IRESite_Id:488 characteristics of AQP4 IRES studied in pBiCAQP4 plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `488`	Version: `3`
Originaly submitted by: Václav Vopálenský
Reviewed by: Václav Vopálenský	Last change: `2008-07-15 08:53:14`

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 in vivo CMV promoter-derived transcript produced from bicistronic plasmid pBiCAQP4 which comprises
beta galactosidase and chloramphenicol acetyl transferase as the first and the second cistron, respectively
and 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.
The sequence ends at its 3'-end right after the poly(A) signal from BGH mRNA and thus the 3'-UTR might be
slightly wrong.

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

agagaaccca ctgcttactg gcttatcgaa attaatacga ctcactatag ggagacccaa gcttggtacc gagctcggat ccactagtaa cggccgccag 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tgtgctggaa ttctgcagat atccatcaca ctggcggccg caattCCCGG GGATCGAAAG AGCCTGCTAA AGCAAAAAAG AAGTCACCAT GTCGTTTACT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TTGACCAACA AGAACGTGAT TTTCGTTGCC GGTCTGGGAG GCATTGGTCT GGACACCAGC AAGGAGCTGC TCAAGCGCGA TCCCGTCGTT TTACAACGTC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTGACTGGGA AAACCCTGGC GTTACCCAAC TTAATCGCCT TGCAGCACAT CCCCCTTTCG CCAGCTGGCG TAATAGCGAA GAGGCCCGCA CCGATCGCCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TTCCCAACAG TTGCGCAGCT GAATGGCGAA TGGCGCTTTG CCTGGTTTCC GGCACCAGAA GCGGTGCCGG AAAGCTGGCT GGAGTTCGAT CTTCCTGAGG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CCGATACTGT CGTCGTCCCC TCAAACTGGC AGATGCACGG TTACGATGCG CCCATCTACA CCAACGTGAC CTATCCCATT ACGGTCAATC CGCCGTTTGT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCCCACGGAG AATCCGACGG GTTGTTACTC GCTCACATTT AATGTTGATG AAAGCTGGCT ACAGGAAGGC CAGACGCGAA TTATTTTTGA TGGCGTTAAC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TCGGCGTTTC ATCTGTGGTG CAACGGGCGC TGGGTCGGTT ACGGCCAGGA CAGTCGTTTG CCGTCTGAAT TTGACCTGAG CGCATTTTTA CGCGCCGGAG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AAAACCGCCT CGCGGTGATG GTGCTGCGTT GGAGTTACGG CAGTTATCTG GAAGATCAGG ATATTTGGCG GATGAGCGGC ATTTTCCGTG ACGTCTCGTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GCTGCATAAA CCGACTACAC AAATCAGCGA TTTCCATGTT GCCACTCGCT TTAATGATGA TTTCAGCCGC GCTGTACTGG AGGCTGAAGT TCAGATGTGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GGCGAGTTGC GTGACTACCT ACGGGTAACA GTTTCTTTAT GGCAGGGTGA AACGCAGGTC GCCAGCGGCA CCGCGCCTTT CGGCGGTGAA ATTATCGATG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AGCGTGGTGG TTATGCCGAT CGCGTCACAC TACGTCTGAA CGTCGAAAAC CCGAAACTGT GGAGCGCCGA AATCCCGAAT CTCTATCGTG CGGTGGTTGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ACTGCACACC GCCGACGGCA CGCTGATTGA AGCAGAAGCC TGCGATGTCG GTTTCCGCGA GGTGCGGATT GAAAATGGTC TGCTGCTGCT GAACGGCAAG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCGTTGCTGA TTCGAGGCGT TAACCGTCAC GAGCATCATC CTCTGCATGG TCAGGTCATG GATGAGCAGA CGATGGTGCA GGATATCCTG CTGATGAAGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AGAACAACTT TAACGCCGTG CGCTGTTCGC ATTATCCGAA CCATCCGCTG TGGTACACGC TGTGCGACCG CTACGGCCTG TATGTGGTGG ATGAAGCCAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TATTGAAACC CACGGCATGG TGCCAATGAA TCGTCTGACC GATGATCCGC GCTGGCTACC GGCGATGAGC GAACGCGTAA CGCGAATGGT GCAGCGCGAT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CGTAATCACC CGAGTGTGAT CATCTGGTCG CTGGGGAATG AATCAGGCCA CGGCGCTAAT CACGACGCGC TGTATCGCTG GATCAAATCT GTCGATCCTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CCCGCCCGGT GCAGTATGAA GGCGGCGGAG CCGACACCAC GGCCACCGAT ATTATTTGCC CGATGTACGC GCGCGTGGAT GAAGACCAGC