IRESite_Id:471 summary record describing characteristics of MYB IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `471`	Version: `2`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2009-09-01 21:48:07`

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: `c-myb`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
46361979

Synonyms of the gene name:

Synonym: efg

Synonym: MYB

The mRNA/+RNA description:

Homo sapiens v-myb myeloblastosis viral oncogene homolog (avian) (MYB), mRNA. Poly(A)-tail sequence was
dropped.

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

AATATCAACC TGTTTCCTCC TCCTCCTTCT CCTCCTCCTC CGTGACCTCC TCCTCCTCTT TCTCCTGAGA AACTTCGCCC CAGCGGTGCG GAGCGCCGCT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGCAGCCGG GGAGGGACGC AGGCAGGCGG CGGGCAGCGG GAGGCGGCAG CCCGGTGCGG TCCCCGCGGC TCTCGGCGGA GCCCCGCGCC CGCCGCGCCA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGGCCCGAAG ACCCCGGCAC AGCATATATA GCAGTGACGA GGATGATGAG GACTTTGAGA TGTGTGACCA TGACTATGAT GGGCTGCTTC CCAAGTCTGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AAAGCGTCAC TTGGGGAAAA CAAGGTGGAC CCGGGAAGAG GATGAAAAAC TGAAGAAGCT GGTGGAACAG AATGGAACAG ATGACTGGAA AGTTATTGCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AATTATCTCC CGAATCGAAC AGATGTGCAG TGCCAGCACC GATGGCAGAA AGTACTAAAC CCTGAGCTCA TCAAGGGTCC TTGGACCAAA GAAGAAGATC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AGAGAGTGAT AGAGCTTGTA CAGAAATACG GTCCGAAACG TTGGTCTGTT ATTGCCAAGC ACTTAAAGGG GAGAATTGGA AAACAATGTA GGGAGAGGTG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GCATAACCAC TTGAATCCAG AAGTTAAGAA AACCTCCTGG ACAGAAGAGG AAGACAGAAT TATTTACCAG GCACACAAGA GACTGGGGAA CAGATGGGCA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GAAATCGCAA AGCTACTGCC TGGACGAACT GATAATGCTA TCAAGAACCA CTGGAATTCT ACAATGCGTC GGAAGGTCGA ACAGGAAGGT TATCTGCAGG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AGTCTTCAAA AGCCAGCCAG CCAGCAGTGG CCACAAGCTT CCAGAAGAAC AGTCATTTGA TGGGTTTTGC TCAGGCTCCG CCTACAGCTC AACTCCCTGC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CACTGGCCAG CCCACTGTTA ACAACGACTA TTCCTATTAC CACATTTCTG AAGCACAAAA TGTCTCCAGT CATGTTCCAT ACCCTGTAGC GTTACATGTA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AATATAGTCA ATGTCCCTCA GCCAGCTGCC GCAGCCATTC AGAGACACTA TAATGATGAA GACCCTGAGA AGGAAAAGCG AATAAAGGAA TTAGAATTGC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TCCTAATGTC AACCGAGAAT GAGCTAAAAG GACAGCAGGT GCTACCAACA CAGAACCACA CATGCAGCTA CCCCGGGTGG CACAGCACCA CCATTGCCGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCACACCAGA CCTCATGGAG ACAGTGCACC TGTTTCCTGT TTGGGAGAAC ACCACTCCAC TCCATCTCTG CCAGCGGATC CTGGCTCCCT ACCTGAAGAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AGCGCCTCGC CAGCAAGGTG CATGATCGTC CACCAGGGCA CCATTCTGGA TAATGTTAAG AACCTCTTAG AATTTGCAGA AACACTCCAA TTTATAGATT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTTTCTTAAA CACTTCCAGT AACCATGAAA ACTCAGACTT GGAAATGCCT TCTTTAACTT CCACCCCCCT CATTGGTCAC AAATTGACTG TTACAACACC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ATTTCATAGA GACCAGACTG TGAAAACTCA AAAGGAAAAT ACTGTTTTTA GAACCCCAGC TATCAAAAGG TCAATCTTAG AAAGCTCTCC AAGAACTCCT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACACCATTCA AACATGCACT TGCAGCTCAA GAAATTAAAT ACGGTCCCCT GAAGATGCTA CCTCAGACAC CCTCTCATCT AGTAGAAGAT CTGCAGGATG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGATCAAACA GGAATCTGAT GAATCTGGAA TTGTTGCTGA GTTTCAAGAA AATGGACCAC CCTTACTGAA GAAAATCAAA CAAGAGGTGG AATCTCCAAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGATAAATCA GGAAACTTCT TCTGCTCACA CCACTGGGAA GGGGACAGTC TGAATACCCA ACTGTTCACG CAGACCTCGC CTGTGGCAGA TGCACCGAAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATTCTTACAA GCTCCGTTTT AATGGCACCA GCATCAGAAG ATGAAGACAA TGTTCTCAAA GCATTTACAG TACCTAAAAA CAGGTCCCTG GCGAGCCCCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGCAGCCTTG TAGCAGTACC TGGGAACCTG CATCCTGTGG AAAGATGGAG GAGCAGATGA CATCTTCCAG TCAAGCTCGT AAATACGTGA ATGCATTCTC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AGCCCGGACG CTGGTCATGT GAGACATTTC CAGAAAAGCA TTATGGTTTT CAGAACACTT CAAGTTGACT TGGGATATAT CATTCCTCAA CATGAAACTT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTCATGAATG GGAGAAGAAC CTATTTTTGT TGTGGTACAA CAGTTGAGAG CAGCACCAAG TGCATTTAGT TGAATGAAGT CTTCTTGGAT TTCACCCAAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TAAAAGGATT TTTAAAAATA AATAACAGTC TTACCTAAAT TATTAGGTAA TGAATTGTAG CCAGTTGTTA ATATCTTAAT GCAGATTTTT TTAAAAAAAA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CATAAAATGA TTTATCTGTA TTTTAAAGGA TCCAACAGAT CAGTATTTTT TCCTGTGATG GGTTTTTTGA AATTTGACAC ATTAAAAGGT ACTCCAGTAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TTCACTTTTC TCGATCACTA AACATATGCA TATATTTTTA AAAATCAGTA AAAGCATTAC TCTAAGTGTA GACTTAATAC CATGTGACAT TTAATCCAGA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTGTAAATGC TCATTTATGG TTAATGACAT TGAAGGTACA TTTATTGTAC CAAACCATTT TATGAGTTTT CTGTTAGCTT GCTTTAAAAA TTATTACTGT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AAGAAATAGT TTTATAAAAA ATTATATTTT TATTCAGTAA TTTAATTTTG TAAATGCCAA ATGAAAAACG TTTTTTGCTG CTATGGTCTT AGCCTGTAGA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CATGCTGCTA GTATCAGAGG GGCAGTAGAG CTTGGACAGA AAGAAAAGAA ACTTGGTGTT AGGTAATTGA CTATGCACTA GTATTTCAGA CTTTTTAATT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TTATATATAT ATACATTTTT TTTCCTTCTG CAATACATTT GAAAACTTGT TTGGGAGACT CTGCATTTTT TATTGTGGTT TTTTTGTTAT TGTTGGTTTA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TACAAGCATG CGTTGCACTT CTTTTTTGGG AGATGTGTGT TGTTGATGTT CTATGTTTTG TTTTGAGTGT AGCCTGACTG TTTTATAATT TGGGAGTTCT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GCATTTGATC CGCATCCCCT GTGGTTTCTA AGTGTATGGT CTCAGAACTG TTGCATGGAT CCTGTGTTTG CAACTGGGGA GACAGAAACT GTGGTTGATA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GCCAGTCACT GCCTTAAGAA CATTTGATGC AAGATGGCCA GCACTGAACT TTTGAGATAT GACGGTGTAC TTACTGCCTT GTAGCAAAAT AAAGATGTGC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CCTTATTTTA CCT
^3301      ^3311

