IRESite_Id:51 summary record describing characteristics of MNT

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `51`	Version: `10`
Originaly submitted by: Václav Vopálenský	Submission date: `2005-09-21 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2009-09-01 16:59:18`

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: `MNT`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
58530884

Synonyms of the gene name:

Synonym: ROX

Synonym: MAD6

Synonym: MXD6

The mRNA/+RNA description:

Homo sapiens MAX binding protein (MNT), mRNA. Poly(A) sequence dropped.

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

GCAGTGCCGC CTTTTTTTTT TTTTTGCATC CCATTTTTTT AAATTTGCAA TTTTATATTT TGCAAATATT TTGAGAGACA TTGATTTTTC TCCCCGTGCT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCCCCGTTCT TCCCTGCGGA GTGCGCTGCG CCGCCCAGCC CTGTCGCCCC CCGGAGGTGA TCCCTCCCTC CTGCCTGCCC GCCAGCCTGA CCTGTGCCCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCTCGCGGGC CGCAGCCTCG GCCCCGGCGC GCCCCCGGCA GCTCTCGGCG CGATGAGCAT AGAGACGCTA CTGGAGGCGG CCCGCTTCCT GGAATGGCAA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GCGCAGCAAC AACAGAGAGC ACGTGAGGAG CAGGAGCGGC TTCGCTTGGA GCAGGAGCGA GAGCAGGAAC AGAAGAAGGC CAATAGCCTG GCCAGGCTGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CACATACCCT TCCTGTGGAG GAACCCCGCA TGGAGGCGCC ACCCCTGCCT CTGTCTCCAC CGGCTCCCCC GCCGGCACCC CCACCACCAC TTGCCACCCC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TGCCCCACTG ACTGTCATCC CTATCCCTGT GGTGACCAAC TCCCCTCAGC CTCTACCCCC ACCCCCACCC TTGCCCGCGG CAGCCCAGCC TCTGCCCCTG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GCGCCTCGTC AGCCGGCCCT GGTTGGCGCC CCCGGACTCA GCATTAAGGA GCCTGCCCCC CTGCCCAGCA GGCCGCAGGT GCCCACCCCT GCTCCCCTAC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGCCGGACTC GAAGGCCACC ATTCCACCCA ATGGCAGCCC CAAGCCTTTG CAGCCCCTCC CCACGCCTGT CCTGACCATA GCGCCACACC CTGGAGTCCA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GCCTCAGCTG GCCCCCCAGC AGCCGCCCCC ACCCACGCTG GGGACCCTGA AGTTGGCACC AGCTGAAGAA GTCAAATCCA GTGAACAGAA GAAGAGGCCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GGGGGGATCG GAACCAGAGA AGTCCACAAC AAATTGGAGA AGAACAGGAG GGCCCATCTG AAAGAGTGCT TTGAGACCCT GAAGCGGAAC ATCCCCAACG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGGATGACAA GAAGACGTCC AATCTGAGCG TGCTGCGGAC GGCGCTGCGG TACATCCAGT CCCTGAAGAG GAAGGAGAAG GAATATGAGC ATGAAATGGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GCGGCTGGCA CGTGAGAAGA TTGCCACGCA GCAGCGGCTG GCAGAGCTCA AGCACGAGCT GAGCCAGTGG ATGGACGTAC TGGAGATTGA CCGCGTGCTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CGGCAGACGG GCCAGCCCGA GGATGACCAG GCCTCCACCT CCACCGCCTC TGAGGGTGAG GACAACATAG ACGAGGATAT GGAGGAGGAC CGGGCGGGCC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TGGGCCCACC TAAGCTGAGC CATCGTCCCC AGCCGGAGCT GCTGAAGTCC ACCCTGCCAC CCCCCAGCAC CACCCCTGCG CCTCTGCCTC