IRESite_Id:475 promoter-less plasmid (deltaCMV)BiCAQP4 used to evaluate potential promoter activity in AQP4 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `475`	Version: `0`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš

IRESite record type:

promoter-less_plasmid_with_putative_IRES

The name of the plasmid:
(deltaCMV)BiCAQP4

Description of the plasmid (facultative for promoter-less plasmid records):
Almost the full length 5' UTR from human AQP4 mRNA (from nt -275 to nt -1 of the original sequence) and the first 7 nts (+1 to +7) from AQP4 ORF has been cloned between the beta galactosidase and chloramphenicol acetyl transferase reporter genes. This promoter-less variant of pBiCAQP4 (IRESite ID: 488) was prepared by removing the CMV promoter using NruI and HindIII restriction sites.

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 origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens HEK 293T/17 (ATCC CRL-11268)

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
AQP4

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

tttttcaata ttattgaagc atttatcagg gttattgtct catgagcgga tacatatttg aatgtattta gaaaaataaa caaatagggg ttccgcgcac 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

atttccccga aaagtgccac ctgacgtcga cggatcggga gatctcccga tcccctatgg tcgactctca gtacaatctg ctctgatgcc gcatagttaa 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

gccagtatct gctccctgct tgtgtgttgg aggtcgctga gtagtgcgcg agcaaaattt aagctacaac aaggcaaggc ttgaccgaca attgcatgaa 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gaatctgctt agggttaggc gttttgcgct gcttcgagct tggtaccgag ctcggatcca ctagtaacgg ccgccagtgt gctggaattc tgcagatatc 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

