IRESite_Id:574 summary record describing characteristics of eIF4GII-long IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `574`	Version: `7`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-03-22 18:28:57`
Reviewed by: Martin Mokrejš	Last change: `2009-10-13 13:22:20`

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: `eIF4GII`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
115529454

Synonyms of the gene name:

Synonym: eIF4G2

The mRNA/+RNA description:

Eukaryotic translation initiation factor 4 gamma, isoform II, long. Poly(A)-tail sequence was dropped.

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

GGAGGCGGCC ACAGCGCCAT GTTGGATGCT ctgctcgttg agtgaagaaa atccaccggc atcgcctgag ccccgctacc gagaagggcg ccgcttcctc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

cggggagggg gataaagatc ccccgccgcc ggcccatgag gatattgccg tgaaaggcac agcgactgca gcaggaaccg gacccggcac cggagcggcg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

gcggcggcgg cagcagcggt accgcctcct cacccggcgg cggcagcagc ggcggcggcg gcggcggcgg cggcggcggc ggcagcggtc ccccctcctc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

acccgaacat cagggccctc cagactcagg cgccccaaca aattcctaga ggacctgtgc aacaacctct tgaggatcga atcttcactc ccgctgtctc 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

agcagtctac agcacggtaa cacaagtggc aagacagccg ggaaccccta ccccatcccc ttattcagca catgaaataa acaaggggca tccaaatctt 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

gcggcaacgc ccccgggaca tgcatcgtcc cctggactct ctcaaacccc ttatccctct ggacagaatg caggtccaac cacgctggta taccctcaaa 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

cccctcagac aatgaattca caacctcaaa cccgttctcc gtttttccag aggcctcaaa tacagcctcc tagagctacc atcccgaaca gcagtccttc 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

cattcgtcct ggtgcacaga cacccactgc agtgtaccag gctaatcagc acatcatgat ggttaaccat ctgcccatgc cgtacccagt gccccagggg 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

cctcagtact gtataccaca gtaccgtcat agtggccctc cttatgttgg gcccccccaa caatatccag ttcaaccacc ggggccaggt cctttttatc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ctggaccagg acctggggac ttccccaatg cttatggaac gcctttttac ccaagtcagc cggtgtatca gtcagcacct atcatagtgc ctacgcagca 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

acagccgcct ccagccaaga gagagaaaaa aactataaga attcgggatc caaaccaggg aggtaaagac ataacagagg agattatgtc tggaggtggc 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

agcagaaatc ctactccacc cataggaaga cccacgtcca cacctactcc tcctcagcag ctgcccagcc aggtccccga gcacagccct gtggtttatg 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ggactgtgga gagcgctcat cttgctgcca gcacccctgt cactgcagct agcgaccaga agcaagagga gaagccaaaa ccagatccag tgttaaagtc 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tccttcccca gtccttaggc tagtcctcag tggagagaag aaagaacaag aaggccagac atctgaaact actgcaatag tatccatagc agagcttcct 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ctgcctccat cacctaccac tgtttcttct gttgctcgaa gtacaattgc agcccccacc tcttctgctc ttagtagcca accaatattc accactgcta 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

tagatgacag atgtgaactc tcatccccaa gagaagacac aattcctata cccagcctca catcttgcac agaaacatca gaccctttac caacaaatga 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

aaatgatgat gatatatgca agaaaccctg tagtgtagca cctaatgata ttccactggt ttctagtact aacctaatta atgaaataaa tggagttagc 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

gaaaaattat cagccacgga gagcattgtg gaaatagtaa aacaggaagt attgccattg actcttgaat tggagattct cgaaaatccc ccagaagaaa 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

tgaaactgga gtgtatccca gctcccatca ccccttccac agttccttcc tttcctccaa ctcctccaac tcctccagct tctcctcctc acactccagt 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

cattgttcct gctgctgcca ctactgttag ttctccgagt gctgccatca cagtccagag agtcctagag gaggacgaga gcataagaac ttgccttagt 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

