IRESite_Id:492 summary record describing characteristics of ELG1 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `492`	Version: `2`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-07-15 11:42:51`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `our_best_guess`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `ELG1`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
34531011

The mRNA/+RNA description:

Homo sapiens cDNA FLJ43058 fis, clone BRTHA3007472, highly similar to Homo sapiens ELG protein (HSA277841),
mRNA.

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

tttaaagaat atcctccagc tcacatcgaa tggttggatg atacctcctg taatgtagtt tggctggatg aaatgacagc cacacgagca cttatcaata 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tgagctccct gcctgcacag gataagatca gaagcaggga tgccagtgag gacaagtcag ctgagaaaag gaaaaaagac aagcaggaag acagttcaga 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

tgatgatgaa gctgaagaag gagaggttga agatgagaac tcaagtgatg tagagttgga tacgttgtct caggtagaag aggagtcttt gttaagaaac 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gatcttcgtc cagctaacaa acttgctaaa ggaaataggt tattcatgag atttgctaca aaaggtaaat gtaatatttg gtattgtttt atattttcaa 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

tcaaaatgat ttattatgga gtgacatcct tcttttttga atagaagtta gatcaagtaa tctcaaagtt cccttcaaac tataatattc tgcgcttatg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

aaataattgc ttgccacctg agttggaatt tctgacttta aaagtgaata ttaactattt gtatatttct gtgacttctg gctaaagtta ttttctgttg 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

aaactggttt gcctcatata ttttcagcca gttaccatct gaattatgaa aactttcaaa tgaaacttta tttattacag caacgtcctc ctgaacattg 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ccagtgtacc attcggttct aattcccttc tcataagatt gtttacacat ggtgactttt ggtgggcatt taaaaatgtg tgtgtatgtg tatatatgta 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

tgtgtatgta tgtgtatata tgtatatgta tgtatgtatc gcgtgtatgt gtgtatgtat gcatgtgtat gtatgtatat gcatgtatgt gtatgtgtat 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

atatgtatgt gtgtgtatgt atatgtgtgt gtatgtgtat gtgtgtgtgt atgtgtgtgt gtatgtatgt atgtatgtat atgtattata cacatataca 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

catattggtt tttttaatca tttgagagtt agttgaagat aaaaacccat cacccctaaa tgtattccaa agaataagaa cattgtttta tacatagcac 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

acttaacaaa atcaagaaat ttaacattaa tacagtactg ttacctaatc cgtagtcgat tttcaaattt tgtcagttgt tccaataatg tcctttatat 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

attccccgcc cagccccagg tctaggatcc atccaggact gagtgtgtaa gtatgtaatg tttccttagt cccccttaag ctgaaactac ttctatcctc 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ccatgttttc caagaatata ggtttactat tttatacaat gtccctcagt ttgggtttgt ctgatgattc ctcctgattg aatttgggtt gtgcatttga 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

gacaggcgtg ccacagaagc gatgtcatgt catttccaga gcatcatgtc aggaggccct ggatacttac tcgtcccagt cctagggacg ttcactttat 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

tcacttggtt aagatgacaa aaaggaactt ggagcagcca gaagaagtca gtattacatg aaatatggga atccaaatta tggaggcatg aaaggaattc 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ttagcaattc atggaagcga agatatcatt cccgtcgtat tcagcgggac gtgatcaaga agagagccct gattggggat gacgttggct tgacgtcgta 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

taaacatcga cattctgggc tagtgaatgt tcccgaggaa cccattgaag aggaggaaga ggaggaggag gaggaagagg aagaggaaga agaagaccag 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

gacatggatg cagatgacag agtggtggta gagtaccacg aggagctccc ggctctcaag cagccccggg agcggagcgc gtctagacga tccagtgcca 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

gcagctcaga ctcagatgaa atggactatg atctagaact gaaaatgatt tccacgcctt caccaaagaa aagcatgaaa atgactatgt atgctgacga 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

agtggaatct cagttgaaaa atattaggaa ctccatgagg gcagatagtg tatcttcaag caatatcaaa aaccgaattg gtaacaaatt accacctgag 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

aaatttgcag atgtccgaca tctattagat gagaaacgtc agcactcccg tccacggcca ccagtcagca gtactaaatc agatatacgc cagcggttag 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