CCTTCCCGGC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGTGCCGAAA TGGTCCATCA AAAAATGGCT TTCGCTACCT GGAGAGACGC GCCCGCTGAT CCTTTGCGAA TACGCCCACG CGATGGGTAA CAGTCTTGGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GGTTTCGCTA AATACTGGCA GGCGTTTCGT CAGTATCCCC GTTTACAGGG CGGCTTCGTC TGGGACTGGG TGGATCAGTC GCTGATTAAA TATGATGAAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACGGCAACCC GTGGTCGGCT TACGGCGGTG ATTTTGGCGA TACGCCGAAC GATCGCCAGT TCTGTATGAA CGGTCTGGTC TTTGCCGACC GCACGCCGCA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TCCAGCGCTG ACGGAAGCAA AACACCAGCA GCAGTTTTTC CAGTTCCGTT TATCCGGGCA AACCATCGAA GTGACCAGCG AATACCTGTT CCGTCATAGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GATAACGAGC TCCTGCACTG GATGGTGGCG CTGGATGGTA AGCCGCTGGC AAGCGGTGAA GTGCCTCTGG ATGTCGCTCC ACAAGGTAAA CAGTTGATTG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AACTGCCTGA ACTACCGCAG CCGGAGAGCG CCGGGCAACT CTGGCTCACA GTACGCGTAG TGCAACCGAA CGCGACCGCA TGGTCAGAAG CCGGGCACAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CAGCGCCTGG CAGCAGTGGC GTCTGGCGGA AAACCTCAGT GTGACGCTCC CCGCCGCGTC CCACGCCATC CCGCATCTGA CCACCAGCGA AATGGATTTT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TGCATCGAGC TGGGTAATAA GCGTTGGCAA TTTAACCGCC AGTCAGGCTT TCTTTCACAG ATGTGGATTG GCGATAAAAA ACAACTGCTG ACGCCGCTGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GCGATCAGTT CACCCGTGCA CCGCTGGATA ACGACATTGG CGTAAGTGAA GCGACCCGCA TTGACCCTAA CGCCTGGGTC GAACGCTGGA AGGCGGCGGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CCATTACCAG GCCGAAGCAG CGTTGTTGCA GTGCACGGCA GATACACTTG CTGATGCGGT GCTGATTACG AACGCTCACG CGTGGCAGCA TCAGGGGAAA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ACCTTATTTA TCAGCCGGAA AACCTACCGG ATTGATGGTA GTGGTCAAAT GGCGATTACC GTTGATGTTG AAGTGGCGAG CGATACACCG CATCCGGCGC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGATTGGCCT GAACTGCCAG CTGGCGCAGG TAGCAGAGCG GGTAAACTGG CTCGGATTAG GGCCGCAAGA AAACTATCCC GACCGCCTTA CTGCCGCCTG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TTTTGACCGC TGGGATCTGC CATTGTCAGA CATGTATACC CCGTACGTCT TCCCGAGCGA AAACGGTCTG CGCTGCGGGA CGCGCGAATT GAATTATGGC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCACACCAGT GGCGCGGCGA CTTCCAGTTC AACATCAGCC GCTACAGTCA ACAGCAACTG ATGGAAACCA GCCATCGCCA TCTGCTGCAC GCGGAAGAAG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GCACATGGCT GAATATCGAC GGTTTCCATA TGGGGATTGG TGGCGACGAC TCCTGGAGCC CGTCAGTATC GGCGGAATTA CAGCTGAGCG CCGGTCGCTA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CCATTACCAG TTGGTCTGGT GTCAAAAATA ATAATAACCG GGCAGGCCAT GTCTGCCCGT ATTTCGCGTA AGGAAATCCA TTATGTACTA TTTAAAAAAC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ACAAACTTTT GGATGTTCGG TTTATTCTTT TTCTTTTACT TTTTTATCAT GGGAGCCTAC TTCCCGTTTT TCCCGATTTG GCTACATGAC ATCAACCATA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TCAGCAAAAG TGATACGGGT ATTATTTTTG CCGCTATTTC TCTGTTCTCG CTATTATTCC AACCGCTGTT TGGTCTGCTT TCTGACAAAC TCGGCCTCGA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CTCTAGGCGG CCGCTCGACG CTAGCAAGGA CAGTTTGGAT AATTTTCCGT GAAACTGGAT GATCTTTGAA TATTAAATGA AAGGAGACTA GAATAACAGT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CTCTTGACTA TTCATGAAGG AGCTTTAGCA GGAGCATTCT TTCTTGGTGT GCAAATCACG CCTGGCAGCC CCTGCCCACA GTACCCGAAG ATGGCAGGCC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TTGTTCCCTT CACCTAAATT CATAAACCTG GGTGTAGTGG CTTCTGATGC TGATTTGTTT CTCTTTTCAG TAAGTGTGGA CCTTTGTGTA CCAGAGAGAA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CATCATGGTG GCTCGAGatg gagaaaaaaa tcactggata taccaccgtt gatatatccc aatggcatcg taaagaacat tttgaggcat ttcagtcagt 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

