IRESite_Id:581 characteristics of FeLV-Notch2_1-579 IRES studied in pSV-CAT/FeLV-Notch2-1-579/LUC plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `581`	Version: `1`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-04-09 02:50:59`
Reviewed by: Martin Mokrejš	Last change: `2009-07-16 15:28:18`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_translationally_characterized

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
only_IRES_fragment

The mRNA/+RNA description:

FeLV-Notch2 IRES fragment 1-579.

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

gcgcaagtct ttgctgagac ttgaccgccc cgggtacccg tgtacgaata aacctcttgc cgattgcatc tgactcgtgg tctcggtgtt ccgtgggcgc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ggggcctcat cgccgaggaa gacccagttc gggggtcttt catttggggg ctcgtccggg atagagaccc ccaacccccg ggaccaccga cccaccatca 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ggaggcacat ttacgcgccc tgcagctggt ccaagaagag atccagagac ctctagcggc ggcctaccga gaaaagctcg aaaccccggt tgtgcctcac 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

cccttcaaac caggagactc cgtctgggtt cggagacatc aaaccaagaa cctcgagcca cggtggaaag gaccacatat cgtcctcctg accaccccca 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

cagccttaaa ggtagacgga gttgctgcct ggattcacgc ctcccatgtg aaagctgcag gaccaaccac caatcaagac ctctcggaca gccccagctc 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

agacgatcca tcgagatgga aagtccaacg cacccaaaac cctctaaaga taagactctc tcgtggaact tagtgtttct g
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581

Warning: available plasmid sequence is exactly same as the mRNA sequence. It seems we never managed to reconstruct the original plasmid sequence used to express the studied mRNA.

Credibility of mRNA sequence:

only_fragment_published_or_from_author

The name of the plasmid:
pSV-CAT/FeLV-Notch2-1-579/LUC The name of the promoter used to express this mRNA:
SV40

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

not tested

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

not tested

A promoter reported in cDNA corresponding to IRES sequence:

not tested

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
FeLV-Notch2

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Felis silvestris 9683

The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:

gcgcaagtct ttgctgagac ttgaccgccc cgggtacccg tgtacgaata aacctcttgc cgattgcatc tgactcgtgg tctcggtgtt ccgtgggcgc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ggggcctcat cgccgaggaa gacccagttc gggggtcttt catttggggg ctcgtccggg atagagaccc ccaacccccg ggaccaccga cccaccatca 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ggaggcacat ttacgcgccc tgcagctggt ccaagaagag atccagagac ctctagcggc ggcctaccga gaaaagctcg aaaccccggt tgtgcctcac 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

cccttcaaac caggagactc cgtctgggtt cggagacatc aaaccaagaa cctcgagcca cggtggaaag gaccacatat cgtcctcctg accaccccca 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

cagccttaaa ggtagacgga gttgctgcct ggattcacgc ctcccatgtg aaagctgcag gaccaaccac caatcaagac ctctcggaca gccccagctc 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

agacgatcca tcgagatgga aagtccaacg cacccaaaac cctctaaaga taagactctc tcgtggaact tagtgtttct g
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

The total number of notable open-reading frames (ORFs):

0

Remarks:

Please note we do not have sequence of the vector not even of the ORFs flanking the putative IRES.

Citations:

Lauring A. S., Overbaugh J. (2000) Evidence that an IRES within the Notch2 coding region can direct expression of a nuclear form of the protein. Mol. Cell. 6(4):939-945

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `FeLV-Notch2_1-579`	The functional status of IRES: `functional`

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

1-581

How IRES boundaries were determined:
experimentally_determined

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

gcgcaagtct ttgctgagac ttgaccgccc cgggtacccg tgtacgaata aacctcttgc cgattgcatc tgactcgtgg tctcggtgtt ccgtgggcgc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ggggcctcat cgccgaggaa gacccagttc gggggtcttt catttggggg ctcgtccggg atagagaccc ccaacccccg ggaccaccga cccaccatca 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ggaggcacat ttacgcgccc tgcagctggt ccaagaagag atccagagac ctctagcggc ggcctaccga gaaaagctcg aaaccccggt tgtgcctcac 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

cccttcaaac caggagactc cgtctgggtt cggagacatc aaaccaagaa cctcgagcca cggtggaaag gaccacatat cgtcctcctg accaccccca 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

cagccttaaa ggtagacgga gttgctgcct ggattcacgc ctcccatgtg aaagctgcag gaccaaccac caatcaagac ctctcggaca gccccagctc 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

agacgatcca tcgagatgga aagtccaacg cacccaaaac cctctaaaga taagactctc tcgtggaact tagtgtttct g
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581

Citations:

Lauring A. S., Overbaugh J. (2000) Evidence that an IRES within the Notch2 coding region can direct expression of a nuclear form of the protein. Mol. Cell. 6(4):939-945

The translation experiments:

Translation results:

IRESite Translation Id: 618

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HeLa (ATCC CCL-2)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

29.000

Name of IRES used as the positive control:

PV

Name of the plasmid used as the positive control. `pSV-CAT/polio/LUC`	Name of the plasmid used as the negative control. `pSV-CAT/mutEMCV/LUC`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `13.000`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

Figure 3B.

Citations:

Lauring A. S., Overbaugh J. (2000) Evidence that an IRES within the Notch2 coding region can direct expression of a nuclear form of the protein. Mol. Cell. 6(4):939-945

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