IRESite_Id:204 summary record describing characteristics of Gtx-133-141 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `204`	Version: `2`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2007-07-24 00:00:00`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `3UTR_possibly_incomplete`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `Gtx`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
193715

The mRNA/+RNA description:

Mus musculus Gtx mRNA sequence.

The mRNA/+RNA sequence represented in the +DNA notation:

CCGCCGCCCA TTCAGCGCAA CAGCCGTCGG TCCTCTCGCT TTCCCGTAGG GGCCGTCGGC GTTCGTTTGA AACGCGGTCC ACCCGTCCCA GCGTAGCCGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGCTCTTCGG CGCCGCGCGC AAACTTCCCG AGCCGGCGGG TGCGGGCGGT GGCAGCGGGG CCCGGATGGG CGCCCGGGTC GGAGGCGGCG GCGCCCATGG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ACGCTAACCG CCCGGGTGCG TTTGTGCTGA GCAGCGCGCC TTTAGCCGCG CTGCACAACA TGGCTGAGAT GAAGACGTCG CTGTTCCCCT ACGCGCTGCA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GGGCCCGGCG GGCTTCAAGA CACCCGCCCT AGGCAGCCTT GGCGCGCAGT TGCCTCTAGG CACTCCGCAC GGCATCAGCG ACATCCTGGG ACGGCCGGTG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GGCGCAGCGG GTGGCGGCCT CCTAGGAAGT CTGCCCCGTC TCAACGGGCT CGCCTCGTCT GCAGGTGTCT ACTTCGGGCC CGCAGCCGCC GTGGCTCGGG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GCTACCCCAA GCCGCTGGCG GAACTGCCTG GGCGCCCGCC CATCTTCTGG CCTGGGGTGG TGCAGGGCTC TCCCTGGAGG GACCCGCGAC TGGCCGGCTC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CGCCCAAGCC GGCGGGGTCC TGGATAAGGA TGGCAAGAAG AAACACTCGC GGCCGACTTT CTCCGGCCAG CAGATCTTCG CGCTGGAGAA GACTTTCGAG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CAGACCAAGT ATTTGGCAGG CCCAGAGCGC GCGCGGCTTG CCTACTCTCT GGGCATGACC GAGAGCCAAG TGAAGGTGTG GTTCCAGAAT CGGCGGACCA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AGTGGCGCAA GCGGCACGCG GCAGAGATGG CGTCGGCTAA AAAGAAGCAA GACTCGGATG CCGAGAAGCT GAAGGTGGGT GGCTCAGACG CGGAGGACGA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGACGAATAC AACCGGCCCC TGGACCCCAA CTCCGATGAC GAGAAGATCA CGCGGCTTCT CAAAAAGCAC AAACCCTCGA ACTTGGCGCT CGTTAGCCCG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGTGGTGGCA GCGCGGGGGA CGCCTTGTGA GGATGCGGCC AGGCCGGAGA ACCCGAGAAC CGGGACTCGC GGCATGCCCC GACGCCAGCC GCCCAGCCGC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AGTGTGTATA TATATTTTTA CAGAATAAGT TATAAAGCGG ACGTTGGCGC GGCCTTGGCG TGATGGCGGA GTACGGGGTT TGGGCCGATC ACTTTGTATA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ATCAATAAAT TATTTAACAC GTCCTCGTCG GAGCCGTGGC TCCC
^1201      ^1211      ^1221      ^1231      ^1241

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:

Mus musculus

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:

Cricetulus griseus CHO-K1 (ATCC CCL-61)

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:
Gtx

The description of the protein encoded in this ORF:
Gtx 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):

197-1030

Remarks:

Promoter activity was confirmed by Hartenbach and Fusseneger (2006). However, they claim IRES activity could
still be observed by direct transfection of uncapped in vitro transcribed RNA into Chinese hamster
ovary cells.

Citations:

Chappell S. A., Edelman G. M., Mauro V. P. (2000) A 9-nt segment of a cellular mRNA can function as an internal ribosome entry site (IRES) and when present in linked multiple copies greatly enhances IRES activity. Proc. Natl. Acad. Sci. U. S. A. 97(4):1536-1541

Hartenbach S., Fussenegger M. (2006) A novel synthetic mammalian promoter derived from an internal ribosome entry site. Biotechnol. Bioeng. 95(4):547-559

IRESs:

IRES:

Version: `2`	Last change: `2007-01-11 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `Gtx-133-141`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

133-141

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

The sequence of IRES region aligned to its secondary structure (if available):

CCGGCGGGT
^133

Remarks:

Synergistic effect was observed when multiple copies of this 9-nt segments were placed besides each other
spaced by beta-globin ORF sequence fragments.

Citations:

IRES:

Version: `1`	Last change: `2007-01-11 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `Gtx-1-166`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

1-166

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

The sequence of IRES region aligned to its secondary structure (if available):

CCGCCGCCCA TTCAGCGCAA CAGCCGTCGG TCCTCTCGCT TTCCCGTAGG GGCCGTCGGC GTTCGTTTGA AACGCGGTCC ACCCGTCCCA GCGTAGCCGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGCTCTTCGG CGCCGCGCGC AAACTTCCCG AGCCGGCGGG TGCGGGCGGT GGCAGCGGGG CCCGGA
^101       ^111       ^121       ^131       ^141       ^151       ^161

Citations:

IRES:

Version: `1`	Last change: `2007-01-11 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `Gtx-1-120`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

1-120

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

The sequence of IRES region aligned to its secondary structure (if available):

CCGCCGCCCA TTCAGCGCAA CAGCCGTCGG TCCTCTCGCT TTCCCGTAGG GGCCGTCGGC GTTCGTTTGA AACGCGGTCC ACCCGTCCCA GCGTAGCCGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGCTCTTCGG CGCCGCGCGC
^101       ^111

Citations:

IRES:

Version: `1`	Last change: `2007-01-11 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `Gtx-1-196`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

1-196

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

The sequence of IRES region aligned to its secondary structure (if available):

CCGCCGCCCA TTCAGCGCAA CAGCCGTCGG TCCTCTCGCT TTCCCGTAGG GGCCGTCGGC GTTCGTTTGA AACGCGGTCC ACCCGTCCCA GCGTAGCCGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGCTCTTCGG CGCCGCGCGC AAACTTCCCG AGCCGGCGGG TGCGGGCGGT GGCAGCGGGG CCCGGATGGG CGCCCGGGTC GGAGGCGGCG GCGCCC
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191

Citations:

Last change to the database: 2019-03-18 09:32:49 GMT+1