The nucleic acid data:
IRESite Id: 111 Version: 2
Originaly submitted by: Martin Mokrejš Submission date: 2006-01-12 00:00:00
Reviewed by: Martin Mokrejš Last change: 2006-04-28 00:00:00
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:
  Scamper
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
21553346
The mRNA/+RNA description: 
Canis familiaris scamper mRNA, complete cds.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_completely_same_as_in_the_experiment
The organism containing this mRNA with IRES segment in its genome:
Canis familiaris MDCK [NBL-2] (ATCC CCL-34)
A promoter reported in cDNA corresponding to IRES sequence:
  yes
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:
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:
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:
Canis familiaris MDCK [NBL-2] (ATCC CCL-34)
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:
Scamper
The description of the protein encoded in this ORF:
putative intracellular Ca2+ channel sensitive to sphingosylphosphocholine; type I integral membrane protein
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):
  366-698
Remarks:
Promoter confirmed in Scamper 5'-UTR in a promoter-less plasmid. The subsequent experiments used cytosolic
vaccinia virus for production of capped (10% efficiency) and polyadenylated transcripts directly in the
cytoplasm. Integrity of any of the transcripts was not studied. Only monocistronic transcripts were tested in
rabbit reticulocyte lysate.
Citations:
De Pietri Tonelli D., Mihailovich M., Schnurbus R., Pesole G., Grohovaz F., Zacchetti D. (2003) Translational control of Scamper expression via a cell-specific internal ribosome entry site. Nucleic Acids Res. 31(10):2508-2513
IRESs:
IRES:
Version: 4 Last change: 2007-01-12 00:00:00
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  Scamper
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-365
Conclusion:
  putative_IRES
How IRES boundaries were determined:
guessed
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
De Pietri Tonelli D., Mihailovich M., Schnurbus R., Pesole G., Grohovaz F., Zacchetti D. (2003) Translational control of Scamper expression via a cell-specific internal ribosome entry site. Nucleic Acids Res. 31(10):2508-2513
Last change to the database: 2015-04-16 16:45:23 GMT+1