IRESite_Id:541 characteristics of AQP4 IRES studied in pBiCAQP4 plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `541`	Version: `1`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-10-28 00:39:18`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_without_translational_characterization

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
only_IRES_fragment

The mRNA/+RNA description:

In vitro T7 transcript used for structure probing experiments of AQP4 IRES. Transcription was done from PCR
template, prepared from pBiCAQP4 vector using AQP4 forward primer with built-in T7 promoter sequence
(taatacgactcactatagggGGACAGTTTGGATAA) and AQP4 reverse primer (cctcgagCCACCATGATGTTCTCT).

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

GGGGGACAGT TTGGATAATT TTCCGTGAAA CTGGATGATC TTTGAATATT AAATGAAAGG AGACTAGAAT AACAGTCTCT TGACTATTCA TGAAGGAGCT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTAGCAGGAG CATTCTTTCT TGGTGTGCAA ATCACGCCTG GCAGCCCCTG CCCACAGTAC CCGAAGATGG CAGGCCTTGT TCCCTTCACC TAAATTCATA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AACCTGGGTG TAGTGGCTTC TGATGCTGAT TTGTTTCTCT TTTCAGTAAG TGTGGACCTT TGTGTACCAG AGAGAACATC ATGGTGGctc gagg
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291

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:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pBiCAQP4 The name of the promoter used to express this mRNA:
T7

Description of the plasmid (facultative for promoter-less plasmid records):
PCR template for structure probing experiments of AQP4 IRES was prepared from pBiCAQP4 vector using AQP4 forward primer with built-in T7 promoter sequence (taatacgactcactatagggGGACAGTTTGGATAA) and AQP4 reverse primer (cctcgagCCACCATGATGTTCTCT).

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:
AQP4

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

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

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 GCTTcgcgat gtacgggcca gatatacgcg ttgacattga ttattgacta gttattaata gtaatcaatt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

acggggtcat tagttcatag cccatatatg gagttccgcg ttacataact tacggtaaat ggcccgcctg gctgaccgcc caacgacccc cgcccattga 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

cgtcaataat gacgtatgtt cccatagtaa cgccaatagg gactttccat tgacgtcaat gggtggacta tttacggtaa actgcccact tggcagtaca 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

tcaagtgtat catatgccaa gtacgccccc tattgacgtc aatgacggta aatggcccgc ctggcattat gcccagtaca tgaccttatg ggactttcct 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

acttggcagt acatctacgt attagtcatc gctattacca tggtgatgcg gttttggcag tacatcaatg ggcgtggata gcggtttgac tcacggggat 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ttccaagtct ccaccccatt gacgtcaatg ggagtttgtt ttggcaccaa aatcaacggg actttccaaa atgtcgtaac aactccgccc cattgacgca 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

aatgggcggt aggcgtgtac ggtgggaggt ctatataagc agagctctct ggctaactag agaacccact gcttactggc ttatcgaaat taatacgact 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

cactataggg agacccaagc ttggtaccga gctcggatcc actagtaacg gccgccagtg tgctggaatt ctgcagatat ccatcacact ggcggccgca 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

