Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release

Table 1 Statistics for Arabidopsis reannotation Release 5.

	Chr. 1	Chr. 2	Chr. 3	Chr.4	Chr. 5	Total
DNA molecules
Length (Mb)	30.269	19.702	23.465	18.582	26.978	118.998
%GC
overall	35.9	35.9	36.3	36.2	35.9	36.0
coding	44.1	44.2	44.3	44.2	44.1	44.2
intronic	32.4	32.3	32.6	32.4	32.3	32.4
intergenic	30.8	31.4	31.6	31.6	31.1	31.2
Genes
# genes	6,772	4,104	5,233	3,985	6,113	26,207
gene density (kb/gene)	4.47	4.80	4.48	4.66	4.41	4.5
Avg. gene length (bp)^a	2,287	2,156	2,197	2,269	2,227	2,232
Avg. protein length	425	398	417	421	419	417
# genes in protein families	4,834	2,884	3,803	2,839	4,281	18,641
#genes duplicated via segmental chromosome duplications	1,868	961	1,315	1,147	1,291	6,582
#genes found tandemly duplicated	993	545	750	636	813	3,737
#genes with alt splicing isoforms	600	412	444	357	517	2,330
#genes with annotated UTRs	4,717	2,936	3,575	2,724	4,147	18,099
#transposons and pseudogenes	748	817	837	652	732	3,786
# tRNA genes	240	96	93	79	123	631
Exons
# exons	37,710	21,428	27,937	21,800	33,255	142,130
total length (Mb)	10.378	5.919	7.812	6.011	9.170	39.290
avg exons/gene	5.57	5.22	5.34	5.47	5.44	5.42
avg exon size	275	276	280	276	276	276
Introns
# introns	30,938	17,324	22,704	17,814	27,191	115,921
total length (Mb)	5.060	2.903	3.657	3.016	4.416	19.053
avg size	164	168	161	169	163	164
Proteome
# distinct proteins	7,176	4,451	5,540	4,231	6,457	27,855
# proteins with interpro domains	6,142	3,686	4,676	3,573	5,441	23,518
# with TM domain	2,047	1,429	1,599	1,316	1,768	8,159
Signal peptides
secretory	1,262	797	974	773	1,103	4,909
chloroplast	1,062	681	845	666	1,021	4,275
mitochondria	820	490	612	430	736	3,088

ISSN: 1741-7007