gaagatgcaa aagagattca gaacaaaata gaggtagaag cagatgggca aacagaagag attttggatt ctcaaaactt aaattcaaga aggagccctg 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

tcccagctca aatagctata actgtaccaa agacatggaa gaaaccaaaa gatcggaccc gaaccactga agagatgtta gaggcagaat tggagcttaa 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

agctgaagag gagctttcca ttgacaaagt acttgaatct gaacaagata aaatgagcca ggggtttcat cctgaaagag acccctctga cctaaaaaaa 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

gtgaaagctg tggaagaaaa tggagaagaa gctgagccag tacgtaatgg tgctgagagt gtttctgagg gtgaaggaat agatgctaat tcaggctcca 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

cagatagttc tggtgatggg gttacatttc catttaaacc agaatcctgg aagcctactg atactgaagg taagaagcag tatgacaggg agtttctgct 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ggacttccag ttcatgcctg cctgtataca aaaaccagag ggcctgcctc ctatcagtga tgtggttctt gacaagatca accaacccaa attgccaatg 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

cgaactctgg atcctcgaat tttgcctcga ggaccagact ttacaccagc ctttgctgat tttggaaggc agacacctgg tggaagaggc gtacctttgt 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

tgaatgttgg gtcacgaaga tctcaacctg gccaaagaag agaacccaga aagatcatca cagtttctgt aaaagaagat gtacacctga aaaaggcaga 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

aaatgcctgg aagccaagcc aaaaacgaga cagccaagcc gatgatcccg aaaacattaa aacccaggag ctttttagaa aagttcgaag tatcttaaat 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

aaattgacac cacagatgtt caatcaactg atgaagcaag tgtcaggact tactgttgac acagaggagc ggctgaaagg agttattgac ctggtctttg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

agaaggctat tgatgaaccc agtttctctg tggcttacgc aaacatgtgt cgatgtctag taacgctgaa agtacccatg gcagacaagc ctggtaacac 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

agtgaatttc cggaagctgc tactgaaccg ttgccagaag gagtttgaaa aagataaagc agatgatgat gtctttgaga agaagcagaa agaacttgag 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

gctgccagtg ctccagagga gaggacaagg cttcatgatg aactggaaga agccaaggac aaagcccggc ggagatccat tggcaacatc aagtttattg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

gagaactctt taaactcaaa atgctgactg aagccatcat gcatgactgt gtggtgaagc tgctaaagaa ccatgatgaa gaatccctgg agtgcctgtg 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

tcgcctgctc accaccattg gcaaagactt ggactttgaa aaagcaaagc cacgtatgga ccagtacttt aatcagatgg agaaaattgt gaaagaaaga 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

aaaacctcat ctaggattcg gttcatgctt caagatgtta tagacctaag gctgtgcaat tgggtatctc gaagagcaga tcaagggcct aaaactatcg 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

aacagattca caaagaggct aaaatagaag aacaagaaga gcaaaggaag gtccagcaac tcatgaccaa agagaagaga agaccaggtg tccagagagt 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ggacgaaggt gggtggaaca ctgtacaagg ggccaagaac agtcgggtac tggacccctc aaaattccta aaaatcacta agcctacaat tgatgaaaaa 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

attcagctgg tacctaaagc acagctaggc agctggggaa aaggcagcag tggtggagca aaggcaagtg agactgatgc cttacggtca agtgcttcca 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

gtttaaacag attctctgcc ctgcaacctc cagcaccctc agggtccacg ccatccacgc ctgtagagtt tgattcccga aggaccttaa ctagtcgtgg 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

aagtatgggc agggagaaga atgacaagcc ccttccatct gcaacagctc ggccaaatac tttcatgagg ggtggcagca gtaaagacct gctagacaat 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

cagtctcaag aagagcagcg gagagagatg ctggagaccg tgaagcagct cacaggaggt gtggatgtgg agaggaacag cactgaggct gagcgaaata 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

