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The nucleic acid data:
IRESite Id: 519 Version: 0
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš
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:
  FGF1 		The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
155573970 
Synonyms of the gene name:
Synonym: AFGF
Synonym: ECGF
Synonym: FGFA
Synonym: ECGFA
Synonym: ECGFB
Synonym: HBGF1
Synonym: GLIO703
Synonym: ECGF-beta
Synonym: FGF-alpha
The mRNA/+RNA description:  
Possibly full-length fibroblast growth factor 1 (acidic) mRNA.
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:
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:
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:
not_tested
Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
no_promoter_confirmed
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:
Mus musculus MEF/3T3 Tet-Off
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:
FGF1A
The description of the protein encoded in this ORF:
fibroblast growth factor 1 (transcript variant A)
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):
  484-951
Citations:
Martineau Y., Le Bec C., Monbrun L., Allo V., Chiu I. M., Danos O., Moine H., Prats H., Prats A. C. (2004) Internal ribosome entry site structural motifs conserved among mammalian fibroblast growth factor 1 alternatively spliced mRNAs. Mol. Cell. Biol. 24(17):7622-7635
IRESs:
IRES:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  FGF1A
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  50-483
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Martineau Y., Le Bec C., Monbrun L., Allo V., Chiu I. M., Danos O., Moine H., Prats H., Prats A. C. (2004) Internal ribosome entry site structural motifs conserved among mammalian fibroblast growth factor 1 alternatively spliced mRNAs. Mol. Cell. Biol. 24(17):7622-7635
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 28
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The function of the 2D structure:
IRES 		The 2D structure causes frameshift:
unknown
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
271-438
The underlying nucleic acid sequence and structure of the mapped region:



Rendering structure of FGF1 mRNA 168 nt long with energy of -54.80 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.
Remarks:
Fig. 7
3.1.1. Enzymes used to characterize at least partially the 2D structure.
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 51
The temperature (in degrees of Celsia):
25 		The enzymatic method used to determine the 2D structure:
ribonuclease T1
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
8.00 		Li+ [mM]
0 		Na+ [mM]
0 		K+ [mM]
0 		Mg2+ [mM]
0 		Ca2+ [mM]
0
Cl- [mM]
0 		Tris [mM]
0 		BSA [mM]
0 		HEPES [mM]
0 		EGTA [mM]
0 		EDTA [mM]
0
cacodylate [mM]
0
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 52
The temperature (in degrees of Celsia):
25 		The enzymatic method used to determine the 2D structure:
ribonuclease T2
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
8.00 		Li+ [mM]
0 		Na+ [mM]
0 		K+ [mM]
0 		Mg2+ [mM]
0 		Ca2+ [mM]
0
Cl- [mM]
0 		Tris [mM]
0 		BSA [mM]
0 		HEPES [mM]
0 		EGTA [mM]
0 		EDTA [mM]
0
cacodylate [mM]
0
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 53
The temperature (in degrees of Celsia):
25 		The enzymatic method used to determine the 2D structure:
ribonuclease V1
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
8.00 		Li+ [mM]
0 		Na+ [mM]
0 		K+ [mM]
0 		Mg2+ [mM]
0 		Ca2+ [mM]
0
Cl- [mM]
0 		Tris [mM]
0 		BSA [mM]
0 		HEPES [mM]
0 		EGTA [mM]
0 		EDTA [mM]
0
cacodylate [mM]
0
3.1.2. Chemicals used to characterize at least partially the 2D structure.
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 24
The temperature (in degrees of Celsia):
25 		The chemical reagent used to determine the 2D structure:
DMS
Chemical reagent used with its respective buffer:
Version: 0
pH
7.50 		Li+ [mM]
0 		Na+ [mM]
0 		K+ [mM]
50.00 		Mg2+ [mM]
2.50 		Ca2+ [mM]
0
Cl- [mM]
55.00 		Tris [mM]
0 		BSA [mM]
0 		HEPES [mM]
10.00 		EGTA [mM]
0 		EDTA [mM]
0
cacodylate [mM]
0
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 25
The temperature (in degrees of Celsia):
25 		The chemical reagent used to determine the 2D structure:
CMCT
Chemical reagent used with its respective buffer:
Version: 0
pH
8.00 		Li+ [mM]
0 		Na+ [mM]
50.00 		K+ [mM]
50.00 		Mg2+ [mM]
0 		Ca2+ [mM]
0
Cl- [mM]
55.00 		Tris [mM]
0 		BSA [mM]
0 		HEPES [mM]
0 		EGTA [mM]
0 		EDTA [mM]
0
cacodylate [mM]
0
Other buffer components and their relative concentrations:
50 mM borate (-)
Citations:
Martineau Y., Le Bec C., Monbrun L., Allo V., Chiu I. M., Danos O., Moine H., Prats H., Prats A. C. (2004) Internal ribosome entry site structural motifs conserved among mammalian fibroblast growth factor 1 alternatively spliced mRNAs. Mol. Cell. Biol. 24(17):7622-7635
Last change to the database: 2019-03-18 09:32:49 GMT+1