATTGAATCGG ACCCAGGATT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CTTTTCCAAT GCTATTGTTG AAGGTGCCAA GAAGTTTCCT AATACTGAAT TTGTCAAAGT AAAAGGTCTT CATTTTTCGC AAGAAGATGC ACCTGATGAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ATGGGAAAAT ATATCAAATC GTTCGTTGAG CGAGTTCTCA AAAATGAACA ATAATTCTAG AGCTTATCGA TACCGTCGAC CTCGAATCAC TAGTCAGCTG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

gaattctggg cggtcaacaa gtgcgggcct ggctcagcgc gggggggcgc ggagaccgcg aggcgaccgg gagcggctgg gttcccggct gcgcgccctt 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

cggccaggcc gggagccgcg ccagtcggag cccccggccc agcgtggtcc gcctccctct gggcgtccac ctgcccggag tactgccagc gggcatgacc 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

gacccaccag gggcgccgcc gccggcgctc gcaggccgcg gatgaagaag aaaacccggc gccgctcgac ccggagcgag gagttgaccc ggagcgagga 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

gttgaccctg agtgaggaag cgacctggag tgaagaggcg acccagagtg aggaggcgac ccagggcgaa gccAgTGGAA GACGCCAAAA ACATAAAGAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGGCCCGGCG CCATTCTATC CGCTGGAAGA TGGAACCGCT GGAGAGCAAC TGCATAAGGC TATGAAGAGA TACGCCCTGG TTCCTGGAAC AATTGCTTTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACAGATGCAC ATATCGAGGT GGACATCACT TACGCTGAGT ACTTCGAAAT GTCCGTTCGG TTGGCAGAAG CTATGAAACG ATATGGGCTG AATACAAATC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACAGAATCGT CGTATGCAGT GAAAACTCTC TTCAATTCTT TATGCCGGTG TTGGGCGCGT TATTTATCGG AGTTGCAGTT GCGCCCGCGA ACGACATTTA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TAATGAACGT GAATTGCTCA ACAGTATGGG CATTTCGCAG CCTACCGTGG TGTTCGTTTC CAAAAAGGGG TTGCAAAAAA TTTTGAACGT GCAAAAAAAG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CTCCCAATCA TCCAAAAAAT TATTATCATG GATTCTAAAA CGGATTACCA GGGATTTCAG TCGATGTACA CGTTCGTCAC ATCTCATCTA CCTCCCGGTT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTAATGAATA CGATTTTGTG CCAGAGTCCT TCGATAGGGA CAAGACAATT GCACTGATCA TGAACTCCTC TGGATCTACT GGTCTGCCTA AAGGTGTCGC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TCTGCCTCAT AGAACTGCCT GCGTGAGATT CTCGCATGCC AGAGATCCTA TTTTTGGCAA TCAAATCATT CCGGATACTG CGATTTTAAG TGTTGTTCCA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTCCATCACG GTTTTGGAAT GTTTACTACA CTCGGATATT TGATATGTGG ATTTCGAGTC GTCTTAATGT ATAGATTTGA AGAAGAGCTG TTTCTGAGGA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCCTTCAGGA TTACAAGATT CAAAGTGCGC TGCTGGTGCC AACCCTATTC TCCTTCTTCG CCAAAAGCAC TCTGATTGAC AAATACGATT TATCTAATTT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ACACGAAATT GCTTCTGGTG GCGCTCCCCT CTCTAAGGAA GTCGGGGAAG CGGTTGCCAA GAGGTTCCAT CTGCCAGGTA TCAGGCAAGG ATATGGGCTC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ACTGAGACTA CATCAGCTAT TCTGATTACA CCCGAGGGGG ATGATAAACC GGGCGCGGTC GGTAAAGTTG TTCCATTTTT TGAAGCGAAG GTTGTGGATC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TGGATACCGG GAAAACGCTG GGCGTTAATC AAAGAGGCGA ACTGTGTGTG AGAGGTCCTA TGATTATGTC CGGTTATGTA AACAATCCGG AAGCGACCAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CGCCTTGATT GACAAGGATG GATGGCTACA TTCTGGAGAC