catcacactg gcggccgcaa ttcccgggga tcgaaagagc ctgctaaagc aaaaaagaag tcaccATGTC GTTTACTTTG ACCAACAAGA ACGTGATTTT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGTTGCCGGT CTGGGAGGCA TTGGTCTGGA CACCAGCAAG GAGCTGCTCA AGCGCGATCC CGTCGTTTTA CAACGTCGTG ACTGGGAAAA CCCTGGCGTT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ACCCAACTTA ATCGCCTTGC AGCACATCCC CCTTTCGCCA GCTGGCGTAA TAGCGAAGAG GCCCGCACCG ATCGCCCTTC CCAACAGTTG CGCAGCTGAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGGCGAATGG CGCTTTGCCT GGTTTCCGGC ACCAGAAGCG GTGCCGGAAA GCTGGCTGGA GTTCGATCTT CCTGAGGCCG ATACTGTCGT CGTCCCCTCA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AACTGGCAGA TGCACGGTTA CGATGCGCCC ATCTACACCA ACGTGACCTA TCCCATTACG GTCAATCCGC CGTTTGTTCC CACGGAGAAT CCGACGGGTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GTTACTCGCT CACATTTAAT GTTGATGAAA GCTGGCTACA GGAAGGCCAG ACGCGAATTA TTTTTGATGG CGTTAACTCG GCGTTTCATC TGTGGTGCAA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CGGGCGCTGG GTCGGTTACG GCCAGGACAG TCGTTTGCCG TCTGAATTTG ACCTGAGCGC ATTTTTACGC GCCGGAGAAA ACCGCCTCGC GGTGATGGTG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CTGCGTTGGA GTTACGGCAG TTATCTGGAA GATCAGGATA TTTGGCGGAT GAGCGGCATT TTCCGTGACG TCTCGTTGCT GCATAAACCG ACTACACAAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TCAGCGATTT CCATGTTGCC ACTCGCTTTA ATGATGATTT CAGCCGCGCT GTACTGGAGG CTGAAGTTCA GATGTGCGGC GAGTTGCGTG ACTACCTACG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGTAACAGTT TCTTTATGGC AGGGTGAAAC GCAGGTCGCC AGCGGCACCG CGCCTTTCGG CGGTGAAATT ATCGATGAGC GTGGTGGTTA TGCCGATCGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GTCACACTAC GTCTGAACGT CGAAAACCCG AAACTGTGGA GCGCCGAAAT CCCGAATCTC TATCGTGCGG TGGTTGAACT GCACACCGCC GACGGCACGC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGATTGAAGC AGAAGCCTGC GATGTCGGTT TCCGCGAGGT GCGGATTGAA AATGGTCTGC TGCTGCTGAA CGGCAAGCCG TTGCTGATTC GAGGCGTTAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CCGTCACGAG CATCATCCTC TGCATGGTCA GGTCATGGAT GAGCAGACGA TGGTGCAGGA TATCCTGCTG ATGAAGCAGA ACAACTTTAA CGCCGTGCGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGTTCGCATT ATCCGAACCA TCCGCTGTGG TACACGCTGT GCGACCGCTA CGGCCTGTAT GTGGTGGATG AAGCCAATAT TGAAACCCAC GGCATGGTGC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CAATGAATCG TCTGACCGAT GATCCGCGCT GGCTACCGGC GATGAGCGAA CGCGTAACGC GAATGGTGCA GCGCGATCGT AATCACCCGA GTGTGATCAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CTGGTCGCTG GGGAATGAAT CAGGCCACGG CGCTAATCAC GACGCGCTGT ATCGCTGGAT CAAATCTGTC GATCCTTCCC GCCCGGTGCA GTATGAAGGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGCGGAGCCG ACACCACGGC CACCGATATT ATTTGCCCGA TGTACGCGCG CGTGGATGAA GACCAGCCCT TCCCGGCTGT GCCGAAATGG TCCATCAAAA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AATGGCTTTC GCTACCTGGA GAGACGCGCC CGCTGATCCT TTGCGAATAC GCCCACGCGA TGGGTAACAG TCTTGGCGGT TTCGCTAAAT ACTGGCAGGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GTTTCGTCAG TATCCCCGTT TACAGGGCGG CTTCGTCTGG GACTGGGTGG ATCAGTCGCT GATTAAATAT GATGAAAACG GCAACCCGTG GTCGGCTTAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GGCGGTGATT TTGGCGATAC GCCGAACGAT CGCCAGTTCT GTATGAACGG TCTGGTCTTT GCCGACCGCA CGCCGCATCC AGCGCTGACG GAAGCAAAAC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ACCAGCAGCA GTTTTTCCAG TTCCGTTTAT CCGGGCAAAC CATCGAAGTG ACCAGCGAAT ACCTGTTCCG TCATAGCGAT AACGAGCTCC TGCACTGGAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GGTGGCGCTG GATGGTAAGC CGCTGGCAAG CGGTGAAGTG CCTCTGGATG TCGCTCCACA AGGTAAACAG TTGATTGAAC TGCCTGAACT ACCGCAGCCG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GAGAGCGCCG GGCAACTCTG GCTCACAGTA CGCGTAGTGC AACCGAACGC GACCGCATGG TCAGAAGCCG GGCACATCAG CGCCTGGCAG CAGTGGCGTC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TGGCGGAAAA CCTCAGTGTG ACGCTCCCCG CCGCGTCCCA CGCCATCCCG CATCTGACCA CCAGCGAAAT GGATTTTTGC ATCGAGCTGG GTAATAAGCG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TTGGCAATTT AACCGCCAGT CAGGCTTTCT TTCACAGATG TGGATTGGCG ATAAAAAACA ACTGCTGACG CCGCTGCGCG ATCAGTTCAC CCGTGCACCG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CTGGATAACG ACATTGGCGT AAGTGAAGCG ACCCGCATTG ACCCTAACGC CTGGGTCGAA CGCTGGAAGG CGGCGGGCCA TTACCAGGCC GAAGCAGCGT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TGTTGCAGTG CACGGCAGAT ACACTTGCTG ATGCGGTGCT GATTACGAAC GCTCACGCGT GGCAGCATCA GGGGAAAACC TTATTTATCA GCCGGAAAAC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CTACCGGATT GATGGTAGTG GTCAAATGGC GATTACCGTT GATGTTGAAG TGGCGAGCGA TACACCGCAT CCGGCGCGGA TTGGCCTGAA CTGCCAGCTG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GCGCAGGTAG CAGAGCGGGT AAACTGGCTC GGATTAGGGC CGCAAGAAAA CTATCCCGAC CGCCTTACTG CCGCCTGTTT TGACCGCTGG GATCTGCCAT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TGTCAGACAT GTATACCCCG TACGTCTTCC CGAGCGAAAA CGGTCTGCGC TGCGGGACGC GCGAATTGAA TTATGGCCCA CACCAGTGGC GCGGCGACTT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CCAGTTCAAC ATCAGCCGCT ACAGTCAACA GCAACTGATG GAAACCAGCC ATCGCCATCT GCTGCACGCG GAAGAAGGCA CATGGCTGAA TATCGACGGT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TTCCATATGG GGATTGGTGG CGACGACTCC TGGAGCCCGT CAGTATCGGC GGAATTACAG CTGAGCGCCG GTCGCTACCA TTACCAGTTG GTCTGGTGTC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AAAAATAATA ATAACCGGGC AGGCCATGTC TGCCCGTATT TCGCGTAAGG AAATCCATTA TGTACTATTT AAAAAACACA AACTTTTGGA TGTTCGGTTT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ATTCTTTTTC TTTTACTTTT TTATCATGGG AGCCTACTTC CCGTTTTTCC CGATTTGGCT ACATGACATC AACCATATCA GCAAAAGTGA TACGGGTATT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ATTTTTGCCG CTATTTCTCT GTTCTCGCTA TTATTCCAAC CGCTGTTTGG TCTGCTTTCT GACAAACTCG GCCTCGACTC TAGGCGGCCG CTCGACGCTA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GCAAGGACAG TTTGGATAAT TTTCCGTGAA ACTGGATGAT CTTTGAATAT TAAATGAAAG GAGACTAGAA TAACAGTCTC TTGACTATTC ATGAAGGAGC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TTTAGCAGGA GCATTCTTTC TTGGTGTGCA AATCACGCCT GGCAGCCCCT GCCCACAGTA CCCGAAGATG GCAGGCCTTG TTCCCTTCAC CTAAATTCAT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AAACCTGGGT GTAGTGGCTT CTGATGCTGA TTTGTTTCTC TTTTCAGTAA GTGTGGACCT TTGTGTACCA GAGAGAACAT CATGGTGGCT CGAGatggag 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

