IRESite_Id:103 summary record describing characteristics of BCL2 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `103`	Version: `17`
Originaly submitted by: Martin Mokrejš	Submission date: `2006-01-11 00:00:00`
Reviewed by: Martin Mokrejš	Last change: `2009-09-01 18:39:29`

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: `BCL2`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
179366

Synonyms of the gene name:

Synonym: Bcl-2

The mRNA/+RNA description:

Human B-cell leukemia/lymphoma 2 (bcl-2) proto-oncogene mRNA encoding bcl-2-alpha protein, complete cds.

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

GCGCCCGCCC CTCCGCGCCG CCTGCCCGCC CGCCCGCCGC GCTCCCGCCC GCCGCTCTCC GTGGCCCCGC CGCGCTGCCG CCGCCGCCGC TGCCAGCGAA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GGTGCCGGGG CTCCGGGCCC TCCCTGCCGG CGGCCGTCAG CGCTCGGAGC GAACTGCGCG ACGGGAGGTC CGGGAGGCGA CCGTAGTCGC GCCGCCGCGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGGACCAGGA GGAGGAGAAA GGGTGCGCAG CCCGGAGGCG GGGTGCGCCG GTGGGGTGCA GCGGAAGAGG GGGTCCAGGG GGGAGAACTT CGTAGCAGTC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATCCTTTTTA GGAAAAGAGG GAAAAAATAA AACCCTCCCC CACCACCTCC TTCTCCCCAC CCCTCGCCGC ACCACACACA GCGCGGGCTT CTAGCGCTCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCACCGGCGG GCCAGGCGCG TCCTGCCTTC ATTTATCCAG CAGCTTTTCG GAAAATGCAT TTGCTGTTCG GAGTTTAATC AGAAGACGAT TCCTGCCTCC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GTCCCCGGCT CCTTCATCGT CCCATCTCCC CTGTCTCTCT CCTGGGGAGG CGTGAAGCGG TCCCGTGGAT AGAGATTCAT GCCTGTGTCC GCGCGTGTGT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GCGCGCGTAT AAATTGCCGA GAAGGGGAAA ACATCACAGG ACTTCTGCGA ATACCGGACT GAAAATTGTA ATTCATCTGC CGCCGCCGCT GCCAAAAAAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AACTCGAGCT CTTGAGATCT CCGGTTGGGA TTCCTGCGGA TTGACATTTC TGTGAAGCAG AAGTCTGGGA ATCGATCTGG AAATCCTCCT AATTTTTACT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CCCTCTCCCC CCGACTCCTG ATTCATTGGG AAGTTTCAAA TCAGCTATAA CTGGAGAGTG CTGAAGATTG ATGGGATCGT TGCCTTATGC ATTTGTTTTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GTTTTACAAA AAGGAAACTT GACAGAGGAT CATGCTGTAC TTAAAAAATA CAAGTAAGTC TCGCACAGGA AATTGGTTTA ATGTAACTTT CAATGGAAAC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CTTTGAGATT TTTTACTTAA AGTGCATTCG AGTAAATTTA ATTTCCAGGC AGCTTAATAC ATTGTTTTTA GCCGTGTTAC TTGTAGTGTG TATGCCCTGC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TTTCACTCAG TGTGTACAGG GAAACGCACC TGATTTTTTA CTTATTAGTT TGTTTTTTCT TTAACCTTTC AGCATCACAG AGGAAGTAGA CTGATATTAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CAATACTTAC TAATAATAAC GTGCCTCATG AAATAAAGAT CCGAAAGGAA TTGGAATAAA AATTTCCTGC GTCTCATGCC AAGAGGGAAA CACCAGAATC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AAGTGTTCCG CGTGATTGAA GACACCCCCT CGTCCAAGAA TGCAAAGCAC ATCCAATAAA ATAGCTGGAT TATAACTCCT CTTCTTTCTC TGGGGGCCGT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GGGGTGGGAG CTGGGGCGAG AGGTGCCGTT GGCCCCCGTT GCTTTTCCTC