The nucleic acid data:
IRESite Id: 52 Version: 8
Originaly submitted by: Václav Vopálenský Submission date: 2005-08-18 00:00:00
Reviewed by: Václav Vopálenský Last change: 2008-07-01 11:57:24
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:
  our_best_guess
The mRNA/+RNA description: 
Putative spliced bicistronic mRNA derived from pSL based plasmid with part of the 5' UTR (nt 1089 to nt 1152)
of human myelin transcription factor 2 (MYT2) mRNA cloned between chloramphenicol acetyltransferase and
firefly luciferase.
The mRNA/+RNA sequence represented in the +DNA notation:


Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)
Credibility of mRNA sequence:
  guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail
The name of the plasmid:
pSL50
The name of the promoter used to express this mRNA:
  CMV
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:
MYT2
The origin of IRES in the plasmid:
  nuclear
The donor organism of the IRES segment:
Homo sapiens
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:


GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:
pSL50.jpg
The total number of notable open-reading frames (ORFs):
  2
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The abbreviated name of this ORF/gene:
CAT
The description of the protein encoded in this ORF:
chloramphenicol acetyltransferase
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):
  71-730
ORF
ORF position:   2
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The abbreviated name of this ORF/gene:
FFluc
The description of the protein encoded in this ORF:
firefly luciferase
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):
  885-2537
Citations:
Kim J. G., Armstrong R. C., Berndt J. A., Kim N. W., Hudson L. D. (1998) A secreted DNA-binding protein that is translated through an internal ribosome entry site (IRES) and distributed in a discrete pattern in the central nervous system. Mol. Cell. Neurosci. 12(3):119-140
IRESs:
IRES:
Version: 2 Last change: 2006-07-25 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The IRES name:
  MYT2_1089-1152
The functional status of IRES:
  defective
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  762-874
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  32
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  144
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -123
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -11
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Fragment nt 1089 to nt 1152 of 5' UTR of human myelin transcription factor 2 (MYT2) mRNA.
Citations:
Kim J. G., Armstrong R. C., Berndt J. A., Kim N. W., Hudson L. D. (1998) A secreted DNA-binding protein that is translated through an internal ribosome entry site (IRES) and distributed in a discrete pattern in the central nervous system. Mol. Cell. Neurosci. 12(3):119-140
The translation experiments:
Translation results:
IRESite Translation Id: 51
Version: 4 Last change: 2006-07-25 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
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:
  41.000
Name of IRES used as the positive control:
  BiP
Name of the plasmid used as the positive control.
pcBIP
Name of the plasmid used as the negative control.
pCAT/LUC
IRESite Id of the plasmid used as negative control.
  218
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  25.000
The size (length) of intercistronic region in the positive control:
264
The size (length) of intercistronic region in the negative control:
76
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:
The pcBIP plasmid is currently not available. It is also not clear whether the pCAT/LUC plasmid used as
negative control was the one with 76b long intercistronic region or whether the plasmid was pCAT/LUC with 17nt
long hairpin structure. However, authors mention luciferase activities in SVG and HeLa cells was same.
Citations:
Kim J. G., Armstrong R. C., Berndt J. A., Kim N. W., Hudson L. D. (1998) A secreted DNA-binding protein that is translated through an internal ribosome entry site (IRES) and distributed in a discrete pattern in the central nervous system. Mol. Cell. Neurosci. 12(3):119-140
Translation results:
IRESite Translation Id: 52
Version: 4 Last change: 2006-07-25 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens SVG
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  14.000
Name of IRES used as the positive control:
  BiP
Name of the plasmid used as the positive control.
pcBIP
Name of the plasmid used as the negative control.
pCAT/LUC
IRESite Id of the plasmid used as negative control.
  218
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  25.000
The size (length) of intercistronic region in the positive control:
264
The size (length) of intercistronic region in the negative control:
76
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:
The pcBIP plasmid is currently not available. It is also not clear whether the pCAT/LUC plasmid used as
negative control was the one with 76b long intercistronic region or whether the plasmid was pCAT/LUC with 17nt
long hairpin structure. However, authors mention luciferase activities in SVG and HeLa cells was same.
Citations:
Kim J. G., Armstrong R. C., Berndt J. A., Kim N. W., Hudson L. D. (1998) A secreted DNA-binding protein that is translated through an internal ribosome entry site (IRES) and distributed in a discrete pattern in the central nervous system. Mol. Cell. Neurosci. 12(3):119-140
Last change to the database: 2015-04-16 16:45:23 GMT+1