The nucleic acid data:
IRESite Id: 138 Version: 10
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2009-09-01 20:32:03
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:
  PIM1
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
31543400 
Synonyms of the gene name:
Synonym: PIM
The mRNA/+RNA description: 
Homo sapiens pim-1 oncogene (PIM1), a serine-threonine kinase, chimeric non-existing mRNA created in silico
for the purpose of IRESite. Poly(A)-tail was dropped.
The mRNA/+RNA sequence represented in the +DNA notation:


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:
  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:
heterogeneous_population_of_molecules_found
Integrity (uniformity) of mRNA tested using RNase protection:
heterogeneous_population_of_molecules_found
Integrity (uniformity) of mRNA tested using 5'-RACE:
heterogeneous_population_of_molecules_found
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:
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 NIH/3T3 (ATCC CRL-1658)
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 2 Last change: 2008-06-26 12:35:57
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
PIM1
The description of the protein encoded in this ORF:
pim-1 oncogene, a serine-threonine kinase
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):
  397-1338
OPTIONAL: The function of the encoded protein
Oncogene PIM1; pim-1 oncogene (proviral integration site 1); pim-1 kinase 44 kDa isoform
Remarks:
The 5'-UTR sequence was replaced by the 5'-UTR sequence used by Wang et al. (2005), which is by 33nt longer on
the 5'-end compared to the GenBank record. The 5'-UTR sequence used hereby was determined by 5'-RACE and thus
should be complete and is by 47nt longer than the sequence used by Johannes et al., 1999. The coding region
and 3'-UTR were taken over from GenBank.

Strong promoter activity was confirmed in human NIH3T3, Jurkat, HEK293, K562 cells. The promoter start sites
relative to ATG (+1) found in human cell lines are as follows: -412, -53, -33, -21. It is unclear whether the
extra 47 bases are necessary for the promoter activity observed by Wang et al. (2005) and not reported
by Johannes et al. (1999).
Citations:
Wang Z., Weaver M., Magnuson N. S. (2005) Cryptic promoter activity in the DNA sequence corresponding to the pim-1 5'-UTR. Nucleic Acids Res. 33(7):2248-2258
IRESs:
IRES:
Version: 9 Last change: 2008-07-08 20:12:35
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  Pim-1
Warning: please make ires_name same as the gene_name and optionally append to it coordinates. E.g. when gene/virus name is EMCV-R use EMCV-R_-222_to_-1 or EMCV-R_1-456, etc. but not Emcv-R-... or EMCV-222_to_-1. Please keep case of letters as well. This rewards when searching through the database.
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-396
Conclusion:
  disproved_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
The formerly published Pim-1 IRES (Johannes et al., 1999) was found to contain promoter and in direct mRNA
transfection assays found not to have IRES activity (Wang et al., 2005, Figure 4C). The originally studied
Pim-1 5'-UTR in HeLa cells (Johannes et al., 1999) was shorter by 47nt compared to the 5'-RACE derived
sequence used by Wang et al. (2005) and was preceded by supposedly defective EMCV IRES (440 nt). The
"defective" EMCV possibly retained some activity, like ability to bind certain protein cofactors which could
have contributed the observed IRES activity of Pim-1.
Citations:
Wang Z., Weaver M., Magnuson N. S. (2005) Cryptic promoter activity in the DNA sequence corresponding to the pim-1 5'-UTR. Nucleic Acids Res. 33(7):2248-2258
Johannes G., Carter M. S., Eisen M. B., Brown P. O., Sarnow P. (1999) Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc. Natl. Acad. Sci. U. S. A. 96(23):13118-13123
Last change to the database: 2015-04-16 16:45:23 GMT+1