IRESite_Id:55 summary record describing characteristics of n-MYC IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `55`	Version: `4`
Originaly submitted by: Václav Vopálenský	Submission date: `2005-07-29 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2010-01-12 21:46:05`

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: `n-MYC`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
62750358

Synonyms of the gene name:

Synonym: NMYC

Synonym: ODED

Synonym: MODED

Synonym: MYCN

The mRNA/+RNA description:

Homo sapiens v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) (MYCN), mRNA.
Poly(A) tail dropped.

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

GTCATCTGTC TGGACGCGCT GGGTGGATGC GGGGGGCTCC TGGGAACTGT GTTGGAGCCG AGCAAGCGCT AGCCAGGCGC AAGCGCGCAC AGACTGTAGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CATCCGAGGA CACCCCCGCC CCCCCGGCCC ACCCGGAGAC ACCCGCGCAG AATCGCCTCC GGATCCCCTG CAGTCGGCGG GAGTGTTGGA GGTCGGCGCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GGCCCCCGCC TTCCGCGCCC CCCACGGGAA GGAAGCACCC CCGGTATTAA AACGAACGGG GCGGAAAGAA GCCCTCAGTC GCCGGCCGGG AGGCGAGCCG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATGCCGAGCT GCTCCACGTC CACCATGCCG GGCATGATCT GCAAGAACCC AGACCTCGAG TTTGACTCGC TACAGCCCTG CTTCTACCCG GACGAAGATG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ACTTCTACTT CGGCGGCCCC GACTCGACCC CCCCGGGGGA GGACATCTGG AAGAAGTTTG AGCTGCTGCC CACGCCCCCG CTGTCGCCCA GCCGTGGCTT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGCGGAGCAC AGCTCCGAGC CCCCGAGCTG GGTCACGGAG ATGCTGCTTG AGAACGAGCT GTGGGGCAGC CCGGCCGAGG AGGACGCGTT CGGCCTGGGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GGACTGGGTG GCCTCACCCC CAACCCGGTC ATCCTCCAGG ACTGCATGTG GAGCGGCTTC TCCGCCCGCG AGAAGCTGGA GCGCGCCGTG AGCGAGAAGC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGCAGCACGG CCGCGGGCCG CCAACCGCCG GTTCCACCGC CCAGTCCCCG GGAGCCGGCG CCGCCAGCCC TGCGGGTCGC GGGCACGGCG GGGCTGCGGG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AGCCGGCCGC GCCGGGGCCG CCCTGCCCGC CGAGCTCGCC CACCCGGCCG CCGAGTGCGT GGATCCCGCC GTGGTCTTCC CCTTTCCCGT GAACAAGCGC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GAGCCAGCGC CCGTGCCCGC AGCCCCGGCC AGTGCCCCGG CGGCGGGCCC TGCGGTCGCC TCGGGGGCGG GTATTGCCGC CCCAGCCGGG GCCCCGGGGG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TCGCCCCTCC GCGCCCAGGC GGCCGCCAGA CCAGCGGCGG CGACCACAAG GCCCTCAGTA CCTCCGGAGA GGACACCCTG AGCGATTCAG ATGATGAAGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TGATGAAGAG GAAGATGAAG AGGAAGAAAT CGACGTGGTC ACTGTGGAGA AGCGGCGTTC CTCCTCCAAC ACCAAGGCTG TCACCACATT CACCATCACT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GTGCGTCCCA AGAACGCAGC CCTGGGTCCC GGGAGGGCTC AGTCCAGCGA GCTGATCCTC AAACGATGCC TTCCCATCCA CCAGCAGCAC AACTATGCCG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCCCCTCTCC CTACGTGGAG AGTGAGGATG CACCCCCACA GAAGAAGATA AAGAGCGAGG CGTCCCCACG TCCGCTCAAG AGTGTCATCC CCCCAAAGGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TAAGAGCTTG AGCCCCCGAA ACTCTGACTC GGAGGACAGT GAGCGTCGCA GAAACCACAA CATCCTGGAG CGCCAGCGCC GCAACGACCT TCGGTCCAGC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTTCTCACGC TCAGGGACCA CGTGCCGGAG TTGGTAAAGA ATGAGAAGGC CGCCAAGGTG GTCATTTTGA AAAAGGCCAC TGAGTATGTC CACTCCCTCC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AGGCCGAGGA GCACCAGCTT TTGCTGGAAA AGGAAAAATT GCAGGCAAGA CAGCAGCAGT TGCTAAAGAA AATTGAACAC GCTCGGACTT GCTAGACGCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TCTCAAAACT GGACAGTCAC TGCCACTTTG CACATTTTGA TTTTTTTTTT AAACAAACAT TGTGTTGACA TTAAGAATGT TGGTTTACTT TCAAATCGGT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CCCCTGTCGA GTTCGGCTCT GGGTGGGCAG TAGGACCACC AGTGTGGGGT TCTGCTGGGA CCTTGGAGAG CCTGCATCCC AGGATGCTGG GTGGCCCTGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGCCTCCTCC ACCTCACCTC CATGACAGCG CTAAACGTTG GTGACGGTTG GGAGCCTCTG GGGCTGTTGA AGTCACCTTG TGTGTTCCAA GTTTCCAAAC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AACAGAAAGT CATTCCTTCT TTTTAAAATG GTGCTTAAGT TCCAGCAGAT GCCACATAAG GGGTTTGCCA TTTGATACCC CTGGGGAACA TTTCTGTAAA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TACCATTGAC ACATCCGCCT TTTGTATACA TCCTGGGTAA TGAGAGGTGG CTTTTGCGGC CAGTATTAGA CTGGAAGTTC ATACCTAAGT ACTGTAATAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TACCTCAATG TTTGAGGAGC ATGTTTTGTA TACAAATATA TTGTTAATCT CTGTTATGTA CTGTACTAAT TCTTACACTG CCTGTATACT TTAGTATGAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GCTGATACAT AACTAAATTT GATACTTATA TTTTCGTATG AAAATGAGTT GTGAAAGTTT TGAGTAGATA TTACTTTATC ACTTTTTGAA CTAAGAAACT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTTGTAAAGA AATTTACTAT ATATATATGC CTTTTTCCTA GCCTGTTTCT TCCTGTTAAT GTATTTGTTC ATGTTTGGTG CATAGAACTG GGTAAATGCA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AAGTTCTGTG TTTAATTTCT TCAAAATGTA TATATTTAGT GCTGCATCTT ATAGCACTTT GAAATACCTC ATGTTTATGA AAATAAATAG CTTAAAATTA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AATG
^2601

