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:


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):


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: 2015-04-16 16:45:23 GMT+1