IRESite_Id:135 characteristics of Hairless IRES studied in I plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `135`	Version: `5`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-12-16 00:51:16`

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:
both_UTRs_incomplete

The mRNA/+RNA description:

mRNA from construct I: lacZ and luc genes with Hairless putative IRES segment with M2 Met codon mutated to
Leu.  Albeit huge the sequence provided here contains just the one polyprotein .

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

atgaccatga ttacggattc actggccgtc gttttacaac gtcgtgactg ggaaaaccct ggcgttaccc aacttaatcg ccttgcagca catccccctt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tcgccagctg gcgtaatagc gaagaggccc gcaccgatcg cccttcccaa cagttgcgca gcctgaatgg cgaatggcgc tttgcctggt ttccggcacc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

agaagcggtg ccggaaagct ggctggagtg cgatcttcct gaggccgata ctgtcgtcgt cccctcaaac tggcagatgc acggttacga tgcgcccatc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

tacaccaacg taacctatcc cattacggtc aatccgccgt ttgttcccac ggagaatccg acgggttgtt actcgctcac atttaatgtt gatgaaagct 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ggctacagga aggccagacg cgaattattt ttgatggcgt taactcggcg tttcatctgt ggtgcaacgg gcgctgggtc ggttacggcc aggacagtcg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

tttgccgtct gaatttgacc tgagcgcatt tttacgcgcc ggagaaaacc gcctcgcggt gatggtgctg cgttggagtg acggcagtta tctggaagat 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

caggatatgt ggcggatgag cggcattttc cgtgacgtct cgttgctgca taaaccgact acacaaatca gcgatttcca tgttgccact cgctttaatg 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

atgatttcag ccgcgctgta ctggaggctg aagttcagat gtgcggcgag ttgcgtgact acctacgggt aacagtttct ttatggcagg gtgaaacgca 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ggtcgccagc ggcaccgcgc ctttcggcgg tgaaattatc gatgagcgtg gtggttatgc cgatcgcgtc acactacgtc tgaacgtcga aaacccgaaa 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ctgtggagcg ccgaaatccc gaatctctat cgtgcggtgg ttgaactgca caccgccgac ggcacgctga ttgaagcaga agcctgcgat gtcggtttcc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

gcgaggtgcg gattgaaaat ggtctgctgc tgctgaacgg caagccgttg ctgattcgag gcgttaaccg tcacgagcat catcctctgc atggtcaggt 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

catggatgag cagacgatgg tgcaggatat cctgctgatg aagcagaaca actttaacgc cgtgcgctgt tcgcattatc cgaaccatcc gctgtggtac 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

acgctgtgcg accgctacgg cctgtatgtg gtggatgaag ccaatattga aacccacggc atggtgccaa tgaatcgtct gaccgatgat ccgcgctggc 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

taccggcgat gagcgaacgc gtaacgcgaa tggtgcagcg cgatcgtaat cacccgagtg tgatcatctg gtcgctgggg aatgaatcag gccacggcgc 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

taatcacgac gcgctgtatc gctggatcaa atctgtcgat ccttcccgcc cggtgcagta tgaaggcggc ggagccgaca ccacggccac cgatattatt 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

tgcccgatgt acgcgcgcgt ggatgaagac cagcccttcc cggctgtgcc gaaatggtcc atcaaaaaat ggctttcgct acctggagag acgcgcccgc 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

tgatcctttg cgaatacgcc cacgcgatgg gtaacagtct tggcggtttc gctaaatact ggcaggcgtt tcgtcagtat ccccgtttac agggcggctt 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

cgtctgggac tgggtggatc agtcgctgat taaatatgat gaaaacggca acccgtggtc ggcttacggc ggtgattttg gcgatacgcc gaacgatcgc 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

cagttctgta tgaacggtct ggtctttgcc gaccgcacgc cgcatccagc gctgacggaa gcaaaacacc agcagcagtt tttccagttc cgtttatccg 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ggcaaaccat cgaagtgacc agcgaatacc tgttccgtca tagcgataac gagctcctgc actggatggt ggcgctggat ggtaagccgc tggcaagcgg 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

