IRESite_Id:436 summary record describing characteristics of PITSLRE

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `436`	Version: `2`
Originaly submitted by: Martin Mokrejš
Reviewed by: Václav Vopálenský	Last change: `2008-06-26 14:58:03`

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
507159

The mRNA/+RNA description:

Human protein kinase PITSLRE alpha 2-2 mRNA, complete cds.

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

ATACAGGAAG TGACGATACT TTTGGCGCGC GCGGTTGCTG TTTCTTCTCT GGCTCCGGGA CCGGCGGCGG CGGCGGCGGC ACGGGCGGCG GCGTAGGGTG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTTTAACTCA AATGGGTGAT GAAAAGGACT CTTGGAAAGT GAAAACTTTA GATGAAATTC TTCAGGAAAA GAAACGAAGG AAGGAACAAG AGGAGAAAGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGAGATAAAA CGCTTAAAAA ATTCTGATGA CCGGGATTCC AAGCGGGATT CCCTTGAGGA GGGGGAGCTG AGAGATCACT GCATGGAGAT CACAATAAGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AACTCCCCGT ATAGAAGAGA AGACTCTATG GAAGACAGAG GAGAAGAAGA TGATTCTTTG GCCATCAAAC CACCCCAGCA AATGTCTCGG AAAGAAAAAG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TTCATCACAG AAAAGATGAA AAGAGAAAAG AGAAAAAGCA TGCTAGAGTG AAGAAGAAAG AAAGAGAGCA CGAACGTCGG AAACGACATC GAGAAGAACA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GGATAAAGCT CGCCGGGAAT GGGAAAGACA GAAGAGAAGG GAAATGGCAA GGGAGCATTC CAGGAGAGAA AGGGGGAATG ATGGCGTGTG CCTCTTCAGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GACCGCTTGG AGCAGTTAGA AAGGAAGCGG GAGCGGGAGC GCAAGATGCG GGAGCAGCAG AAGGAGCAGC GGGAGCAGAA GGAGCGCGAG CGGCGGGCGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGGAGCGGCG CAAGGAGCGG GAGGCCCGCA GGGAAGTGTC TGCACATCAC CGAACGATGA GAGAGGACTA CAGCGACAAA GTGAAAGCCA GCCACTGGAG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TCGCAGCCCG CCTCGGCCGC CGCGGGAGCG GTTCGAGTTG GGAGACGGCC GGAAGCCAGT AAAAGAAGAG AAAATGGAAG AAAGGGACCT GCTGTCCGAC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTACAGGACA TCAGCGACAG CGAGAGGAAG ACCAGCTCGG CCGAGTCCTC GTCAGCAGAA TCAGGCTCAG GTTCTGAGGA AGAAGAGGAG GAGGAGGAAG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGGAGGAGGA GGAAGGGAGC ACCAGTGAAG AATCAGAGGA GGAAGAGGAA GAGGAGGAGG AGGAGACCGG CAGCAACTCT GAGGAGGCAT CAGAGCAGTC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TGCCGAAGAA GTAAGTGAGG AAGAAATGAG TGAAGATGAA GAACGAGAAA ATGAAAACCA CCTCTTGGTT GTTCCAGAGT CACGGTTCGA CCGAGATTCC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GGGGAGAGTG AAGAAGCAGA GGAAGAAGTG GGTGAGGGAA CGCCGCAGAG CAGCGCCCTG ACAGAGGGCG ACTATGTGCC CGACTCCCCT GCCCTGTCGC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCATCGAGCT CAAGCAGGAG CTGCCCAAGT ACCTGCCGGC CCTGCAGGGC TGCCGGAGCG TCGAGGAGTT CCAGTGCCTG AACAGGATCG AGGAGGGCAC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTATGGAGTG GTCTACAGAG CAAAAGACAA GAAAACAGAT GAAATTGTGG CTCTAAAGCG GCTGAAGATG GAGAAGGAGA AGGAGGGCTT CCCGATCACG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCGCTGAGGG AGATCAACAC CATCCTCAAG GCCCAGCATC CCAACATCGT CACCGTTAGA GAGATTGTGG TGGGCAGCAA CATGGACAAG ATCTACATCG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TGATGAACTA TGTGGAGCAC GACCTCAAGA GCCTGATGGA GACCATGAAA CAGCCCTTCC TGCCAGGGGA GGTGAAGACC CTGATGATCC AGCTGCTGCG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGGGGTGAAA CACCTGCACG ACAACTGGAT CCTGCACCGT GACCTCAAGA CGTCCAACCT GCTGCTGAGC CACGCCGGCA TCCTCAAGGT GGGTGACTTC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GGGCTGGCGC GGGAGTACGG ATCCCCTCTG AAGGCCTACA CCCCGGTCGT GGTGACCCTG TGGTACCGCG CCCCAGAGCT GCTGCTTGGT GCCAAGGAAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ACTCCACGGC CGTGGACATG TGGTCAGTGG GTTGCATCTT CGGGGAGCTG CTGACTCAGA AGCCTCTGTT CCCCGGGAAG TCAGAAATCG ATCAGATCAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CAAGGTGTTC AAGGATCTGG GGACCCCTAG TGAGAAAATC TGGCCCGGCT ACAGCGAGCT CCCAGCAGTC AAGAAGATGA CCTTCAGCAG ACACCCCTAC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AACAACCTCC GCAAGCGCTT CGGGGCTCTG CTCTCAGACC AGGGCTTCGA CCTCATGAAC AAGTTCCTGA CCTACTTCCC CGGGAGGAGG ATCAGCGCTG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AGGACGGCCT CAAGCATGAG TATTTCCGCG AGACCCCCCT CCCCATCGAC CCCTCCATGT TCCCCACGTG GCCCGCCAAG AGCGAGCAGC AGCGTGTGAA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GCGGGGCACC AGCCCGAGGC CCCCTGAGGG AGGCCTGGGC TACAGCCAGC TGGGTGACGA CGACCTGAAG GAGACGGGCT TCCACCTTAC CACCACGAAC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CAGGGGGCCT CTGCCGCGGG CCCCGGCTTC AGCCTCAAGT TCTGAAGGTC AGAGTGGACC CCGTCATGGG G
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471

