IRESite_Id:139 summary record describing characteristics of HRV-2 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `139`	Version: `8`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-12-16 02:32:56`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `hopefully_full-length_mRNA`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `HRV2`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
61098

The mRNA/+RNA description:

Human rhinovirus (HRV) 5'-UTR

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

ttaaaactgg atccaggttg ttcccacctg gatttcccac agggagtggt actctgttat tacggtaact ttgtacgcca gttttatctc ccttccccca 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tgtaacttag aagtttttca caaagaccaa tagccggtaa tcagccagat tactgaaggt caagcacttc tgtttccccg gtcaatgttg atatgctcca 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

acagggcaaa aacaactgcg atcgttaacc gcaaagcgcc tacgcaaagc ttagtagcat ctttgaaatc gtttggctgg tcgatccgcc atttcccctg 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gtagacctgg cagatgaggc tagaaatacc ccactggcga cagtgttcta gcctgcgtgg ctgcctgcac accctatggg tgtgaagcca aacaatggac 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

aaggtgtgaa gagccccgtg tgctcgcttt gagtcctccg gcccctgaat gtggctaacc ttaaccctgc agctagagca cgtaacccaa tgtgtatcta 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

gtcgtaatga gcaattgcgg gatgggacca actactttgg gtgtccgtgt ttcacttttt cctttatatt tgcttatggt gacaatatat acaatatata 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

tattggcacc atgggtgcac aggtttcaag acaaaatgtt ggaactcact ccacgcaaaa ctctgtatca aatgggtcta gtttaaatta ttttaacatc 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

aattatttca aagatgctgc ttcaaatggt gcatcaaaac tggaattcac acaagatcct agtaaattta ctgacccagt taaggatgtt ttggaaaagg 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gaataccaac actacagtcc cccacagtgg aggcttgtgg atactctgat aggattatac agattaccag aggagattca accataacct cacaagatgt 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ggctaatgct atcgttgcgt atggtgtttg gccacattat ctatcctcca aggatgcctc tgcaattgat aaaccctctc aaccagatac atcttctaat 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

agattttata ctctaaggag tgtgacctgg agcagttcct caaagggttg gtggtggaaa ctacctgatg cactcaagga catgggtatt tttggtgaaa 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

acatgtttta tcattacctg ggtaggagtg gatacacaat acatgtgcag tgtaatgcta gtaaatttca ccagggtaca ctaattgttg ctctgatacc 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tgagcatcag attgcaagtg ccttacatgg caatgtgaat gttggttaca actacacaca cccaggtgaa acaggcaggg aagttaaagc tgagacgaga 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ttgaatcctg atctacaacc tactgaagag tattggctaa actttgatgg gacactcctt ggaaatatta ccatattccc tcatcaattt atcaacttga 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ggagtaataa ttctgccaca ataattgccc cttatgtcaa tgcagttcct atggattcaa tgcggagcca caataattgg agtttggtaa taataccaat 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

atgtcccctt gagacatcaa gtgcaattaa cacaatacct attacaatat ctataagccc catgtgtgca gagttttccg gcgcgcgtgc caagcgtcaa 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ggattaccag ttttcatcac accaggttca ggacagtttt tgacaacaga tgatttccaa tccccatgtg cacttccctg gtatcaccca actaaggaaa 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

tttctattcc aggtgaggtt aaaaatttgg ttgaaatttg tcaagtagac agcctagtac caataaataa cactgacacc tacatcaata gtgaaaatat 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

gtattctgtt gtattgcaat catcaattaa tgcaccagat aagatcttct ctattcgaac agatgttgct tcccaacctt tagctactac tttgattggt 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

gagatatcta gctatttcac ccactggaca gggagtctcc gtttcagctt catgttttgt ggtactgcca acactactgt taagcttttg ttggcataca 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

caccacctgg tatcgcagaa cccaccacaa gaaaggatgc aatgctaggc actcatgtta tatgggatgt ggggttgcag tctacaatat caatggtagt 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gccatggatt agcgctagtc attatagaaa cacatcacca ggtagatcta catctgggta cataacatgc tggtatcaga ctagattagt cattccacct 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