attCCCGGGG ATCGAAAGAG CCTGCTAAAG CAAAAAAGAA GTCACCATGT CGTTTACTTT GACCAACAAG AACGTGATTT TCGTTGCCGG TCTGGGAGGC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ATTGGTCTGG ACACCAGCAA GGAGCTGCTC AAGCGCGATC CCGTCGTTTT ACAACGTCGT GACTGGGAAA ACCCTGGCGT TACCCAACTT AATCGCCTTG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CAGCACATCC CCCTTTCGCC AGCTGGCGTA ATAGCGAAGA GGCCCGCACC GATCGCCCTT CCCAACAGTT GCGCAGCTGA ATGGCGAATG GCGCTTTGCC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TGGTTTCCGG CACCAGAAGC GGTGCCGGAA AGCTGGCTGG AGTTCGATCT TCCTGAGGCC GATACTGTCG TCGTCCCCTC AAACTGGCAG ATGCACGGTT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACGATGCGCC CATCTACACC AACGTGACCT ATCCCATTAC GGTCAATCCG CCGTTTGTTC CCACGGAGAA TCCGACGGGT TGTTACTCGC TCACATTTAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TGTTGATGAA AGCTGGCTAC AGGAAGGCCA GACGCGAATT ATTTTTGATG GCGTTAACTC GGCGTTTCAT CTGTGGTGCA ACGGGCGCTG GGTCGGTTAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GGCCAGGACA GTCGTTTGCC GTCTGAATTT GACCTGAGCG CATTTTTACG CGCCGGAGAA AACCGCCTCG CGGTGATGGT GCTGCGTTGG AGTTACGGCA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTTATCTGGA AGATCAGGAT ATTTGGCGGA TGAGCGGCAT TTTCCGTGAC GTCTCGTTGC TGCATAAACC GACTACACAA ATCAGCGATT TCCATGTTGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CACTCGCTTT AATGATGATT TCAGCCGCGC TGTACTGGAG GCTGAAGTTC AGATGTGCGG CGAGTTGCGT GACTACCTAC GGGTAACAGT TTCTTTATGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CAGGGTGAAA CGCAGGTCGC CAGCGGCACC GCGCCTTTCG GCGGTGAAAT TATCGATGAG CGTGGTGGTT ATGCCGATCG CGTCACACTA CGTCTGAACG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TCGAAAACCC GAAACTGTGG AGCGCCGAAA TCCCGAATCT CTATCGTGCG GTGGTTGAAC TGCACACCGC CGACGGCACG CTGATTGAAG CAGAAGCCTG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CGATGTCGGT TTCCGCGAGG TGCGGATTGA AAATGGTCTG CTGCTGCTGA ACGGCAAGCC GTTGCTGATT CGAGGCGTTA ACCGTCACGA GCATCATCCT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CTGCATGGTC AGGTCATGGA TGAGCAGACG ATGGTGCAGG ATATCCTGCT GATGAAGCAG AACAACTTTA ACGCCGTGCG CTGTTCGCAT TATCCGAACC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ATCCGCTGTG GTACACGCTG TGCGACCGCT ACGGCCTGTA TGTGGTGGAT GAAGCCAATA TTGAAACCCA CGGCATGGTG CCAATGAATC GTCTGACCGA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TGATCCGCGC TGGCTACCGG CGATGAGCGA ACGCGTAACG CGAATGGTGC AGCGCGATCG TAATCACCCG AGTGTGATCA TCTGGTCGCT GGGGAATGAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TCAGGCCACG GCGCTAATCA CGACGCGCTG TATCGCTGGA TCAAATCTGT CGATCCTTCC CGCCCGGTGC AGTATGAAGG CGGCGGAGCC GACACCACGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CCACCGATAT TATTTGCCCG ATGTACGCGC GCGTGGATGA AGACCAGCCC TTCCCGGCTG TGCCGAAATG GTCCATCAAA AAATGGCTTT CGCTACCTGG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AGAGACGCGC CCGCTGATCC TTTGCGAATA CGCCCACGCG ATGGGTAACA GTCTTGGCGG TTTCGCTAAA TACTGGCAGG CGTTTCGTCA GTATCCCCGT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TTACAGGGCG GCTTCGTCTG GGACTGGGTG GATCAGTCGC TGATTAAATA TGATGAAAAC GGCAACCCGT GGTCGGCTTA CGGCGGTGAT TTTGGCGATA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CGCCGAACGA