IRESite_Id:49 summary record describing characteristics of MYT2

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `49`	Version: `5`
Originaly submitted by: Václav Vopálenský	Submission date: `2005-07-20 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2008-07-12 17:53:30`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `possibly_wrong`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `MYT2`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
2246660

The mRNA/+RNA description:

Homo sapiens myelin transcription factor 2 (MYT2) mRNA

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

TATTTTAGTT AGTGAAAGGA CATAATCATC AATGTTTATA ATCTGGAGTG CGTTATCATG GTTTATAGCA ATTAGTTCAT TTGCATTTAT GTTTTTATAT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TCATCAGCAA AATTGCAATG GGTATTTGGA TTGATTGGAA TTAGTCAGAT ACTTTTATGG CTACTAATAT GGCGTTTTTC ACGTTCAGAC AAGAACGGTA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCGATTAAAA TATTTCGGCA GACATGTGCG TAGCACGTTT ATAGCGTCCG CTTTGTTAGC ATGTATTAGA CGTTAACGAA CGATTCGCTT ATCAAATTTG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AACGATACGG TTGCTACATG GTATAATTTT GTTAGAAGAA TTGTGGTTTG GAGTCTTATC TTCAATCCAG AGCTTGTCGT CTGTCAACGA TGAGCTTTTT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TTGTGCAAAA AAATAGCCCC GTCCTGTCAA ACGAGGCACT TGTATTAGCG ACGATTGTCG AAATACTTTT GCAACAAGAT TAATACTAAG CCAGCAAAAA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCTGCCAAAG TGTGGCTTGG AGCTGTTGCA TTAGAAGGAT TGCGGTTTGC ATGGAGTCTC ACCTCCCTTC TGGGCGTCTA ATCTCAACGC CACGAGAAAT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AGTATACCAT GACTTTAAAA TGGCTTAGAA CGCAAATAAG AGCCGTTTAA GAGTATTTAA GTTTGCGGTG GTATCTTCGT ATCGGTGGCG CGACCAAAGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GAGCGACAGA CGACACACAG CAGGACACTC CAAGTGTCCA GTGTGCTGGG GTGCCGTTAA GAAATGACGA CCAGTCATTT TAGGCATCTC GTCCTTGCCG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATATGGAGAT ACCACCTCTA GGCGAAATGA GGAGAGCTCT GCTCGACGAT TGGAGACTTT TTGACGGGAG GCGATCAGCC GACCAGAAAA AAGCGGGCTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTACTAACAG CCCGCTAACA GCCCGCTAGA GGTTTCCTTT AGGTAACCGC ACAACCAAAA AAGCAGTCAG AATGACAAGC CAAATAACTA GTAATTCGCC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CGTAAAATGG GAACGTAGAA CTCGTCATGA CACTTGTGGT AAAATAACAT TATTCGCTTG CAAAAAACGA TGTACTTTGA CAATTTAAGA CACAAAAAAA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CACAACCTCG ACAATTTAGG AGTTAGAGAG GTCGTGTTTT GAGATTAGTG AGACTATGGA TAGTTCATTA AGTATTATAA CATACTCAAT GAGTGTACAT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AGTCTCCAGA AAAATGGAGA ACCCATGAAA CAAGAAAAAC AGCAGTTTAT AAAAACGGAT TGGACGATTG ACATGATAAA TGCCGTCGGC AATTTGAGAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ATATGCCATT GATATTTCTC ACAGCTACTA AGGATATTCA TCGCGGTGGA TGGGTAGAAC GAATTGATAA TAAGGCTTGG CAGTATGTCA GAGTTTATGA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAATGGCGAC ATTGAAGTTT TAATTACACT TCAGATAATA AGATTCCACA AATATTTTGA TACACCAGTT TGGTTACAGT TTAACCCGAA TCATCTTTTA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CCCGCAGATT ATGTGCAACT TGATCATGTG ATGAAATATG TTGATCACTC ACATTTAACT CGCGCCGATT TAGCAAATGA TATTTATAAC ATCAACTTGC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AACGTTACGA TTTTGGATTG TTTGGAGGAA CTAGAGATAT CTATCGTAGT TTATCTGGTG ATTTAGAAAC ACGGTATTGG GGACGCCGAA AAAGTGAGCG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CCAAATTCGT CTTTATGACA AAATGCGCGA GATGAAAAAA CATGGCAAAG CAGATGATAT TCCAGACGGT ATTACTGATT GGTGGCGTTT AGAATTTCAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TTTAGAGGTG GCAAGGTTGA GTCATGGCAA GAAGAAGTAA TGGACAAAAT GCAGTCGTTC CATGTTCTTG CTGTTGATGA TAATGATGAT TTAAGTGAAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TAGATAAAGC CATTTTAGCA CGTGTTAATG CCGATAAATT TGATTTTAAA AGAGTCGGTA AACGTTATGC TGCAAAAATT CGGAAAATGG TACGTGAAAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CGTTGGTTTT GATACGACCG TTGCAGAATT ATCTCTCAAA ACATTCAACG AACAAAAAGA TGAGTTGCAG AGACAACTAG ATAGCATGCT TGCAAAATAT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AATATCGGTG CACAAACAGA AGAAATGACA GCATATTTTG AGGAAGAGCT TAAACAAACA GGTAATCTTG ATTTTTCTGT TGTTGAGAGT GAATCTGCGT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TAGAGCGTAA TGTGATACGA AATATTGCTA AAAGTTGGCG TGAAGAAAAT AGTTTAACGC ACAGAACTAA TACTAATAGT TGATGCGTAT TTTTTATTTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TCTAATAT
^2301