aaaaaaatca ctggatatac caccgttgat atatcccaat ggcatcgtaa agaacatttt gaggcatttc agtcagttgc tcaatgtacc tataaccaga 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ccgttcagct ggatattacg gcctttttaa agaccgtaaa gaaaaataag cacaagtttt atccggcctt tattcacatt cttgcccgcc tgatgaatgc 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

tcatccggaa ttccgtatgg caatgaaaga cggtgagctg gtgatatggg atagtgttca cccttgttac accgttttcc atgagcaaac tgaaacgttt 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

tcatcgctct ggagtgaata ccacgacgat ttccggcagt ttctacacat atattcgcaa gatgtggcgt gttacggtga aaacctggcc tatttcccta 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

aagggtttat tgagaatatg tttttcgtct cagccaatcc ctgggtgagt ttcaccagtt ttgatttaaa cgtggccaat atggacaact tcttcgcccc 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

cgttttcacc atgggcaaat attatacgca aggcgacaag gtgctgatgc cgctggcgat tcaggttcat catgccgtct gtgatggctt ccatgtcggc 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

agaatgctta atgaattaca acagtactgc gatgagtggc agggcggggc gtaaTTTTTT TAAGGCAGTT ATTGGTGCCC TTAAACGCCT GGTTCTACGC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CTGAATAAGT GATAATAAGC GGATGAATGG CAGAAATTCG CCGgatcttt gtgaaggaac cttacttctg tggtgtgaca taattggaca aactacctac 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

agagatttaa agctctaagg taaatataaa atttttaagt gtataatgtg ttaaactact gattctaatt gtttgtgtat tttagattcc aacctatgga 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