ATAGCTTACT GGGACGAAGA CGAACACTTC TTCATCGTTG ACCGCCTGAA GTCTCTGATT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AAGTACAAAG GCTATCAGGT GGCTCCCGCT GAATTGGAAT CCATCTTGCT CCAACACCCC AACATCTTCG ACGCAGGTGT CGCAGGTCTT CCCGACGATG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ACGCCGGTGA ACTTCCCGCC GCCGTTGTTG TTTTGGAGCA CGGAAAGACG ATGACGGAAA AAGAGATCGT GGATTACGTC GCCAGTCAAG TAACAACCGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GAAAAAGTTG CGCGGAGGAG TTGTGTTTGT GGACGAAGTA CCGAAAGGTC TTACCGGAAA ACTCGACGCA AGAAAAATCA GAGAGATCCT CATAAAGGCC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AAGAAGGGCG GAAAGATCGC CGTGTAATTC TAGAGTCGGG GCGGCCGGCC GCTTCGAGCA GACATGATAA GATACATTGA TGAGTTTGGA CAAACCACAA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CTAGAATGCA GTGAAAAAAA TGCTTTATTT GTGAAATTTG TGATGCTATT GCTTTATTTG TAACCATTAT AAGCTGCAAT AAACAAGTTA ACAACAACAA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TTGCATTCAT TTTATGTTTC AGGTTCAGGG GGAGGTGTGG GAGGTTTTTT AAAGCAAGTA AAACCTCTAC AAATGTGGTA AAATCGATAA GGATCTGAAC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GATGGAGCGG AGAATGGGCG GAACTGGGCG GAGTTAGGGG CGGGATGGGC GGAGTTAGGG GCGGGACTAT GGTTGCTGAC TAATTGAGAT GCATGCTTTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CATACTTCTG CCTGCTGGGG AGCCTGGGGA CTTTCCACAC CTGGTTGCTG ACTAATTGAG ATGCATGCTT TGCATACTTC TGCCTGCTGG GGAGCCTGGG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GACTTTCCAC ACCCTAACTG ACACACATTC CACAGCGGAT CCGTCGACCG ATGCCCTTGA GAGCCTTCAA CCCAGTCAGC TCCTTCCGGT GGGCGCGGGG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CATGACTATC GTCGCCGCAC TTATGACTGT CTTCTTTATC ATGCAACTCG TAGGACAGGT GCCGGCAGCG CTCTTCCGCT TCCTCGCTCA CTGACTCGCT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GCGCTCGGTC GTTCGGCTGC GGCGAGCGGT ATCAGCTCAC TCAAAGGCGG TAATACGGTT ATCCACAGAA TCAGGGGATA ACGCAGGAAA GAACATGTGA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GCAAAAGGCC AGCAAAAGGC CAGGAACCGT AAAAAGGCCG CGTTGCTGGC GTTTTTCCAT AGGCTCCGCC CCCCTGACGA GCATCACAAA AATCGACGCT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CAAGTCAGAG GTGGCGAAAC CCGACAGGAC TATAAAGATA CCAGGCGTTT CCCCCTGGAA GCTCCCTCGT GCGCTCTCCT GTTCCGACCC TGCCGCTTAC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CGGATACCTG TCCGCCTTTC TCCCTTCGGG AAGCGTGGCG CTTTCTCAAT GCTCACGCTG TAGGTATCTC AGTTCGGTGT AGGTCGTTCG CTCCAAGCTG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GGCTGTGTGC ACGAACCCCC CGTTCAGCCC GACCGCTGCG CCTTATCCGG TAACTATCGT CTTGAGTCCA ACCCGGTAAG ACACGACTTA TCGCCACTGG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CAGCAGCCAC TGGTAACAGG ATTAGCAGAG CGAGGTATGT AGGCGGTGCT ACAGAGTTCT TGAAGTGGTG GCCTAACTAC GGCTACACTA GAAGGACAGT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ATTTGGTATC TGCGCTCTGC TGAAGCCAGT TACCTTCGGA AAAAGAGTTG GTAGCTCTTG ATCCGGCAAA CAAACCACCG CTGGTAGCGG TGGTTTTTTT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GTTTGCAAGC AGCAGATTAC GCGCAGAAAA AAAGGATCTC AAGAAGATCC TTTGATCTTT TCTACGGGGT CTGACGCTCA GTGGAACGAA AACTCACGTT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