TGGGAAGGAT GGCGCACGCT GGGAGAACGG GGTACGACAA CCGGGAGATA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GTGATGAAGT ACATCCATTA TAAGCTGTCG CAGAGGGGCT ACGAGTGGGA TGCGGGAGAT GTGGGCGCCG CGCCCCCGGG GGCCGCCCCC GCACCGGGCA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TCTTCTCCTC CCAGCCCGGG CACACGCCCC ATCCAGCCGC ATCCCGCGAC CCGGTCGCCA GGACCTCGCC GCTGCAGACC CCGGCTGCCC CCGGCGCCGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CGCGGGGCCT GCGCTCAGCC CGGTGCCACC TGTGGTCCAC CTGGCCCTCC GCCAAGCCGG CGACGACTTC TCCCGCCGCT ACCGCGGCGA CTTCGCCGAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ATGTCCAGCC AGCTGCACCT GACGCCCTTC ACCGCGCGGG GACGCTTTGC CACGGTGGTG GAGGAGCTCT TCAGGGACGG GGTGAACTGG GGGAGGATTG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGGCCTTCTT TGAGTTCGGT GGGGTCATGT GTGTGGAGAG CGTCAACCGG GAGATGTCGC CCCTGGTGGA CAACATCGCC CTGTGGATGA CTGAGTACCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GAACCGGCAC CTGCACACCT GGATCCAGGA TAACGGAGGC TGGGATGCCT TTGTGGAACT GTACGGCCCC AGCATGCGGC CTCTGTTTGA TTTCTCCTGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTGTCTCTGA AGACTCTGCT CAGTTTGGCC CTGGTGGGAG CTTGCATCAC CCTGGGTGCC TATCTGAGCC ACAAGTGAAG TCAACATGCC TGCCCCAAAC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AAATATGCAA AAGGTTCACT AAAGCAGTAG AAATAATATG CATTGTCAGT GATGTACCAT GAAACAAAGC TGCAGGCTGT TTAAGAAAAA ATAACACACA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TATAAACATC ACACACACAG ACAGACACAC ACACACACAA CAATTAACAG TCTTCAGGCA AAACGTCGAA TCAGCTATTT ACTGCCAAAG GGAAATATCA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTTATTTTTT ACATTATTAA GAAAAAAGAT TTATTTATTT AAGACAGTCC CATCAAAACT CCGTCTTTGG AAATCCGACC ACTAATTGCC AAACACCGCT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TCGTGTGGCT CCACCTGGAT GTTCTGTGCC TGTAAACATA GATTCGCTTT CCATGTTGTT GGCCGGATCA CCATCTGAAG AGCAGACGGA TGGAAAAAGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ACCTGATCAT TGGGGAAGCT GGCTTTCTGG CTGCTGGAGG CTGGGGAGAA GGTGTTCATT CACTTGCATT TCTTTGCCCT GGGGGCGTGA TATTAACAGA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GGGAGGGTTC CCGTGGGGGG AAGTCCATGC CTCCCTGGCC TGAAGAAGAG ACTCTTTGCA TATGACTCAC ATGATGCATA CCTGGTGGGA GGAAAAGAGT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TGGGAACTTC AGATGGACCT AGTACCCACT GAGATTTCCA CGCCGAAGGA CAGCGATGGG AAAAATGCCC TTAAATCATA GGAAAGTATT TTTTTAAGCT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ACCAATTGTG CCGAGAAAAG CATTTTAGCA ATTTATACAA TATCATCCAG TACCTTAAAC CCTGATTGTG TATATTCATA TATTTTGGAT ACGCACCCCC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CAACTCCCAA TACTGGCTCT GTCTGAGTAA GAAACAGAAT CCTCTGGAAC TTGAGGAAGT GAACATTTCG GTGACTTCCG ATCAGGAAGG CTAGAGTTAC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCAGAGCATC AGGCCGCCAC AAGTGCCTGC TTTTAGGAGA CCGAAGTCCG CAGAACCTAC CTGTGTCCCA GCTTGGAGGC CTGGTCCTGG AACTGAGCCG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GGCCCTCACT GGCCTCCTCC AGGGATGATC AACAGGGTAG TGTGGTCTCC GAATGTCTGG AAGCTGATGG ATGGAGCTCA GAATTCCACT