aaacaaggga gtcagcaaaa ccagaaattt cagcaatgtc agctcatgac aaggctgcat tatcagaaga ggaactggag aggaagtcga aatctatcat 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

tgatgaattt ctacacatta atgattttaa ggaagccatg cagtgtgtgg aagagctgaa tgcccagggc ctactacatg tttttgtgag agtgggagtg 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

gagtccaccc tggaaaggag ccagatcacc agggatcaca tgggccaatt actctatcag ctggtacagt cagaaaaact cagcaaacag gactttttca 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

aaggtttttc agaaactttg gaattggcag atgacatggc cattgatatt ccccatattt ggttgtacct tgctgaactg gtgaccccca tgttaaaaga 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

aggtggaatc tccatgagag aacttaccat agaatttagc aaacctttac ttcctgttgg aagagctggg gtcttgctat ctgaaatatt gcacctacta 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

tgcaaacaaa tgagccataa gaaagtggga gccttatgga gggaggctga cctcagctgg aaggactttt taccagaagg agaagatgta cataattttc 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ttttggagca gaagttggac ttcatagagt ctgacagtcc ctgttcctct gaagcacttt caaagaaaga actgtctgcc gaagagctgt ataagcgact 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

cgagaaactc attattgagg acaaagcgaa tgatgaacag atctttgact gggtagaggc taatctagac gaaatccaga tgagttcacc tacattcctt 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

agagctttaa tgactgctgt ttgtaaagca gctattatag ccgactcttc taccttcaga gtggacactg ctgttatcaa gcagagagtg ccgatcttac 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

tcaagtacct agactcagat acagagaagg aactgcaagc actttatgca ctacaagcat cgatagtaaa acttgatcaa cctgccaatt tgctgcggat 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

gttttttgat tgtctatatg acgaggaggt gatctccgag gatgccttct acaaatggga gagcagcaag gaccctgcag agcagaatgg gaagggcgtg 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

gctctgaaat ctgtcacggc attcttcacg tggctgcggg aagcagaaga ggagtctgag gataactaaa acttcaaata cacaaaatga aacaaaagaa 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

acaatttaag tattttttta aaaagtttca cgtcttcgcc aatcacagtg cagcaaggcc aattctcgca gaaaccccca cgtgtgcacg agtgggagag 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

gggaaagaga aaaaaaggtg atcatggagg aaaaaggtac tggataaaag taaacttcaa accttagggc gggagcacta aaaccaaaat acatgtatta 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

tttatagaaa atattttctg ttttaatctt ttctttttaa acaaggactc atacttaaaa aaatgtttag caaaaaaaaa aaaagttgag aacttttaat 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ttattttaag gactgcaaat gccagtgtaa ttttttaatt tgcagtttct gtaaacaact tgtataatag aaaagcagag aaataaattt ccctcccctt 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

caagatgcac ctcatgtttg ttttaaggta tagcatttag tccagatttg agaaagtttg gggtgaacaa ggtaagaaag attttttttt ttttggcatc 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

aaatctttct gcctgcctct cagcttgctt cagaaaattt aaaaaatcac aatagtaatc aaaacataca taacattgaa acagaaggaa atgctgtgga 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ccacagaact ccaagaattg tttaaaaaaa aaaaagtgct accctgagaa aagtactctt aatactcttg aaatctttag agcaacttta aggcttgtaa 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

atacatagaa caaatattta aaaaaacaaa aagaaattga ctcagtacta tttcttttca ctttgaaaat ataaagaaca aaataaagac aaacattgca 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

agttt
^6201

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

A promoter reported in cDNA corresponding to IRES sequence:
not tested 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:
eIF4GII

The description of the protein encoded in this ORF:
Eukaryotic translation initiation factor 4 gamma, isoform II.