gaaaaagacc acattctccg gaaaaggctt ttagtagtaa ccccgtcgtt cggagagagc cctcttctga tgtgcatagt aggctaggtg ttcccaggca 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ggatagtaaa ggcctctacg ccgatactcg ggagaagaaa tcaggtaatt tatggactcg cctaggatct gcacccaaga ccaaagaaaa gaatacgaag 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

aaagtggatc acagggcgcc tggcgctgag gaagacgact ctgagctgca aagggcatgg ggggctctga ttaaggagaa agagcagtct cgccaaaaga 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

agagccggtt agataactta ccatctctcc agattgaagt tagtcgggaa agcagctctg gttcagaggc agagtcctga tgcccctggg gcctatggca 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

gctgccctaa agcctgacat tcttgcacag ggtggggcgc gcagtaggaa cctcccccgc aggagctggc gccctctcgc tcctgctcac acagtcaccc 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

tccgctcttg ctacttcggc aagacatctt aagaatgtga cacattttca agggcatctc tatctttcgc tgcggagttg tagttctggg ccctcgattc 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ctttcccacc accccacagg ctttaccctt tgagaaaaag gcagccctcc agattttgta gacatttttc ttaatatttt taacattgtg tcttttaaaa 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

gaaatgtttt acacagttca tccaaagagc agagaactga acttctcact attgccttgg ccctgacagc tgttaccagc acccttttcc caagaaaagt 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

caattcccag gtgcttattg gacatccttc gagggggaag aggagggaag cggccagctc acccttccgg gaccctagtg tggggcgaat ctcacggacc 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

tgacctcaga ggtgcaccag tgccgcccag gtagataaga gctgcagcat tgactgtgct tccgttcttc cctcggggat tgctcatggc atgggcctct 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

tacgtgctgt cagcttgatg tgaagatcaa gttcagtgct gtgggatttt taggaacaaa aaactgtgac gtctggattt ggggttgatt tttgtgctgg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ggtgggatta tgggtcaatg ttgaagaatt tttaagtctg tattatgttt aaaacatgaa tgatttgaaa gtttaaattt ttaattttta tatgtggaaa 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ttcttcctgt tggctaaagg ggaagctcaa gtggtgtcgt cttttgtgct gttaaatata tattctattc tttggaagaa ggcagagaga ggagtcttat 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

tatttttaaa tgctcctagt tgtatagtct gtctgttgta catagagttc agcttgtttt ttggctccag taggaaaaaa aatccatcca tctgagatgg 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ggtcctgttg tttattatca ctctagaagt tatacattga tatttattct ttctgtcccc acgttgtggc acctgaagac atcttcaaaa ttggcagaaa 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

agataatagt tataaaaatt ttagttcatt tatttttaaa ctcctttcag attattttac cattaggagg aggtagattg tttcgtcttc ctgtctgatt 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

tttgttttgt agtatttaat tttgtattcc tctgcagttt taagaaacag tgtttttctt cggtttgctg gaacatgggc gttagagatg gtaataaacc 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

gtggtccttt ttgcgatgtc acgactcttc acctgcctgg gctgttgtgc acacagtgca gcctggatcc tgtcgatctt tacttgtggc ggagctaatg 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

gtcacattga tagttgatta cactgtggca cgaattaatg cagaacactg ttattaataa aggaagtaaa gggctgcaag atttgagagc tgcaac
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

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

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

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:
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)

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: Martin Mokrejš

The abbreviated name of this ORF/gene:
ELG1

The description of the protein encoded in this ORF:
unknown function

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):

1558-2580

Remarks:

Tested ELG1 5' UTR sequence contains 35 AUG repeats.

Citations:

Baird S. D., Lewis S. M., Turcotte M., Holcik M. (2007) A search for structurally similar cellular internal ribosome entry sites. Nucleic. Acids. Res. 35(14):4664-4677

IRESs:

IRES:

