ENCODE Project: Comparative Sequencing

The ENCODE Project is an NHGRI-led initiative that aims to identify all the functional elements in the human genome. Its initial effort is a pilot-scale program that is focusing on 1% of the human genome, distributed across 44 discrete regions. A major component of the ENCODE Project is the comparative sequencing of these regions in multiple vertebrate species. In partnership with the Genome Technology Branch of NHGRI, NISC is extensively involved in generating these multi-species sequences and analyzing the resulting data. This and subsequent pages provide a summary of the progress to date in mapping and sequencing the 44 ENCODE regions in various species. For further information, contact NISC@nhgri.nih.gov.  For information about genome-wide DNA sequencing efforts, see the International Sequencing Consortium web page http://www.intlgenome.org.
Overall progress in sequencing ENCODE targets in various species, listed in general anticipated order (species-by-species) for data generation: Species Total Sequenced BACs Multi-BAC Assembled Targets Current BAC Gaps in Assembly % Human Sequence Represented Species Progress by Target Galago (small-eared) 285/285 (100%) 44/44  11  96%  Data File  Baboon (olive) 302/302 (100%) 44/44  8  97%  Data File  Marmoset (white-tufted-ear) 275/275 (100%) 44/44  5  99%  Data File  Armadillo (nine-banded) 386/386 (100%) 44/44  24  94%  Data File  Platypus 230/236 (97%) 41/42  12  80%  Data File  Bat (greater horseshoe) 259/260 (100%) 44/44  3  98%  Data File  Elephant (African) 397/398 (100%) 44/44  19  96%  Data File  Hedgehog (middle-African) 313/322 (97%) 42/44  22  82%  Data File  Rabbit 234/234 (100%) 43/44  5  91%  Data File  Shrew (European) 290/296 (98%) 44/44  9  91%  Data File  Dusky titi 232/236 (98%) 44/44  3  97%  Data File  Monkey (owl) 234/236 (99%) 44/44  4  98%  Data File  Monkey (colobus) 213/216 (99%) 44/44  7  97%  Data File  Lemur (gray mouse) 181/188 (96%) 44/44  6  95%  Data File  Guinea Pig 251/263 (95%) 44/44  12  95%  Data File  Cat 282/284 (99%) 44/44  9  97%  Data File  Tenrec (lesser hedgehog) 262/263 (100%) 44/44  13  94%  Data File  Bat (little brown) 189/198 (95%) 44/44  15  89%  Data File  Squirrel (13-lined ground) 247/254 (97%) 44/44  10  94%  Data File  Gibbon (northern white-cheeked) 227/229 (99%) 44/44  9  98%  Data File  Monkey (Bolivian squirrel) 193/197 (98%) 44/44  4  94%  Data File  Monkey (African green) 243/249 (98%) 44/44  7  97%  Data File  Horse 188/205 (92%) 43/43  8  90%  Data File  Flying Fox (Malayan) 189/193 (98%) 43/44  9  87%  Data File  Rock hyrax 218/219 (100%) 44/44  14  84%  Data File  Shrew (northern tree) 246/252 (98%) 43/43  33  86%  Data File  Opossum (gray short-tailed) 346/355 (97%) 41/43  15  76%  Data File  Ferret (domestic) 145/159 (91%) 31/39  18  54%  Data File  Sloth (two-toed) 300/318 (94%) 41/43  39  71%  Data File  Alpaca 151/162 (93%) 44/44  8  92%  Data File  Pika (American) 134/200 (67%) 20/44  3  38%  Data File  Download data file for all species
	Target-by-Target, Species-by-Species Sequencing Summary
		Summary of BAC Maps
		Summary of BAC Sequencing
		Summary of Multi-BAC Assemblies
	NHGRI Homepage for ENCODE project
	UCSC Homepage for ENCODE project