actgatgaat gggagcagtg gtggaatgcc tttaatgagg aaaacctgtt ttgctcagaa gaaatgccat ctagtgatga tgaggctact gctgactctc 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

aacattctac tcctccaaaa aagaagagaa aggtagaaga ccccaaggac tttccttcag aattgctaag ttttttgagt catgctgtgt ttagtaatag 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

aactcttgct tgctttgcta tttacaccac aaaggaaaaa gctgcactgc tatacaagaa aattatggaa aaatattctg taacctttat aagtaggcat 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

aacagttata atcataacat actgtttttt cttactccac acaggcatag agtgtctgct attaataact atgctcaaaa attgtgtacc tttagctttt 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

taatttgtaa aggggttaat aaggaatatt tgatgtatag tgccttgact agagatcata atcagccata ccacatttgt agaggtttta cttgctttaa 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

aaaacctccc acacctcccc ctgaacctga aacataaaat gaatgcaatt gttgttgtta acttgtttat tgcagcttat aatggttaca aataaagcaa 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

tagcatcaca aatttcacaa ataaagcatt tttttcactg cattctagtt gtggtttgtc caaactcatc aatgtatctt atcatgtctg TCCTAGAGGG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CCCTATTcta tagtgtcacc taaatgctag agctcgctga tcagcctcga ctgtgccttc tagttgccag ccatctgttg tttgcccctc ccccgtgcct 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

tccttgaccc tggaaggtgc cactcccact gtcctttcct aataaaatga ggaaattgca tcgcattgtc tgagtaggtg tcattctatt ctggggggtg 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

gggtggggca ggacagcaag ggggaggatt gggaagacaa tagcaggcat gctggggatg cggTGGGCTC TATGGCTTCT GAGGCGGAAA GAACCAGCTG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GGGCTCTAGG GGGTATCCCC ACGCGCCCTG TAGCGGCgca ttaagcgcgg cgggtgtggt ggttacgcgc agcgtgaccg ctacacttgc cagcgcccta 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

gcgcccgctc ctttcgcttt cttcccttcc tttctcgcca cgttcgccgg ctttccccgt caagctctaa atcggggcat ccctttaggg ttccgattta 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

gtgctttacg gcacctcgac cccaaaaaac ttgattaggg tgatggttca cgtagtgggc catcgccctg atagacggtt tttcgccctt tgacgttgga 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

gtccacgttc tttaatagtg gactcttgtt ccaaactgga acaaCACTCA ACCCTATCTC GGTCTATTCT TTTGATTTAT AAGGGATTTT GGGGATTTCG 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

GCCTATTGGT TAAAAAATGA GCTGATTTAA CAAAAATTTA ACGCGAATTA ATTCTGTGGA ATGTGTGTCA GTTAGGGTGT GGAAAGTCCC CAGGCTCCcc 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

aggcaggcag aagtatgcaa agcatgcatc tcaattagtc agcaaccagg tgtggaaagt ccccaggctc cccagcaggc agaagtatgc aaagcatgca 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

tctcaattag tcagcaacca tagtcccgcc cctaactccg cccatcccgc ccctaactcc gcccagttcc gcccattctc cgccccatgg ctgactaatt 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ttttttattt atgcagaggc cgaggccgcc tctgcctctg agctattcca gaagtagtga ggaggctttt ttggaggcct aggcttttgc aaaaagctcc 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

cgggagcttg tatatccatt ttcggATCTG ATCAAGAGAC AGGATGAGGA TCGTTTCGCa tgattgaaca agatggattg cacgcaggtt ctccggccgc 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

ttgggtggag aggctattcg gctatgactg ggcacaacag acaatcggct gctctgatgc cgccgtgttc cggctgtcag cgcaggggcg cccggttctt 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

tttgtcaaga ccgacctgtc cggtgccctg aatgaactgc aggacgaggc agcgcggcta tcgtggctgg ccacgacggg cgttccttgc gcagctgtgc 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