AAGGGATTTT GGTCATGAGA TTATCAAAAA GGATCTTCAC CTAGATCCTT TTAAATTAAA AATGAAGTTT TAAATCAATC TAAAGTATAT ATGAGTAAAC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TTGGTCTGAC AGTTACCAAT GCTTAATCAG TGAGGCACCT ATCTCAGCGA TCTGTCTATT TCGTTCATCC ATAGTTGCCT GACTCCCCGT CGTGTAGATA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ACTACGATAC GGGAGGGCTT ACCATCTGGC CCCAGTGCTG CAATGATACC GCGAGACCCA CGCTCACCGG CTCCAGATTT ATCAGCAATA AACCAGCCAG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CCGGAAGGGC CGAGCGCAGA AGTGGTCCTG CAACTTTATC CGCCTCCATC CAGTCTATTA ATTGTTGCCG GGAAGCTAGA GTAAGTAGTT CGCCAGTTAA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TAGTTTGCGC AACGTTGTTG CCATTGCTAC AGGCATCGTG GTGTCACGCT CGTCGTTTGG TATGGCTTCA TTCAGCTCCG GTTCCCAACG ATCAAGGCGA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

GTTACATGAT CCCCCATGTT GTGCAAAAAA GCGGTTAGCT CCTTCGGTCC TCCGATCGTT GTCAGAAGTA AGTTGGCCGC AGTGTTATCA CTCATGGTTA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TGGCAGCACT GCATAATTCT CTTACTGTCA TGCCATCCGT AAGATGCTTT TCTGTGACTG GTGAGTACTC AACCAAGTCA TTCTGAGAAT AGTGTATGCG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

GCGACCGAGT TGCTCTTGCC CGGCGTCAAT ACGGGATAAT ACCGCGCCAC ATAGCAGAAC TTTAAAAGTG CTCATCATTG GAAAACGTTC TTCGGGGCGA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

AAACTCTCAA GGATCTTACC GCTGTTGAGA TCCAGTTCGA TGTAACCCAC TCGTGCACCC AACTGATCTT CAGCATCTTT TACTTTCACC AGCGTTTCTG 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

GGTGAGCAAA AACAGGAAGG CAAAATGCCG CAAAAAAGGG AATAAGGGCG ACACGGAAAT GTTGAATACT CATACTCTTC CTTTTTCAAT ATTATTGAAG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CATTTATCAG GGTTATTGTC TCATGAGCGG ATACATATTT GAATGTATTT AGAAAAATAA ACAAATAGGG GTTCCGCGCA CATTTCCCCG AAAAGTGCCA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CCTGACGCGC CCTGTAGCGG CGCATTAAGC GCGGCGGGTG TGGTGGTTAC GCGCAGCGTG ACCGCTACAC TTGCCAGCGC CCTAGCGCCC GCTCCTTTCG 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

CTTTCTTCCC TTCCTTTCTC GCCACGTTCG CCGGCTTTCC CCGTCAAGCT CTAAATCGGG GGCTCCCTTT AGGGTTCCGA TTTAGTGCTT TACGGCACCT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

CGACCCCAAA AAACTTGATT AGGGTGATGG TTCACGTAGT GGGCCATCGC CCTGATAGAC GGTTTTTCGC CCTTTGACGT TGGAGTCCAC GTTCTTTAAT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AGTGGACTCT TGTTCCAAAC TGGAACAACA CTCAACCCTA TCTCGGTCTA TTCTTTTGAT TTATAAGGGA TTTTGCCGAT TTCGGCCTAT TGGTTAAAAA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

