IRESite_Id:474 summary record describing characteristics of MTG8a IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `474`	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: `MTG8a`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
28329413

Synonyms of the gene name:

Synonym: RUNX1T1

Synonym: CDR

Synonym: ETO

Synonym: AML1T1

Synonym: ZMYND2

Synonym: CBFA2T1

Synonym: MGC2796

The mRNA/+RNA description:

Homo sapiens runt-related transcription factor 1; translocated to, 1 (cyclin D-related) (RUNX1T1), transcript
variant 1, mRNA.

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

TGAATAAATT ATTCGGCATT TAGCTTATCA TTCTGAATTT CACTTTTTGC TTTTTGGTGC TCTGAAACTT GCAGAGAGAG GTGGAGTGCT AAGGGGAGGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TAGGGGTTGT GATACTTTGC ACACACATCC CTGTCATTGT TCTGCCTAAA GAGACAGGGC TGGGTTCAAG GCCACATGTG CTCCTGTCAT CCTCCACATT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCTGCTCCAA GTGCAATCCG GAGTGTCAGC TCTCCATCTG TCTCTGCCTG GCAGGCGCAC GCGCCCAGCA CCCTGCCTCC GGCGATGCCG CCCCAGCCCC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TCTGATGGCC CTCCTCTCTG CTGCCACTCA TTCCAGAACA GGAGGCATGA GCCCGGAACG CGCTTGCTTT TAGGAGACAG CCACTTTCTG TGTGGTACGC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TGGATTCAAG GATGCCTGAT CGTACTGAGA AGCACTCCAC AATGCCAGAC TCACCTGTGG ATGTGAAGAC GCAATCTAGG CTGACTCCTC CAACAATGCC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACCTCCCCCA ACTACTCAAG GAGCTCCAAG AACCAGTTCA TTTACACCGA CAACGTTAAC TAATGGCACG AGCCATTCTC CTACAGCCTT GAATGGCGCC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCCTCACCAC CCAATGGCTT CAGCAATGGG CCTTCCTCTT CTTCCTCCTC CTCTCTGGCT AATCAACAGC TGCCCCCAGC CTGTGGTGCC AGGCAACTCA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GCAAGCTGAA AAGGTTCCTT ACTACCCTGC AGCAGTTTGG CAATGACATT TCACCCGAGA TAGGAGAAAG AGTTCGCACC CTCGTTCTGG GACTAGTGAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTCCACTTTG ACAATTGAAG AATTTCATTC CAAACTGCAA GAAGCTACTA ACTTCCCACT GAGACCTTTT GTCATCCCAT TTTTGAAGGC CAACTTGCCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CTGCTGCAGC GTGAGCTCCT CCACTGCGCA AGACTGGCCA AACAGAACCC TGCCCAGTAC CTCGCCCAGC ATGAACAGCT GCTTCTGGAT GCCAGCACCA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCTCACCTGT TGACTCCTCA GAGCTGCTTC TCGATGTGAA CGAAAACGGG AAGAGGCGAA CTCCAGACAG AACCAAAGAA AATGGCTTTG ACAGAGAGCC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TTTGCACTCA GAACATCCAA GCAAGCGACC ATGCACTATT AGCCCAGGCC AGCGGTACAG TCCAAATAAC GGCTTATCCT ACCAGCCCAA TGGCCTGCCT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CACCCTACCC CACCTCCACC TCAGCATTAC CGTTTGGATG ATATGGCCAT TGCCCACCAC TACAGGGACT CCTATCGACA CCCCAGCCAC AGGGACCTCA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGGACAGAAA CAGACCTATG GGGTTGCATG GCACACGTCA AGAAGAAATG ATTGATCACA GACTAACAGA CAGAGAATGG GCAGAAGAGT GGAAACATCT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TGACCATCTG TTAAACTGCA TAATGGACAT GGTAGAAAAA ACAAGGCGAT CTCTCACCGT ACTAAGGCGG TGTCAAGAAG CAGACCGGGA AGAATTGAAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TACTGGATCC GGCGGTACAG TGACGCCGAG GACTTAAAAA AAGGTGGCGG CAGTAGCAGC AGCCACTCTA GGCAGCAGAG