IRESite_Id:46 summary record describing characteristics of Hsp101 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `46`	Version: `6`
Originaly submitted by: Martin Pospíšek	Submission date: `2005-07-19 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2009-09-01 16:39:00`

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: `Hsp101`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
4928487

The mRNA/+RNA description:

Zea mays heat shock protein 101 (HSP101) gene. Poly(A) sequence was dropped.

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

GGCACGAGAG AAAAACTAGC CGAAGCAAAC CCATTCCACA AGCACCTGGT GGGATCATCT CATCATCAGA AACAAAGAGA GAGATTCCGT GCCCACTTGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGTAGTAGAT TGTGAGGATT GAGGAGTAGC AAAGAGAAGC AGCCATGAAT CCGGACAACT TCACCCACAA GACGAACGAG GCGATCGTGG GGGCGCACGA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GATTGCGGTG GAGGCCGGCC ACGCGCAGCT CACGCCGCTG CACCTGGCCG CAGTGCTGGC TGCGGACAAG GGCGGCATCC TGCGGCAGGC CATCACGGGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GCGTCGGGGG GCGACGGAGC GGCCGGGGAC TCGTTCGAGC GCGTGCTGAA CAACTCGCTC AAGAAGCTGC CGTCGCAGTC CCCGCCGCCG GACTCCGTCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CGGCGTCCAC GGCACTGATC AAGGTCATCC GCCGGGCGCA GTCCGCGCAG AAAAAACGCG GGGACTCTCA CCTCGCCGTC GACCAGCTGC TGCTCGGCCT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GCTCGAGGAC TCGCAGATCT CCGACTGCCT CAAGGAGGCC GGCGTGTCCG CGGCGCGGGT GCGCGCCGAG CTTGAGAAGC TCCGCGGCGG GGAGGGGCGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CGCGTGGAGT CCGCGTCGGG GGACACCAAC TTCCAGGCGC TCAAGACATA CGGCCGGGAC CTCGTTGAGC AGGCCGGGAA GCTGGACCCC GTCATCGGCC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GCGACGAGGA GATCCGCCGC GTGGTGCGCA TCCTCTCGCG CCGCACTAAG AACAACCCCG TCCTCATCGG CGAGCCCGGC GTTGGCAAGA CGGCCGTCGT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GGAGGGCCTC GCGCAGCGCA TCGTTCGCGG CGACGTGCCC AGTAACCTCC TCGACGTCCG CCTCATCGCG CTCGACATGG GCGCGCTCGT CGCGGGCGCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAGTACCGCG GCGAGTTCGA GGAGCGGCTC AAGGCCGTGC TCAAGGAGGT GGAAGAGGCC GAGGGGAAGG TCATTCTCTT CATCGACGAG ATACACCTCG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TCCTGGGCGC GGGCAGGACG GAGGGTTCCA TGGACGCGGC CAACCTGTTC AAGCCAATGC TGGCGAGGGG ACAGCTCAGG TGCATCGGCG CCACCACGCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GGAGGAGTAC CGCAAGTACG TGGAGAAGGA CGCAGCGTTC GAGCGGCGGT TCCAGCAGGT GTTCGTCGCG GAGCCGAGCG TGCCCGACAC CGTCAGCATT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CTGAGGGGAC TCAAGGAGAA GTACGAGGGG CACCATGGCG TGAGGATCCA GGACCGCGCC CTCGTGGTCG CGGCACAGCT ATCCGCGAGG TACATCATGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GTCGGCACCT GCCTGACAAA GCCATAGACC TGGTGGACGA GGCCTGCGCC AATGTGAGGG TGCAGCTCGA CAGCCAGCCG GAGGAGATTG ATAACCTGGA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GAGGAAGAGA ATCCAGCTTG AGGTTGAGCT CCACGCGCTC GAGAAGGAGA AGGACAAGGC CAGCAAAGCC CGGCTGATCG AGGTCAGGAA GGAATTGGAC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GATCTGAGGG ACAAGCTGCA GCCCCTGACC ATGAAGTACA GGAAGGAGAA GGAGAGAATC GATGAGATCA GGAAGCTGAA GCAGCGCCGC GAGGAGCTCC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AGTTCACCCT GCAGGAGGCC GAGCGCCGGA TGGACCTGGC CCGTGTGGCC GACCTCAAGT ACGGCGCCCT CCAGGAAATC GACGCCGCGA TCTCCAAGCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GGAGAGCGAA ACAGGGGAGA ACCTGATGCT CACCGAAACC GTCGGCCCTG AACAAATTGC AGAGGTGGTG AGCCGTTGGA CGGGTATTCC AGTGACCCGG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTTGGCCAGA ACGACAAGGA GAGGCTGGTC GGCCTGGCTG ACAGGCTTCA CCAGAGGGTG GTCGGCCAGA CAGAGGCTGT GAGCGCCGTC GCAGAGGCGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGCTGAGGTC GAGGGCCGGT CTTGGCAGGC CACAACAGCC CACTGGCTCG TTCCTGTTCC TGGGTCCGAC TGGCGTGGGG AAAACTGAGC TAGCCAAGGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCTAGCCGAA CAGCTGTTCG ACGACGAGAA CCTTCTTGTC CGCATCGACA TGTCGGAGTA CATGGAGCAG CACTCGGTTG CTCGCCTCAT CGGAGCACCG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CCTGGCTACG TCGGCCATGA AGAGGGTGGG CAGCTGACTG AACAAGTGAG GAGGAGGCCG TACAGCGTGA TCCTGTTCGA CGAGGTCGAG AAGGCCCATG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TCGCCGTGTT CAACACCCTG CTCCAGGTCC TCGACGACGG CAGGTTGACG GATGGGCAAG GCAGGACGGT GGACTTCAGG AACACCGTGA TCATCATGAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ATCGAACCTC GGCGCCGAGC ACCTCCTCGC TGGGATGGTG GGCAAGAACT CCATGAAGGT CGCTCGCGAT CTGGTCATGC AGGAGGTGAG GAGGCACTTC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CGACCCGAGC TGCTGAACCG TCTCGACGAG ATCGTGATCT TCGATCCTCT GTCCCACGAG CAGCTGAGGA AGGTCGCTCG CCTTCAGATG AAGGATGTGG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CCGTCCGTCT TGCCGAAAGG GGCATCGCTC TGGCTGTGAC CGACGCCGCA TTGGACATCA TCTTGTCTCT CTCTTACGAT CCGGTGTACG GCGCGCGGCC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AATCAGGAGG TGGATCGAGA AGAGGGTGGT GACGCAGCTG TCGAAGATGC TGATCCAGGA GGAGATCGAC GAGAACTGCA CGGTCTACAT CGACGCCGCG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CCCGGCAAGG ACGAGCTGGT CTACAGGGTG GACCGGAGCG GCGGTCTGGT GAACGCTGAG ACGGGGATGA AGTCGGACAT CCTGATCCAG GTCCCCAACA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GCTCCACCAG GAGCGACGCT GCGCAGGCCG TCAAGAAGAT GAGGATCATG GAGGAGGACG AGGACGGTAT GGACGAGGAG TAAAAGGCGG GCCGGAGGAC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GCGGAGCTGC GCCCAGGCCG CAGGTCTGGC GCCGGCATCA TCGAGTGTCT TTTGAATAAG CGTGTAGATA AGCCCGTGAA TATGCAGACG AGGTTGAGAT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GATGTTCTTG TAACGCTGCT GTTTGTCAAG CATGGACGAA TGGTCTCTCA TATAGTATCA AAGTGACAAG TCTCTC
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071

