IRESite_Id:138 summary record describing characteristics of Pim-1 IRES

IRESite: The database of experimentally verified IRES structures

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:

CAGCCTCTGC AGCGGCCGCG GTGGCTGAGG AGGCCCGAGA GGAGTCGGTG GCAGCGGCGG CGGCGGGACC GGCAGCAGCA GCAGCAGCAG CAGCAGCAAC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CACTAGCCTC CTGCCCCGCG GCGCTGCCGC ACGAGCCCCA CGAGCCGCTC ACCCCGCCGT TCTCAGCGCT GCCCGACCCC GCTGGCGCGC CCTCCCGCCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCAGTCCCGG CAGCGCCCTC AGTTGTCCTC CGACTCGCCC TCGGCCTTCC GCGCCAGCCG CAGCCACAGC CGCAACGCCA CCCGCAGCCA CAGCCACAGC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CACAGCCCCA GGCATAGCCT TCGGCACAGC CCCGGCTCCG GCTCCTGCGG CAGCTCCTCT GGGCACCGTC CCTGCGCCGA CATCCTGGAG GTTGGGATGC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TCTTGTCCAA AATCAACTCG CTTGCCCACC TGCGCGCCGC GCCCTGCAAC GACCTGCACG CCACCAAGCT GGCGCCCGGC AAGGAGAAGG AGCCCCTGGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GTCGCAGTAC CAGGTGGGCC CGCTACTGGG CAGCGGCGGC TTCGGCTCGG TCTACTCAGG CATCCGCGTC TCCGACAACT TGCCGGTGGC CATCAAACAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GTGGAGAAGG ACCGGATTTC CGACTGGGGA GAGCTGCCTA ATGGCACTCG AGTGCCCATG GAAGTGGTCC TGCTGAAGAA GGTGAGCTCG GGTTTCTCCG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GCGTCATTAG GCTCCTGGAC TGGTTCGAGA GGCCCGACAG TTTCGTCCTG ATCCTGGAGA GGCCCGAGCC GGTGCAAGAT CTCTTCGACT TCATCACGGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AAGGGGAGCC CTGCAAGAGG AGCTGGCCCG CAGCTTCTTC TGGCAGGTGC TGGAGGCCGT GCGGCACTGC CACAACTGCG GGGTGCTCCA CCGCGACATC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAGGACGAAA ACATCCTTAT CGACCTCAAT CGCGGCGAGC TCAAGCTCAT CGACTTCGGG TCGGGGGCGC TGCTCAAGGA CACCGTCTAC ACGGACTTCG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ATGGGACCCG AGTGTATAGC CCTCCAGAGT GGATCCGCTA CCATCGCTAC CATGGCAGGT CGGCGGCAGT CTGGTCCCTG GGGATCCTGC TGTATGATAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GGTGTGTGGA GATATTCCTT TCGAGCATGA CGAAGAGATC ATCAGGGGCC AGGTTTTCTT CAGGCAGAGG GTCTCTTCAG AATGTCAGCA TCTCATTAGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGGTGCTTGG CCCTGAGACC ATCAGATAGG CCAACCTTCG AAGAAATCCA GAACCATCCA TGGATGCAAG ATGTTCTCCT GCCCCAGGAA ACTGCTGAGA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TCCACCTCCA CAGCCTGTCG CCGGGGCCCA GCAAATAGCA GCCTTTCTGG CAGGTCCTCC CCTCTCTTGT CAGATGCCCG AGGGAGGGGA AGCTTCTGTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCCAGCTTCC CGAGTACCAG TGACACGTCT CGCCAAGCAG GACAGTGCTT GATACAGGAA CAACATTTAC AACTCATTCC AGATCCCAGG CCCCTGGAGG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CTGCCTCCCA ACAGTGGGGA AGAGTGACTC TCCAGGGGTC CTAGGCCTCA ACTCCTCCCA TAGATACTCT CTTCTTCTCA TAGGTGTCCA GCATTGCTGG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACTCTGAAAT ATCCCGGGGG TGGGGGGTGG GGGTGGGTCA GAACCCTGCC ATGGAACTGT TTTCTTCATC ATGAGTTCTG CTGAATGCCG CGATGGGTCA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GGTAGGGGGG AAACAGGTTG GGATGGGATA GGACTAGCAC CATTTTAAGT CCCTGTCACC TCTTCCGACT CTTTCTGAGT GCCTTCTGTG GGGACTCCGG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTGTGCTGGG AGAAATACTT GAACTTGCCT CTTTTACCTG CTGCTTCTCC AAAAATCTGC CTGGGTTTTG TTCCCTATTT TTCTCTCCTG TCCTCCCTCA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CCCCCTCCTT CATATGAAAG GTGCCATGGA AGAGGCTACA GGGCCAAACG CTGAGCCACC TGCCCTTTTT TCTGCCTCCT TTAGTAAAAC TCCGAGTGAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CTGGTCTTCC TTTTTGGTTT TTACTTAACT GTTTCAAAGC CAAGACCTCA CACACACAAA AAATGCACAA ACAATGCAAT CAACAGAAAA GCTGTAAATG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGTGTACAGT TGGCATGGTA GTATACAAAA AGATTGTAGT GGATCTAATT TTTAAGAAAT TTTGCCTTTA AGTTATTTTA CCTGTTTTTG TTTCTTGTTT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGAAAGATGC GCATTCTAAC CTGGAGGTCA ATGTTATGTA TTTATTTATT TATTTATTTG GTTCCCTTCC TATTCCAAGC TTCCATAGCT GCTGCCCTAG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTTTCTTTCC TCCTTTCCTC CTCTGACTTG GGGACCTTTT GGGGGAGGGC TGCGACGCTT GCTCTGTTTG TGGGGTGACG GGACTCAGGC GGGACAGTGC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGCAGCTCCC TGGCTTCTGT GGGGCCCCTC ACCTACTTAC CCAGGTGGGT CCCGGCTCTG TGGGTGATGG GGAGGGGCAT TGCTGACTGT GTATATAGGA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TAATTATGAA AAGCAGTTCT GGATGGTGTG CCTTCCAGAT CCTCTCTGGG GCTGTGTTTT GAGCAGCAGG TAGCCTGCTG GTTTTATCTG AGTGAAATAC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TGTACAGGGG AATAAAAGAG ATCTTATTTT TTTTTTTATA CTTGGCGTTT TTTGAATAAA AACCTTTTGT CTT
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671

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):

CAGCCTCTGC AGCGGCCGCG GTGGCTGAGG AGGCCCGAGA GGAGTCGGTG GCAGCGGCGG CGGCGGGACC GGCAGCAGCA GCAGCAGCAG CAGCAGCAAC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CACTAGCCTC CTGCCCCGCG GCGCTGCCGC ACGAGCCCCA CGAGCCGCTC ACCCCGCCGT TCTCAGCGCT GCCCGACCCC GCTGGCGCGC CCTCCCGCCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCAGTCCCGG CAGCGCCCTC AGTTGTCCTC CGACTCGCCC TCGGCCTTCC GCGCCAGCCG CAGCCACAGC CGCAACGCCA CCCGCAGCCA CAGCCACAGC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CACAGCCCCA GGCATAGCCT TCGGCACAGC CCCGGCTCCG GCTCCTGCGG CAGCTCCTCT GGGCACCGTC CCTGCGCCGA CATCCTGGAG GTTGGG
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391

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: 2019-03-18 09:32:49 GMT+1