IRESite_Id:118 summary record describing characteristics of hsp70 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `118`	Version: `7`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2009-09-01 20:29:00`

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: `HSPA1A`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
194248071

Synonyms of the gene name:

Synonym: HSP72

Synonym: HSPA1

Synonym: HSPA1B

Synonym: HSP70-1

The mRNA/+RNA description:

Homo sapiens heat shock 70kDa protein 1A (HSPA1A), mRNA. Poly(A)-tail was dropped.

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

ATAAAAGCCC AGGGGCAAGC GGTCCGGATA ACGGCTAGCC TGAGGAGCTG CTGCGACAGT CCACTACCTT TTTCGAGAGT GACTCCCGTT GTCCCAAGGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTCCCAGAGC GAACCTGTGC GGCTGCAGGC ACCGGCGCGT CGAGTTTCCG GCGTCCGGAA GGACCGAGCT CTTCTCGCGG ATCCAGTGTT CCGTTTCCAG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCCCCAATCT CAGAGCGGAG CCGACAGAGA GCAGGGAACC GGCATGGCCA AAGCCGCGGC GATCGGCATC GACCTGGGCA CCACCTACTC CTGCGTGGGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTGTTCCAAC ACGGCAAGGT GGAGATCATC GCCAACGACC AGGGCAACCG CACCACCCCC AGCTACGTGG CCTTCACGGA CACCGAGCGG CTCATCGGGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ATGCGGCCAA GAACCAGGTG GCGCTGAACC CGCAGAACAC CGTGTTTGAC GCGAAGCGGC TGATTGGCCG CAAGTTCGGC GACCCGGTGG TGCAGTCGGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CATGAAGCAC TGGCCTTTCC AGGTGATCAA CGACGGAGAC AAGCCCAAGG TGCAGGTGAG CTACAAGGGG GAGACCAAGG CATTCTACCC CGAGGAGATC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCGTCCATGG TGCTGACCAA GATGAAGGAG ATCGCCGAGG CGTACCTGGG CTACCCGGTG ACCAACGCGG TGATCACCGT GCCGGCCTAC TTCAACGACT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CGCAGCGCCA GGCCACCAAG GATGCGGGTG TGATCGCGGG GCTCAACGTG CTGCGGATCA TCAACGAGCC CACGGCCGCC GCCATCGCCT ACGGCCTGGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CAGAACGGGC AAGGGGGAGC GCAACGTGCT CATCTTTGAC CTGGGCGGGG GCACCTTCGA CGTGTCCATC CTGACGATCG ACGACGGCAT CTTCGAGGTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAGGCCACGG CCGGGGACAC CCACCTGGGT GGGGAGGACT TTGACAACAG GCTGGTGAAC CACTTCGTGG AGGAGTTCAA GAGAAAACAC AAGAAGGACA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TCAGCCAGAA CAAGCGAGCC GTGAGGCGGC TGCGCACCGC CTGCGAGAGG GCCAAGAGGA CCCTGTCGTC CAGCACCCAG GCCAGCCTGG AGATCGACTC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CCTGTTTGAG GGCATCGACT TCTACACGTC CATCACCAGG GCGAGGTTCG AGGAGCTGTG CTCCGACCTG TTCCGAAGCA CCCTGGAGCC CGTGGAGAAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GCTCTGCGCG ACGCCAAGCT GGACAAGGCC CAGATTCACG ACCTGGTCCT GGTCGGGGGC TCCACCCGCA TCCCCAAGGT GCAGAAGCTG CTGCAGGACT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TCTTCAACGG GCGCGACCTG AACAAGAGCA TCAACCCCGA CGAGGCTGTG GCCTACGGGG CGGCGGTGCA GGCGGCCATC CTGATGGGGG ACAAGTCCGA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GAACGTGCAG GACCTGCTGC TGCTGGACGT GGCTCCCCTG TCGCTGGGGC TGGAGACGGC CGGAGGCGTG ATGACTGCCC TGATCAAGCG CAACTCCACC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ATCCCCACCA AGCAGACGCA GATCTTCACC ACCTACTCCG ACAACCAACC CGGGGTGCTG ATCCAGGTGT ACGAGGGCGA GAGGGCCATG ACGAAAGACA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACAATCTGTT GGGGCGCTTC GAGCTGAGCG GCATCCCTCC GGCCCCCAGG GGCGTGCCCC AGATCGAGGT GACCTTCGAC ATCGATGCCA ACGGCATCCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GAACGTCACG GCCACGGACA AGAGCACCGG CAAGGCCAAC AAGATCACCA TCACCAACGA CAAGGGCCGC CTGAGCAAGG AGGAGATCGA GCGCATGGTG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CAGGAGGCGG AGAAGTACAA AGCGGAGGAC GAGGTGCAGC GCGAGAGGGT GTCAGCCAAG AACGCCCTGG AGTCCTACGC CTTCAACATG AAGAGCGCCG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGGAGGATGA GGGGCTCAAG GGCAAGATCA GCGAGGCGGA CAAGAAGAAG GTGCTGGACA AGTGTCAAGA GGTCATCTCG TGGCTGGACG CCAACACCTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGCCGAGAAG GACGAGTTTG AGCACAAGAG GAAGGAGCTG GAGCAGGTGT GTAACCCCAT CATCAGCGGA CTGTACCAGG GTGCCGGTGG TCCCGGGCCT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GGGGGCTTCG GGGCTCAGGG TCCCAAGGGA GGGTCTGGGT CAGGCCCCAC CATTGAGGAG GTAGATTAGG GGCCTTTCCA AGATTGCTGT TTTTGTTTTG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GAGCTTCAAG ACTTTGCATT TCCTAGTATT TCTGTTTGTC AGTTCTCAAT TTCCTGTGTT TGCAATGTTG AAATTTTTTG GTGAAGTACT GAACTTGCTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTTTTCCGGT TTCTACATGC AGAGATGAAT TTATACTGCC ATCTTACGAC TATTTCTTCT TTTTAATACA CTTAACTCAG GCCATTTTTT AAGTTGGTTA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CTTCAAAGTA AATAAACTTT AAAATTC
^2401      ^2411      ^2421

