A draft annotation and overview of the human genome

Table 1 Identification of exons on the genome after vector screening using transcript, rodent, and protein databases.

Category	Database	Total Records	Percent Placed	Unique Exons	Exon Length (bp)	Putative genes (Non-Splicing Singletons)	Protein Homology (Pfam Hit)	CpG Isplands
Known genes	UTR-DB	40,258	80%	19,195	6,925,762	10,007 (426)	5,701 (3,813)	3,866
HTDB	15,305	89%	48,477	11,893,081	4,816 (148)	2,938 (1,943)	1,960
Consensus Transcripts	HINT	87,000	77%	103,817	23,381,024	20,357 (959)	9,121 (6,453)	7,557
EG	62,064	80%	13,085	4,562,954	4,800 (154)	2,177 (1,679)	2,462
THC	84,837	81%	38,806	12,406,081	8,604 (322)	2,907 (2,026)	3,983
Transcripts	GenBank CDS	110,222	81%	41,917	5,303,064	2,634 (227)	1,858 (1,607)	1,178
DbEST Human	2,154,995	73%	273,881	32,288,385	20,073 (7,136)	5,377 (3,745)	11,807
Rodent Transcripts	MINT	92,531	30%	8,284	866,046	777	123 (56)	486
RINT	37,367	46%	5,600	592,788	458	65 (32)	255
EMBL Rodent	43,488	28%	5,819	724,630	202	68 (72)	135
Protein Homology	SWISS-PROT	86,593	38%	27,526	9,858,797	1,648	1,648 (1,244)	158
TrEMBL	351,834	13%	22,670	4,385,497	1,185	1,185 (654)	92
PIR	182,106	16%	4,106	1,355,644	321	321 (132)	20
Total				613,183	114,543,753	75,982 (9,372)	33,489 (23,008)	33,959

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%. Protein homology required BlastX E < 10^-15. Pfam hits required score > 20 using hmmpfam (http://hmmer.wustl.edu). CpG islands were identified using cpgreport (http://www.emboss.org) using standard criteria [24].

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