Credibility of mRNA sequence:

guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail

The organism containing this mRNA with IRES segment in its genome:

Homo sapiens

A promoter reported in cDNA corresponding to IRES sequence:
not tested The total number of notable open-reading frames (ORFs):
1

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

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
MYT2

The description of the protein encoded in this ORF:
Myelin transcription factor 2

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):

1156-2283

OPTIONAL: The function of the encoded protein

GO:0005615;  Cellular component: extracellular space
GO:0005634;  Cellular component: nucleus
GO:0003697;  Molecular function: single-stranded DNA binding
GO:0003700;  Molecular function: transcription factor activity
GO:0008270;  Molecular function: zinc ion binding
GO:0008283;  Biological process: cell proliferation

Remarks:

MYT2 mRNA can only be translated efficiently in vitro in rabbit reticulocyte lysates only when upstream ATGs
(and possibly secondary structures) are removed. This mRNA is said to be low-abundant and undetectable using
Northern blot or RNase-protection assay in total cellular RNA. It seems the MYT2 gene contains an intron. The
IRES activity was studied only in vivo using bicistronic constructs. The underlying sequence probably differs
from the clone used by the authors. RT-PCR analysis of mouse mRNA has shown 2 types of MYT2 mRNA. One
full-length as expected and one shorter by 40 bases in 5'-UTR (missing bases 948-987, but not resembling
splice junction).

Citations:

Kim J. G., Armstrong R. C., Berndt J. A., Kim N. W., Hudson L. D. (1998) A secreted DNA-binding protein that is translated through an internal ribosome entry site (IRES) and distributed in a discrete pattern in the central nervous system. Mol. Cell. Neurosci. 12(3):119-140

IRESs:

IRES:

Version: `6`	Last change: `2008-07-12 17:53:30`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `MYT2_997-1152`

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

997-1152

Conclusion:
putative_IRES

How IRES boundaries were determined:
guessed

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

CGCCCGTAAA ATGGGAACGT AGAACTCGTC ATGACACTTG TGGTAAAATA ACATTATTCG CTTGCAAAAA ACGATGTACT TTGACAATTT AAGACACAAA 
^997       ^1007      ^1017      ^1027      ^1037      ^1047      ^1057      ^1067      ^1077      ^1087      

AAAACACAAC CTCGACAATT TAGGAGTTAG AGAGGTCGTG TTTTGAGATT AGTGAG
^1097      ^1107      ^1117      ^1127      ^1137      ^1147

Remarks:

Fragment of 5' UTR nt 997 to nt 1152 (determined by primer location) is 156-nt IRES module, which is
functional as IRES when it is tested in bicistronic vector. The sequence of the IRES regions differs from the
sequence shown in Fig. 1 which claims complete 5' UTR was tested [shown underlined].

Citations:

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