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:
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:
MYB

The description of the protein encoded in this ORF:
v-myb myeloblastosis viral oncogene homolog

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):

200-2122

Remarks:

Several splice variants exist in human. A great survey of them is annotated in GI:1872199. The same 5'-UTR as
within this IRESite record is present in splice variant 8 (GI:45502008), 8A (GI:45502002), 8B (GI:45502010),
9Ai (GI:45502004), 9Aii (GI:45502006), 10A (GI:45502012), 13A (GI:45502014), 14A (GI:45502016).


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

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: `2`	Last change: `2008-07-11 16:55:18`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `MYB` Warning: please make ires_name same as the gene_name and optionally append to it coordinates. E.g. when gene/virus name is EMCV-R use EMCV-R_-222_to_-1 or EMCV-R_1-456, etc. but not Emcv-R-... or EMCV-222_to_-1. Please keep case of letters as well. This rewards when searching through the database.

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

2-151

Conclusion:
weakly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

ATATCAACCT GTTTCCTCCT CCTCCTTCTC CTCCTCCTCC GTGACCTCCT CCTCCTCTTT CTCCTGAGAA ACTTCGCCCC AGCGGTGCGG AGCGCCGCTG 
.......((( ((((((.((. ((((((((.( (((((((((. ..((...... .........) )....))).. ....(((.(( ........)) .)))..(((. 
^2         ^12        ^22        ^32        ^42        ^52        ^62        ^72        ^82        ^92        

CGCAGCCGGG GAGGGACGCA GGCAGGCGGC GGGCAGCGGG AGGCGGCAGC
...))).))) ))))))...) )).))).)). ))).)))))) .(((....))
^102       ^112       ^122       ^132       ^142

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:

Results of mutational IRES analysis were shown in Figure 6A, left column.

Citations:

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

Version: `3`	Last change: `2008-07-12 10:28:19`
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):
15-39

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 4A,B (in vitro). The binding region and changed 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):
15-39

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 4A,B (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):
15-39

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:
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 4A,B (in vitro).

Citations:

IRES trans-acting factor (ITAF):

Version: `1`	Last change: `2008-07-12 15:02:46`
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: `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 4A,B (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 4A,B (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 4A,B (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 4A,B (in vitro).

Citations:

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 17

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):
2-202

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

ATATCAACCT GTTTCCTCCT CCTCCTTCTC CTCCTCCTCC GTGACCTCCT CCTCCTCTTT CTCCTGAGAA ACTTCGCCCC AGCGGTGCGG AGCGCCGCTG 
.......((( ((((((.((. ((((((((.( (((((((((. ..((...... .........) )....))).. ....(((.(( ........)) .)))..(((. 
^2         ^12        ^22        ^32        ^42        ^52        ^62        ^72        ^82        ^92        

CGCAGCCGGG GAGGGACGCA GGCAGGCGGC GGGCAGCGGG AGGCGGCAGC CCGGTGCGGT CCCCGCGGCT CTCGGCGGAG CCCCGCGCCC GCCGCGCCAT 
...))).))) ))))))...) )).))).)). ))).)))))) .(((....)) ).(((((((( ...(((((.. (((....))) ..)))))... )))))))).. 
^102       ^112       ^122       ^132       ^142       ^152       ^162       ^172       ^182       ^192       

G
.
^202

Rendering structure of c-myb mRNA 201 nt long with energy of -73.90 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 5B(i) based on Supplementary material B, part B(i).

Citations:

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