cagaccccac caacagctag attgttatgt tttgtatctg ggtgcaaaga cttttgcttg cgcatggcac gagatactaa cctacacctg caaagtggtg 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

caatagcaca gaaccctgtt gagaattata tagatgaagt tcttaatgaa gttttagttg tcccaaatat taatagtagt aaccccacaa catcaaattc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

tgccccagca ttagatgctg cagaaacagg gcacactagt agtgttcaac cagaggatgt cattgaaact aggtatgtgc agacatcaca aacaagagat 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

gaaatgagtt tagagagttt tcttggcaga tcaggatgca tacatgaatc taaattagag gttacacttg caaattataa caaggagaat tttacagtgt 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

gggctattaa tctacaagaa atggctcaaa ttagaaggaa atttgaattg ttcacctata ctaggtttga ttctgaaata accctagttc catgcatttc 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

cgcccttagt caggacattg gacacatcac aatgcaatac atgtatgttc caccaggtgc accggtgccc aatagtaggg acgattatgc atggcagtct 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ggcactaatg cctctgtttt ctggcaacat ggacaggctt atccaagatt ttccttacct ttcctaagtg tggcatctgc ttattacatg ttttatgatg 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ggtatgatga acaagatcaa aactatggta cagcaaacac aaataacatg gggtcactat gctctaggat agtaacagag aaacacattc ataaagtaca 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

tataatgaca agaatctatc acaaggctaa acatgtcaag gcatggtgtc cacgcccacc cagagcgctt gagtatactc gtgctcatcg cactaatttt 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

aaaattgagg ataggagtat tcagacagca attgtgacca gaccaattat cactacagct ggccccagtg acatgtatgt tcatgtaggt aaccttattt 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

atagaaatct tcatcttttc aactctgaga tgcatgaatc tattttggta tcttattcat cagatttaat catttaccga acaaacactg taggtgatga 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ttacattccc tcttgtgatt gtacccaagc tacttattat tgcaaacata aaaatagata cttcccaatt acagttacaa gccatgactg gtatgaaata 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

caggaaagtg agtactatcc caaacacata cagtacaatt tgttgattgg tgagggccct tgtgaaccag gtgactgtgg tggaaagttg ctatgcaaac 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

atggtgtcat aggtatagta acagctggtg gtgataatca tgtggctttt attgacctta gacacttcca ttgtgctgaa gaacaagggg ttacagatta 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

tatacatatg ctaggagaag catttggaaa tggatttgtg gatagtgtaa aagaacatat acatgccata aacccagtag gaaatatcag caagaaaatt 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

attaaatgga tgttgagaat aatatcagca atggtcataa taattagaaa ctcttctgac ccccaaacta tattagcaac actcacactg attgggtgtt 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ctggatcacc ctggagattt ttaaaggaaa aattctgtaa atggacacag cttaattata tacacaaaga atcagattca tggttaaaga aatttactga 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

agcatgcaat gcagctagag ggcttgaatg gatagggaat aagatatcta aatttattga atggatgaag tcgatgctcc cgcaagctca attgaaggtt 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

aagtacttaa acgagcttaa aaaactcaac ctatacgaaa agcaagttga gagcttgcgg gtggctgaca tgaaaacaca agaaaaaatt aaaatggaaa 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

tagacacttt acatgatttg tcacgtaaat ttctaccttt gtatgcaagt gaggcaaaaa ggataaaaac cctatacatt aaatgtgata atatcatcaa 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

gcagaagaaa agatgtgaac cagtagctat agttattcat ggaccacctg gtgctggcaa atctataaca acaaatttcc tggccaaaat gataactaat 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

gatagtgaca tatactctct acctcctgat ccaaaatatt ttgatggtta tgaccaacag agtgtagtaa taatggatga cattatgcag aatccagccg 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

gggatgacat gacactgttc tgccaaatgg tttctagtgt tacatttata ccaccaatgg ctgatctacc agataaaggc aaggcttttg attctaggtt 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

