IRESite_Id:48 summary record describing characteristics of c-jun IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `48`	Version: `6`
Originaly submitted by: Václav Vopálenský	Submission date: `2006-01-12 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2009-09-01 16:46:27`

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: `c-jun`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
212221

The mRNA/+RNA description:

Chicken jun oncogene.

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

GCGCCGGAGC GGGCAGGGCC GAGCGGCAGC GCGGAGCCGG GGTACTCGCG GCGGCGGCGG CGGCGGCAGG AGCGGCGCGG CCCGGCCCGG CGGCGGCACA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGCGGCGAG GCGGCCCGGG AAGCACAGCG AGGCCCGCGG GGCGCCGCCC GCGCCGGGAG GAGCGGCGGC GTCCCGGCGA GAAGTAAGAG CTCCGCGCAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCCTTCCTCC AACCCGCGCG GCCGGGAGCG GTGTGGGGCG GCGGCCGGGA CCGTCCAGCG CGCTGCCGCG GCTCCCGGCG CCACTCCGCG GGCTCTGTTC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TATGAGTGCA AAGATGGAGC CTACTTTCTA CGAGGATGCC CTGAACGCCA GCTTCGCGCC GCCGGAGAGC GGCGGCTATG GATATAATAA CGCCAAGGTG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTGAAGCAGA GCATGACGCT GAACCTGTCC GACGCGGCCA GCAGCCTGAA GCCGCACCTG AGGAACAAGA ACGCCGACAT CCTCACCTCC CCCGACGTGG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GGCTGCTGAA GCTGGCCTCC CCGGAGCTGG AACGGCTCAT CATCCAGTCC AGCAACGGGT TAATCACCAC CACGCCGACC CCGACGCAGT TCCTCTGCCC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CAAGAACGTT ACCGACGAGC AAGAGGGGTT CGCCGAAGGC TTCGTGAGAG CGCTGGCGGA ACTGCACAAC CAGAACACGC TGCCCAGCGT CACCTCAGCC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GCACAACCTG TTAGCGGCGG CATGGCACCT GTGTCCTCCA TGGCCGGCGG CGGCAGCTTC AACACGAGTT TGCACAGCGA GCCCCCGGTG TATGCCAATC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TCAGCAACTT CAACCCCAAC GCGCTCAACT CTGCACCCAA CTACAACGCC AACGGCATGG GCTACGCGCC GCAGCATCAC ATAAACCCCC AGATGCCCGT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GCAGCATCCC AGGCTTCAGG CTCTGAAAGA AGAGCCTCAG ACTGTACCTG AAATGCCGGG GGAAACCCCT CCCCTGTCCC CTATTGACAT GGAGTCGCAG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GAGAGAATCA AAGCCGAGAG AAAACGCATG AGAAACAGAA TTGCGGCGTC CAAATGCCGG AAAAGGAAGT TGGAAAGGAT TGCCAGGTTG GAAGAAAAAG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TGAAAACTTT GAAAGCCCAG AACTCAGAGC TGGCATCCAC GGCCAACATG CTCAGAGAAC AGGTTGCACA GCTTAAGCAG AAGGTCATGA ACCATGTCAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CAGCGGGTGC CAGCTAATGC TAACACAACA GTTGCAAACG TTTTGAAGAG ACGGACTTAA ATAGGAACTG TGATGTTGTG GTATAACCAA ACAACAAACC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AAAAGCGGCG GACGCGTAAA GCTGACGGTA GAAGCTGAGA GGCTGAGTCC TGCCTGCGTG CTCGAAAGCG CATGTGTGGA AAGACTGGCG AGCCTTCAGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TTGAGTTGGT GAAGCAGCCA GCACCGCTCC AAGGAGGGCT GTTCCTGCTC CGATGAGGCG TCAGATCTTC GTTTAACATT GACCAAGACC TGCATGGACC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TAACATTCGA TGATCATTCA GTATTAAAGG TTAAACTGCA ATTGAAACTG TAGATTGCTT TATGTAGTAT TCCTTAAGAA AAAAAAAAAA AAAGCGGGAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGAGGTTTGT GGGAGGCTGA TAAAGAAACA AGAACTGTTC TGCCTGCCTT CAGTAAATGG TGTATGTACA TATCCTTTTT TTATTTTATT TTATGAAAGT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGATTAATGT CAATAAA
^1701      ^1711

Credibility of mRNA sequence:

guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail

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

Gallus gallus

A promoter reported in cDNA corresponding to IRES sequence:
no (not convincing) 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:
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 NIH/3T3 (ATCC CRL-1658)

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

ORF

ORF position:

1

Version: `1`	Last change: `2006-08-10 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
c-jun

The description of the protein encoded in this ORF:
Transcription factor AP-1 and proto-oncogene c-jun.

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):

302-1246

OPTIONAL: The function of the encoded protein

Transcription factor that recognizes and binds to the enhancer heptamer motif 5'-TGA[CG]TCA-3'.

Remarks:

c-jun 5'-UTR containing SP6 synthesized, uncapped, monocistronic mRNA is poorly translated in rabbit
reticulocyte lysate (the shorter 5'-UTR is the more protein is obtained). In contrast, capped, monocistronic
5'-UTR_c-jun + CAT could be read-through in vivo in transiently transfected cells. Transcript integrity
from cells expressing bicistronic mRNA was verified by Northern blot. No bicistronic mRNA tested in
vitro.


Warning: the ORF coordinates do not correspond to the GenBank annotation. According to the article the ORF is
302-1447. But, there is only one sequence from chicken in Genbank (a chromosomal fragment) which IRESite used
for this entry which (dropped the very first 499bp of the DNA and trailing sequence right after the first
poly(A) signal, as annotated in the GenBank file M57467.

Citations:

Sehgal A., Briggs J., Rinehart-Kim J., Basso J., Bos T. J. (2000) The chicken c-Jun 5' untranslated region directs translation by internal initiation. Oncogene. 19(24):2836-2845

IRESs:

IRES:

Version: `5`	Last change: `2007-01-11 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `c-jun`

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

1-301

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GCGCCGGAGC GGGCAGGGCC GAGCGGCAGC GCGGAGCCGG GGTACTCGCG GCGGCGGCGG CGGCGGCAGG AGCGGCGCGG CCCGGCCCGG CGGCGGCACA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGCGGCGAG GCGGCCCGGG AAGCACAGCG AGGCCCGCGG GGCGCCGCCC GCGCCGGGAG GAGCGGCGGC GTCCCGGCGA GAAGTAAGAG CTCCGCGCAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCCTTCCTCC AACCCGCGCG GCCGGGAGCG GTGTGGGGCG GCGGCCGGGA CCGTCCAGCG CGCTGCCGCG GCTCCCGGCG CCACTCCGCG GGCTCTGTTC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

T
^301

Citations:

Sehgal A., Briggs J., Rinehart-Kim J., Basso J., Bos T. J. (2000) The chicken c-Jun 5' untranslated region directs translation by internal initiation. Oncogene. 19(24):2836-2845

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