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Table 1 ESTS encoding chimeric miRNA precursor mRNA transcripts

From: EST analyses predict the existence of a population of chimeric microRNA precursor-mRNA transcripts expressed in normal human and mouse tissues

miRNA Example EST Source Number of ESTs with mRNA Any with poly(A)+ tail? mRNA Length of mRNA contained in nucleotides Location of mRNA contained
21, 104 BF326048 Human normal amnion 3 No NM_030938 vesicular membrane protein 1 290 3' UTR
22 BQ887833 Human pigmented retinal epithelium 13 Yes AF070569* clone 24659 472 5' UTR
93, 94 AW990440 Mouse lactating mammary gland 1 No XM_124678 mini chromosome maintenance deficient 7 159 Coding sequence
123, 126 BI395608 Rat mixed tissues 1 No NM_139104 estrogen-regulated protein 167 Coding sequence
124a BF402302 Rat brain 2 Yes XM_139109 kinesin-like 164 Coding sequence
125b BG000222 Human normal placenta 1 No NM_147207 ischemia related factor vof-16 73 5' UTR
142-s, 142-as BM994627 Human metastatic chondrosarcoma 6 Yes XM_173924 hypothetical protein 21 Coding sequence
  1. Each of the miRNAs reported in [2] and [3] were characterized against the NCBI Entrez combined EST database using BLAST (parameters optimized for short sequences: expect = 1,000, word size = 7, no filtering) [14, 15]. Each EST that matched a miRNA perfectly in either orientation was characterized by BLAST against the nr database (using default parameters). An EST was deemed to be a likely miRNA precursor if its sequence matched the miRNA exactly and if the mfold secondary-sequence prediction algorithm [16, 17] predicted that this sequence lies on the arm of an imperfect hairpin of around 70 nucleotides. Note that several different miRNA sequences are often represented in the same EST. *Although this mRNA is not annotated, it overlaps in sense direction with two other annotated mRNAs BC007813 and NM_032895, allowing it to be assigned unambiguously. After this paper was initially submitted for publication, these records were removed from GenBank as a result of standard genome annotation processing (though still visible upon query of the database). However, that does not imply that the records are necessarily obsolete or in error. EST 990440 matched not only XM_124678, but numerous other mRNAs that are still in GenBank - for example, NM_008568. Thus, the finding is not restricted to a single rogue mRNA entry. The entire sequence of XM_173924 maps with no discrepancies to two human chromosome 17 genomic clones (for example, AC023992), suggesting that it does not contain sequencing errors.