TCGCCAGTTC TGTATGAACG GTCTGGTCTT TGCCGACCGC ACGCCGCATC CAGCGCTGAC GGAAGCAAAA CACCAGCAGC AGTTTTTCCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GTTCCGTTTA TCCGGGCAAA CCATCGAAGT GACCAGCGAA TACCTGTTCC GTCATAGCGA TAACGAGCTC CTGCACTGGA TGGTGGCGCT GGATGGTAAG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CCGCTGGCAA GCGGTGAAGT GCCTCTGGAT GTCGCTCCAC AAGGTAAACA GTTGATTGAA CTGCCTGAAC TACCGCAGCC GGAGAGCGCC GGGCAACTCT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GGCTCACAGT ACGCGTAGTG CAACCGAACG CGACCGCATG GTCAGAAGCC GGGCACATCA GCGCCTGGCA GCAGTGGCGT CTGGCGGAAA ACCTCAGTGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GACGCTCCCC GCCGCGTCCC ACGCCATCCC GCATCTGACC ACCAGCGAAA TGGATTTTTG CATCGAGCTG GGTAATAAGC GTTGGCAATT TAACCGCCAG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TCAGGCTTTC TTTCACAGAT GTGGATTGGC GATAAAAAAC AACTGCTGAC GCCGCTGCGC GATCAGTTCA CCCGTGCACC GCTGGATAAC GACATTGGCG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TAAGTGAAGC GACCCGCATT GACCCTAACG CCTGGGTCGA ACGCTGGAAG GCGGCGGGCC ATTACCAGGC CGAAGCAGCG TTGTTGCAGT GCACGGCAGA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TACACTTGCT GATGCGGTGC TGATTACGAA CGCTCACGCG TGGCAGCATC AGGGGAAAAC CTTATTTATC AGCCGGAAAA CCTACCGGAT TGATGGTAGT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GGTCAAATGG CGATTACCGT TGATGTTGAA GTGGCGAGCG ATACACCGCA TCCGGCGCGG ATTGGCCTGA ACTGCCAGCT GGCGCAGGTA GCAGAGCGGG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TAAACTGGCT CGGATTAGGG CCGCAAGAAA ACTATCCCGA CCGCCTTACT GCCGCCTGTT TTGACCGCTG GGATCTGCCA TTGTCAGACA TGTATACCCC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GTACGTCTTC CCGAGCGAAA ACGGTCTGCG CTGCGGGACG CGCGAATTGA ATTATGGCCC ACACCAGTGG CGCGGCGACT TCCAGTTCAA CATCAGCCGC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TACAGTCAAC AGCAACTGAT GGAAACCAGC CATCGCCATC TGCTGCACGC GGAAGAAGGC ACATGGCTGA ATATCGACGG TTTCCATATG GGGATTGGTG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GCGACGACTC CTGGAGCCCG TCAGTATCGG CGGAATTACA GCTGAGCGCC GGTCGCTACC ATTACCAGTT GGTCTGGTGT CAAAAATAAT AATAACCGGG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CAGGCCATGT CTGCCCGTAT TTCGCGTAAG GAAATCCATT ATGTACTATT TAAAAAACAC AAACTTTTGG ATGTTCGGTT TATTCTTTTT CTTTTACTTT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TTTATCATGG GAGCCTACTT CCCGTTTTTC CCGATTTGGC TACATGACAT CAACCATATC AGCAAAAGTG ATACGGGTAT TATTTTTGCC GCTATTTCTC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TGTTCTCGCT ATTATTCCAA CCGCTGTTTG GTCTGCTTTC TGACAAACTC GGCCTCGACT CTAGGCGGCC GCTCGACGCT AGCAAGGACA GTTTGGATAA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TTTTCCGTGA AACTGGATGA TCTTTGAATA TTAAATGAAA GGAGACTAGA ATAACAGTCT CTTGACTATT CATGAAGGAG CTTTAGCAGG AGCATTCTTT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CTTGGTGTGC AAATCACGCC TGGCAGCCCC TGCCCACAGT ACCCGAAGAT GGCAGGCCTT GTTCCCTTCA CCTAAATTCA TAAACCTGGG TGTAGTGGCT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TCTGATGCTG ATTTGTTTCT CTTTTCAGTA AGTGTGGACC TTTGTGTACC AGAGAGAACA TCATGGTGGC TCGAGatgga gaaaaaaatc actggatata 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

