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Table 1 Genes with pseudogene features (GPFs) and pseudogenes

From: Identification and characterization of pseudogenes in the rice gene complement

Category

No. of GPFs

Pseudogenes (%)1

Transcribed pseudogenes

Unsupported2

17792

1191 (7%)

101 (8.5%)

Long UTR3

831

104 (12%)

35 (34%)

Short CDS4

734

5(4%)

0 (0%)

Poly-A tail5

475

30(6%)

1 (3%)

Segmentally duplicated6

248

40(16%)

14 (35%)

Single-exon singletons7

4833

202(4%)

31 (15%)

Total (non redundant)

22033

1439(6.5%)

170 (13%)

  1. 1 Pseudogenes (with parent gene and at least one frameshift or premature stop codon)
  2. 2 GPFs not supported by cDNA or EST evidence
  3. 3 The UTRs of the GPFs are longer than mean + 2 standard deviations
  4. 4 The CDS of the GPFs are shorter than 50 amino acids
  5. 5 The GPFs contain a stretch of 18 adenines in a 20-base window, within -200 to 400 bases from the end of the annotated UTR, or within 600 bases of the stop codon if no UTR is annotated
  6. 6 The CDS of the GPFs are significantly shorter than their respective paralog or, the GPFs have a significantly smaller number of exons
  7. 7 The GPFs contain a single exon and are within a segmentally duplicated region but have no paralog in the duplicated region