tcgacgttgt cactgaagcg ggaagggact ggctgctatt gggcgaagtg ccggggcagg atctcctgtc atctcacctt gctcctgccg agaaagtatc 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

catcatggct gatgcaatgc ggcggctgca tacgcttgat ccggctacct gcccattcga ccaccaagcg aaacatcgca tcgagcgagc acgtactcgg 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

atggaagccg gtcttgtcga tcaggatgat ctggacgaag agcatcaggg gctcgcgcca gccgaactgt tcgccaggct caaggcgcgc atgcccgacg 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

gcgaggatct cgtcgtgacc catggcgatg cctgcttgcc gaatatcatg gtggaaaatg gccgcttttc tggattcatc gactgtggcc ggctgggtgt 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

ggcggaccgc tatcaggaca tagcgttggc tacccgtgat attgctgaag agcttggcgg cgaatgggct gaccgcttcc tcgtgcttta cggtatcgcc 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

gctcccgatt cgcagcgcat cgccttctat cgccttcttg acgagttctt ctgagcgGGA CTCTGGGGTT CGAAATGACC GACCAAGCGA CGCCCAACCT 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

GCCATCACGA GATTTCGATT CCACCGCCGC CTTCTATGAA AGGTTGGGCT TCGGAATCGT TTTCCGGGAC GCCGGCTGGA TGATCCTCCA GCGCGGGGAT 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

CTCATGCTGG AGTTCTTCGC CCACCCCAac ttgtttattg cagcttataa tggttacaaa taaagcaata gcatcacaaa tttcacaaat aaagcatttt 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

tttcactgca ttctagttgt ggtttgtcca aactcatcaa tgtatcttat catgtctgta taccgtcgac ctctagctag agcttggcgt aatcatggtc 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

atagctgttt cctgtgtgaa attgttatcc gctcacaatt ccacacaACA TACGAGCCGG AAGCATAAAG TGTAAAGCCT GGGGTGCCTA ATGAGTGAGC 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

TAACTCACAT TAATTGCGTT GCGCTCACTG CCCGCTTTCC AGTCGGGAAA CCTGTCGTGC CAGCTGCATT AATGAATCGG CCAACGCGCG GGGAGAGGCG 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

GTTTGCGTAT TGGGCGCTCT TCCGCTTCCT CGCTCACTGA CTCGCTGCGC TCGGTCGTTC GGCTGCGGCG AGCGGTATCA GCTCACTCAA AGGCGGTAAT 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

ACGGTTATCC ACAGAATCAG GGGATAACGC AGGAAAGAAC ATGTGAGCAA AAGGCCAGCA AAAGGCCAGG AACCGTAAAA Aggccgcgtt gctggcgttt 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcaatgctc 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

acgctgtagg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

tatcgtcttg agtccaaccc ggtaagacac gacttatcgc cactggcagc agccactggt aacaggatta gcagagcgag gtatgtaggc ggtgctacag 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

agttcttgaa gtggtggcct aactacggct acactagaag gacagtattt ggtatctgcg ctctgctgaa gccagttacc ttcggaaaaa gagttggtag 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

ctcttgatcc ggcaaacaaa ccaccgctgg tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga agatcctttg 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

atcttttcta cggggtctga cgctcagtgg aacgaaaact cacgttaagg gattttggtc atgagattat caaaaaggat cttcacctag atccttttaa 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

attaaaaatg aagttttaaa tcaatctaaa gtatatatga gtaaacttgg tctgacagtt accaatgctt aatcagtgag gcacctatct cagcgatctg 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

tctatttcgt tcatccatag ttgcctgact ccccgtcgtg tagataacta cgatacggga gggcttacca tctggcccca gtgctgcaat gataccgcga 
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391      

gacccacgct caccggctcc agatttatca gcaataaacc agccagccgg aagggccgag cgcagaagtg gtcctgcaac tttatccgcc tccatccagt 
^9401      ^9411      ^9421      ^9431      ^9441      ^9451      ^9461      ^9471      ^9481      ^9491      