tgaagtgcct ctggatgtcg ctccacaagg taaacagttg attgaactgc ctgaactacc gcagccggag agcgccgggc aactctggct cacagtacgc 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gtagtgcaac cgaacgcgac cgcatggtca gaagccgggc acatcagcgc ctggcagcag tggcgtctgg cggaaaacct cagtgtgacg ctccccgccg 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

cgtcccacgc catcccgcat ctgaccacca gcgaaatgga tttttgcatc gagctgggta ataagcgttg gcaatttaac cgccagtcag gctttctttc 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

acagatgtgg attggcgata aaaaacaact gctgacgccg ctgcgcgatc agttcacccg tgcaccgctg gataacgaca ttggcgtaag tgaagcgacc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

cgcattgacc ctaacgcctg ggtcgaacgc tggaaggcgg cgggccatta ccaggccgaa gcagcgttgt tgcagtgcac ggcagataca cttgctgatg 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

cggtgctgat tacgaccgct cacgcgtggc agcatcaggg gaaaacctta tttatcagcc ggaaaaccta ccggattgat ggtagtggtc aaatggcgat 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

taccgttgat gttgaagtgg cgagcgatac accgcatccg gcgcggattg gcctgaactg ccagctggcg caggtagcag agcgggtaaa ctggctcgga 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ttagggccgc aagaaaacta tcccgaccgc cttactgccg cctgttttga ccgctgggat ctgccattgt cagacatgta taccccgtac gtcttcccga 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

gcgaaaacgg tctgcgctgc gggacgcgcg aattgaatta tggcccacac cagtggcgcg gcgacttcca gttcaacatc agccgctaca gtcaacagca 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

actgatggaa accagccatc gccatctgct gcacgcggaa gaaggcacat ggctgaatat cgacggtttc catatgggga ttggtggcga cgactcctgg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

agcccgtcag tatcggcgga attccagctg agcgccggtc gctaccatta ccagttggtc tggtgtcaaa aatgtcgtcg acAGACAACA TTGACCGATG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AGCATAAAAG TAACATTAAC AGTAACAGCA GTCACTCCAG CAACAACAAC AACAACGGCA GCAGCAGCAA TAACGACAAC AACAGCAACG ACGACGCAGC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AAGTAGCAGC AACAGCAAAA ACAACAACAC CAGCAACGAG AGCAGCCACA GCAACAACAA TACTAGTAGC ATAATTGCAG AGGCGGCCGC CAAGTTTCTA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CTGAAAAATG GCCTAAACGG CAGTAGCAGC ACCAGCTACC CCCCTCTGCC ACCGCCTCTG CCCGCCAACT TAAGCAGGAC GACCACGCCC ACGACAACGA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CAACGCCCTC ATCCTCCAGC TCCACCGCCT CAAATGGCTT TTTGCCGCAT GCCAAGACGC CCAAAAGTAG TAGCATTATG GCTGCGTCCG CCGCAGTGGC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGCCAGCGTC GTTGGAtcct tcaacttccc tgagctcgaa gacgccaaaa acataaagaa aggcccggcg ccattctatc ctctagagga tggaaccgct 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ggagagcaac tgcataaggc tatgaagaga tacgccctgg ttcctggaac aattgctttt acagatgcac atatcgaggt gaacatcacg tacgcggaat 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

acttcgaaat gtccgttcgg ttggcagaag ctatgaaacg atatgggctg aatacaaatc acagaatcgt cgtatgcagt gaaaactctc ttcaattctt 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

tatgccggtg ttgggcgcgt tatttatcgg agttgcagtt gcgcccgcga acgacattta taatgaacgt gaattgctca acagtatgaa catttcgcag 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

cctaccgtag tgtttgtttc caaaaagggg ttgcaaaaaa ttttgaacgt gcaaaaaaaa ttaccaataa tccagaaaat tattatcatg gattctaaaa 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

cggattacca gggatttcag tcgatgtaca cgttcgtcac atctcatcta cctcccggtt ttaatgaata cgattttgta ccagagtcct ttgatcgtga 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

