Proposed list of taxa for Comparative Analysis of Eukaryotic Promoter Architecture
R. Taylor Raborn** and Krishnakumar Sridharan**
May 9th, 2011
List of proposed taxa (common name)
Animalia
H. sapiens (human)
Reference
Available TSS and transcript Data (Number of
clones)
-Yamashita et al., 2011
[~140 million tags in 12 human tissues]
-Mammalian Gene Collection-MGC (29,818 fulllength cDNA) and dbEST (8,314,509 EST sequences)
M. musculus (house mouse)
-Yamashita et al., 2010
20,246,303 (tags from cultured cells)
-MGC (27,285 full-length cDNA) and dbEST
(4,853,542 ESTs)
D. rerio (Zebrafish)
-Yamashita et al., 2006
32,263 clones/15,198 TSSs
-MGC (16,739 full-length cDNA) and dbEST
(1,488,275 ESTs)
D. melanogaster (fruit fly)
-Hoskins et al., 2011
CAGE 21 million tags
- BDGP (full-length cDNAs) and dbEST (821,005
ESTs)
C. elegans (nematode worm)
-WormBase- SAGE and other data
-dbEST (396,687 ESTs)
P. falciparum (Malarial protozoan parasite)
-Yamashita et al., 2006
10,236 clones/ 6908 TSS
-Comparasite ftp
-P.Falciparum 3D7 dbEST (53,293) P.Falciparum
dbEST (40,620)
T. gondii (Protozoan parasite
Cause of Toxoplasmosis)
-Yamagishi et al., 2010
TSS-seq 1.24*105 TSSs, clustered into 103 TSRs
-Comparasite ftp TSS tags (6,801,945 )
-dbEST (136,229)
Fungi
S. pombe (fission yeast)
C. cinerea (gray shag mushroom)
-Wilhelm et al., 2008
High density tiling array giving TSS assignments
-dbEST (109,202)
-5’SAGE project completed by Tommy Chu
(personal communication) Publication status
unknown
L. edodes (Shittake mushroom)**
Plantae
C. merolae (red algae)
A. thaliana (thale cress)
-dbEST (15,777)
-WWY Chum et al., 2011
454 GS 20
cDNAs pooled from sporeless (FB) and sporebearing (FBS) fruiting bodies
-dbEST (26,541)
-Yamagishi et al., 2010
22,923 clones/14,029 TSSs
-U Tokyo link (see below)
-Yamamoto et al., 2009
CT-MPSS 158,237tags/38,311 TSS
-RIKEN Arabidosis full-length (RAFL cdnas) -> 155,144
RAFL cDNAs clustered into 14,668 nonredundant cDNA
groups (about 60% of predicted genes)
-dbEST/plantGDB/Brendel grp (1,529,700 ESTs)
Z. mays (maize)
O. Sativa(Rice)
-Li et al., 2010
120 million reads (RNA-seq)
- dbEST/plantGDB/Brendel grp (2,019,105
ESTs)
-Maize full-length cDNA project (Varying number
of FLcDNA based on strictness)
- 28,469 full-length cDNA clones for japonica
strain
-dbEST/plantGDB/Brendel grp (1,252,989
ESTs)
RESOURCES AND LINKS:
1. Mammalian Gene Collection (ftp://ftp.ncbi.nih.gov/repository/MGC/MGC_project/MGC_project_data/)
2. Full-length cDNA links – (http://www.ncbi.nlm.nih.gov/genome/flcdna/)
3. Berkeley Drosophila Genome Project – (http://www.fruitfly.org/sequence/dlcDNA.shtml)
4. WormBase for c.elegans – (ftp://ftp.wormbase.org/pub/wormbase/genomes/c_elegans/)
5. Full-length cDNA database for parasites-- http://comparasite.hgc.jp/ (see lower left of
webpage)
6. C.Merolae Genome resource -- http://merolae.biol.s.u-tokyo.ac.jp/download/
7. RARGE = RIKEN Arabidopsis Genome Encyclopedia -- http://rarge.psc.riken.jp/cdna/cdna.pl
and http://rarge.psc.riken.jp/archives/rafl/
8. Maize full-length cDNA resource -- http://www.maizecdna.org/download/
9. Rice Oryza Sativa japonica strain FL cDNA resource -ftp://cdna01.dna.affrc.go.jp/pub/data/
10. Plant EST and genome information and sequences -http://grinch2.gdcb.iastate.edu/PlantGenome/plantGenomeTable.php
* Genome sequence currently unavailable- genome project underway at Chinese University of Hong Kong