GTCAAGAAAG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AGCAGTAGAG GGGTGTGGCT GGGCCTGTCA CCCTGGGGCC CTCCAGGTAG GCCCGTTTTC ACGTGGAGCA TAGGAGCCAC GACCCTTCTT AAGACATGTA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TCACTGTAGA GGGAAGGAAC AGAGGCCCTG GGCCTTCCTA TCAGAAGGAC ATGGTGAAGG CTGGGAACGT GAGGAGAGGC AATGGCCACG GCCCATTTTG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GCTGTAGCAC ATGGCACGTT GGCTGTGTGG CCTTGGCCAC CTGTGAGTTT AAAGCAAGGC TTTAAATGAC TTTGGAGAGG GTCACAAATC CTAAAAGAAG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CATTGAAGTG AGGTGTCATG GATTAATTGA CCCCTGTCTA TGGAATTACA TGTAAAACAT TATCTTGTCA CTGTAGTTTG GTTTTATTTG AAAACCTGAC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AAAAAAAAAG TTCCAGGTGT GGAATATGGG GGTTATCTGT ACATCCTGGG GCATTAAAAA AAAATCAATG GTGGGGAACT ATAAAGAAGT AACAAAAGAA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GTGACATCTT CAGCAAATAA ACTAGGAAAT TTTTTTTTCT TCCAGTTTAG AATCAGCCTT GAAACATTGA TGGAATAACT CTGTGGCATT ATTGCATTAT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ATACCATTTA TCTGTATTAA CTTTGGAATG TACTCTGTTC AATGTTTAAT GCTGTGGTTG ATATTTCGAA AGCTGCTTTA AAAAAATACA TGCATCTCAG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CGTTTTTTTG TTTTTAATTG TATTTAGTTA TGGCCTATAC ACTATTTGTG AGCAAAGGTG ATCGTTTTCT GTTTGAGATT TTTATCTCTT GATTCTTCAA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AAGCATTCTG AGAAGGTGAG ATAAGCCCTG AGTCTCAGCT ACCTAAGAAA AACCTGGATG TCACTGGCCA CTGAGGAGCT TTGTTTCAAC CAAGTCATGT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GCATTTCCAC GTCAACAGAA TTGTTTATTG TGACAGTTAT ATCTGTTGTC CCTTTGACCT TGTTTCTTGA AGGTTTCCTC GTCCCTGGGC AATTCCGCAT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TTAATTCATG GTATTCAGGA TTACATGCAT GTTTGGTTAA ACCCATGAGA TTCATTCAGT TAAAAATCCA GATGGCGAAT GACCAGCAGA TTCAAATCTA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TGGTGGTTTG ACCTTTAGAG AGTTGCTTTA CGTGGCCTGT TTCAACACAG ACCCACCCAG AGCCCTCCTG CCCTCCTTCC GCGGGGGCTT TCTCATGGCT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GTCCTTCAGG GTCTTCCTGA AATGCAGTGG TCGTTACGCT CCACCAAGAA AGCAGGAAAC CTGTGGTATG AAGCCAGACC TCCCCGGCGG GCCTCAGGGA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ACAGAATGAT CAGACCTTTG AATGATTCTA ATTTTTAAGC AAAATATTAT TTTATGAAAG GTTTACATTG TCAAAGTGAT GAATATGGAA TATCCAATCC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TGTGCTGCTA TCCTGCCAAA ATCATTTTAA TGGAGTCAGT TTGCAGTATG CTCCACGTGG TAAGATCCTC CAAGCTGCTT TAGAAGTAAC AATGAAGAAC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GTGGACGTTT TTAATATAAA GCCTGTTTTG TCTTTTGTTG TTGTTCAAAC GGGATTCACA GAGTATTTGA AAAATGTATA TATATTAAGA GGTCACGGGG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GCTAATTGCT AGCTGGCTGC CTTTTGCTGT GGGGTTTTGT TACCTGGTTT TAATAACAGT AAATGTGCCC AGCCTCTTGG CCCCAGAACT GTACAGTATT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GTGGCTGCAC TTGCTCTAAG AGTAGTTGAT GTTGCATTTT CCTTATTGTT AAAAACATGT TAGAAGCAAT GAATGTATAT AAAAGC
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

