IRESite_Id:241 summary record describing characteristics of ELH IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `241`	Version: `2`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2007-07-24 00:00:00`

IRESite record type:

natural_transcript

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

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
155731

The mRNA/+RNA description:

A. californica egg-laying hormone mRNA, complete cds. The 5'-UTR of 293nt has been replaced by IRESite
annotator with the 319nt long 5'-UTR actually studied.

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

CTTTACCGAC AACGTCCAGC GGTCCAGTCG AGAAGTAAGT AGTCCGCGCT GCGAGCATAA CTCTACCAGA GAAACGCGCA CTTTATTGGT CAAGACAGAC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GGAAGCCGGC GGTTGGACGC AAAGGTTGAC TCGGAAGCTG AGAGATTGTT GAGTAACACG CAGAAGTCTT GAAAGTATCA AGTATTGAAC ATATTTCAAG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GGACTTGGTT TCGGTGAAGT CGTCAATTCC TTTTATCGTC AACGTTTCCA CAGCCCTCAG AATAGAAATT TCCAACAAGC CAAAGCCTAC GTAATGAAGC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GCCCCAATAA CCGGCCGACA AACACAATGT CTCTCATTCT GTGCCTCACC CTCTCCTCTC ATAATGGCGA GGACGTATTT AGCAACGAGA AAAGGAGATT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ACGGTTCCAC AAAAGGAGAC TCCGATTCGA CAGGAGAGAT CAAGATGAAG GTAACTTTCG GCGGATCCCG ACCAACGCAG TTTCTATGTC AGCAGATGAA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AACTCTCCTT TCGATCTTTC TAATGAAGAG GGCGCTGTTT ATCAACGTGA TCTGAGGGCT CCGAGACTAC GCTTCTACTC CTTACGCAAA AGAGCTGCAG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GGGAAATGGA GCAGTCGGAA GGACAAAATC CTGAAACGGA AAGCCACTCA AGGAGAAAAC GGTCTGTCCT AACGCCTTCG CTTTCGAGTC TTGGTGAGTC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACTCGAGTCT GGAATCTCGA AACGAATCTC CATCAACCAG GACTTGAAGG CTATCACAGA CATGCTGCTT ACAGAGCAAA TCCGAGAAAG GCAAAGGTAT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTCGCTGACT TACGCCCACG TCTCTTGGAA AAGGGCAAGC GGAGTTCTGG CGTCAGTCTG CTCACCTCCA ACAAGGACGA GGAACAGAGG GAACTGCTGA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAGCGATAAG CAACCTCTTG GACTAATGGA ACAGTCTGTA AAGCGAACGA CACAAACCCA AACGGTGTCG GTAGGGTCGT AAAACATTAA ACATTTTACA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ACC
^1001

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

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

Aplysia californica

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:
homogeneous_population_of_molecules_confirmed

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:

Aplysia californica

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:
ELH

The description of the protein encoded in this ORF:
egg-laying hormone

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):

294-926

Remarks:

There is no complete mRNA sequence in GenBank which would match reasonably the IRES sequence tested. Probably
the best overall match is to 155731. The sequence of GI:155731 has been edited for IRESite aims - so the
5'-UTR is replaced completely by the tested sequence with extra sequences 1-13nt and 196-208nt and few
mismatches. The edited record has 5'-UTR with 319nt instead of 293 as originally. Below is the original
pairwise alignment as reported by BLAST:


>gi|155731|gb|M29347.1|APLELHABJ
 A.californica egg-laying hormone mRNA, complete cds Length=1003

 Score =  297 bits (150),  Expect = 1e-77
 Identities = 174/182 (95%), Gaps = 0/182 (0%)
 Strand=Plus/Plus

Query  14   CTTTACCGACAACGTCCAGCGTCCCAGTCGAGAAGTAAGTAGTCCGAGCTGTGAGCATAA  73
Sbjct  1    .....................GT.......................C....C........  60

Query  74   CTCTACCAGAGAAACGCGCGCTTTATTGGTCAAGATAGACGGAAGCCGGCGGTTGAAGGC  133
Sbjct  61   ...................A...............C...................G.C..  120

Query  134  AAAGGTTGACTCGGAAGCTGAGAGATTGTTGAGTAACACGCAGAAGTCTTGAAAGTATCA  193
Sbjct  121  ............................................................  180

Query  194  AG  195
Sbjct  181  ..  182


 Score =  210 bits (106),  Expect = 2e-51
 Identities = 109/110 (99%), Gaps = 0/110 (0%)
 Strand=Plus/Plus

Query  209  ATTGAACATATTTCAAGGAACTTGGTTTCGGTGAAGTCGTCAATTCCTTTTATCGTCAAC  268
Sbjct  184  ..................G.........................................  243

Query  269  GTTTCCACAGCCCTCAGAATAGAAATTTCCAACAAGCCAAAGCCTACGTA  318
Sbjct  244  ..................................................  293



Presence of a cryptic promoter and possibility of aberrant splicing were ruled out using RNase protection
and RT-PCR.

Citations:

Dyer J. R., Michel S., Lee W., Castellucci V. F., Wayne N. L., Sossin W. S. (2003) An activity-dependent switch to cap-independent translation triggered by eIF4E dephosphorylation. Nat. Neurosci. 6(3):219-220

IRESs:

IRES:

Version: `2`	Last change: `2007-07-24 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `ELH`

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

1-319

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

CTTTACCGAC AACGTCCAGC GGTCCAGTCG AGAAGTAAGT AGTCCGCGCT GCGAGCATAA CTCTACCAGA GAAACGCGCA CTTTATTGGT CAAGACAGAC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GGAAGCCGGC GGTTGGACGC AAAGGTTGAC TCGGAAGCTG AGAGATTGTT GAGTAACACG CAGAAGTCTT GAAAGTATCA AGTATTGAAC ATATTTCAAG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GGACTTGGTT TCGGTGAAGT CGTCAATTCC TTTTATCGTC AACGTTTCCA CAGCCCTCAG AATAGAAATT TCCAACAAGC CAAAGCCTAC GTAATGAAGC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GCCCCAATAA CCGGCCGAC
^301       ^311

Remarks:

It is not clear what is the ELH IRES activity in scale to other IRESs, especially to some known positive
controls.

Citations:

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