IRESite_Id:62 summary record describing characteristics of reaper IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `62`	Version: `9`
Originaly submitted by: Petra Sekyrová	Submission date: `2006-01-12 00:00:00`
Reviewed by: Martin Mokrejš	Last change: `2008-05-13 21:56:32`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `both_UTRs_possibly_incomplete`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `Rpr`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
24666289

Synonyms of the gene name:

Synonym: rp

Synonym: Rpr

Synonym: CG4319

Synonym: Reaper L

The mRNA/+RNA description:

Drosophila melanogaster CG4319-PA (rpr) mRNA, complete cds.

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

tgaataagag agacaccaga acaaagtgaa cgaactcgaa aatacgaaag aaaagtgtgt gcgccagcaa caaagaacta actcgataaa tattcattgt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

gcagaagaga aagttattga gtcactacca gttgtgtaat tccgaacgag aagaaagata aaccaacaat ggcagtggca ttctacatac ccgatcaggc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

gactctgttg cgggaggcgg agcagaagga gcagcagatc cttcgcttgc gggagtcaca gtggagattc ctggccaccg tcgtcctgga aaccctgcgc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

cagtacactt catgtcatcc gaagaccgga agaaagtccg gcaaatatcg caagccatcg caatgaggat tcgagtaact aacaaatacg gggaaaacca 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

atagtccagt ccaaaatcca gagtacaaag gaaataagca tgagccaacc caaaacccaa acacagtcac cactcatcag ccgacggcac tcgatttcta 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ctgcagtcaa ggacacagag ccacaacacc cacccaattt tagtttactc atcaaagcga ttgtgataat ggttttgttt ctacaaaaaa gcggaggaaa 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

aatttgaaaa aataacgttt ttataaagtc cccaattttt tacaaaaatg tttcaatgat ataaatcaac ttttttagaa ataatttact cttaaagcct 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

atttaaatga attactactg taatagtttg taagttcttt tgtaagacga gtttttctaa gtttttttta agaagaaacc ccagaaaaaa acgaagatga 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gtcgaagttg gctaaaaatt gcatcaattt tttgtcaaac aaaaagtcaa t
^801       ^811       ^821       ^831       ^841       ^851

Credibility of mRNA sequence:

guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail

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

Drosophila melanogaster

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:
unclear_result

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:

Drosophila melanogaster SL2

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

ORF

ORF position:

1

Version: `1`
Originaly submitted by: Petra Sekyrová	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
rpr

The description of the protein encoded in this ORF:
reaper

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):

169-366

OPTIONAL: The function of the encoded protein

down-regulates inhibitors of apoptosis by inhibition of general protein synthesis and by protein degradation

Remarks:

White et al. (1994) refer to 5'UTR sequence GI:476009 (L31631) 854 bp. There is a similar record
GI:24666289 (NM_079414) 851bp which has similar sequence as well. In contrast, White et al. (1994)
stated that rpr appears to encode single polyadenylated transcript of approx. 1300bp. IRESite annotation is
based on NM_079414 sequence. A BLAST search against EST databases reveals that only regions 347-584 650-851 of
the NM_079414 record appear to be expressed.

It appears GenBank annotators took over the putative gene prediction from GI:476009 (L31631) 854 bp published
in 1994. Subsequently GI:17737620 (NM_079414.1) and finally GI:24666289 (NM_079414.2) were published by NCBI
staff. All these records lack the very last 2 nucleotides of the TGA stop codon shown in Fig. 7 in White et
al. (1994). FlyBase annotation at http://flybase.bio.indiana.edu/reports/FBgn0011706.html took over the
annotation again and annotated the "Reported size (kD)" to be "65 aa" and in "Comments" they claim "GO
molecular function: physical interaction reported".

Hernandez et al. (2004) used also Drosophila embryo lysates for in vitro translation of
both, capped and uncapped mRNAs obtained by T3 polymerase. They used pFluc-Rluc plasmid, so have swapped the
reporter genes than usual. Integrity of the transcripts was not verified convincingly (Northern-blots only).
In contrary, direct RNA transfection shown in Figure 2G demonstrates cap-independent mode of translation.

Possible promoter existence was eliminated for reaper 5'-UTR using promoter-less construct in vivo
using SL2 cells (while it was confirmed for eIF4E1 of Drosophila). Integrity of bicistronic constructs used
in vivo was tested by Northern blot. Integrity of the in vitro transcripts was monitored using traces
of 32P-labeled co-reporter RNA. Most of the experiments performed utilized in vitro translation of
capped/uncapped monocistronic mRNAs.

Citations:

Hernandez G., Vazquez-Pianzola P., Sierra J. M., Rivera-Pomar R. (2004) Internal ribosome entry site drives cap-independent translation of reaper and heat shock protein 70 mRNAs in Drosophila embryos. RNA. 10(11):1783-1797

White K., Grether M. E., Abrams J. M., Young L., Farrell K., Steller H. (1994) Genetic control of programmed cell death in Drosophila. Science. 264(5159):677-683

IRESs:

IRES:

Version: `11`	Last change: `2008-05-13 21:56:32`
Originaly submitted by: Petra Sekyrová	Reviewed by: Martin Mokrejš
The IRES name: `reaper` 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):

1-168

Conclusion:
weakly_supported_IRES

How IRES boundaries were determined:
guessed

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

tgaataagag agacaccaga acaaagtgaa cgaactcgaa aatacgaaag aaaagtgtgt gcgccagcaa caaagaacta actcgataaa tattcattgt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

gcagaagaga aagttattga gtcactacca gttgtgtaat tccgaacgag aagaaagata aaccaaca
^101       ^111       ^121       ^131       ^141       ^151       ^161

Remarks:

Authors do not specify the length of 5'-UTR sequence tested, thus the whole 5'UTR sequence is marked here as
containing IRES. The translational activity of rpr 5'-UTR was confirmed in a cell-free Drosophila-embryo
translation system and in Drosophila S2 cells. See Figure 2G and 5D in Hernadez et al. (2004).

Citations:

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