ccaccgttga tatatcccaa tggcatcgta aagaacattt tgaggcattt cagtcagttg ctcaatgtac ctataaccag accgttcagc tggatattac 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

ggccttttta aagaccgtaa agaaaaataa gcacaagttt tatccggcct ttattcacat tcttgcccgc ctgatgaatg ctcatccgga attccgtatg 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

gcaatgaaag acggtgagct ggtgatatgg gatagtgttc acccttgtta caccgttttc catgagcaaa ctgaaacgtt ttcatcgctc tggagtgaat 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

accacgacga tttccggcag tttctacaca tatattcgca agatgtggcg tgttacggtg aaaacctggc ctatttccct aaagggttta ttgagaatat 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

gtttttcgtc tcagccaatc cctgggtgag tttcaccagt tttgatttaa acgtggccaa tatggacaac ttcttcgccc ccgttttcac catgggcaaa 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

tattatacgc aaggcgacaa ggtgctgatg ccgctggcga ttcaggttca tcatgccgtc tgtgatggct tccatgtcgg cagaatgctt aatgaattac 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

aacagtactg cgatgagtgg cagggcgggg cgtaaTTTTT TTAAGGCAGT TATTGGTGCC CTTAAACGCC TGGTTCTACG CCTGAATAAG TGATAATAAG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CGGATGAATG GCAGAAATTC GCCGgatctt tgtgaaggaa ccttacttct gtggtgtgac ataattggac aaactaccta cagagattta aagctctaag 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

gtaaatataa aatttttaag tgtataatgt gttaaactac tgattctaat tgtttgtgta ttttagattc caacctatgg aactgatgaa tgggagcagt 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ggtggaatgc ctttaatgag gaaaacctgt tttgctcaga agaaatgcca tctagtgatg atgaggctac tgctgactct caacattcta ctcctccaaa 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

aaagaagaga aaggtagaag accccaagga ctttccttca gaattgctaa gttttttgag tcatgctgtg tttagtaata gaactcttgc ttgctttgct 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

atttacacca caaaggaaaa agctgcactg ctatacaaga aaattatgga aaaatattct gtaaccttta taagtaggca taacagttat aatcataaca 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

tactgttttt tcttactcca cacaggcata gagtgtctgc tattaataac tatgctcaaa aattgtgtac ctttagcttt ttaatttgta aaggggttaa 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

taaggaatat ttgatgtata gtgccttgac tagagatcat aatcagccat accacatttg tagaggtttt acttgcttta aaaaacctcc cacacctccc 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

cctgaacctg aaacataaaa tgaatgcaat tgttgttgtt aacttgttta ttgcagctta taatggttac aaataaagca atagcatcac aaatttcaca 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

aataaagcat ttttttcact gcattctagt tgtggtttgt ccaaactcat caatgtatct tatcatgtct gTCCTAGAGG GCCCTATTct atagtgtcac 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

ctaaatgcta gagctcgctg atcagcctcg actgtgcctt ctagttgcca gccatctgtt gtttgcccct cccccgtgcc ttccttgacc ctggaaggtg 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

ccactcccac tgtcctttcc taataaaatg aggaaattgc atcgcattgt ctgagtaggt gtcattctat tctggggggt ggggtggggc aggacagcaa 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

gggggaggat tgggaagaca atagcaggca tgctggggat gcggTGGGCT CTATGGCTTC TGAGGCGGAA AGAACCAGCT GGGGCTCTAG GGGGTATCCC 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

CACGCGCCCT GTAGCGGCgc attaagcgcg gcgggtgtgg tggttacgcg cagcgtgacc gctacacttg ccagcgccct agcgcccgct cctttcgctt 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

tcttcccttc ctttctcgcc acgttcgccg gctttccccg tcaagctcta aatcggggca tccctttagg gttccgattt agtgctttac ggcacctcga 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

ccccaaaaaa cttgattagg gtgatggttc acgtagtggg ccatcgccct gatagacggt ttttcgccct ttgacgttgg agtccacgtt ctttaatagt 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

ggactcttgt tccaaactgg aacaaCACTC AACCCTATCT CGGTCTATTC TTTTGATTTA TAAGGGATTT TGGGGATTTC GGCCTATTGG TTAAAAAATG 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