Credibility of mRNA sequence:

only_fragment_published_or_from_author

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

Zea mays

A promoter reported in cDNA corresponding to IRES sequence:
not tested The total number of notable open-reading frames (ORFs):
1

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

ORF

ORF position:

1

Version: `2`	Last change: `2009-09-01 16:37:24`
Originaly submitted by: Martin Pospíšek	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
Hsp101

The description of the protein encoded in this ORF:
heat shock protein 101

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):

145-2883

Remarks:

The underlying mRNA sequence used for this record has start codon at base 145 instead of 147. It also lacks
the region of 60nt upstream the transcription start which has been included in the bicistronic tests. See
GI:68160574 for sequence of the relevant Zea mays chromosome region. Also, a full-length cDNA under
GI:223975968 has only 68bp as the 5'-UTR. A third mRNA sequence available has 114bp as the 5'-UTR
(GI:40060484).
Please refer also to sequence 39 from Patent WO03020928.

Citations:

Dinkova T. D., Zepeda H., Martinez-Salas E., Martinez L. M., Nieto-Sotelo J., de Jimenez E. S. (2005) Cap-independent translation of maize Hsp101. Plant J. 41(5):722-731

IRESs:

IRES:

Version: `9`	Last change: `2007-01-12 00:00:00`
Originaly submitted by: Martin Pospíšek	Reviewed by: Václav Vopálenský
The IRES name: `Hsp101`

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

1-161

Conclusion:
putative_IRES

How IRES boundaries were determined:
guessed

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

GGCACGAGAG AAAAACTAGC CGAAGCAAAC CCATTCCACA AGCACCTGGT GGGATCATCT CATCATCAGA AACAAAGAGA GAGATTCCGT GCCCACTTGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGTAGTAGAT TGTGAGGATT GAGGAGTAGC AAAGAGAAGC AGCCATGAAT CCGGACAACT T
^101       ^111       ^121       ^131       ^141       ^151       ^161

Remarks:

In described experiment is Hsp101 5' UTR cloned in bicistronic plasmids contained chloramphenicol acetyl
transferase as first cistron and firefly luciferase as second cistron. The maize "Hsp101 5' UTR" used in the
bicistronic constructs included 60 nt upstream of the transcription start site, the entire 5' UTR (146 bp),
and the first 15 bp of the coding region in frame with the LUC ORF. Here is shown mRNA (UTR (146 nt) and open
reading frame (15 nt)) only. Therefore, T3/T7 capped transcripts used for in vitro translations contained in
roughly the first 60nt of a plant promoter. In vitro translation was let to proceed for 1 hour at 30
oC. FMDV Lb protease was supplemented to rabbit reticulocyte lysates used for translation of the bicistronic
mRNAs. Protein products were detected by antibodies. Alternatively, wheat germ extracts (and also rabbit
reticulocyte lysates) were depleted of eIF4E because plant eIF4G proteins are not susceptible to FMDV Lb
protease.

Citations:

Dinkova T. D., Zepeda H., Martinez-Salas E., Martinez L. M., Nieto-Sotelo J., de Jimenez E. S. (2005) Cap-independent translation of maize Hsp101. Plant J. 41(5):722-731

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