caaaacaatt gcactgataa tgaattcctc tggatctact gggttaccta agggtgtggc ccttccgcat agaactgcct gcgtcagatt ctcgcatgcc 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

agagatccta tttttggcaa tcaaatcatt ccggatactg cgattttaag tgttgttcca ttccatcacg gttttggaat gtttactaca ctcggatatt 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

tgatatgtgg atttcgagtc gtcttaatgt atagatttga agaagagctg tttttacgat cccttcagga ttacaaaatt caaagtgcgt tgctagtacc 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

aaccctattt tcattcttcg ccaaaagcac tctgattgac aaatacgatt tatctaattt acacgaaatt gcttctgggg gcgcacctct ttcgaaagaa 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

gtcggggaag cggttgcaaa acgcttccat cttccaggga tacgacaagg atatgggctc actgagacta catcagctat tctgattaca cccgaggggg 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

atgataaacc gggcgcggtc ggtaaagttg ttccattttt tgaagcgaag gttgtggatc tggataccgg gaaaacgctg ggcgttaatc agagaggcga 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

attatgtgtc agaggaccta tgattatgtc cggttatgta aacaatccgg aagcgaccaa cgccttgatt gacaaggatg gatggctaca ttctggagac 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

atagcttact gggacgaaga cgaacacttc ttcatagttg accgcttgaa gtctttaatt aaatacaaag gatatcaggt ggcccccgct gaattggaat 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

cgatattgtt acaacacccc aacatcttcg acgcgggcgt ggcaggtctt cccgacgatg acgccggtga acttcccgcc gccgttgttg ttttggagca 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

cggaaagacg atgacggaaa aagagatcgt ggattacgtc gccagtcaag taacaaccgc gaaaaagttg cgcggaggag ttgtgtttgt ggacgaagta 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ccgaaaggtc ttaccggaaa actcgacgca agaaaaatca gagagatcct cataaaggcc aagaagggcg gaaagtccaa attgtaa
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181

Warning: available plasmid sequence is exactly same as the mRNA sequence. It seems we never managed to reconstruct the original plasmid sequence used to express the studied mRNA.

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

The name of the plasmid:
I The name of the promoter used to express this mRNA:
actin_5C

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:

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:
homogeneous_population_of_molecules_confirmed

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):
not_tested

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:

Drosophila melanogaster S2

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

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Drosophila melanogaster

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

atgaccatga ttacggattc actggccgtc gttttacaac gtcgtgactg ggaaaaccct ggcgttaccc aacttaatcg ccttgcagca catccccctt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tcgccagctg gcgtaatagc gaagaggccc gcaccgatcg cccttcccaa cagttgcgca gcctgaatgg cgaatggcgc tttgcctggt ttccggcacc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

agaagcggtg ccggaaagct ggctggagtg cgatcttcct gaggccgata ctgtcgtcgt cccctcaaac tggcagatgc acggttacga tgcgcccatc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

tacaccaacg taacctatcc cattacggtc aatccgccgt ttgttcccac ggagaatccg acgggttgtt actcgctcac atttaatgtt gatgaaagct 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ggctacagga aggccagacg cgaattattt ttgatggcgt taactcggcg tttcatctgt ggtgcaacgg gcgctgggtc ggttacggcc aggacagtcg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

tttgccgtct gaatttgacc tgagcgcatt tttacgcgcc ggagaaaacc gcctcgcggt gatggtgctg cgttggagtg acggcagtta tctggaagat 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

caggatatgt ggcggatgag cggcattttc cgtgacgtct cgttgctgca taaaccgact acacaaatca gcgatttcca tgttgccact cgctttaatg 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

atgatttcag ccgcgctgta ctggaggctg aagttcagat gtgcggcgag ttgcgtgact acctacgggt aacagtttct ttatggcagg gtgaaacgca 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ggtcgccagc ggcaccgcgc ctttcggcgg tgaaattatc gatgagcgtg gtggttatgc cgatcgcgtc acactacgtc tgaacgtcga aaacccgaaa 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ctgtggagcg ccgaaatccc gaatctctat cgtgcggtgg ttgaactgca caccgccgac ggcacgctga ttgaagcaga agcctgcgat gtcggtttcc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

