IRESite_Id:612 summary record describing characteristics of NtHSF1 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `612`	Version: `0`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-25 21:39:21`
Reviewed by: Martin Mokrejš

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: `NtHSF1`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
5821135

The mRNA/+RNA description:

Nicotiana tabacum NtHSF1 mRNA for heat shock factor, complete cds.

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

GGCACGAGGC TCCCATTAAT ATTTCTTCTT CTGTGTAATT CCATTATTCT GTAGTAGATT CACGTCCGAG TTTAAAGAAG AGAGAAAACT GAAAAGGCAG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAAATTCCAG AGCTTTAGAT TTAGCCAAAG ATAGTTATGG TCGTGTTGTT CTTGGTGAAG ATTGGCAAAG TAGGAGCCAA TGGAAGAAAC TAAGATCATA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ATCAATCGCC CCAAAAACAA CCTTGTTCAT TCTATGGTTT TTCTCTTCGG TTTCTATGTT TGGGATTGGG AATTCCTCAC TGTCCTTTTG CTTTTCAGTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATTGCTCCTT CTAATTTTCC CTAGCTAGGA TCTTCTCAAT TAATTTCCTT TTTCATTTTC AACTAACTCA TAATTAGCCC AAATCTTCAA AAGAGTTTTG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TGTAAGTTGA TAGACGTTTA GAGAAACAGA GAAATACAGG GGAAAAACAA GGGATGTCGC AGAGGACAGT TCCGGCGCCG TTTCTGACGA AGACGTACCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ATTGGTAGAT GATGCGACCA CCGACGACGT CGTATCTTGG AACGAGAGCG GCACTACTTT TGTGGTTTGG AAAACTGCTG AATTTGCAAA GGATTTGGTG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCCACTTACT TCAAGCACAA CAATTTCTCC AGCTTCGTTC GTCAGCTTAA CACTTATGGC TTTCGAAAGA TTGTGCCAGA CAAATGGGAA TTCGCCAACG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGAACTTCAA AAGAGGACAG AAGGAGCTCC TCACGGCAAT ACGCCGTCGG AAAACCGTGA CACCAACCCC AGCTGGTGGT AAGTCCGTGG TACCAGGCAC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATCAGCATCT CCGGACAATT CGGGGGAAGA CTTAGGCTCA AGTTCCACCT CTTCCCCTGA CTCGAAGAAC CCGGGGTCTG TTGATACTCC GGGAAAGTCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CAATTCGCAG ACTTGTCGGA CGAAAACGAG AAGCTAAAGA AAGACAACCA GATGCTGAGC TCTGAGCTCG CGCAGGCCAA GAAACAGTGC GACGAGCTAG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGGCTTTCTT GAATCAGTAT GTGAAGGTTG CACCTGACAT GATCAACCGT ATCATTAGCC AAGGAACCTC AGGGTCCAGC TATGGGGAGT TGGTCAAGGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GGTAATTGGT GGTGTTAATG ATTTAGAAGC ACAAGGTAGT GATGATGACG AAAAGGGTGA TACTTTGAAA CTATTTGGTG TGTTACTGAA AGAGAACAAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AAAAAAAGGG GTCCAGACGA GAATGCTGAT ATTTCTGGGT CCCGTGGGAA AATGATGAAA ACTATGGACT ACAATTTGCC TTGGATGAAA ATGTCTTCGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCCCTGGAGA GAGTAACAAG GTCTGTAACT GAAATTGTGA TCCAAATATT AAGGGAAGCT AGAGAATGGA CTTCTGCAGA TTAGCTTCAT GCATCCTTTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GTTTTAGTGC CTGTTAGTTT ACAAGTTCAG TGATTATGAA ATAACGGAGT ATTTAGTATG AGTAGTATTG GGGTTAGATT ACTACGAGCA GTAACCCCAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CATATTAAAC AAGAAATATA TATACATAGG GGACTATCAA AGTCATATCC CACTGCCTCA AGGTCGGTTG GTTTGTGTAG TCCAAACTCA TAATAATGGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTCTTATTTA TGATTTCGTT TTGGT
^1601      ^1611      ^1621

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:

Nicotiana tabacum

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: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
NtHSF1

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

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):

454-1332

Citations:

Dorokhov YL, Skulachev MV, Ivanov PA, Zvereva SD, Tjulkina LG, Merits A, Gleba YY, Hohn T, Atabekov JG (2002) Polypurine (A)-rich sequences promote cross-kingdom conservation of internal ribosome entry. Proc. Natl. Acad. Sci. U.S.A. 8(99):5301-5306

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `NtHSF1`

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

1-453

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GGCACGAGGC TCCCATTAAT ATTTCTTCTT CTGTGTAATT CCATTATTCT GTAGTAGATT CACGTCCGAG TTTAAAGAAG AGAGAAAACT GAAAAGGCAG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAAATTCCAG AGCTTTAGAT TTAGCCAAAG ATAGTTATGG TCGTGTTGTT CTTGGTGAAG ATTGGCAAAG TAGGAGCCAA TGGAAGAAAC TAAGATCATA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ATCAATCGCC CCAAAAACAA CCTTGTTCAT TCTATGGTTT TTCTCTTCGG TTTCTATGTT TGGGATTGGG AATTCCTCAC TGTCCTTTTG CTTTTCAGTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATTGCTCCTT CTAATTTTCC CTAGCTAGGA TCTTCTCAAT TAATTTCCTT TTTCATTTTC AACTAACTCA TAATTAGCCC AAATCTTCAA AAGAGTTTTG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TGTAAGTTGA TAGACGTTTA GAGAAACAGA GAAATACAGG GGAAAAACAA GGG
^401       ^411       ^421       ^431       ^441       ^451

Remarks:

The IRES was postulated based on the fact the 5'-UTR contains two polypurine-rich tracts. Brief experiments
involved transfection of tobacco protoplasts using Agrobacterium vector, and in vitro test using WGE. In HeLa
cells transfected by recombinant vaccinia virus it was also scaled to EMCV-R IRES (Figure 5C). The NtHSF1 IRES
appeared to be about 2.5x stronger.

Citations:

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