Table 1

Identification of exons on the genome
Category
 Database
 Total records
 Percent placed (%)
 Total unique exons
 Exons in complete ORFs
 Exons in partial ORFs
 Exon length (bp)
 ORF length (bp)
 Putative genes (non-splicing singletons)
 Protein homology (Pfam hits)
 CpG islands
Known
 UTR-DB
 40,258
 80
 19,195
 5,075
 1,895
 6,925,762
 1,990,818
 10,007 (426)
 5,701 (3,813)
 3,866
genes
 HTDB
 15,305
 89
 48,477
 12,077
 7,706
 11,893,081
 4,043,544
 4,816 (148)
 2,938 (1,943)
 1,960
Consensus
 HINT
 87,125
 77
 103,817
 47,055
 15,061
 23,381,024
 10,144,988
 20,357 (959)
 9,121 (6,453)
 7,557
transcripts
 EG
 62,064
 80
 13,085
 5,389
 1,904
 4,562,954
 1,873,723
 4,800 (154)
 2,177 (1,679)
 2,462

THC
 84,837
 81
 38,806
 15,463
 6,671
 12,406,081
 5,078,661
 8,604 (322)
 2,907 (2,026)
 3,983
Transcripts
 GenBank CDS
 110,222
 81
 41,917
 31,626
 1,452
 5,303,064
 4,299,272
 2,634 (227)
 1,858 (1,607)
 1,178

dbEST Human
 2,154,995
 73
 273,881
 147,819
 17,694
 32,288,385
 14,975,758
 20,073 (7,136)
 5,377 (3,745)
 11,807
Rodent
 MINT
 92,531
 30
 8,284
 5,433
 120
 866,046
 780,566
 777
 123 (56)
 486
transcripts
 RINT
 37,367
 46
 5,600
 3,588
 75
 592,788
 546,932
 458
 65 (32)
 255

EMBL
 43,488
 28
 5,819
 4,108
 59
 724,630
 655,993
 202
 68 (72)
 135
Protein
 SWISS-PROT
 86,593
 38
 27,526
 12,072
 1,163
 9,858,797
 7,784,205
 1,648
 1,648 (1,244)
 158
homology
 TrEMBL
 351,834
 13
 22,670
 8,134
 1,677
 4,385,497
 2,886,034
 1,185
 1,185 (654)
 92

PIR
 182,106
 16
 4,106
 1,175
 383
 1,355,644
 764,339
 321
 321 (132)
 20
Total


613,183
 299,014
 55,860
 114,543,753
 55,824,833
 75,982 (9,372)
 33,489 (23,008)
 33,959

Exons were identified after vector screening using transcript, rodent, and protein databases. The definition of a record varies according to the database, while 'exons' refer to high-scoring segment pairs in BlastN comparisons (E < 10-15 and sequence identity >90%) to the genome. Unique exons and all subsequent columns refer to placements that were possible after considering the preceding databases. Placement of rodent transcripts required evidence of splicing and sequence identity >80%. ORFs were identified using getorf [84] using a minimum size of 30bp to report. Protein homology required BlastX E < 10-15. Pfam hits required score >20 using hmmpfam [92]. Gene prediction programs are described in Table 2. CpG islands were identified using cpgreport [84] using standard criteria [45].

Wright et al. Genome Biology 2001 2:research0025.1   doi:10.1186/gb-2001-2-7-research0025