tgctcaatgt acctataacc agaccgttca gctggatatt acggcctttt taaagaccgt aaagaaaaat aagcacaagt tttatccggc ctttattcac 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

attcttgccc gcctgatgaa tgctcatccg gaattccgta tggcaatgaa agacggtgag ctggtgatat gggatagtgt tcacccttgt tacaccgttt 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

tccatgagca aactgaaacg ttttcatcgc tctggagtga ataccacgac gatttccggc agtttctaca catatattcg caagatgtgg cgtgttacgg 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

tgaaaacctg gcctatttcc ctaaagggtt tattgagaat atgtttttcg tctcagccaa tccctgggtg agtttcacca gttttgattt aaacgtggcc 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

aatatggaca acttcttcgc ccccgttttc accatgggca aatattatac gcaaggcgac aaggtgctga tgccgctggc gattcaggtt catcatgccg 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

tctgtgatgg cttccatgtc ggcagaatgc ttaatgaatt acaacagtac tgcgatgagt ggcagggcgg ggcgtaaTTT TTTTAAGGCA GTTATTGGTG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CCCTTAAACG CCTGGTTCTA CGCCTGAATA AGTGATAATA AGCGGATGAA TGGCAGAAAT TCGCCGgatc tttgtgaagg aaccttactt ctgtggtgtg 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

acataattgg acaaactacc tacagagatt taaagctcta aggtaaatat aaaattttta agtgtataat gtgttaaact actgattcta attgtttgtg 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

tattttagat tccaacctat ggaactgatg aatgggagca gtggtggaat gcctttaatg aggaaaacct gttttgctca gaagaaatgc catctagtga 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

tgatgaggct actgctgact ctcaacattc tactcctcca aaaaagaaga gaaaggtaga agaccccaag gactttcctt cagaattgct aagttttttg 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

agtcatgctg tgtttagtaa tagaactctt gcttgctttg ctatttacac cacaaaggaa aaagctgcac tgctatacaa gaaaattatg gaaaaatatt 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ctgtaacctt tataagtagg cataacagtt ataatcataa catactgttt tttcttactc cacacaggca tagagtgtct gctattaata actatgctca 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

aaaattgtgt acctttagct ttttaatttg taaaggggtt aataaggaat atttgatgta tagtgccttg actagagatc ataatcagcc ataccacatt 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

tgtagaggtt ttacttgctt taaaaaacct cccacacctc cccctgaacc tgaaacataa aatgaatgca attgttgttg ttaacttgtt tattgcagct 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

tataatggtt acaaataaag caatagcatc acaaatttca caaataaagc atttttttca ctgcattcta gttgtggttt gtccaaactc atcaatgtat 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

cttatcatgt ctgTCCTAGA GGGCCCTATT ctatagtgtc acctaaatgc tagagctcgc tgatcagcct cgactgtgcc ttctagttgc cagccatctg 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ttgtttgccc ctcccccgtg ccttccttga ccctggaagg tgccactccc actgtccttt cctaataa
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

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

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.

