Table 3.

Summary of cDNA clones recovered

Classification	Clone counta
ORF identical to gene annotationb	43
ORF alters gene annotationc:
5′ extension	10
3′ extension	3
5′ short with upstream in-frame stop codon	2
Exon variant	12
Dicistronic	1
Gene merge	1
Subtotal: high-quality, full-length cDNAs	72
Compromised clones:
Nucleotide discrepancyd	6
Shorte
5′ short	1
3′ short	5
5′and 3′ short	1
Co-ligated insertf	7
Antisense transcriptg	1
Genomic contaminanth	4
Retained introni	3
SLIP artifact	4
Subtotal: compromised cDNAs	32
Gene-specific clones recovered	104

^aOne cDNA clone was selected per target gene.

^bThe clone encodes a protein that is identical to the corresponding Release 4.1 annotation.

^cThese clones encode proteins that differ from their corresponding annotation. ‘5′ extension’ and ‘3′ extension’ clones encode additional N-terminal and C-terminal residues, respectively, relative to the annotation. ‘5′ short with upstream in-frame stop codon’ clones encode full-length ORFs that are missing sequences encoding N-terminal residues relative to the annotation and may represent alternatively spliced products. ‘Exon variant’ clones contain sequence differences relative to the annotation at internal positions in the CDS and represent alternatively spliced products.

^dThe sequence of these clones have nucleotide differences, most likely the result of errors generated by reverse transcriptase during library construction, that introduce a missense or frameshift change in the ORF relative to the annotated CDS.

^eThese clones are missing sequences encoding the N-terminal portion of the predicted protein sequence of the annotation for the ‘5′ short’ class, the C-terminal portion for the ‘3′ short’ class, or both for the ‘5′ and 3′ short’ class.

^fThese clones contain sequences from two unrelated genes and are almost certainly the result of two cDNA molecules being cloned into the same plasmid vector during library construction. In three such cases, the clones encode proteins that are identical to the targeted annotation.

^gThe sequence of the clone overlaps the annotated gene model but is transcribed from the opposite strand.

^hThese clones do not include a poly-adenylated tail. These are genomic clones that contaminate the cDNA libraries.

ⁱThese clones are poly-adenylated and include unprocessed intron.