gcgaggtgcg gattgaaaat ggtctgctgc tgctgaacgg caagccgttg ctgattcgag gcgttaaccg tcacgagcat catcctctgc atggtcaggt 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

catggatgag cagacgatgg tgcaggatat cctgctgatg aagcagaaca actttaacgc cgtgcgctgt tcgcattatc cgaaccatcc gctgtggtac 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

acgctgtgcg accgctacgg cctgtatgtg gtggatgaag ccaatattga aacccacggc atggtgccaa tgaatcgtct gaccgatgat ccgcgctggc 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

taccggcgat gagcgaacgc gtaacgcgaa tggtgcagcg cgatcgtaat cacccgagtg tgatcatctg gtcgctgggg aatgaatcag gccacggcgc 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

taatcacgac gcgctgtatc gctggatcaa atctgtcgat ccttcccgcc cggtgcagta tgaaggcggc ggagccgaca ccacggccac cgatattatt 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

tgcccgatgt acgcgcgcgt ggatgaagac cagcccttcc cggctgtgcc gaaatggtcc atcaaaaaat ggctttcgct acctggagag acgcgcccgc 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

tgatcctttg cgaatacgcc cacgcgatgg gtaacagtct tggcggtttc gctaaatact ggcaggcgtt tcgtcagtat ccccgtttac agggcggctt 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

cgtctgggac tgggtggatc agtcgctgat taaatatgat gaaaacggca acccgtggtc ggcttacggc ggtgattttg gcgatacgcc gaacgatcgc 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

cagttctgta tgaacggtct ggtctttgcc gaccgcacgc cgcatccagc gctgacggaa gcaaaacacc agcagcagtt tttccagttc cgtttatccg 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ggcaaaccat cgaagtgacc agcgaatacc tgttccgtca tagcgataac gagctcctgc actggatggt ggcgctggat ggtaagccgc tggcaagcgg 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

tgaagtgcct ctggatgtcg ctccacaagg taaacagttg attgaactgc ctgaactacc gcagccggag agcgccgggc aactctggct cacagtacgc 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gtagtgcaac cgaacgcgac cgcatggtca gaagccgggc acatcagcgc ctggcagcag tggcgtctgg cggaaaacct cagtgtgacg ctccccgccg 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

cgtcccacgc catcccgcat ctgaccacca gcgaaatgga tttttgcatc gagctgggta ataagcgttg gcaatttaac cgccagtcag gctttctttc 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

acagatgtgg attggcgata aaaaacaact gctgacgccg ctgcgcgatc agttcacccg tgcaccgctg gataacgaca ttggcgtaag tgaagcgacc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

cgcattgacc ctaacgcctg ggtcgaacgc tggaaggcgg cgggccatta ccaggccgaa gcagcgttgt tgcagtgcac ggcagataca cttgctgatg 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

cggtgctgat tacgaccgct cacgcgtggc agcatcaggg gaaaacctta tttatcagcc ggaaaaccta ccggattgat ggtagtggtc aaatggcgat 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

taccgttgat gttgaagtgg cgagcgatac accgcatccg gcgcggattg gcctgaactg ccagctggcg caggtagcag agcgggtaaa ctggctcgga 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ttagggccgc aagaaaacta tcccgaccgc cttactgccg cctgttttga ccgctgggat ctgccattgt cagacatgta taccccgtac gtcttcccga 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

gcgaaaacgg tctgcgctgc gggacgcgcg aattgaatta tggcccacac cagtggcgcg gcgacttcca gttcaacatc agccgctaca gtcaacagca 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

actgatggaa accagccatc gccatctgct gcacgcggaa gaaggcacat ggctgaatat cgacggtttc catatgggga ttggtggcga cgactcctgg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