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:
not_tested

Integrity (uniformity) of mRNA tested using RNase protection:
homogeneous_population_of_molecules_confirmed

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:
homogeneous_population_of_molecules_confirmed

The organism used:

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

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

ORF

ORF position:

1

Version: `2`	Last change: `2009-09-01 20:29:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
HSPA1A

The description of the protein encoded in this ORF:
heat shock 70kDa protein 1A

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):

244-2169

Remarks:

The sequence used for this IRESite (NM_005345.5) is longer by 27bp at the very 5'-end than the 5'-UTR shown in
the article in Figure 1.

Slightly conflicting annotation of the chromosomal region in DQ451402 shows that the 5'-UTR of our entry
(taken over from RefSeq) might be too long. Seemingly complete cDNAs in CR624878 and DA486842.


The promoter-less plasmid was created by destroying the SV40 promoter. Activity of both Renilla and firefly
luciferases was monitored (primary data were not published) and no promoter activity was concluded. RNase
protection was used to confirm that only bicistronic transcripts were produced (Fig. 3).

Citations:

Rubtsova M. P., Sizova D. V., Dmitriev S. E., Ivanov D. S., Prassolov V. S., Shatsky I. N. (2003) Distinctive properties of the 5'-untranslated region of human hsp70 mRNA. J. Biol. Chem. 278(25):22350-22356

IRESs:

IRES:

Version: `5`	Last change: `2009-09-01 20:29:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `hsp70` 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):

51-243

Conclusion:
strongly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

CTGCGACAGT CCACTACCTT TTTCGAGAGT GACTCCCGTT GTCCCAAGGC TTCCCAGAGC GAACCTGTGC GGCTGCAGGC ACCGGCGCGT CGAGTTTCCG 
^51        ^61        ^71        ^81        ^91        ^101       ^111       ^121       ^131       ^141       

GCGTCCGGAA GGACCGAGCT CTTCTCGCGG ATCCAGTGTT CCGTTTCCAG CCCCCAATCT CAGAGCGGAG CCGACAGAGA GCAGGGAACC GGC
^151       ^161       ^171       ^181       ^191       ^201       ^211       ^221       ^231       ^241

Remarks:

Deletion of the 5' end to nt 23 had no effect on the IRES activity. The HSP70 IRES appeared about 5x stronger
than HRV IRES.

Citations:

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