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

Homo sapiens

A promoter reported in cDNA corresponding to IRES sequence:
yes 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):
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:
weak_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:
heterogeneous_population_of_molecules_found

The organism used:

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

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:
BCL2

The description of the protein encoded in this ORF:
BCL2 protein

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):

1459-2178

Remarks:

The sequence of the BCL2 mRNA (1458b 5'-UTR, 5086b total) corresponds to the sequence in Fig. 3A in Tsujimoto
and Croce, 1986 which has in addition to the GenBank record also the polyA tail stretch. According to Sherrill
et al., 2004, this mRNA sequence corresponds to the so called 5.5 kb variant and should originate from the P1
promoter. The 1458b long 5'-UTR contains an intron, which is only optionally spliced out in vivo.
Excision of the intron does not affect IRES activity (K. Sherrill, personal communication).

BTW, the 3.5kb variant (146b 5'-UTR, 911b total) is stored under GI:179368 and is in Tsujimoto and Croce, 1986
in Fig. 3B.

Back to Sherrill et al., 2004, the transcript integrity was verified by RT-PCR. Cells were transfected by DNA
and also directly by in vitro transcribed mRNA. RNAi targeted against renilla luciferase in the first cistron
was contransfected into the cells to lower background noise by ~80%. Possible promoter presence within part of
the BCL2 5'-UTR studied was examined by use of a promoter-less plasmid (Fig. 3A) and also judged from the
effect of RNAi on levels of Rluc and Fluc (although such result could be biased by the fact aberrant splicing
was detected as pointed above it seems excision of the intron does not affect IRES activity; K. Sherrill,
personal communication). In case of BCL2 and XIAP IRESs it was found that RNAi decreased RLuc luciferase but
not FLuc activity in same scale (Fig. 3B). The Northern blot analysis and RNAi assay confirmed the BCL2 region
studied had a weak promoter activity (should be the P2 promoter described elsewhere?). The experiments have
shown/confirmed that the pRL-BCL2-FL plasmid contains previously known 3' splice acceptor site within the BCL2
region. The presence of the acceptor site resulted in both bicistronic Rluc-BCL2-Fluc mRNA and also Fluc
monocistronic mRNA being produced in vivo. Note: The IRES region studied by Sherrill et al., 2004 was only
1138b upstream the START codon -- instead of 1146b upstream as misreported in the article (K. Sherrill,
personal communication) because longer region could not be amplified by RT-PCR, possibly due to the very high
GC content.

Additional comments from K. Sherrill:

A key point is that our evidence for BCL-2 IRES activity is based exclusively
upon transfection of mRNA transcripts containing the BCL-2 IRES 5'UTR, and not
DNA transfection. Our RT-PCR results and RNAi work were performed only to
show the dangers inherent with defining an IRES solely by transfecting DNA
alone. The minor BCL-2 promoter that is present within this sequence is not
cryptic, but rather well-defined in the literature. However, it is primarily
active in lymphocytes. There is nothing to be taken "with a grain of salt"
as these data are not the supporting data of the paper. They simply show why
we had to obtain all of our REAL data via direct transfection of capped and
poly-adenylated mRNA, which is to avoid the possibility that promoter and/or
splicing activity might have affected our data.

In addition, I'd like to note that the presence (or absence) of the
alternatively-spliced intron within this BCL-2 5'UTR doesn't appear to
affect IRES activity, as we selectively deleted this intron and saw no
apparent effect.

Cammas et al. (2007) used the Bcl2 IRES in their RNAi experiments showing that either the splicing issue or
the promoter make the RNAi-based approach not unsuccessful (Supplemental Figure S2 of their publication).

Citations:

Tsujimoto Y., Croce C. M. (1986) Analysis of the structure, transcripts, and protein products of bcl-2, the gene involved in human follicular lymphoma. Proc. Natl. Acad. Sci. U. S. A. 83(14):5214-5218

Sherrill K. W., Byrd M. P., Van Eden M. E., Lloyd R. E. (2004) BCL-2 translation is mediated via internal ribosome entry during cell stress. J. Biol. Chem. 279(28):29066-29074

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: `4`	Last change: `2007-01-23 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `BCL2`

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

322-1458

Conclusion:
weakly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

AAAAAATAAA ACCCTCCCCC ACCACCTCCT TCTCCCCACC CCTCGCCGCA CCACACACAG CGCGGGCTTC TAGCGCTCGG CACCGGCGGG CCAGGCGCGT 
^322       ^332       ^342       ^352       ^362       ^372       ^382       ^392       ^402       ^412       