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:
not_tested

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: `3`	Last change: `2009-09-01 17:19:12`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
n-myc

The description of the protein encoded in this ORF:
v-myc myelocytomatosis viral related oncogene, neuroblastoma derived

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):

301-1695

Remarks:

Integrity of the bicistronic transcript in transiently transfected cells was tested by RNase-protection assay.
The GenBank underlying sequence is possibly shorter on the 5'-end when compared to the clone used by authors.



The sequence IRESite used for this record (NM_005378.4) does not align well to mRNA entry. Note the seemingly
overly long 5'-UTR we have which could be spanning into a promoter region and that most of this region belongs
to the IRES:

>gb|BC002712.2| UniGene infoGeoGene info Homo sapiens v-myc myelocytomatosis viral related oncogene,
neuroblastoma derived (avian), mRNA (cDNA clone MGC:3962 IMAGE:3627330),
complete cds
Length=2458

 Score = 4481 bits (2426),  Expect = 0.0
 Identities = 2430/2432 (99%), Gaps = 0/2432 (0%)
 Strand=Plus/Plus

Query  182   AGTGTTGGAGGTCGGCGCCGGCCCCCGCCTTCCGCGCCCCCCACGGGAAGGAAGCACCCC  241
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  23    AGTGTTGGAGGTCGGCGCCGGCCCCCGCCTTCCGCGCCCCCCACGGGAAGGAAGCACCCC  82

[cut]



A hit to a full-length cDNA (by oligo-capping) shows this entry has an extra exon(s) or the exon is extended:

>dbj|AK298225.1| UniGene infoGene info Homo sapiens cDNA FLJ51262 complete cds, highly similar to N-myc
proto-oncogene protein
Length=2015

Query  1    GTCATCTGTCTGGACGCGCTGGGTGGATGCGGGGGGCTCCTGGGAACTGTGTTGGAGCCG  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  4    GTCATCTGTCTGGACGCGCTGGGTGGATGCGGGGGGCTCCTGGGAACTGTGTTGGAGCCG  63

[cut]

Query  361  TTTGACTCGCTACAGCCCTGCTTCTACCCGGACGAAGATGACTTCTACTTCGG-CGGCCC  419
            ||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||
Sbjct  364  TTTGACTCGCTACAGCCCTGCTTCTACCCGGACGAAGATGACTTCTACTTCGGTCG-CCC  422

Query  420  C  420
            |
Sbjct  423  C  423

[cut]

Query  999   ggTCGCCCCTCCGCGCCCAGGCGGCCGCCAGACCAGCGGCGGCGACCACAAGGCCCTCAG  1058
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  415   GGTCGCCCCTCCGCGCCCAGGCGGCCGCCAGACCAGCGGCGGCGACCACAAGGCCCTCAG  474

[cut]

Query  2559  TTGAAATACCTCATGTTTATGAAAATAAATAGCTTAAAATT  2599
             |||||||||||||||||||||||||||||||||||||||||
Sbjct  1975  TTGAAATACCTCATGTTTATGAAAATAAATAGCTTAAAATT  2015



More information on the various exons in entries: M13241, X03295, X02363, X03919.

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

IRESs:

IRES:

Version: `4`	Last change: `2008-06-26 02:14:16`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `n-MYC`

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

8-327

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GTCTGGACGC GCTGGGTGGA TGCGGGGGGC TCCTGGGAAC TGTGTTGGAG CCGAGCAAGC GCTAGCCAGG CGCAAGCGCG CACAGACTGT AGCCATCCGA 
^8         ^18        ^28        ^38        ^48        ^58        ^68        ^78        ^88        ^98        

GGACACCCCC GCCCCCCCGG CCCACCCGGA GACACCCGCG CAGAATCGCC TCCGGATCCC CTGCAGTCGG CGGGAGTGTT GGAGGTCGGC GCCGGCCCCC 
^108       ^118       ^128       ^138       ^148       ^158       ^168       ^178       ^188       ^198       

GCCTTCCGCG CCCCCCACGG GAAGGAAGCA CCCCCGGTAT TAAAACGAAC GGGGCGGAAA GAAGCCCTCA GTCGCCGGCC GGGAGGCGAG CCGATGCCGA 
^208       ^218       ^228       ^238       ^248       ^258       ^268       ^278       ^288       ^298       

GCTGCTCCAC GTCCACCATG
^308       ^318

Remarks:

n-myc UTR (293 nt) and putative open reading frame (27 nt). Please refer also to GI:11692795.

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

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