tgtattatgc agcacaaatc attcccttct aacacccccg acaataactt cactacctgc aatgaataga agatttttcc tagatttaga tataatagta 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

catgataact tcaaagatcc acagggcaaa cttaatgtgg cagcagcgtt tcgaccatgt gatgtagata atagaatagg aaatgcacgt tgttgtccat 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ttgtgtgtgg aaaagcagtt tctttcaaag atcgtaactc ttgcaacaaa tacagccttg cgcaggtgta caacataatg attgaagaag acagacggag 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

aagacaagtg gttgatgtca tgacagctat attccaaggg ccaattgata tgaaaaaccc accaccacct gctattactg acttgctcca gtctgttaga 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

acccctgaag ttattaagta ttgtgagggt aatagatgga taattccagc agaatgcaag atagaaaagg agttgaactt ggctaacaca atcataacaa 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

tcattgcaaa tgttattggt atggcgagaa taatatatgt tatttacaaa cttttttgca cattacaggg accatattca ggagaaccaa agcccaagac 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

taaaatccca gaaaggcgtg tagtaacaca gggaccagag gaggaatttg ggatgtcttt aattaaacat aactcatgtg ttattacaac agaaaatggg 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

aaattcacag gtcttggagt atacgacaga tttgtggtcg taccaacaca tgcagatcct ggaaaggaaa ttcaggttga tggtataact acaaaagtca 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

ttgactcata tgacctatac aacaagaatg ggataaagct agaaataaca gtacttaaat tagatagaaa tgaaaaattt agagatatca ggagatatat 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

acctaacaat gaagatgatt accccaattg caacttagca ctgctagcaa accagcctga accaactata atcaatgttg gagatgttgt atcctatggc 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

aatatactgc tcagtggcaa ccaaacggct agaatgctta aatacagtta cccaactaaa tctggttact gtggaggtgt cttatacaaa attgggcaag 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

tgcttggaat acatgttggg ggcaatggta gggatggttt ctcagctatg ttactcagat cctatttcac tgatgttcag ggccaaataa cgttatcaaa 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

gaagaccagt gaatgtaacc tacccagtat acacacccca tgcaaaacca aattgcagcc tagtgttttc tatgatgtat tccctggttc aaaagaacca 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

gctgtgttgt ctgaaaaaga tgcccggtta caagttgatt tcaatgaagc actattttct aaatacaaag ggaatacaga ttgctccatt aatgaccaca 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

taagaattgc atcatcacat tatgcagcac aactcattac cttagatatt gacccaaaac ctattacact tgaggacagt gtctttggca ctgatggatt 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

agaggctctt gatttgaaca ctagcgcagg atttccatat attgcaatgg gagttaaaaa gagagattta ataaacaaca agaccaagga tataagcaaa 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

cttaaagaag caattgacaa atacggagtt gacttaccta tggtcacctt cttgaaagat gaactcagaa agcatgaaaa ggtaattaaa ggtaaaacta 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

gagttattga agctagtagt gtgaatgata ccctattatt tagaacaact tttggcaacc tcttttcaaa gttccacttg aatcctggaa ttgttactgg 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

atcagcagtt ggatgtgatc cagaggtgtt ttggtcaaaa ataccagcaa tgttggatga taaatgtatt atggcttttg attatacaaa ttatgatggt 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

agtatacacc ctatttggtt tgaagctctt aaacaggtac tggtagatct atcatttaat ccaacattaa tagatagact atgcaagtct aaacacatct 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

tcaaaaatac atactatgaa gtggagggag gtgtaccatc tgggtgttca ggtactagta tttttaacac tatgatcaat aatattatca taaggacctt 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

agtgttagat gcatacaaga atatagatct agataagctt aagataattg cctatggtga tgatgtcata ttctcataca tacatgaact ggacatggag 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

gctatagcaa tagagggtgt taaatatggt ttgactataa ctcctgctga taaatctaac acatttgtaa aattagacta tagcaatgtt acttttttaa 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