TCCCGTCAAC CCAGACCCAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTGCACTAGA CGCGCATCGG GAATTCCTTC ACAGGCCTGC GTCTGGATAC GTGCCAGAGG AGATCTGGAA GAAAGCTGAG GAGGCCGTCA ATGAGGTGAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCGCCAGGCG ATGACGGAGC TGCAGAAGGC CGTGTCTGAG GCGGAGCGGA AAGCCCACGA CATGATCACA ACAGAGAGGG CCAAGATGGA GCGCACGGTC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCCGAGGCCA AACGGCAGGC GGCGGAGGAC GCACTGGCAG TTATCAATCA GCAGGAGGAT TCAAGCGAGA GTTGCTGGAA TTGTGGCCGT AAAGCGAGTG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AAACCTGCAG TGGCTGTAAC ACAGCCCGAT ACTGTGGCTC ATTTTGCCAG CACAAAGACT GGGAGAAGCA CCATCACATC TGTGGACAGA CCCTGCAGGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCAGCAGCAG GGAGACACAC CTGCAGTCAG CTCCTCTGTC ACGCCCAACA GCGGGGCTGG GAGCCCGATG GACACACCAC CAGCAGCCAC TCCGAGGTCA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACCACCCCGG GAACCCCTTC CACCATAGAG ACAACCCCTC GCTAGACGTG AACTCAGAAC TGTCGGAGGA AAGACAACAC AACCAACGCG AAACCAATTC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CTCATCCTCA GATGCTCAAA GTTGTTTTTT TTGTTTGTTT GTTTATTAGA TGAATTATCC TATTTCAGTA CTTCAGCAAG AGAGAACCTA ACTGTATCTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GAGGTGGTAG TAAAACACAG AGGGCCAGTA ACGGGTCGTA ATGACTTATT GTGGATAACA AAGATATCTT TTCTTTAGAG AACTGAAAAG AGAGCAGAGA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ATATAACATG AAATGATAGA TTTGACCTCC TCCCTGTTAT TTTCAAGTAG CTGGGATTTT AAACTAGATG ACCTCATTAA CCGATGCTTT ACCAAACAGC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AAACCAAGAG ATTGCTAATT GCTGTTGAAA GCAAAAATGC TAATATTAAA AGTCACAATG TTCTTTATAT ACAATAATGG AAAAAAAAAA AAGAGGAAAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CCCTCAAGGG CATGAGCATT GGATACAGCA GTAGACATTT TAACAAGAAG ATGAATGGCG TCCGTGGGTT GCTAACTGAA CTTTGAAGAC CCGCTACAAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ACGCGCAGAT GTGCAGCAGA TTGGAAGGAG ACACAGATGT TCGGTTTTTT TCCTGTTTCT GAAAAGAAAT AATAATATCC AGGTCAACAG AATGAAAAAT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GAAAGATGAT TTGCAATGGG ATGTATGAAT ACAGCAGCAA GAAAAAAAAA TGCCATAATA CAAAAGGCTC CATATATATA TATATATATA TATATATACA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CACACACACA CGCACATATA CACACACACA CACACACACA CACACACACA CACACACACA CACACACACA CACAAGTAAG AGACTCAGCC TGCAGTTAAT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TAGCATTCTG GCAGTTTTGA CATCAGCCAG CTGCCCTAAA TAACCCTTCA ACGTTTCTTC ACTTTTGCAA GGTTCCACAG AGTAAGACAT TGGGTCTATT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCAGCTCATT CATTTTATAT TGAAAAAAAT AATTTTAAAA ATGGTGGCTT CAGCTCCAGC CCCTTTCCAA AATTTTTCAA CCCCACCCTG TTTGGATTTT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TAATTAAAAA CTAGTAGTTC TCTTGGTGTT AAAACACTTC TGTCCTGTGA GGTTTCCCAA TGGTGTTTTT CTTGTAAATG TGTTGGACAA ATGTGAAGAT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GCATTGTAGT TTAACCATAT GCCCACATTT AGTCTCTTTA TTCCTAGTTG GTGAGAAACC TGTATCTTTC TATGCTGCTT TTATATCTGT ATGTATTAGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GATATTTCTC TAGTAGTTAA AAAAAAAAAA AGGAAAAAAA GACTCTTTTT GGTTGTCCTC AAG
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461

