IRESite_Id:107 summary record describing characteristics of ODC1 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `107`	Version: `7`
Originaly submitted by: Martin Mokrejš	Submission date: `2005-12-22 00:00:00`
Reviewed by: Martin Mokrejš	Last change: `2009-04-15 13:10:04`

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: `ODC1`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
205803

The mRNA/+RNA description:

Rat ornithine decarboxylase (ODC) mRNA, complete cds.

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

GTCAGTCCCT GCAGCCGCCG CCGCCGGCCG CCTTCAGTCA GCAGCTCGGC GCCACCTCCG GTCGGCGACT GCGGCGGGCT CGACGAGGCG GCTGACGGGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGGCGGCGGG AAGACGGCCG GGTGCGCCTT GGGGTTTAGT GGCGGCTTCT CCATGGGTCC AGCCAGCCGC TTCCCTGTGC TGTGAGTGTT TCCACCACTC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CAGGAGACAG CATTCAGAGT TGACCTTGTG AGAGCTGGCC ATAATTTAAT TCCATCTCTA GGTTTTCTGT CTTATTGTTT CAGAGGCACA TCGAGAACCA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ACCATGGGCA GCTTTACTAA GGAAGAGTTT GACTGCCATA TCCTCGATGA AGGTTTCACT GCTAAGGACA TTCTGGACCA AAAAATCAAT GAAGTTTCTT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCTCTGATGA TAAGGATGCT TTCTATGTTG CGGACCTCGG AGACGTTCTA AAGAAGCATC TGAGGTGGCT GAAAGCTCTT CCCCGTGTTA CTCCCTTCTA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TGCTGTCAAG TGTAATGACA GCAGAGCCAT AGTGAGCACC CTGGCTGCCA TTGGGACAGG ATTTGATTGT GCAAGCAAGA CTGAAATACA GTTGGTGCAG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GGGCTTGGGG TGCCTCCAGA GAGGATTATC TATGCAAATC CTTGTAAGCA AGTGTCTCAG ATCAAGTATG CTGCCAGTAA TGGAGTCCAG ATGATGACTT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TTGACAGTGA AATTGAGTTG ATGAAAGTTG CCAGAGCACA TCCAAAGGCA AAGTTGGTTT TGCGGATTGC CACTGATGAT TCCAAAGCAG TTTGTCGGCT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CAGTGTTAAG TTTGGTGCCA CACTGAAAAC CAGCAGGCTT CTCTTGGAAC GGGCAAAAGA GCTAAATATT GATGTCATTG GTGTCAGCTT CCATGTGGGC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AGTGGGTGTA CTGACCCTGA GACCTTCGTG CAGGCAGTGT CAGATGCCCG GTGTGTCTTT GACATGGGAA CAGAAGTTGG TTTCAGCATG TATCTGCTTG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ACATTGGTGG TGGCTTTCCT GGGTCTGAAG ACACGAAGCT TAAATTTGAG GAGATCACCA GTGTAATCAA CCCAGCTCTG GACAAGTACT TCCCATCGGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CTCTGGAGTG AGAATCATAG CTGAGCCAGG CAGATACTAC GTCGCATCAG CTTTCACACT TGCAGTGAAT ATCATTGCCA AAAAAACCGT GTGGAAGGAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CAGACCGGCT CGGACGATGA AGATGAGTCA AACGAGCAAA CTTTGATGTA TTACGTGAAT GATGGAGTGT ATGGGTCATT TAACTGCATT CTTTATGACC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ATGCACATGT GAAGGCCCTG CTGCAGAAGA GACCCAAGCC AGATGAGAAG TATTACTCAT CCAGCATCTG GGGACCAACA TGTGATGGCC TTGATCGGAT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CGTCGAGCGC TGTAGCCTGC CTGAAATGCA TGTGGGTGAT TGGATGCTGT TTGAGAACAT GGGTGCATAC ACTGTTGCTG CTGCTTCTAC TTTCAATGGG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTCCAGAGGC CAAACATCTA CTACGTAATG TCACGGTCAA TGTGGCAACT CATGAAGCAA ATCCAGAGCC ATGGCTTCCC GCCAGAAGTG GAGGAGCAGG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ATGTTGGCAC TCTGCCCATG TCTTGTGCCC AGGAGAGCGG GATGGACCGT CACCCTGCAG CCTGTGCTTC TGCTAGTATC AATGTATAGA TGCCATTCTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GTAGCTCTTA CCTGCAAGTT TAGCTTGAGT TCACGGCATT TGGGGGGACC ATTTAACTTA ATTACTGCTA GTTTGGAATG TCTTTGTAAG AGTAGGGTTG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCACCAATGC AGTATGGAAA GACTAGGAGA TGGGGGTCAC ACTTACTGTG TTCCTATGGA AACTTTGAAT ATTTTATATG GATTTTTATT CACTTTTCAG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ACCTGATACT AATGAGTGCC CCTCGGCTGC TGAGCAAGCA TTTGTAGCTT GTACATTGGC AGAATGGGCT AAAAGCTTAT GTTGTGACCC ATTTTGAAAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TAAAGTATCT TGAAATGATT GGACATTGGA GAATGTGTGC AAGTATCCCT TACAGAAGGC ACAAACTTCT GCACAGGCTG TGTGTTACAG CAGTGAGTCT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AGCCCAGCAG AGATGTGGAT GATACAAAGC TGTGCCCCCT CTGTACAGCA TCAATGTGCT TAGCCCATCT CAAGTGTTTA CTGTGAACTT GGTGCCCAAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GTCTCTTAAG AGTGTCATCT GCCTAGTGGC CTCTTGACTT GGCCACTTCC TAAGGAGAGG GCATCTGAGG CTCTTTGAAC CTTGCCTGCA GAAACCCTGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CTGCTCCCTC AACCCTTGGC CG
^2301      ^2311      ^2321

