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.
|