agcccgtcag tatcggcgga attccagctg agcgccggtc gctaccatta ccagttggtc tggtgtcaaa aatgtcgtcg acAGACAACA TTGACCGATG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AGCATAAAAG TAACATTAAC AGTAACAGCA GTCACTCCAG CAACAACAAC AACAACGGCA GCAGCAGCAA TAACGACAAC AACAGCAACG ACGACGCAGC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AAGTAGCAGC AACAGCAAAA ACAACAACAC CAGCAACGAG AGCAGCCACA GCAACAACAA TACTAGTAGC ATAATTGCAG AGGCGGCCGC CAAGTTTCTA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CTGAAAAATG GCCTAAACGG CAGTAGCAGC ACCAGCTACC CCCCTCTGCC ACCGCCTCTG CCCGCCAACT TAAGCAGGAC GACCACGCCC ACGACAACGA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CAACGCCCTC ATCCTCCAGC TCCACCGCCT CAAATGGCTT TTTGCCGCAT GCCAAGACGC CCAAAAGTAG TAGCATTATG GCTGCGTCCG CCGCAGTGGC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGCCAGCGTC GTTGGAtcct tcaacttccc tgagctcgaa gacgccaaaa acataaagaa aggcccggcg ccattctatc ctctagagga tggaaccgct 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ggagagcaac tgcataaggc tatgaagaga tacgccctgg ttcctggaac aattgctttt acagatgcac atatcgaggt gaacatcacg tacgcggaat 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

acttcgaaat gtccgttcgg ttggcagaag ctatgaaacg atatgggctg aatacaaatc acagaatcgt cgtatgcagt gaaaactctc ttcaattctt 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

tatgccggtg ttgggcgcgt tatttatcgg agttgcagtt gcgcccgcga acgacattta taatgaacgt gaattgctca acagtatgaa catttcgcag 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

cctaccgtag tgtttgtttc caaaaagggg ttgcaaaaaa ttttgaacgt gcaaaaaaaa ttaccaataa tccagaaaat tattatcatg gattctaaaa 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

cggattacca gggatttcag tcgatgtaca cgttcgtcac atctcatcta cctcccggtt ttaatgaata cgattttgta ccagagtcct ttgatcgtga 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

caaaacaatt gcactgataa tgaattcctc tggatctact gggttaccta agggtgtggc ccttccgcat agaactgcct gcgtcagatt ctcgcatgcc 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

agagatccta tttttggcaa tcaaatcatt ccggatactg cgattttaag tgttgttcca ttccatcacg gttttggaat gtttactaca ctcggatatt 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

tgatatgtgg atttcgagtc gtcttaatgt atagatttga agaagagctg tttttacgat cccttcagga ttacaaaatt caaagtgcgt tgctagtacc 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

aaccctattt tcattcttcg ccaaaagcac tctgattgac aaatacgatt tatctaattt acacgaaatt gcttctgggg gcgcacctct ttcgaaagaa 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

gtcggggaag cggttgcaaa acgcttccat cttccaggga tacgacaagg atatgggctc actgagacta catcagctat tctgattaca cccgaggggg 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

atgataaacc gggcgcggtc ggtaaagttg ttccattttt tgaagcgaag gttgtggatc tggataccgg gaaaacgctg ggcgttaatc agagaggcga 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

attatgtgtc agaggaccta tgattatgtc cggttatgta aacaatccgg aagcgaccaa cgccttgatt gacaaggatg gatggctaca ttctggagac 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

atagcttact gggacgaaga cgaacacttc ttcatagttg accgcttgaa gtctttaatt aaatacaaag gatatcaggt ggcccccgct gaattggaat 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

cgatattgtt acaacacccc aacatcttcg acgcgggcgt ggcaggtctt cccgacgatg acgccggtga acttcccgcc gccgttgttg ttttggagca 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

cggaaagacg atgacggaaa aagagatcgt ggattacgtc gccagtcaag taacaaccgc gaaaaagttg cgcggaggag ttgtgtttgt ggacgaagta 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ccgaaaggtc ttaccggaaa actcgacgca agaaaaatca gagagatcct cataaaggcc aagaagggcg gaaagtccaa attgtaa
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181

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

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

1

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

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
LacZ-Hairless_IRES-luc-fusion

The description of the protein encoded in this ORF:
beta-galactosidase protein fused with part of the Hairless 5'UTR fused to luciferase. The protein had luciferase activity at least.