CACACCCACA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CCCTCACCCC CACTCCGTGG CCCTACCTCC TGCCCACCTC CCCGTGCAGC AGCAGCAGCC ACAGCAGAAG ACCCCTCTGC CAGCCCCTCC TCCCCCACCG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GCTGCCCCTG CCCAGACACT GGTGCCAGCT CCAGCCCATC TGGTGGCGAC GGCTGGGGGT GGCTCCACGG TCATCGCCCA CACAGCCACC ACTCACGCTT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CAGTCATCCA GACTGTGAAC CACGTTCTGC AGGGGCCAGG CGGCAAGCAC ATCGCCCACA TCGCCCCCTC GGCCCCCAGC CCTGCGGTGC AACTGGCGCC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGCCACACCC CCCATTGGGC ACATCACTGT GCACCCTGCC ACCCTCAACC ATGTGGCCCA CCTGGGCTCC CAGCTGCCCT TGTACCCGCA GCCCGTGGCA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTGAGCCACA TCGCCCACAC CCTCTCGCAC CAGCAAGTCA ACGGCACGGC CGGCCTGGGG CCCCCGGCTA CTGTCATGGC AAAGCCGGCC GTGGGGGCTC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGGTGGTGCA CCACCCCCAG CTGGTGGGCC AGACCGTGCT CAACCCTGTG ACCATGGTCA CCATGCCCTC CTTCCCAGTC AGCACACTCA AGCTGGCTTG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGGACGAGGC CACTCAGAGG CCCCCAGTGG GGACAGGGAG GGGGACCTGT CCCCCACTCT CTCACCCACC AGCTCCACAC ATTCCAGCCA GGCCCAGGCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AGCCCCCCCA CCCACCCCCA GGCCTCCTAG GGGAAGGGGG TGCAAAGACT CTGAGCCAAG GGAGGGAAGG GCCACCCTGC TGCACTAGGA CTTGGTAAGA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGACTCTGAG AAAATGCGAG ACTCTGATGG AATGTGCCAC CTGTCCGGCC CAGTGCCAGC TCCAGTGCCG CTCCTGCTTC CCCTCCCTAC CCTCGGAAAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CAGTGCGATG TGGACGTCAC GCTCCCTGAC TTCTCCCCCG CCCTGCCCCG CCTTCGTGTG CTGCTGCTGC TATTGCTGTC TGGTGAGGTG GCCCAGGCCC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCGGCTTTCC TCCGGAGCCT CATGTTCTCT TCCCAGGCCT TTGGAGGGGA AATGGGGAAA GCAGAACTGA AGCCACTTGG CCCAGAAAGC TGCGGATTGG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GGTGATAAGG GGCCTTGCTC TGAGCACAGG TGACAGATCA TAGGAAGTGG CTGGTCTGGA GTCCCACCCG GACAGGTGGG GCCTCAGCCT GGGGCTCTCT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GACCCGGTTG CAGTCACTGT GATTCGTTAC CGTAGATACT ACTTAAAATG ATTCTCTACC AACAATAAAC CAAACCCAGC CACTGCCAAG CTTCCTGTGC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CCTCACCCCA ATCCCTGCCA CTGGGCTCTG GACCTCAGGA GGGCAGGCTG AGGTGGGGAA GGAGGGACTT GGCTGTCCTT CCCCTTCCCC GTCCCCTGCA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GCCTGGGTCT GGATGGGAGG AGAGCCACTG GGCCCCTGTC CCCAGTCCCC AGTCCCCAGC CCTGGGCTTG GCTCTTGGCT TCCAGAAGGC AGCAAAGAGG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGCGCTGTCC TGCGTTCAGC CCCTGATCTC TGACCTCTGC TGAGTGCTGG GCACTGCTCC AAGGGACAGG TGGGCCTGGC GGCCTGTGGG TTTGGGTGCC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TCCTGCAGTT TGGGAGACAT GGACCAGCAT CTGGTCTTGT TTCCAGGAGC ATAGAAGCCA CATCGTTGAG ACATCAGGAA GGTAAAAACC CAGCGGCTTA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GCCAAGCCCT AAGCCTGTCC