IRESite_Id:570 summary record describing characteristics of BiP_-222

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `570`	Version: `3`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-03-16 17:41:34`
Reviewed by: Martin Mokrejš	Last change: `2009-09-03 12:47:06`

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
1143491

Synonyms of the gene name:

Synonym: GRP78

The mRNA/+RNA description:

H.sapiens mRNA for BiP protein mRNA. Poly(A)-tail sequence was dropped.

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

AGGTCGACGC CGGCCAAGAC AGCACAGACA GATTGACCTA TTGGGGTGTT TCGCGAGTGT GAGAGGGAAG CGCCGCGGCC TGTATTTCTA GACCTGCCCT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TCGCCTGGTT CGTGGCGCCT TGTGACCCCG GGCCCCTGCC GCCTGCAAGT CGGAAATTGC GCTGTGCTCC TGTGCTACGG CCTGTGGCTG GACTGCCTGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGCTGCCCAA CTGGCTGGCA AGATGAAGCT CTCCCTGGTG GCCGCGATGC TGCTGCTGCT CAGCGCGGCG CGGGCCGAGG AGGAGGACAA GAAGGAGGAC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTGGGCACGG TGGTCGGCAT CGACTTGGGG ACCACCTACT CCTGCGTCGG CGTGTTCAAG AACGGCCGCG TGGAGATCAT CGCCAACGAT CAGGGCAACC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCATCACGCC GTCCTATGTC GCCTTCACTC CTGAAGGGGA ACGTCTGATT GGCGATGCCG CCAAGAACCA GCTCACCTCC AACCCCGAGA ACACGGTCTT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TGACGCCAAG CGGCTCATCG GCCGCACGTG GAATGACCCG TCTGTGCAGC AGGACATCAA GTTCTTGCCG TTCAAGGTGG TTGAAAAGAA AACTAAACCA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TACATTCAAG TTGATATTGG AGGTGGGCAA ACAAAGACAT TTGCTCCTGA AGAAATTTCT GCCATGGTTC TCACTAAAAT GAAAGAAACC GCTGAGGCTT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATTTGGGAAA GAAGGTTACC CATGCAGTTG TTACTGTACC AGCCTATTTT AATGATGCCC AACGCCAAGC AACCAAAGAC GCTGGAACTA TTGCTGGCCT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AAATGTTATG AGGATCATCA ACGAGCCTAC GGCAGCTGCT ATTGCTTATG GCCTGGATAA GAGGGAGGGG GAGAAGAACA TCCTGGTGTT TGACCTGGGT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GGCGGAACCT TCGATGTGTC TCTTCTCACC ATTGACAATG GTGTCTTCGA AGTTGTGGCC ACTAATGGAG ATACTCATCT GGGTGGAGAA GACTTTGACC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGCGTGTCAT GGAACACTTC ATCAAACTGT ACAAAAAGAA GACGGGCAAA GATGTCAGGA AGGACAATAG AGCTGTGCAG AAACTCCGGC GCGAGGTAGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AAAGGCCAAG GCCCTGTCTT CTCAGCATCA AGCAAGAATT GAAATTGAGT CCTTCTATGA AGGAGAAGAC TTTTCTGAGA CCCTGACTCG GGCCAAATTT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GAAGAGCTCA ACATGGATCT GTTCCGGTCT ACTATGAAGC CCGTCCAGAA AGTGTTGGAA GATTCTGATT TGAAGAAGTC TGATATTGAT GAAATTGTTC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TTGTTGGTGG CTCGACTCGA ATTCCAAAGA TTCAGCAACT GGTTAAAGAG TTCTTCAATG GCAAGGAACC ATCCCGTGGC ATAAACCCAG ATGAAGCTGT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AGCGTATGGT GCTGCTGTCC AGGCTGGTGT GCTCTCTGGT GATCAAGATA CAGGTGACCT GGTACTGCTT CATGTATGTC CCCTTACACT TGGTATTGAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACTGTAGGAG GTGTCATGAC CAAACTGATT CCAAGTAATA CAGTGGTGCC TACCAAGAAC TCTCAGATCT TTTCTACAGC TTCTGATAAT CAACCAACTG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTACAATCAA GGTCTATGAA GGTGAAAGAC CCCTGACAAA AGACAATCAT CTTCTGGGTA CATTTGATCT GACTGGAATT CCTCCTGCTC CTCGTGGGGT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CCCACAGATT GAAGTCACCT TTGAGATAGA TGTGAATGGT ATTCTTCGAG TGACAGCTGA AGACAAGGGT ACAGGGAACA AAAATAAGAT CACAATCACC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AATGACCAGA ATCGCCTGAC ACCTGAAGAA ATCGAAAGGA TGGTTAATGA TGCTGAGAAG TTTGCTGAGG AAGACAAAAA GCTCAAGGAG CGCATTGATA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CTAGAAATGA GTTGGAAAGC TATGCCTATT CTCTAAAGAA TCAGATTGGA GATAAAGAAA AGCTGGGAGG TAAACTTTCC TCTGAAGATA AGGAGACCAT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGAAAAAGCT GTAGAAGAAA AGATTGAATG GCTGGAAAGC CACCAAGATG CTGACATTGA AGACTTCAAA GCTAAGAAGA AGGAACTGGA AGAAATTGTT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CAACCAATTA TCAGCAAACT CTATGGAAGT GCAGGCCCTC CCCCAACTGG TGAAGAGGAT ACAGCAGAAA AAGATGAGTT GTAGACACTG ATCTGCTAGT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GCTGTAATAT TGTAAATACT GGACTCAGGA ACTTTTGTTA GGAAAAAATT GAAAGAACTT AAGTCTCGAA TGTAATTGGA ATCTTCACCT CAGAGTGGAG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTGAACTGCT ATAGCCTAAG CGGCTGTTTA CTGCTTTTCA TTAGCAGTTG CTCACATGTC TTTGGGTGGG GGGGGAGAAG AAGAATTGGC CATCTTAAAA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AGCGGGTAAA AAACCTGGGT TAGGGTGTGT GTTCACCTTC AAAATGTTCT ATTTAACAAC TGGGTCATGT GCATCTGGTG TAGGAAGTTT TTTCTACCAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AAGTGACACC AATAAATGTT TGTTATTTAC ACTGGTC
^2501      ^2511      ^2521      ^2531