aaagagggtt taagcaagat gagaagtata actttctaat acatccaact ttccctgaag atgaaatatt tgaatccatc agatggacaa agaaaccatc 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

acaaatgcat gaacatgtgt tgtctctgtg tcacttaatg tggcacaatg gacgtgacgc atacaaaaaa tttgtggaga agatacgcag tgtaagcgct 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

ggtcgtgcac tgtacatccc tccgtatgat ttgcttttgc atgagtggta tgaaaaattt taaagatata gaaatagtaa actgatagtt tattagtttt 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

at
^7101

Credibility of mRNA sequence:

reverse_engineered_fragment_and_the_rest_is_a_guess

The organism containing this mRNA with IRES segment in its genome:

Human rhinovirus 2

A promoter reported in cDNA corresponding to IRES sequence:
no The total number of notable open-reading frames (ORFs):
1

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:

Cercopithecus aethiops COS-7 (ATCC CRL-1651)

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):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
homogeneous_population_of_molecules_confirmed

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

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

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 HeLa (ATCC CCL-2)

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

ORF

ORF position:

1

Version: `1`	Last change: `2008-12-16 02:32:56`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
polyprotein

The description of the protein encoded in this ORF:
genome polyprotein

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:

no

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

611-7063

Remarks:

The sequence of the HRV2 IRES was inferred from pR-HRV-F plasmid sequence provided by N. S. Magnuson which was
actually provided from the lab of A. Willis (who copied the sequence from R. Jacksons plasmid pXLJ(10-605)).
However, A. Willis utilized PvuII/NcoI sites of the plasmid whereas N. S. Magnuson utilized SpeI/NcoI sites
(it is unclear which HRV-2 sequence used was thus shorter).

Cammas et al. (2007) excluded both splicing and cryptic promoter issues with the pR-HRV-F plasmid in DNA
transfections (Supplemental Figure S2).

Citations:

Wang Z., Weaver M., Magnuson N. S. (2005) Cryptic promoter activity in the DNA sequence corresponding to the pim-1 5'-UTR. Nucleic Acids Res. 33(7):2248-2258

Stoneley M., Subkhankulova T., Le Quesne J. P., Coldwell M. J., Jopling C. L., Belsham G. J., Willis A. E. (2000) Analysis of the c-myc IRES; a potential role for cell-type specific trans-acting factors and the nuclear compartment. Nucleic Acids Res. 28(3):687-694

Cammas A., Pileur F., Bonnal S., Lewis S. M., Leveque N., Holcik M., Vagner S. (2007) Cytoplasmic relocalization of heterogeneous nuclear ribonucleoprotein A1 controls translation initiation of specific mRNAs. Mol. Biol. Cell. 18(12):5048-5059

IRESs:

IRES:

Version: `7`	Last change: `2008-12-16 02:37:29`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `HRV-2` Warning: please make ires_name same as the gene_name and optionally append to it coordinates. E.g. when gene/virus name is EMCV-R use EMCV-R_-222_to_-1 or EMCV-R_1-456, etc. but not Emcv-R-... or EMCV-222_to_-1. Please keep case of letters as well. This rewards when searching through the database.

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

11-614

Conclusion:
strongly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

atccaggttg ttcccacctg gatttcccac agggagtggt actctgttat tacggtaact ttgtacgcca gttttatctc ccttccccca tgtaacttag 
^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        ^101       

aagtttttca caaagaccaa tagccggtaa tcagccagat tactgaaggt caagcacttc tgtttccccg gtcaatgttg atatgctcca acagggcaaa 
^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       ^201       

aacaactgcg atcgttaacc gcaaagcgcc tacgcaaagc ttagtagcat ctttgaaatc gtttggctgg tcgatccgcc atttcccctg gtagacctgg 
^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       ^301       

cagatgaggc tagaaatacc ccactggcga cagtgttcta gcctgcgtgg ctgcctgcac accctatggg tgtgaagcca aacaatggac aaggtgtgaa 
^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       ^401       

gagccccgtg tgctcgcttt gagtcctccg gcccctgaat gtggctaacc ttaaccctgc agctagagca cgtaacccaa tgtgtatcta gtcgtaatga 
^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       ^501       

gcaattgcgg gatgggacca actactttgg gtgtccgtgt ttcacttttt cctttatatt tgcttatggt gacaatatat acaatatata tattggcacc 
^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       ^601       

atgg
^611

Remarks:

The 5'-UTR tested was confirmed to be functional as IRES and without cryptic promoter activity. No integrity
of the transcripts was studied in case of in vivo DNA plasmid transfections. But, direct RNA
transfections have confirmed IRES activity (Stoneley et al. (2000), Figure 6C). The IRES sequence is
terminated here after the naturally occurring NcoI site (ccATGg).

Citations:

Wang Z., Weaver M., Magnuson N. S. (2005) Cryptic promoter activity in the DNA sequence corresponding to the pim-1 5'-UTR. Nucleic Acids Res. 33(7):2248-2258

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

Version: `1`	Last change: `2008-12-10 10:49:21`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

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:
Unr

ITAF fullname:
upstream of N-ras

ITAF description (long):
Unr protein is known to bind to gaagaaguaa

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_vivo

The organism where action of this ITAF was studied:

Homo sapiens HeLa (ATCC CCL-2)

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_vivo

The organism where action of this ITAF was studied:

Mus musculus ES

Remarks:

Depletion of Unr reduces HRV2 IRES activity or knocking-out of the gene in mouse embryonic stem cells.

Citations:

Hunt S. L., Hsuan J. J., Totty N., Jackson R. J. (1999) unr, a cellular cytoplasmic RNA-binding protein with five cold-shock domains, is required for internal initiation of translation of human rhinovirus RNA. Genes. Dev. 13(4):437-448

Boussadia O., Niepmann M., Creancier L., Prats A. C., Dautry F., Jacquemin-Sablon H. (2003) Unr is required in vivo for efficient initiation of translation from the internal ribosome entry sites of both rhinovirus and poliovirus. J. Virol. 77(6):3353-3359

IRES trans-acting factor (ITAF):

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

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

ITAF protein characteristics:

Version: `3`	Last change: `2009-08-30 14:16:52`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
PCBP-2

ITAF fullname:
poly(rC)-binding protein 2 (39 kDa)

ITAF description (long):
Required for poliovirus IRES activity (Blyn et al. 1996 and 1997) and replication (Toyoda et al., 2007). Its amount is not limiting in rabbit reticulocyte lysates (RRL) (Hunt and Jackson 1999).

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:
in_vivo

The organism where action of this ITAF was studied:

Homo sapiens HeLa (ATCC CCL-2)

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:
rabbit reticulocytes lysate

Citations:

IRES trans-acting factor (ITAF):

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

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: Martin Mokrejš

ITAF abbreviated name:
PTB

ITAF fullname:
polypyrimidine-tract binding protein (unspecified isoform)

ITAF description (long):
polypyrimidine-tract binding protein

3.3.2. 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_vivo

The organism where action of this ITAF was studied:

Homo sapiens HeLa (ATCC CCL-2)

Organism or in vitro system where ITAF was shown:

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

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Citations:

Hunt S. L., Jackson R. J. (1999) Polypyrimidine-tract binding protein (PTB) is necessary, but not sufficient, for efficient internal initiation of translation of human rhinovirus-2 RNA. RNA. 5(3):344-359

RNA:protein interactions:

The RNA:protein interaction:

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

The description of the protein interacting with the RNA:
Heterogeneous nuclear ribonucleoprotein (hnRNP) A1

The organism where this RNA:protein interaction occurs:

Homo sapiens HeLa (ATCC CCL-2)

Remarks:

The interaction was confirmed by several methods using HeLa cell nuclear extracts (NE) with 32P-labeled RNAs.
Data in Figure 1. In Supplemental Figure S1 are describe HRV-2 mutant IRESs lacking the binding activity.

Citations:

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