ATGAGCTGAT TTAACAAAAA TTTAACGCGA ATTTTAACAA AATATTAACG TTTACAATTT CCCATTCGCC ATTCAGGCTG CGCAACTGTT GGGAAGGGCG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

ATCGGTGCGG GCCTCTTCGC TATTACGCCA GCCCAAGCTA CCATGATAAG TAAGTAATAT TAAGGTACGG GAGGTACTTG GAGCGGCCGC AATAAAATAT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

CTTTATTTTC ATTACATCTG TGTGTTGGTT TTTTGTGTGA ATCGATAGTA CTAACATACG CTCTCCATCA AAACAAAACG AAACAAAACA AACTAGCAAA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ATAGGCTGTC CCCAGTGCAA GTGCAGGTGC CAGAACATTT CTCTATCGAT A
^6801      ^6811      ^6821      ^6831      ^6841      ^6851

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: `1`	Last change: `2008-05-22 17:50:00`
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):

192-1127

Remarks:

Although this construct has mutated authentic initiator AUG codon of FLuc there are many ORFs remaining
throughout the sequence of firefly luciferase while it is not clear whether any of the protein products are
functional. Below are the positions of ORFs C-co-terminal with the full-length protein form within the
putative transcript:

1548-3200 550aa (AUG to AGG mutation)
1635-3200 521aa
1722-3200 492aa
1746-3200 484aa
1815-3200 461aa
1899-3200 433aa
2001-3200 399aa
2037-3200 387aa
2133-3200 355aa
2292-3200 302aa
2340-3200 286aa
2733-3200 155aa
2739-3200 153aa
3024-3200 58aa

Citations:

Coldwell M. J., deSchoolmeester M. L., Fraser G. A., Pickering B. M., Packham G., Willis A. E. (2001) The p36 isoform of BAG-1 is translated by internal ribosome entry following heat shock. Oncogene. 20(30):4095-4100

IRESs:

IRES:

Version: `1`	Last change: `2008-05-22 17:50:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `BAG1_p36`	The functional status of IRES: `defective`

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

1179-1544

How IRES boundaries were determined:
experimentally_determined

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

ctgggcggtc aacaagtgcg ggcctggctc agcgcggggg ggcgcggaga ccgcgaggcg accgggagcg gctgggttcc cggctgcgcg cccttcggcc 
^1179      ^1189      ^1199      ^1209      ^1219      ^1229      ^1239      ^1249      ^1259      ^1269      

aggccgggag ccgcgccagt cggagccccc ggcccagcgt ggtccgcctc cctctgggcg tccacctgcc cggagtactg ccagcgggca tgaccgaccc 
^1279      ^1289      ^1299      ^1309      ^1319      ^1329      ^1339      ^1349      ^1359      ^1369      

accaggggcg ccgccgccgg cgctcgcagg ccgcggatga agaagaaaac ccggcgccgc tcgacccgga gcgaggagtt gacccggagc gaggagttga 
^1379      ^1389      ^1399      ^1409      ^1419      ^1429      ^1439      ^1449      ^1459      ^1469      

ccctgagtga ggaagcgacc tggagtgaag aggcgaccca gagtgaggag gcgacccagg gcgaag
^1479      ^1489      ^1499      ^1509      ^1519      ^1529      ^1539

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 412

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:

Homo sapiens HeLa (ATCC CCL-2)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

5.000

Name of IRES used as the positive control:

BAG1_p36

Name of the plasmid used as the positive control. `pRBF`
`IRESite Id` of the plasmid used as positive control. `323`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `419`

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:

Values from Figure 5B. Expression of FLuc from this plasmid could be due to ribosomal re-initiation as well as
initiation at a downstream AUG codon. However, the firefly luciferase proteins produced from shorter ORFs seem
to be non-functional or not produced.

Citations:

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