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 HeLa (ATCC CCL-2)

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:
not_tested

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:
weak_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: `1`	Last change: `2009-03-16 18:29:27`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
BiP

The description of the protein encoded in this ORF:
glucose-regulated protein (78 kDa)

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):

223-2184

Remarks:

Thoma et al. (2004) did not show activity of BiP IRES in contrast to any other IRES. The negative control
was either BiP IRES in sense orientation on an in vitro run-off transcript without poly(A) tail or BiP IRES
in anti-sense orientation.

The region -93 to -1 does not contain functional 3'-splice acceptor site in the setup used by Baranick et al.
(2008), Supplementary Images 7 and 8. These authors also report no IRES activity of this region as well
in their in vivo based experiments (Figures 1, 2, 3).

We hypothesize that if there is a problematic 3'-splice acceptor site it must be in the region -222 to -94.

Young et al. (2008) tested BiP in a promoter-less construct (Figure 2) and reported a weak promoter. They also
showed that most of the "IRES" activity is related to this cryptic promoter (compare Figure 2B vs. 2C; scale
of 2C higher).

Citations:

Thoma C., Bergamini G., Galy B., Hundsdoerfer P., Hentze M. W. (2004) Enhancement of IRES-mediated translation of the c-myc and BiP mRNAs by the poly(A) tail is independent of intact eIF4G and PABP. Mol. Cell. 15(6):925-935

Baranick B. T., Lemp N. A., Nagashima J., Hiraoka K., Kasahara N., Logg C. R. (2008) Splicing mediates the activity of four putative cellular internal ribosome entry sites. Proc. Natl. Acad. Sci. U. S. A. 105(12):4733-4738

Young RM, Wang SJ, Gordan JD, Ji X, Liebhaber SA, Simon MC (2008) Hypoxia-mediated selective mRNA translation by an internal ribosome entry site-independent mechanism. J. Biol. Chem. 283(24):16309-16319

IRESs:

IRES:

Version: `2`	Last change: `2009-09-03 12:47:06`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `BiP_-222_-3`

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

1-222

Conclusion:
disproved_IRES

How IRES boundaries were determined:
experimentally_determined

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

AGGTCGACGC CGGCCAAGAC AGCACAGACA GATTGACCTA TTGGGGTGTT TCGCGAGTGT GAGAGGGAAG CGCCGCGGCC TGTATTTCTA GACCTGCCCT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TCGCCTGGTT CGTGGCGCCT TGTGACCCCG GGCCCCTGCC GCCTGCAAGT CGGAAATTGC GCTGTGCTCC TGTGCTACGG CCTGTGGCTG GACTGCCTGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGCTGCCCAA CTGGCTGGCA AG
^201       ^211       ^221

Remarks:

The BiP IRES was reported by Young et al. (2008) not to be functional in direct RNA transfection (Figure 3).
In Figure 2BC they show that most of the "IRES" activity in NIH3T3 cells is related to the cryptic promoter.

Citations:

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