AGCTGATTTA ACAAAAATTT AACGCGAATT AATTCTGTGG AATGTGTGTC AGTTAGGGTG TGGAAAGTCC CCAGGCTCCc caggcaggca gaagtatgca 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

aagcatgcat ctcaattagt cagcaaccag gtgtggaaag tccccaggct ccccagcagg cagaagtatg caaagcatgc atctcaatta gtcagcaacc 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

atagtcccgc ccctaactcc gcccatcccg cccctaactc cgcccagttc cgcccattct ccgccccatg gctgactaat tttttttatt tatgcagagg 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

ccgaggccgc ctctgcctct gagctattcc agaagtagtg aggaggcttt tttggaggcc taggcttttg caaaaagctc ccgggagctt gtatatccat 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

tttcggATCT GATCAAGAGA CAGGATGAGG ATCGTTTCGC atgattgaac aagatggatt gcacgcaggt tctccggccg cttgggtgga gaggctattc 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

ggctatgact gggcacaaca gacaatcggc tgctctgatg ccgccgtgtt ccggctgtca gcgcaggggc gcccggttct ttttgtcaag accgacctgt 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

ccggtgccct gaatgaactg caggacgagg cagcgcggct atcgtggctg gccacgacgg gcgttccttg cgcagctgtg ctcgacgttg tcactgaagc 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

gggaagggac tggctgctat tgggcgaagt gccggggcag gatctcctgt catctcacct tgctcctgcc gagaaagtat ccatcatggc tgatgcaatg 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

cggcggctgc atacgcttga tccggctacc tgcccattcg accaccaagc gaaacatcgc atcgagcgag cacgtactcg gatggaagcc ggtcttgtcg 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

atcaggatga tctggacgaa gagcatcagg ggctcgcgcc agccgaactg ttcgccaggc tcaaggcgcg catgcccgac ggcgaggatc tcgtcgtgac 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

ccatggcgat gcctgcttgc cgaatatcat ggtggaaaat ggccgctttt ctggattcat cgactgtggc cggctgggtg tggcggaccg ctatcaggac 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

atagcgttgg ctacccgtga tattgctgaa gagcttggcg gcgaatgggc tgaccgcttc ctcgtgcttt acggtatcgc cgctcccgat tcgcagcgca 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

tcgccttcta tcgccttctt gacgagttct tctgagcgGG ACTCTGGGGT TCGAAATGAC CGACCAAGCG ACGCCCAACC TGCCATCACG AGATTTCGAT 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

TCCACCGCCG CCTTCTATGA AAGGTTGGGC TTCGGAATCG TTTTCCGGGA CGCCGGCTGG ATGATCCTCC AGCGCGGGGA TCTCATGCTG GAGTTCTTCG 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

CCCACCCCAa cttgtttatt gcagcttata atggttacaa ataaagcaat agcatcacaa atttcacaaa taaagcattt ttttcactgc attctagttg 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

tggtttgtcc aaactcatca atgtatctta tcatgtctgt ataccgtcga cctctagcta gagcttggcg taatcatggt catagctgtt tcctgtgtga 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

aattgttatc cgctcacaat tccacacaAC ATACGAGCCG GAAGCATAAA GTGTAAAGCC TGGGGTGCCT AATGAGTGAG CTAACTCACA TTAATTGCGT 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

TGCGCTCACT GCCCGCTTTC CAGTCGGGAA ACCTGTCGTG CCAGCTGCAT TAATGAATCG GCCAACGCGC GGGGAGAGGC GGTTTGCGTA TTGGGCGCTC 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

TTCCGCTTCC TCGCTCACTG ACTCGCTGCG CTCGGTCGTT CGGCTGCGGC GAGCGGTATC AGCTCACTCA AAGGCGGTAA TACGGTTATC CACAGAATCA 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