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:
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 HeLa (ATCC CCL-2)

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:
RUNX1T1

The description of the protein encoded in this ORF:
acute myelogenous leukemia 1 translocation 1 protein isoform MTG8a

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):

412-2145

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

IRESs:

IRES:

Version: `1`	Last change: `2008-07-11 16:56:35`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `MTG8a`

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

213-411

Conclusion:
weakly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

GCAATCCGGA GTGTCAGCTC TCCATCTGTC TCTGCCTGGC AGGCGCACGC GCCCAGCACC CTGCCTCCGG CGATGCCGCC CCAGCCCCTC TGATGGCCCT 
).))).)))) )))....... .......((. ((.(((.((( (((.((.... .....))..) )))))...)) ))).)).((( .(((.....) ))..)))... 
^213       ^223       ^233       ^243       ^253       ^263       ^273       ^283       ^293       ^303       

CCTCTCTGCT GCCACTCATT CCAGAACAGG AGGCATGAGC CCGGAACGCG CTTGCTTTTA GGAGACAGCC ACTTTCTGTG TGGTACGCTG GATTCAAGG
.......... .......... (((..((((( ((((.((... ...(((.((. ...)).))). .....))))) ...)))))). )))....... .........
^313       ^323       ^333       ^343       ^353       ^363       ^373       ^383       ^393       ^403

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:

).))).)))))))..............((.((.(((.((((((.((.........))..))))))...))))).)).(((.(((.....)))..))).......................(((..(((((((((.((......(((.((....)).)))......)))))...)))))).)))................
ERROR: unbalanced brackets in make_pair_table

STDOUT was:

Remarks:

Mutational analysis of shortened 5'-UTR regions was shown in Figure 6A, right column.

Citations:

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

Version: `1`	Last change: `2008-07-11 23:31:11`
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):
268-286,310-326

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 4E,F (in vitro). The binding region and unchanged structure due to the
binding was shown in Figure 6D(i) 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):
268-286,310-326

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 4E,F (in vitro).

Citations:

IRES trans-acting factor (ITAF):

Version: `1`	Last change: `2008-07-12 15:08:23`
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 4E,F (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:
direct_interaction_with_rna

OPTIONAL: The interacting RNA base range (if any):
268-286,310-326

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:
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 4E,F (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 4E,F (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 4E,F (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 4E,F (in vitro).

Citations:

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 18

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):
1-414

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

TGAATAAATT ATTCGGCATT TAGCTTATCA TTCTGAATTT CACTTTTTGC TTTTTGGTGC TCTGAAACTT GCAGAGAGAG GTGGAGTGCT AAGGGGAGGG 
.......... .......... ........(( (((((.(((. (((((((((( (((((..((( .......... )))..))))) ))))))((.. ((..(((((( 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TAGGGGTTGT GATACTTTGC ACACACATCC CTGTCATTGT TCTGCCTAAA GAGACAGGGC TGGGTTCAAG GCCACATGTG CTCCTGTCAT CCTCCACATT 
(((((((((( (...(((((. ((.((...(( (((((.((.( .......).) ).))))))). )).)).)))) ).))))...) )))))...)) )))))...)) 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCTGCTCCAA GTGCAATCCG GAGTGTCAGC TCTCCATCTG TCTCTGCCTG GCAGGCGCAC GCGCCCAGCA CCCTGCCTCC GGCGATGCCG CCCCAGCCCC 
..)).....) ))).))).)) )))))..... .........( (.((.(((.( (((((.((.. .......)). .))))))... ))))).)).( ((.(((.... 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TCTGATGGCC CTCCTCTCTG CTGCCACTCA TTCCAGAACA GGAGGCATGA GCCCGGAACG CGCTTGCTTT TAGGAGACAG CCACTTTCTG TGTGGTACGC 
.)))..))). .......... .......... ..(((..((( ((((((.((. .....(((.( (....)).)) )......))) ))...))))) ).)))..... 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TGGATTCAAG GATG
.......... ....
^401       ^411

Rendering structure of MTG8a mRNA 414 nt long with energy of -89.40 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:

Data from Figure 5(iii).

Citations:

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