CCAGACCAAC CCTGGGACCT ATACAGAACA GAGGGCCAGA GCTAGGGCTG CTGCTTCTGC TCCAGCCCCT TTGCCTCTGT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CCTCCCATCC CCTCAACACC CTGCTTCTCC CGGGGACGCT TTTGAGTGGG CCCTGCCCGG GGAGCTGCAG AGCAGCAGCA CCTTTCTCTG AGAAGAGGTC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CTTGGTTGGG TCAAGGACAG GGCTGAGCGT GGAAGGGGGA GGAGTCAGGG GCTCTGTGTT AGGATGCGGC TTTCTCTGCC TCTGGGCAGC CTGCTTTGGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CTTTCCTTGT ATGTGGGTGT TTATTACAAG TGGCTTTGTG TCAGACACGC TCGGCTCCCC ACCTGGACAC ACACTCACCA GTGGCCTTTC AGTGTAGCGG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GAGGAAGCCG GTGTCCCTGG ATGTGAAGCT CACACTGATG GGCTGGGGCA GGGGCCTGGG CCGGCGAGGG GGCCGGGGGG AGGGGACAGA GCTGAGGATT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TCCTGGAGTG CCCTGCAGGC ACAGAGGAGG TCAGCAAAGG TCTTGAATAG ATTTTCTCTG GAAATAAAGA ATCCTTAGAT GCCTAAAAAT TCCCTTCCTG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TTCCCTCCTG GTCCTGGACA CCTCCCAGGG GACTGTTCCT TATTTCTCTC TCCTGGTGTG GGTAAAGGGA CAGTTACAAA CCAGGTCACC ATCCTCAGAG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GCTGAGCCCT GTACCCACCC CAGCACAGCC ACCTCCGCCA GACCCCGTGG CTCTGGGAGA GCCAGCTTTG CTATTCCCAT TGTGACAGCG ATGGCAGGCC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TGACCCACGG GGCAGTTAGA GCAGCCTCGT GGAGCTCGCC CCTCCCCTCA GCCTGCCCAC CTCTCCCTGC ATCCTGAGGC CAGTGGCCCC CGGGCCTGCA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CAGATACCTC ATCATCCACC CGCTGCCCCT CCCCGTCCCT GTCCCCCAGC ATCGGGGGCC TGCAAATCTA GTGCCGAATG ACTATGTCCA GATTGGTGAC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GATGGGTGTT GCTGTTTTTC TTGTCGTTTG TGAACGCTGT GATGCTGTGT GCCCAAGTGG GCAGTCACCA CCCAGCCCTT CCTTGGGCGT CTCCCCCAGA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GTGCTGTCGG GACCACATCT GTCCTCACCC TGTGGGACCG CCTGGCCCTC CCTCCCTAGC CCTTCCAGCC TGGGACACAC ACACACACAC ACACACACAC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ACACGCACGC ACACGCACAC ATCTTACCTC TCATGCGTGT TTTACCTTTT GATGTTCAGA GTGGCTCACT GGCTGGGAGT CCTTACCTCG GGGAGAGGGG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GAGGTTGGTT CCTTGGGGGG CCAAAGAAGG CAGGGAATGC CTGGAGGGTA ACTGGGGGGC CACCATGACC CCTTCTCTCT CCAGAAACAG CTGCTTCTCC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CCCCATCCCA GGGTCCCACC CCCAACCCCC AGAGGTGGCC CTTGTTTACA GTGAGGACTC GGCCACTGTG TCTCTGTTTC CTGAAATATA AACTGTAGCG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ACCCCAGACT GTAGAGATTT TTATGTGTTT GGATACATCT GCTGTGTGGA AAAAAAAAAA AACTACAAAA ACCCTAATTT TGTACATACT GTATTTTTAC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TATTGAACTG TATTCTAGTG GCTGTTCATG CTCCAAGACT TTAGTTACCG AGACATGAAT ACTATCCATG TAATAAGCAC TTGCCTGGAA TAAAATATAA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AACTGAAATA AACCTGCACT GAAACCTGAG ATGGAGCTGC C
^4801      ^4811      ^4821      ^4831      ^4841

