The nucleic acid data:
IRESite Id: 81 Version: 4
Originaly submitted by: Václav Vopálenský Submission date: 2005-10-21 00:00:00
Reviewed by: Václav Vopálenský Last change: 2007-01-24 00:00:00
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  hopefully_full-length_mRNA
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  UNR
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
56117851
Synonyms of the gene name:
Synonym: CSDE1
Synonym: D1S155E
Synonym: DKFZp779B0247
Synonym: DKFZp779J1455
Synonym: RP5-1000E10.3
The mRNA/+RNA description: 
Homo sapiens cold shock domain containing E1, RNA-binding (CSDE1), transcript variant 1, mRNA.

In transcript variant 2 lacks an in-frame exon, compared to variant 1, resulting in a shorter protein (isoform
2) that is missing an internal segment relative to isoform 1.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  unknown
The organism containing this mRNA with IRES segment in its genome:
Homo sapiens
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:
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:
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:
Homo sapiens HEK 293T/17 (ATCC CRL-11268)
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 1 Last change: 2006-01-15 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The abbreviated name of this ORF/gene:
UNR
The description of the protein encoded in this ORF:
upstream of NRAS isoform 1
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):
  467-2863
OPTIONAL: The function of the encoded protein
isoform 1 is encoded by transcript variant 1;
NRAS-related gene; upstream of NRAS;
go_function: DNA binding [goid 0003677] [evidence IEA];
go_function: RNA binding [goid 0003723] [evidence IEA];
go_function: peroxidase activity [goid 0004601] [evidence IEA];
go_process: male gonad development [goid 0008584] [evidence TAS] [pmid 2204029];
go_process: response to oxidative stress [goid 0006979] [evidence IEA];
go_process: regulation of transcription, DNA-dependent [goid 0006355] [evidence IEA]
Remarks:
Presence of a cryptic promoter in human HEK293 cells was ruled out using a cryptic promoter where the
activity observed was 1/15 of the positive control with SV40 promoter (pGL3-basic) and the delta335-355
variant had 1/24 activity of the SV40 based control.
Citations:
Cornelis S., Tinton S. A., Schepens B., Bruynooghe Y., Beyaert R. (2005) UNR translation can be driven by an IRES element that is negatively regulated by polypyrimidine tract binding protein. Nucleic Acids Res. 33(10):3095-3108
IRESs:
IRES:
Version: 2 Last change: 2007-01-24 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The IRES name:
  UNR
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  36-464
Conclusion:
  putative_IRES
How IRES boundaries were determined:
unknown
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
UNR 5' UTR from nt -431 nt to nt -3.
Citations:
Cornelis S., Tinton S. A., Schepens B., Bruynooghe Y., Beyaert R. (2005) UNR translation can be driven by an IRES element that is negatively regulated by polypyrimidine tract binding protein. Nucleic Acids Res. 33(10):3095-3108
RNA:protein interactions:
The RNA:protein interaction:
Version: 2 Last change: 2007-01-24 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The description of the protein interacting with the RNA:
PTB bound to UNR IRES in UV cross-linking experiments
The organism where this RNA:protein interaction occurs:
Homo sapiens HEK 293T/17 (ATCC CRL-11268)
Remarks:
Ultraviolet cross-linking analysis and RNA affinity chromatography revealed the binding of polypyrimidine
tract binding protein (PTB) to the UNR IRES, requiring a pyrimidine-rich region (nucleotides 354-374). Whereas
overexpression of PTB in several cell lines inhibited UNR IRES activity and UNR protein expression, depletion
of endogenous PTB using RNAi increased UNR IRES activity. Moreover, a mutant version of the UNR IRES lacking
the PTB binding site was more efficient at directing IRES-mediated translation.
Citations:
Cornelis S., Tinton S. A., Schepens B., Bruynooghe Y., Beyaert R. (2005) UNR translation can be driven by an IRES element that is negatively regulated by polypyrimidine tract binding protein. Nucleic Acids Res. 33(10):3095-3108
Last change to the database: 2015-04-16 16:45:23 GMT+1