IRESite_Id:137 characteristics of Hairless IRES studied in IS plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `137`	Version: `3`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-12-16 00:47:02`

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:
both_UTRs_incomplete

The mRNA/+RNA description:

Incomplete reverse engineered bicistronic mRNA molecule coding for LacZ and Luc reporter genes, with putative
Hairless IRES segment in the intercistronic region in which the M2 START codon is replaced by STOP codon.
Thus, two protein products are produced from this plasmid. Albeit huge the sequence provided here contains
just the two CDS and the intercistronic region.

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 TGAACCGATG 
^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:
IS 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:

not tested

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 TGAACCGATG 
^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):

2

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

ORF

ORF position:

1

Version: `1`	Last change: `2007-09-04 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

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

The description of the protein encoded in this ORF:
beta-galactosidase fused to few aminoacid residues of Hairless

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):

1-3093

ORF

ORF position:

2

Version: `1`	Last change: `2007-09-04 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
Hairless-Luc-fusion

The description of the protein encoded in this ORF:
20 aminoacid residues from 3'-end of the putative Hairless IRES sequence (initiated by M3 start codon) fused with luciferase

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

not tested

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

3478-5187

Remarks:

The plasmid sequence is not complete and could have not been completed even upon communication with Dieter
Maier. The sequence available was partly reconstructed from public sequences or reporter genes and of regions
actually cloned/verified by D. Maier. The actin 5C promoter is constitutive.

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

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 GAACCGATGA 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

The translation experiments:

Translation results:

IRESite Translation Id: 98

Version: `5`	Last change: `2007-09-07 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Drosophila melanogaster S2

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

74.200

Name of IRES used as the positive control:

Antp

Name of the plasmid used as the positive control. `CI`	Name of the plasmid used as the negative control. `pA_LL`
	`IRESite Id` of the plasmid used as negative control. `136`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0.800`
	The size (length) of intercistronic region in the negative control: `29`

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:

The galactosidase and luciferase activities were determined after 2 days in cellular lysates. Both
galactosidase and luciferase protein activities were measured spectrophotometrically and luminometrically,
respectively (Fig. 2B left). Presence of both proteins was confirmed immunologically from Western blots (Fig.
2B right). Raw Luc measurements published in the paper:

Construct I	2 584 684  (pAC5.1B based monocistronic plasmid with constitutive actin 5C promoter producing
		2 580 534   lacZ-Hairless_IRES-luc fusion product)

Construct IS	  15 096   avg. 15 564, 74.2% (pAC5.1B based bicistronic plasmid with constitutive actin 5C
                  16 032                       promoter producing IRES-Luc fusion product)

Construct CI      19 733   avg. 20978, 100% (SV40 promoter based plasmid with CAT-Antp_IRES-Luc, not in
alias pBGLPLCys   22 223                     IRESite)

Construct BT I     1 573   avg. 1 528, 7.2% (pBluescript based promoter-less plasmid (with/without bacterial
 		   1 483                     Lac promoter?), not in IRESite)

Construct pA LL      158   avg. 163.5, 0.8% (empty pBluescript-based monocistronic (Lac promoter) plasmid with
                     169                     very short intercistronic sequence with LacZ-luc ORFs although
Luc                                              should not be translated)

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