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

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:
homogeneous_population_of_molecules_confirmed

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 HeLa (ATCC CCL-2)

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `2`	Last change: `2008-07-09 19:14:48`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
MNT

The description of the protein encoded in this ORF:
MAX binding 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:

no

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

253-2001

Remarks:

Promoter of the MNT gene is approx. -200 bases from the translations start. The region -180/+1 was tested in a
promoter-less construct and was without promoter activity. The region to -400 bases from the translations
start had about 5/27 activity of the SV40 promoter. Transcript integrity was verified by RNase-protection
assay. [Stoneley et al. (2001)]

According to very few human mRNAs available in GenBank this sequence (NM_020310.2) protrudes at the 5'-end by
40bp (compared to mRNA entry X96401 which could have been an incomplete RT-PCR product, of course). Hits to
mRNAs of other mammals seem to confirm that this RefSeq sequence is rather correct.

Possibility of cryptic promoter presence was excluded by the use of a promoter-less plasmid (Figure 3D).
Possibility of aberrantly spliced products was only studied by Northern blot (Figure 3C).
[Mitchell et al. (2005)]

The sequence shown in Mitchell et al. (2005) in Figure 5B(ii) as 5'-UTR is shorter by 52 bp on the left to our
belief. The sequence used in IRESite (NM_020310.2) is matching with some short insertions full-length cDNA
sequence from H-INV database HIT000324941.7 but in overall it seems to be quite OK. In contrast, a GenBank
record AK291596 seems to be different splice variant with extended 5'-UTR.

Citations:

Stoneley M., Spencer J. P., Wright S. C. (2001) An internal ribosome entry segment in the 5' untranslated region of the mnt gene. Oncogene. 20(7):893-897

IRESs:

IRES:

Version: `6`	Last change: `2008-07-11 16:53:53`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `MNT_75-267`

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

75-267

Conclusion:
weakly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

GAGACATTGA TTTTTCTCCC CGTGCTCCCC CGTTCTTCCC TGCGGAGTGC GCTGCGCCGC CCAGCCCTGT CGCCCCCCGG AGGTGATCCC TCCCTCCTGC 
^75        ^85        ^95        ^105       ^115       ^125       ^135       ^145       ^155       ^165       

CTGCCCGCCA GCCTGACCTG TGCCCGGCTC GCGGGCCGCA GCCTCGGCCC CGGCGCGCCC CCGGCAGCTC TCGGCGCGAT GAGCATAGAG ACG
^175       ^185       ^195       ^205       ^215       ^225       ^235       ^245       ^255       ^265

Remarks:

part of 5' UTR (178 nts) and 15 nts from ORF. The Mnt IRES appears slightly weaker than c-myc IRES in vivo.

Citations:

Stoneley M., Spencer J. P., Wright S. C. (2001) An internal ribosome entry segment in the 5' untranslated region of the mnt gene. Oncogene. 20(7):893-897

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `MNT_36-160`

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

36-160

Conclusion:
weakly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

TTTTTAAATT TGCAATTTTA TATTTTGCAA ATATTTTGAG AGACATTGAT TTTTCTCCCC GTGCTCCCCC GTTCTTCCCT GCGGAGTGCG CTGCGCCGCC 
^36        ^46        ^56        ^66        ^76        ^86        ^96        ^106       ^116       ^126       

CAGCCCTGTC GCCCCCCGGA GGTGA
^136       ^146       ^156

Remarks:

This regions was found to be the minimal but functional IRES region spanning the many PTB-binding sites.
Data shown in Figure 6, middle column.

Citations:

Mitchell S. A., Spriggs K. A., Bushell M., Evans J. R., Stoneley M., Le Quesne J. P., Spriggs R. V., Willis A. E. (2005) Identification of a motif that mediates polypyrimidine tract-binding protein-dependent internal ribosome entry. Genes Dev. 19(13):1556-1571

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

Version: `3`	Last change: `2008-07-11 23:38:46`
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):
102-136

ITAF protein characteristics:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský

ITAF abbreviated name:
PTB-1

ITAF fullname:
polypyrimidine tract-binding protein isoform 1

ITAF description (long):
polypyrimidine tract-binding protein isoform 1 binds dsRNA with (CCU)n motif where n is at least 3. By SELEX approach it was found it binds to 5'-CAGCCUGGUGCCUCUCUUUCGG-3' (Singh et al. (1995) Science 268:1173-1176) but also UCUU or UCUUC within pyrimidine-rich sequence (Perez et al. (1997) RNA3:1334-1347).

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:

Homo sapiens HeLa (ATCC CCL-2)

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_and_must_be_supplemented

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figures 3 (in vivo) and 4C,D (in vitro). The binding region and unaffected structure due to the
binding was shown in Figure 6D(ii) and Supplementary material C.

Citations:

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):
102-136

ITAF protein characteristics:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
PTB-2

ITAF fullname:
polypyrimidine tract-binding protein isoform 2

ITAF description (long):
polypyrimidine tract-binding protein isoform 2 binds (CCU)n motif

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_and_must_be_supplemented

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figures 4C,D (in vitro).