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:
no 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:
no_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 293T (ATCC CRL-1573)

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

ORF

ORF position:

1

Version: `1`	Last change: `2008-06-26 04:30:09`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
p58_PITSLRE

The description of the protein encoded in this ORF:
PITSLRE alpha 2-2

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):

1126-2445

Remarks:

The p58 protein is produced by IRES-mediated translation initiation whereas p110 is initiated by cap-dependent
manner. Survey of the ATG codons within 5'-UTR was shown in Cornelis et al. (2000), Table 1.

Promoter-less plasmid was used to show at least 20x less-active promoter could be located in 745-1125 PITSLRE
IRES as compared to SV40 early promoter (Tinton et al. (2005), Figure 1D).

Citations:

Cornelis S., Bruynooghe Y., Denecker G., Van Huffel S., Tinton S., Beyaert R. (2000) Identification and characterization of a novel cell cycle-regulated internal ribosome entry site. Mol. Cell. 5(4):597-605

IRESs:

IRES:

Version: `4`	Last change: `2008-06-26 14:58:03`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský
The IRES name: `PITSLRE_p58`

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

745-1125

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

CATCACCGAA CGATGAGAGA GGACTACAGC GACAAAGTGA AAGCCAGCCA CTGGAGTCGC AGCCCGCCTC GGCCGCCGCG GGAGCGGTTC GAGTTGGGAG 
^745       ^755       ^765       ^775       ^785       ^795       ^805       ^815       ^825       ^835       

ACGGCCGGAA GCCAGTAAAA GAAGAGAAAA TGGAAGAAAG GGACCTGCTG TCCGACTTAC AGGACATCAG CGACAGCGAG AGGAAGACCA GCTCGGCCGA 
^845       ^855       ^865       ^875       ^885       ^895       ^905       ^915       ^925       ^935       

GTCCTCGTCA GCAGAATCAG GCTCAGGTTC TGAGGAAGAA GAGGAGGAGG AGGAAGAGGA GGAGGAGGAA GGGAGCACCA GTGAAGAATC AGAGGAGGAA 
^945       ^955       ^965       ^975       ^985       ^995       ^1005      ^1015      ^1025      ^1035      

GAGGAAGAGG AGGAGGAGGA GACCGGCAGC AACTCTGAGG AGGCATCAGA GCAGTCTGCC GAAGAAGTAA GTGAGGAAGA A
^1045      ^1055      ^1065      ^1075      ^1085      ^1095      ^1105      ^1115      ^1125

Remarks:

Sequence 6 from patent US 6764852. Originally IRES has been mapped to 121-1125 and with finer mapping
published in Tinton et al. (2005) to 745-1125 in Di-4 plasmid and 976-1125 (Di-4 mut C).

Citations:

Tinton S. A., Schepens B., Bruynooghe Y., Beyaert R., Cornelis S. (2005) Regulation of the cell-cycle-dependent internal ribosome entry site of the PITSLRE protein kinase: roles of Unr (upstream of N-ras) protein and phosphorylated translation initiation factor eIF-2alpha. Biochem. J. 385(Pt 1):155-163

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

OPTIONAL: The interacting RNA base range (if any):
745-1125

ITAF protein characteristics:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský

ITAF abbreviated name:
Unr

ITAF fullname:
upstream of N-ras

ITAF description (long):
Unr protein is known to bind to gaagaaguaa

3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
stimulatory

Method used to demonstrate ITAF effect:
in_vivo In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

The organism where action of this ITAF was studied:

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

Citations:

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