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):

612-5369

Remarks:

This sequence encompasses the region studied by Johannes and Sarnow (1998) and named eIF4GII-long. The region
they studied as the 5'-UTR is located in this transcript between 288-614.

To assemble sequence of this entry curator IRESite extended at the 5'-end sequence of NM_003760.3 by 30 bp
long GGAGGCGGCCACAGCGCCATGTTGGATGCT sequence inferred from these ESTs: CN402456 DA260816. This record is
further supported by ESTs: DB451482, DB449034, CN402457, BU155832, BQ644097, DR002014, BF897694, BF897695.

An EST record with accession BD644097 is somewhat different inside the 5'-UTR region and could represent yet
another splice variant of eIF4GII.

Please note the RefSeq entry NM_003760 was not listed in the Supplementary Figure 12 of Baranick et al. (2008)
nor Byrd et al. (2005). That is probably because this gene is on chromosome 1 while their variants are from
chromosome 3.

Our extended mRNA sequence using ESTs in this entry spans in front of the genomic contig NC_000001:

>NC_000001 Homo sapiens chromosome 1, GRCh37 primary reference assembly.; LEN=370369
>IRESite_Id:574 eIF4GII-long (chromosome1); LEN=6205

1-126  (31-156)                100% -> (GT/AG) 24   (126bp exon)
490-673  (157-340)             100% -> (GT/AG) 24   (184bp exon)
87635-87710  (341-416)         100% -> (GT/AG) 24   (76bp exon)
125854-125982  (417-545)       100% -> (GT/AG) 24   (129bp exon)

>NT_004610 Homo sapiens chromosome 1 genomic contig, GRCh37 reference primary assembly.; LEN=16558170
>IRESite_Id:574 eIF4GII-long (chromosome1); LEN=6205

(complement)

[cut]
8057447-8057575  (5661-5789)   100% <- (GT/AG) 24   (129bp exon)
8095719-8095794  (5790-5865)   100% <- (GT/AG) 24   (76 bp exon)
8182756-8182939  (5866-6049)   100% <- (GT/AG) 24   (184bp exon)
8183303-8183458  (6050-6205)   100%                 (156bp exon)

Citations:

Johannes G., Sarnow P. (1998) Cap-independent polysomal association of natural mRNAs encoding c-myc, BiP, and eIF4G conferred by internal ribosome entry sites. RNA. 4(12):1500-1513

IRESs:

IRES:

Version: `3`	Last change: `2009-10-13 13:41:30`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `eIF4GII-long`

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

288-614

Conclusion:
never_claimed_to_be_IRES

How IRES boundaries were determined:
experimentally_determined

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

gtcccccctc ctcacccgaa catcagggcc ctccagactc aggcgcccca acaaattcct agaggacctg tgcaacaacc tcttgaggat cgaatcttca 
^288       ^298       ^308       ^318       ^328       ^338       ^348       ^358       ^368       ^378       

ctcccgctgt ctcagcagtc tacagcacgg taacacaagt ggcaagacag ccgggaaccc ctaccccatc cccttattca gcacatgaaa taaacaaggg 
^388       ^398       ^408       ^418       ^428       ^438       ^448       ^458       ^468       ^478       

gcatccaaat cttgcggcaa cgcccccggg acatgcatcg tcccctggac tctctcaaac cccttatccc tctggacaga atgcaggtcc aaccacgctg 
^488       ^498       ^508       ^518       ^528       ^538       ^548       ^558       ^568       ^578       

gtataccctc aaacccctca gacaatg
^588       ^598       ^608

Remarks:

Actually this region (325bp) was never claimed to harbor an IRES and has no IRES activity. In Figure 8 is
shown that eIF4GII-long performed badly in comparison with eIG4GI-ext and especially with PV IRES.

Citations:

Johannes G., Sarnow P. (1998) Cap-independent polysomal association of natural mRNAs encoding c-myc, BiP, and eIF4G conferred by internal ribosome entry sites. RNA. 4(12):1500-1513

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