The nucleic acid data:
IRESite Id: 438 Version: 1
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2008-06-26 12:56:09
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  our_best_guess
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  Cat-1
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
33943114 
Synonyms of the gene name:
Synonym: Cat1
The mRNA/+RNA description: 
Rattus norvegicus cationic amino acid transporter-1 (Cat1) gene, merged from GI:18542255 and GI:33943114.
The mRNA/+RNA sequence represented in the +DNA notation:


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:
Rattus norvegicus Wistar
A promoter reported in cDNA corresponding to IRES sequence:
  no (not convincing)
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:
homogeneous_population_of_molecules_confirmed
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:
not_tested
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:
Rattus norvegicus C6
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 1 Last change: 2008-06-26 12:56:09
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
Cat-1
The description of the protein encoded in this ORF:
cationic amino acid transporter 1 (arginine/lysine)
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):
  271-2145
Remarks:
The first 60bp have been added in front of GI:33943114 from GI:18542255. The leftmost 45 nt were not
determined by authors by 5'-RACE as shown in Fernandez et al. (2001), Figure 1A. Additional primer-extension
studies were published in Fernandez et al. (2003) in Figure 2A and have identified transcription start site
'G' residues -254 and -260 nt upstream of initiator ATG. The mRNA sequence used here in IRESite is the one
defined by S1 nuclease protection as shown in Fernandez et al. (2003) in Figure 2B,D (black arrow) and is
longer by 10 or 16 nt then the transcripts mapped by primer-extension (gray arrows).
Citations:
Fernandez J., Yaman I., Mishra R., Merrick W. C., Snider M. D., Lamers W. H., Hatzoglou M. (2001) Internal ribosome entry site-mediated translation of a mammalian mRNA is regulated by amino acid availability. J. Biol. Chem. 276(15):12285-12291
Fernandez J., Yaman I., Merrick W. C., Koromilas A., Wek R. C., Sood R., Hensold J., Hatzoglou M. (2002) Regulation of internal ribosome entry site-mediated translation by eukaryotic initiation factor-2alpha phosphorylation and translation of a small upstream open reading frame. J. Biol. Chem. 277(3):2050-2058
Fernandez J., Lopez A. B., Wang C., Mishra R., Zhou L., Yaman I., Snider M. D., Hatzoglou M. (2003) Transcriptional control of the arginine/lysine transporter, cat-1, by physiological stress. J. Biol. Chem. 278(50):50000-50009
Finley K. D., Kakuda D. K., Barrieux A., Kleeman J., Huynh P. D., MacLeod C. L. (1995) A mammalian arginine/lysine transporter uses multiple promoters. Proc. Natl. Acad. Sci. U. S. A. 92(20):9378-9382
IRESs:
IRES:
Version: 1 Last change: 2008-06-26 12:56:09
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  Cat-1_224
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  47-270
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
IRES coordinates located from GI:18542255.
Citations:
Fernandez J., Yaman I., Mishra R., Merrick W. C., Snider M. D., Lamers W. H., Hatzoglou M. (2001) Internal ribosome entry site-mediated translation of a mammalian mRNA is regulated by amino acid availability. J. Biol. Chem. 276(15):12285-12291
Fernandez J., Yaman I., Merrick W. C., Koromilas A., Wek R. C., Sood R., Hensold J., Hatzoglou M. (2002) Regulation of internal ribosome entry site-mediated translation by eukaryotic initiation factor-2alpha phosphorylation and translation of a small upstream open reading frame. J. Biol. Chem. 277(3):2050-2058
Fernandez J., Lopez A. B., Wang C., Mishra R., Zhou L., Yaman I., Snider M. D., Hatzoglou M. (2003) Transcriptional control of the arginine/lysine transporter, cat-1, by physiological stress. J. Biol. Chem. 278(50):50000-50009
Lopez A. B., Wang C., Huang C. C., Yaman I., Li Y., Chakravarty K., Johnson P. F., Chiang C. M., Snider M. D., Wek R. C., Hatzoglou M. (2007) A feedback transcriptional mechanism controls the level of the arginine/lysine transporter cat-1 during amino acid starvation. Biochem. J. 402(1):163-173
IRES trans-acting factor (ITAFS):
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
OPTIONAL: The interacting RNA base range (if any):
107-112
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
PTB
ITAF fullname:
polypyrimidine-tract binding protein (unspecified isoform)
ITAF description (long):
polypyrimidine-tract binding protein
3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vivo
The organism where action of this ITAF was studied:
Rattus norvegicus C6
Remarks:
Predicted secondary structure and the binding regions were shown in Figure 3A.
Citations:
Majumder M, Yaman I, Gaccioli F, Zeenko VV, Wang C, Caprara MG, Venema RC, Komar AA, Snider MD, Hatzoglou M (2009) The hnRNA-binding proteins hnRNP L and PTB are required for efficient translation of the Cat-1 arginine/lysine transporter mRNA during amino acid starvation. Mol. Cell. Biol. 29(10):2899-2912
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
OPTIONAL: The interacting RNA base range (if any):
127-137
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
hnRNP_L
ITAF fullname:
heterogeneous ribonucleoprotein L
ITAF description (long):
heterogeneous ribonucleoprotein L (68 kDa)
3.2.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vivo
The organism where action of this ITAF was studied:
Rattus norvegicus C6
Remarks:
Predicted secondary structure and the binding regions were shown in Figure 3A.
Citations:
Majumder M, Yaman I, Gaccioli F, Zeenko VV, Wang C, Caprara MG, Venema RC, Komar AA, Snider MD, Hatzoglou M (2009) The hnRNA-binding proteins hnRNP L and PTB are required for efficient translation of the Cat-1 arginine/lysine transporter mRNA during amino acid starvation. Mol. Cell. Biol. 29(10):2899-2912
Last change to the database: 2015-04-16 16:45:23 GMT+1