GGGGATAACG CAGGAAAGAA CATGTGAGCA AAAGGCCAGC AAAAGGCCAG GAACCGTAAA AAggccgcgt tgctggcgtt tttccatagg ctccgccccc 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

ctgacgagca tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct ccctcgtgcg 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcaatgct cacgctgtag gtatctcagt 
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391      

tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc 
^9401      ^9411      ^9421      ^9431      ^9441      ^9451      ^9461      ^9471      ^9481      ^9491      

cggtaagaca cgacttatcg ccactggcag cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga agtggtggcc 
^9501      ^9511      ^9521      ^9531      ^9541      ^9551      ^9561      ^9571      ^9581      ^9591      

taactacggc tacactagaa ggacagtatt tggtatctgc gctctgctga agccagttac cttcggaaaa agagttggta gctcttgatc cggcaaacaa 
^9601      ^9611      ^9621      ^9631      ^9641      ^9651      ^9661      ^9671      ^9681      ^9691      

accaccgctg gtagcggtgg tttttttgtt tgcaagcagc agattacgcg cagaaaaaaa ggatctcaag aagatccttt gatcttttct acggggtctg 
^9701      ^9711      ^9721      ^9731      ^9741      ^9751      ^9761      ^9771      ^9781      ^9791      

acgctcagtg gaacgaaaac tcacgttaag ggattttggt catgagatta tcaaaaagga tcttcaccta gatcctttta aattaaaaat gaagttttaa 
^9801      ^9811      ^9821      ^9831      ^9841      ^9851      ^9861      ^9871      ^9881      ^9891      

atcaatctaa agtatatatg agtaaacttg gtctgacagt taccaatgct taatcagtga ggcacctatc tcagcgatct gtctatttcg ttcatccata 
^9901      ^9911      ^9921      ^9931      ^9941      ^9951      ^9961      ^9971      ^9981      ^9991      

gttgcctgac tccccgtcgt gtagataact acgatacggg agggcttacc atctggcccc agtgctgcaa tgataccgcg agacccacgc tcaccggctc 
^10001     ^10011     ^10021     ^10031     ^10041     ^10051     ^10061     ^10071     ^10081     ^10091     

cagatttatc agcaataaac cagccagccg gaagggccga gcgcagaagt ggtcctgcaa ctttatccgc ctccatccag tctattaatt gttgccggga 
^10101     ^10111     ^10121     ^10131     ^10141     ^10151     ^10161     ^10171     ^10181     ^10191     

agctagagta agtagttcgc cagttaatag tttgcgcaac gttgttgcca ttgctacagg catcgtggtg tcacgctcgt cgtttggtat ggcttcattc 
^10201     ^10211     ^10221     ^10231     ^10241     ^10251     ^10261     ^10271     ^10281     ^10291     

agctccggtt cccaacgatc aaggcgagtt acatgatccc ccatgttgtg caaaaaagcg gttagctcct tcggtcctcc gatcgttgtc agaagtaagt 
^10301     ^10311     ^10321     ^10331     ^10341     ^10351     ^10361     ^10371     ^10381     ^10391     

tggccgcagt gttatcactc atggttatgg cagcactgca taattctctt actgtcatgc catccgtaag atgcttttct gtgactggtg agtactcaac 
^10401     ^10411     ^10421     ^10431     ^10441     ^10451     ^10461     ^10471     ^10481     ^10491     

caagtcattc tgagaatagt gtatgcggcg accgagttgc tcttgcccgg cgtcaatacg ggataatacc gcgccacata gcagaacttt aaaagtgctc 
^10501     ^10511     ^10521     ^10531     ^10541     ^10551     ^10561     ^10571     ^10581     ^10591     

atcattggaa aacgttcttc ggggcgaaaa ctctcaagga tcttaccgct gttgagatcc agttcgatgt aacccactcg tgcacccaac tgatcttcag 
^10601     ^10611     ^10621     ^10631     ^10641     ^10651     ^10661     ^10671     ^10681     ^10691     

catcttttac tttcaccagc gtttctgggt gagcaaaaac aggaaggcaa aatgccgcaa aaaagggaat aagggcgaca cggaaatgtt gaatactcat 
^10701     ^10711     ^10721     ^10731     ^10741     ^10751     ^10761     ^10771     ^10781     ^10791     

actcttCC
^10801

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

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

0

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: `0`
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):

