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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.
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Genome Biology

ISSN: 1474-760X

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