ctattaattg ttgccgggaa gctagagtaa gtagttcgcc agttaatagt ttgcgcaacg ttgttgccat tgctacaggc atcgtggtgt cacgctcgtc 
^9501      ^9511      ^9521      ^9531      ^9541      ^9551      ^9561      ^9571      ^9581      ^9591      

gtttggtatg gcttcattca gctccggttc ccaacgatca aggcgagtta catgatcccc catgttgtgc aaaaaagcgg ttagctcctt cggtcctccg 
^9601      ^9611      ^9621      ^9631      ^9641      ^9651      ^9661      ^9671      ^9681      ^9691      

atcgttgtca gaagtaagtt ggccgcagtg ttatcactca tggttatggc agcactgcat aattctctta ctgtcatgcc atccgtaaga tgcttttctg 
^9701      ^9711      ^9721      ^9731      ^9741      ^9751      ^9761      ^9771      ^9781      ^9791      

tgactggtga gtactcaacc aagtcattct gagaatagtg tatgcggcga ccgagttgct cttgcccggc gtcaatacgg gataataccg cgccacatag 
^9801      ^9811      ^9821      ^9831      ^9841      ^9851      ^9861      ^9871      ^9881      ^9891      

cagaacttta aaagtgctca tcattggaaa acgttcttcg gggcgaaaac tctcaaggat cttaccgctg ttgagatcca gttcgatgta acccactcgt 
^9901      ^9911      ^9921      ^9931      ^9941      ^9951      ^9961      ^9971      ^9981      ^9991      

gcacccaact gatcttcagc atcttttact ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa atgccgcaaa aaagggaata agggcgacac 
^10001     ^10011     ^10021     ^10031     ^10041     ^10051     ^10061     ^10071     ^10081     ^10091     

ggaaatgttg aatactcata ctcttCC
^10101     ^10111     ^10121

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: Václav Vopálenský	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
LacZ

The description of the protein encoded in this ORF:
beta galactosidase

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):

810-3608

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
CAT

The description of the protein encoded in this ORF:
chloramphenicol acetyl transferase

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):

4195-4854

Remarks:

The plasmid was used as the negative control for experiments in article A search for structurally similar
cellular internal ribosome entry sites (Baird et al., 2007; PMID:17591613).

Citations:

Baird S. D., Lewis S. M., Turcotte M., Holcik M. (2007) A search for structurally similar cellular internal ribosome entry sites. Nucleic. Acids. Res. 35(14):4664-4677

IRESs:

IRES:

Version: `2`	Last change: `2008-07-15 08:48:18`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `AQP4`	The functional status of IRES: `functional`

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

3905-4188

How IRES boundaries were determined:
guessed

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `297`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `580`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-290`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-7`

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

GGACAGTTTG GATAATTTTC CGTGAAACTG GATGATCTTT GAATATTAAA TGAAAGGAGA CTAGAATAAC AGTCTCTTGA CTATTCATGA AGGAGCTTTA 
^3905      ^3915      ^3925      ^3935      ^3945      ^3955      ^3965      ^3975      ^3985      ^3995      

GCAGGAGCAT TCTTTCTTGG TGTGCAAATC ACGCCTGGCA GCCCCTGCCC ACAGTACCCG AAGATGGCAG GCCTTGTTCC CTTCACCTAA ATTCATAAAC 
^4005      ^4015      ^4025      ^4035      ^4045      ^4055      ^4065      ^4075      ^4085      ^4095      

CTGGGTGTAG TGGCTTCTGA TGCTGATTTG TTTCTCTTTT CAGTAAGTGT GGACCTTTGT GTACCAGAGA GAACATCATG GTGG
^4105      ^4115      ^4125      ^4135      ^4145      ^4155      ^4165      ^4175      ^4185

Citations:

Baird S. D., Lewis S. M., Turcotte M., Holcik M. (2007) A search for structurally similar cellular internal ribosome entry sites. Nucleic. Acids. Res. 35(14):4664-4677

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