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):

1-5187

Remarks:

The construct I was based on pAC5.1B (Invitrogen) and the M2 start codon present in the putative IRES segment
was replaced by Leu codon. The construct I shows very high luciferase activity, more than two orders higher
than the IS construct, where the M2 start codon was replaced with stop codon (instead of the leucine as in the
case of construct I) and so no fusion protein was produced. It might be the IRES-like activity was observed
because of fusion Gal-Luc protein being still active in I. The IS plasmid construct was used in the
experiments published in the article instead of this plasmid I. Both vectors use strong actin 5C promoter.

The BT_I plasmid (not in IRESite) construct was used to test cryptic promoter activity in the putative IRES
segment (the M2 start codon was replaced by Leu as in monocistronic-fusion I plasmid instead of being based on
the bicistronic IS plasmid which would be more tempting).

The positive control IRES used was the Antp IRES segment in CI plasmid, which sequence is completely
unavailable so far and which had different reporter genes (SV40-CAT-Antp-Luc).

Additional comment from Dieter Maier: We found in northern blots no indication for a mRNA corresponding to
the short protein. It is true that there is luc activity in the BTI (Bluescript without promoter) construct,
but much less than with the IS construct. In addition the BTI construct showed also beta Gal activity, with
other words the luc activity was maybe a result of the fusion lacZ-luc protein. However, never say never
again, I cannot 100% exclude a week promoter in our sequence.

The actin 5C promoter was described by Bond and Davidson (1986).

Citations:

Maier D., Nagel A. C., Preiss A. (2002) Two isoforms of the Notch antagonist Hairless are produced by differential translation initiation. Proc. Natl. Acad. Sci. U. S. A. 99(24):15480-15485

Bond B. J., Davidson N. (1986) The Drosophila melanogaster actin 5C gene uses two transcription initiation sites and three polyadenylation sites to express multiple mRNA species. Mol. Cell. Biol. 6(6):2080-2088

IRESs:

IRES:

Version: `1`	Last change: `2007-09-04 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `Hairless`	The functional status of IRES: `functional`

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

3082-3516

How IRES boundaries were determined:
experimentally_determined

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

cAGACAACAT TGACCGATGA GCATAAAAGT AACATTAACA GTAACAGCAG TCACTCCAGC AACAACAACA ACAACGGCAG CAGCAGCAAT AACGACAACA 
^3082      ^3092      ^3102      ^3112      ^3122      ^3132      ^3142      ^3152      ^3162      ^3172      

ACAGCAACGA CGACGCAGCA AGTAGCAGCA ACAGCAAAAA CAACAACACC AGCAACGAGA GCAGCCACAG CAACAACAAT ACTAGTAGCA TAATTGCAGA 
^3182      ^3192      ^3202      ^3212      ^3222      ^3232      ^3242      ^3252      ^3262      ^3272      

GGCGGCCGCC AAGTTTCTAC TGAAAAATGG CCTAAACGGC AGTAGCAGCA CCAGCTACCC CCCTCTGCCA CCGCCTCTGC CCGCCAACTT AAGCAGGACG 
^3282      ^3292      ^3302      ^3312      ^3322      ^3332      ^3342      ^3352      ^3362      ^3372      

ACCACGCCCA CGACAACGAC AACGCCCTCA TCCTCCAGCT CCACCGCCTC AAATGGCTTT TTGCCGCATG CCAAGACGCC CAAAAGTAGT AGCATTATGG 
^3382      ^3392      ^3402      ^3412      ^3422      ^3432      ^3442      ^3452      ^3462      ^3472      

CTGCGTCCGC CGCAGTGGCA GCCAGCGTCG TTGGA
^3482      ^3492      ^3502      ^3512

Citations:

Maier D., Nagel A. C., Preiss A. (2002) Two isoforms of the Notch antagonist Hairless are produced by differential translation initiation. Proc. Natl. Acad. Sci. U. S. A. 99(24):15480-15485

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