Credibility of mRNA sequence:

reverse_engineered_fragment_and_the_rest_is_a_guess

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

Rattus norvegicus AR4-2J

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: `2`	Last change: `2009-04-15 13:10:04`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
ODC1

The description of the protein encoded in this ORF:
ornithine decarboxylase

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):

304-1689

Remarks:

The GI:205803 mRNA sequence from rat (2442b) contains 1-423 5'-UTR and 1810-2442b 3'-UTR and aligns well to
the sequence available in IRESdb which acquired the sequence directly from S. Pyronnet. However, the 5'-UTR
sequence matching in GenBank (and used by IRESite since position 121) is longer by 120 bp on the left (only
the overlap shown below):

>gb|M16982.1|RATODC UniGene infoGeoGene info Rat ornithine decarboxylase (ODC) mRNA, complete cds
Length=2442

 GENE ID: 24609 Odc1 | ornithine decarboxylase 1 [Rattus norvegicus]
(Over 10 PubMed links)

 Score =  558 bits (302),  Expect = 7e-159
 Identities = 305/306 (99%), Gaps = 1/306 (0%)
 Strand=Plus/Plus

Query  1    GTCAGTCCCTGCAGCCGCCGCCGCCGGCCGCCTTCAGTCAGCAGCTcggcgccacctccg  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  121  GTCAGTCCCTGCAGCCGCCGCCGCCGGCCGCCTTCAGTCAGCAGCTCGGCGCCACCTCCG  180

Query  61   gtcggcgactgcggcgggctcgacgaggcggctgacggggcggcggcgggaagacggccg  120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  181  GTCGGCGACTGCGGCGGGCTCGACGAGGCGGCTGACGGGGCGGCGGCGGGAAGACGGCCG  240

Query  121  ggTGCGCCTTGGGGTTTAGTGGCGGCTTCTCCATGGGTCCAGCCAGCCGCTTCCCTGTGC  180
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  241  GGTGCGCCTTGGGGTTTAGTGGCGGCTTCTCCATGGGTCCAGCCAGCCGCTTCCCTGTGC  300

Query  181  TGTGAGTGTTTCCACCACTCCAGGAGACAG-ATTCAGAGTTGACCTTGTGAGAGCTGGCC  239
            |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct  301  TGTGAGTGTTTCCACCACTCCAGGAGACAGCATTCAGAGTTGACCTTGTGAGAGCTGGCC  360

Query  240  ATAATTTAATTCCATCTCTAGGTTTTCTGTCTTATTGTTTCAGAGGCACATCGAGAACCA  299
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  361  ATAATTTAATTCCATCTCTAGGTTTTCTGTCTTATTGTTTCAGAGGCACATCGAGAACCA  420

Query  300  ACCATG  305
            ||||||
Sbjct  421  ACCATG  426


A BLAST-based search for ESTs using the GI:205803 rat sequence results in no EST sequence covering completely
the 5'-UTR region. Instead, introns are seen in various positions. It seems the transcription start site is
at the best at position 120 if not downstream. Therefore, the RefSeq record is probably an over-prediction.


The best EST match in terms of sequence identity is:

>gb|CK469804.1| AGENCOURT_17644639 NIH_MGC_237 Rattus norvegicus cDNA clone IMAGE:7113571 5', mRNA sequence.
Length=828

 Score =  558 bits (302),  Expect = 1e-157
 Identities = 302/302 (100%), Gaps = 0/302 (0%)
 Strand=Plus/Plus

Query  122  TCAGTCCCTGCAGCCGCCGCCGCCGGCCGCCTTCAGTCAGCAGCTcggcgccacctccgg  181
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1    TCAGTCCCTGCAGCCGCCGCCGCCGGCCGCCTTCAGTCAGCAGCTCGGCGCCACCTCCGG  60