Citations:

IRES trans-acting factor (ITAF):

Version: `1`	Last change: `2008-07-12 15:14:06`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Type of the interaction between ITAF and the RNA subject to translation:
no_direct_interaction_with_rna

ITAF protein characteristics:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
PTB-4

ITAF fullname:
polypyrimidine tract-binding protein isoform 4

ITAF description (long):
polypyrimidine tract-binding protein isoform 4 binds (CCU)n motif

3.3.2. 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:
no_effect_on_translation

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figures 4C,D (in vitro) show very weak interaction with PTB-4.

Citations:

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):
102-136

ITAF protein characteristics:

Version: `1`	Last change: `2008-07-11 23:17:15`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
nPTB

ITAF fullname:
polypyrimidine tract-binding protein isoform n

ITAF description (long):
neuronal polypyrimidine tract-binding protein isoform binds (CCU)n motif

3.4.2. 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:
no_effect_on_translation

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figures 4C,D (in vitro).

Citations:

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:
no_direct_interaction_with_rna

ITAF protein characteristics:

Version: `2`	Last change: `2009-08-29 12:19:15`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
La

ITAF fullname:
La autoantigen

ITAF description (long):
La autoantigen (p52), 52 kDa RNA binding protein, predominantly localized to nucleus, unwinds the dsRNA in ATP-dependent manner, forms a dimer

3.5.2. 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:
no_effect_on_translation

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figures 4C,D (in vitro).

Citations:

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:
no_direct_interaction_with_rna

ITAF protein characteristics:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
p97/DAP5/NAT1

ITAF fullname:
p97/DAP5/NAT1

ITAF description (long):
p97/DAP5/NAT1 cleavage product p86 oe eIF4G, 86 kDa, RNA binding protein

3.6.2. 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:
no_effect_on_translation

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figures 4C,D (in vitro).

Citations:

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:
no_direct_interaction_with_rna

ITAF protein characteristics:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
ITAF45

ITAF fullname:
ITAF45 (murine proliferation-associated protein, Mpp1)

ITAF description (long):
proliferation-dependent protein that is not expressed in murine brain cells, its human homolog is called PAG24

3.7.2. 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:
no_effect_on_translation

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figures 4C,D (in vitro).

Citations:

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 16

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):
53-255

The underlying nucleic acid sequence and structure of the mapped region:

TTATATTTTG CAAATATTTT GAGAGACATT GATTTTTCTC CCCGTGCTCC CCCGTTCTTC CCTGCGGAGT GCGCTGCGCC GCCCAGCCCT GTCGCCCCCC 
.......... .......... ((((((.... ....)))))) .(((.((((( .((((..... ...)))).(( ((((((.((( (......... ((((((.... 
^53        ^63        ^73        ^83        ^93        ^103       ^113       ^123       ^133       ^143       

GGAGGTGATC CCTCCCTCCT GCCTGCCCGC CAGCCTGACC TGTGCCCGGC TCGCGGGCCG CAGCCTCGGC CCCGGCGCGC CCCCGGCAGC TCTCGGCGCG 
...)))))). ........(( ((..(((((( (((((..... .......))) )))))))).) )))...)))) ..)))))))) ....)).))) ...))).... 
^153       ^163       ^173       ^183       ^193       ^203       ^213       ^223       ^233       ^243       

ATG
...
^253

There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:

WARNING: bases 131 and 152 (CC) can't pair!

STDOUT was:

UUAUAUUUUGCAAAUAUUUUGAGAGACAUUGAUUUUUCUCCCCGUGCUCCCCCGUUCUUCCCUGCGGAGUGCGCUGCGCCGCCCAGCCCUGUCGCCCCCCGGAGGUGAUCCCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGGCUCGCGGGCCGCAGCCUCGGCCCCGGCGCGCCCCCGGCAGCUCUCGGCGCGAUG
....................((((((........)))))).(((.(((((.((((........)))).((((((((.((((.........((((((.......)))))).........((((..(((((((((((............))))))))))).))))...))))..))))))))....)).)))...)))....... (-69.10)

Rendering structure of MNT mRNA 203 nt long with energy of -69.10 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:

The sequence data were shown in Figure 5A while structural data in Figures 5B(ii) and with raw results in
Supplementary data B, Figure B(ii).

Citations:

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