4-287

How IRES boundaries were determined:
experimentally_determined

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

GGACAGTTTG GATAATTTTC CGTGAAACTG GATGATCTTT GAATATTAAA TGAAAGGAGA CTAGAATAAC AGTCTCTTGA CTATTCATGA AGGAGCTTTA 
((.((((((( (........) )...)))))) ....(((((( (......... ......(((( ((........ )))))).((( ....))).(( (((((((((. 
^4         ^14        ^24        ^34        ^44        ^54        ^64        ^74        ^84        ^94        

GCAGGAGCAT TCTTTCTTGG TGTGCAAATC ACGCCTGGCA GCCCCTGCCC ACAGTACCCG AAGATGGCAG GCCTTGTTCC CTTCACCTAA ATTCATAAAC 
...))))).. ))))))..(( ((((.....) ))))).((.. ...))..... ........)) ))))).(((. ....)))..) )))((((((. .......... 
^104       ^114       ^124       ^134       ^144       ^154       ^164       ^174       ^184       ^194       

CTGGGTGTAG TGGCTTCTGA TGCTGATTTG TTTCTCTTTT CAGTAAGTGT GGACCTTTGT GTACCAGAGA GAACATCATG GTGG
.))))))..( ((((...... .)).(((((( ((.(((.... .......... .......... ........)) )))))..... ....
^204       ^214       ^224       ^234       ^244       ^254       ^264       ^274       ^284

There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:

((.((((((((........))...))))))....(((((((...............((((((........)))))).(((....))).(((((((((((....)))))..))))))..((((((.....)))))).((.....)).............))))))).(((.....)))..))))((((((............))))))..(((((.......)).((((((((.(((................................))))))).........
ERROR: unbalanced brackets in make_pair_table

STDOUT was:

Remarks:

AQP4 IRES represents 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.

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

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 29

Version: `0`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `no`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
4-293

The underlying nucleic acid sequence and structure of the mapped region:

GGACAGTTTG GATAATTTTC CGTGAAACTG GATGATCTTT GAATATTAAA TGAAAGGAGA CTAGAATAAC AGTCTCTTGA CTATTCATGA AGGAGCTTTA 
((.((((((( (........) )...)))))) ....(((((( (......... ......(((( ((........ )))))).((( ....))).(( (((((((((. 
^4         ^14        ^24        ^34        ^44        ^54        ^64        ^74        ^84        ^94        

GCAGGAGCAT TCTTTCTTGG TGTGCAAATC ACGCCTGGCA GCCCCTGCCC ACAGTACCCG AAGATGGCAG GCCTTGTTCC CTTCACCTAA ATTCATAAAC 
...))))).. ))))))..(( ((((.....) ))))).((.. ...))..... ........)) ))))).(((. ....)))..) )))((((((. .......... 
^104       ^114       ^124       ^134       ^144       ^154       ^164       ^174       ^184       ^194       

CTGGGTGTAG TGGCTTCTGA TGCTGATTTG TTTCTCTTTT CAGTAAGTGT GGACCTTTGT GTACCAGAGA GAACATCATG GTGGctcgag
.))))))..( ((((...... .)).(((((( ((.(((.... .......... .......... ........)) )))))..... ..........
^204       ^214       ^224       ^234       ^244       ^254       ^264       ^274       ^284

There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:

((.((((((((........))...))))))....(((((((...............((((((........)))))).(((....))).(((((((((((....)))))..))))))..((((((.....)))))).((.....)).............))))))).(((.....)))..))))((((((............))))))..(((((.......)).((((((((.(((................................)))))))...............
ERROR: unbalanced brackets in make_pair_table

STDOUT was:

Remarks:

2D structure of AQP4 from Fig 5B.

3.1.1. Enzymes used to characterize at least partially the 2D structure.