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

no

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

no

A promoter reported in cDNA corresponding to IRES sequence:

no

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
not_tested

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
homogeneous_population_of_molecules_confirmed

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
no_promoter_confirmed

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Homo sapiens HEK293 (ATCC CRL-1573)

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):

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: Václav Vopálenský

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):

533-3331

ORF

ORF position:

2

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

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):

3918-4577

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: `3`	Last change: `2008-07-15 09:11:54`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `AQP4`	The functional status of IRES: `functional`

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

3626-3911

How IRES boundaries were determined:
guessed

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `295`	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: `-292`	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):

AAGGACAGTT TGGATAATTT TCCGTGAAAC TGGATGATCT TTGAATATTA AATGAAAGGA GACTAGAATA ACAGTCTCTT GACTATTCAT GAAGGAGCTT 
^3626      ^3636      ^3646      ^3656      ^3666      ^3676      ^3686      ^3696      ^3706      ^3716      

TAGCAGGAGC ATTCTTTCTT GGTGTGCAAA TCACGCCTGG CAGCCCCTGC CCACAGTACC CGAAGATGGC AGGCCTTGTT CCCTTCACCT AAATTCATAA 
^3726      ^3736      ^3746      ^3756      ^3766      ^3776      ^3786      ^3796      ^3806      ^3816      

ACCTGGGTGT AGTGGCTTCT GATGCTGATT TGTTTCTCTT TTCAGTAAGT GTGGACCTTT GTGTACCAGA GAGAACATCA TGGTGG
^3826      ^3836      ^3846      ^3856      ^3866      ^3876      ^3886      ^3896      ^3906

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

The translation experiments:

Translation results:

IRESite Translation Id: 540

Version: `1`	Last change: `2009-09-03 19:20:08`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HEK293 (ATCC CRL-1573)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

2.000

Name of IRES used as the positive control:

XIAP

Name of the plasmid used as the positive control. `pbetaGAL/5'(-162)/CAT`	Name of the plasmid used as the negative control. `pBiCmod`
`IRESite Id` of the plasmid used as positive control. `486`	`IRESite Id` of the plasmid used as negative control. `636`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0.300`
The size (length) of intercistronic region in the positive control: `504`	The size (length) of intercistronic region in the negative control: `294`

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:

Translational data are derived from Fig. 4A.

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

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

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

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

ITAF protein characteristics:

Version: `2`	Last change: `2009-08-29 12:19:15`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
La

ITAF fullname:
La autoantigen

ITAF description (long):
La autoantigen (p52), 52 kDa RNA binding protein, predominantly localized to nucleus, unwinds the dsRNA in ATP-dependent manner, forms a dimer

3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
other

Remarks:

HEK 293T cell extracts were used to demonstrate in vitro binding to AQP4 RNA. Data from Figure 8A.

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

IRES trans-acting factor (ITAF):

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

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

ITAF protein characteristics:

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

ITAF abbreviated name:
PTB-1

ITAF fullname:
polypyrimidine tract-binding protein isoform 1

ITAF description (long):
polypyrimidine tract-binding protein isoform 1 binds dsRNA with (CCU)n motif where n is at least 3. By SELEX approach it was found it binds to 5'-CAGCCUGGUGCCUCUCUUUCGG-3' (Singh et al. (1995) Science 268:1173-1176) but also UCUU or UCUUC within pyrimidine-rich sequence (Perez et al. (1997) RNA3:1334-1347).

3.2.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally

Method used to demonstrate ITAF effect:
both In vitro system used to demonstrate ITAF effect:
other

The organism where action of this ITAF was studied:

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

Remarks:

Deletion of the AQP4 5' UTR polypyrimidine tract causes a loss of PTB binding and a complete loss of IRES
activity, but does not disrupt the binding of other ITAFs.
Overexpression of PTB enhances AQP4 IRES activity approximately 2-fold.

HEK 293T cell extracts were used to demonstrate in vitro binding to AQP4 RNA. Data from Figure 8A/B/C.

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