CCTGCCTTCA TTTATCCAGC AGCTTTTCGG AAAATGCATT TGCTGTTCGG AGTTTAATCA GAAGACGATT CCTGCCTCCG TCCCCGGCTC CTTCATCGTC 
^422       ^432       ^442       ^452       ^462       ^472       ^482       ^492       ^502       ^512       

CCATCTCCCC TGTCTCTCTC CTGGGGAGGC GTGAAGCGGT CCCGTGGATA GAGATTCATG CCTGTGTCCG CGCGTGTGTG CGCGCGTATA AATTGCCGAG 
^522       ^532       ^542       ^552       ^562       ^572       ^582       ^592       ^602       ^612       

AAGGGGAAAA CATCACAGGA CTTCTGCGAA TACCGGACTG AAAATTGTAA TTCATCTGCC GCCGCCGCTG CCAAAAAAAA ACTCGAGCTC TTGAGATCTC 
^622       ^632       ^642       ^652       ^662       ^672       ^682       ^692       ^702       ^712       

CGGTTGGGAT TCCTGCGGAT TGACATTTCT GTGAAGCAGA AGTCTGGGAA TCGATCTGGA AATCCTCCTA ATTTTTACTC CCTCTCCCCC CGACTCCTGA 
^722       ^732       ^742       ^752       ^762       ^772       ^782       ^792       ^802       ^812       

TTCATTGGGA AGTTTCAAAT CAGCTATAAC TGGAGAGTGC TGAAGATTGA TGGGATCGTT GCCTTATGCA TTTGTTTTGG TTTTACAAAA AGGAAACTTG 
^822       ^832       ^842       ^852       ^862       ^872       ^882       ^892       ^902       ^912       

ACAGAGGATC ATGCTGTACT TAAAAAATAC AAGTAAGTCT CGCACAGGAA ATTGGTTTAA TGTAACTTTC AATGGAAACC TTTGAGATTT TTTACTTAAA 
^922       ^932       ^942       ^952       ^962       ^972       ^982       ^992       ^1002      ^1012      

GTGCATTCGA GTAAATTTAA TTTCCAGGCA GCTTAATACA TTGTTTTTAG CCGTGTTACT TGTAGTGTGT ATGCCCTGCT TTCACTCAGT GTGTACAGGG 
^1022      ^1032      ^1042      ^1052      ^1062      ^1072      ^1082      ^1092      ^1102      ^1112      

AAACGCACCT GATTTTTTAC TTATTAGTTT GTTTTTTCTT TAACCTTTCA GCATCACAGA GGAAGTAGAC TGATATTAAC AATACTTACT AATAATAACG 
^1122      ^1132      ^1142      ^1152      ^1162      ^1172      ^1182      ^1192      ^1202      ^1212      

TGCCTCATGA AATAAAGATC CGAAAGGAAT TGGAATAAAA ATTTCCTGCG TCTCATGCCA AGAGGGAAAC ACCAGAATCA AGTGTTCCGC GTGATTGAAG 
^1222      ^1232      ^1242      ^1252      ^1262      ^1272      ^1282      ^1292      ^1302      ^1312      

ACACCCCCTC GTCCAAGAAT GCAAAGCACA TCCAATAAAA TAGCTGGATT ATAACTCCTC TTCTTTCTCT GGGGGCCGTG GGGTGGGAGC TGGGGCGAGA 
^1322      ^1332      ^1342      ^1352      ^1362      ^1372      ^1382      ^1392      ^1402      ^1412      

GGTGCCGTTG GCCCCCGTTG CTTTTCCTCT GGGAAGG
^1422      ^1432      ^1442      ^1452

Remarks:

The BCL2 IRES has 6% activity of the HCV IRES in direct mRNA transfection (capped transcripts and 35bp long
polyA in human HEK 293T cells).

Citations:

Sherrill K. W., Byrd M. P., Van Eden M. E., Lloyd R. E. (2004) BCL-2 translation is mediated via internal ribosome entry during cell stress. J. Biol. Chem. 279(28):29066-29074

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