Query  182  tcggcgactgcggcgggctcgacgaggcggctgacggggcggcggcgggaagacggccgg  241
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  61   TCGGCGACTGCGGCGGGCTCGACGAGGCGGCTGACGGGGCGGCGGCGGGAAGACGGCCGG  120

Query  242  gTGCGCCTTGGGGTTTAGTGGCGGCTTCTCCATGGGTCCAGCCAGCCGCTTCCCTGTGCT  301
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  121  GTGCGCCTTGGGGTTTAGTGGCGGCTTCTCCATGGGTCCAGCCAGCCGCTTCCCTGTGCT  180

Query  302  GTGAGTGTTTCCACCACTCCAGGAGACAGCATTCAGAGTTGACCTTGTGAGAGCTGGCCA  361
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  181  GTGAGTGTTTCCACCACTCCAGGAGACAGCATTCAGAGTTGACCTTGTGAGAGCTGGCCA  240

Query  362  TAATTTAATTCCATCTCTAGGTTTTCTGTCTTATTGTTTCAGAGGCACATCGAGAACCAA  421
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  241  TAATTTAATTCCATCTCTAGGTTTTCTGTCTTATTGTTTCAGAGGCACATCGAGAACCAA  300

Query  422  CC  423
            ||
Sbjct  301  CC  302


There are several other GenBank records covering ODC1 in human but lets say two should be considered more
seriously. The GI:19263695 (2039 b, 29-JUN-2004, 5'-UTR 1-301, 3'-UTR 1688-2039) and GI:33869436 (2043 b,
24-JUN-2004, 5'-UTR 1-484, 3'-UTR 1676-2043). Pyronnet et al., 2000 refer to ODC1 from Rattus norvegicus
having 303b long 5'-UTR. Multiple sequence alignment shows human GI:35135 (2035 b, 18-MAR-1996, 5'-UTR
1-302, 3'-UTR 1689-2035) and GI:19263695 are very similar except about 5 mismatches while one removes an
upstream ATG codon.


Pyronnet et al., Gastroentrology 108(4):xx-xx reported a 53bp shorter variant of ODC1 transcript amplified
by RT-PCR compared to full-legth variant of rat caused by alternative splicing with splice sites moved inwards
of exon1 while both splice donor and acceptor sites appeared in a direct repeat heptanucleotide GGCGGCU and
that the motif was reconstituted in the spliced product. The shorter variant was found to be 3x more
translated than the full-length transcript in which 5'-end 130bp were reported to contain strong secondary
structure.

The ODC1 IRES sequence present in BCCM plasmid repository (not sequence, only guessed based on some GenBank
record) is different. See http://bccm.belspo.be/db/lmbp_plasmid_details.php?NM=pcDNA3-di-RF-ODC for more
details.

Citations:

Pyronnet S., Pradayrol L., Sonenberg N. (2000) A cell cycle-dependent internal ribosome entry site. Mol. Cell. 5(4):607-616

Pyronnet S., Pradayrol L., Sonenberg N. (2005) Alternative splicing facilitates internal ribosome entry on the ornithine decarboxylase mRNA. Cell. Mol. Life Sci. 62(11):1267-1274

IRESs:

IRES:

Version: `5`	Last change: `2009-04-15 13:10:04`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `ODC1`

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

1-303

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GTCAGTCCCT GCAGCCGCCG CCGCCGGCCG CCTTCAGTCA GCAGCTCGGC GCCACCTCCG GTCGGCGACT GCGGCGGGCT CGACGAGGCG GCTGACGGGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGGCGGCGGG AAGACGGCCG GGTGCGCCTT GGGGTTTAGT GGCGGCTTCT CCATGGGTCC AGCCAGCCGC TTCCCTGTGC TGTGAGTGTT TCCACCACTC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CAGGAGACAG CATTCAGAGT TGACCTTGTG AGAGCTGGCC ATAATTTAAT TCCATCTCTA GGTTTTCTGT CTTATTGTTT CAGAGGCACA TCGAGAACCA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ACC
^301

Remarks:

Bicistronic constructs studied by Pyronnet et al., 2000 were tested by in vitro translation in rabbit
reticulocytes (optionally treated with rhinoviral 2A protease) and in transiently transfected cells. Integrity
of bicistronic transcripts used in rabbit reticulocyte lysates was tested by Northern blot. IRES activity is
impaired when UUUC segment is mutated to AAAC (authors mutated the one about 20b upstream from translation
start). But, there are more such short stretches in the 5'-UTR of ODC1.

Citations:

Pyronnet S., Pradayrol L., Sonenberg N. (2000) A cell cycle-dependent internal ribosome entry site. Mol. Cell. 5(4):607-616

Pyronnet S., Pradayrol L., Sonenberg N. (2005) Alternative splicing facilitates internal ribosome entry on the ornithine decarboxylase mRNA. Cell. Mol. Life Sci. 62(11):1267-1274

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