Version: `0`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `ELG1`

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

755-1214

Conclusion:
weakly_supported_IRES

How IRES boundaries were determined:
guessed

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

acttttggtg ggcatttaaa aatgtgtgtg tatgtgtata tatgtatgtg tatgtatgtg tatatatgta tatgtatgta tgtatcgcgt gtatgtgtgt 
.......((. (......... .(((..((.. ((..(((((( ((((((..(( (....))).. )))))))))) ))..))..)) ..)))))).. .((((((((( 
^755       ^765       ^775       ^785       ^795       ^805       ^815       ^825       ^835       ^845       

atgtatgcat gtgtatgtat gtatatgcat gtatgtgtat gtgtatatat gtatgtgtgt gtatgtatat gtgtgtgtat gtgtatgtgt gtgtgtatgt 
((((((((.. ...(((((.. ......)))) ).....)))) )))))))))) ))).(((((( .((((((((. ..(((((((( (((((((((( (((((.(((. 
^855       ^865       ^875       ^885       ^895       ^905       ^915       ^925       ^935       ^945       

gtgtgtgtat gtatgtatgt atgtatatgt attatacaca tatacacata ttggtttttt taatcatttg agagttagtt gaagataaaa acccatcacc 
.((((..((. .(....)..) )..))))..) )))))))))) )))))))))) )(((((.... .))))).... .......... .......... .......... 
^955       ^965       ^975       ^985       ^995       ^1005      ^1015      ^1025      ^1035      ^1045      

cctaaatgta ttccaaagaa taagaacatt gttttataca tagcacactt aacaaaatca agaaatttaa cattaataca gtactgttac ctaatccgta 
.......... .......... .....)))). ....)))))) )))))))).. .......... .......... .......... ....((.... .))....... 
^1055      ^1065      ^1075      ^1085      ^1095      ^1105      ^1115      ^1125      ^1135      ^1145      

gtcgattttc aaattttgtc agttgttcca ataatgtcct ttatatattc cccgcccagc
.......... .....(((.. ........)) )..((.((.. .......... ..........
^1155      ^1165      ^1175      ^1185      ^1195      ^1205

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

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

STDOUT was:

Remarks:

ELG1 IRES represents part (from nt -803 to nt -461 of the original sequence) of 5' UTR from human ELG1 mRNA.

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: Martin Mokrejš

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 ELG1 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: Martin Mokrejš

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

ITAF protein characteristics:

Version: `1`	Last change: `2008-06-27 20:14:51`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
hnRNP_A1

ITAF fullname:
heterogeneous nuclear ribonucleoprotein A1

ITAF description (long):
heterogeneous nuclear ribonucleoprotein A1 (p37), 37 kDa

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_vitro In vitro system used to demonstrate ITAF effect:
other

Remarks:

HEK 293T cell extracts were used to demonstrate in vitro binding to ELG1 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

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 25

Version: `0`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `unknown`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
755-1214

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

acttttggtg ggcatttaaa aatgtgtgtg tatgtgtata tatgtatgtg tatgtatgtg tatatatgta tatgtatgta tgtatcgcgt gtatgtgtgt 
.......((. (......... .(((..((.. ((..(((((( ((((((..(( (....))).. )))))))))) ))..))..)) ..)))))).. .((((((((( 
^755       ^765       ^775       ^785       ^795       ^805       ^815       ^825       ^835       ^845       

atgtatgcat gtgtatgtat gtatatgcat gtatgtgtat gtgtatatat gtatgtgtgt gtatgtatat gtgtgtgtat gtgtatgtgt gtgtgtatgt 
((((((((.. ...(((((.. ......)))) ).....)))) )))))))))) ))).(((((( .((((((((. ..(((((((( (((((((((( (((((.(((. 
^855       ^865       ^875       ^885       ^895       ^905       ^915       ^925       ^935       ^945       

gtgtgtgtat gtatgtatgt atgtatatgt attatacaca tatacacata ttggtttttt taatcatttg agagttagtt gaagataaaa acccatcacc 
.((((..((. .(....)..) )..))))..) )))))))))) )))))))))) )(((((.... .))))).... .......... .......... .......... 
^955       ^965       ^975       ^985       ^995       ^1005      ^1015      ^1025      ^1035      ^1045      

cctaaatgta ttccaaagaa taagaacatt gttttataca tagcacactt aacaaaatca agaaatttaa cattaataca gtactgttac ctaatccgta 
.......... .......... .....)))). ....)))))) )))))))).. .......... .......... .......... ....((.... .))....... 
^1055      ^1065      ^1075      ^1085      ^1095      ^1105      ^1115      ^1125      ^1135      ^1145      

gtcgattttc aaattttgtc agttgttcca ataatgtcct ttatatattc cccgcccagc
.......... .....(((.. ........)) )..((.((.. .......... ..........
^1155      ^1165      ^1175      ^1185      ^1195      ^1205

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

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

STDOUT was:

Remarks:

2D structure of ELG1 from Fig 5A.

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