Table 1 Chlamydomonas sequence data collected for the ChlamyCyc web-portal
From: ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii
Name | Type | Source | Mapping |
|---|---|---|---|
| Â | Genomic sequence data | Â | Â |
Chlre3_1_genome_scaffolds | DNA genomic scaffolds (all1) | JGI2 | - |
JGI 4.0 genome_scaffolds | DNA genomic scaffolds | JGI3 | - |
Chlamy chloroplast | DNA complete genome sequence (. NC_005353) | Genbank | - |
Chlamy mitochondrion | DNA complete genome sequence (. NC_001638) | Genbank | - |
Chlamy GSS | DNA (15574 GSS sequences from Genbank4) | PlantGDB5 | razerS12 |
Chlamy STS | DNA (8 STS sequences from Genbank7) | PlantGDB5 | razerS12 |
Chlamy HTG | DNA (2 HTG sequences from Genbank8) | PlantGDB5 | razerS12 |
| Â | Transcript sequence data | Â | Â |
Chlre3_1.GeneCatalog_2007_09_13.transcripts | mRNA transcripts (frozen gene catalog 3.1) | JGI2 | GFF (from JGI) |
Chlamy Chlre3.1M dna | mRNA transcripts (Science paper) | JGI2 | GFF (from JGI) |
Chlre3_1_allESTs.fasta | mRNA transcripts | JGI2 | gmap6 |
Chlre3_1_ESTcluster.cr.171 | mRNA transcripts | JGI2 | gmap6 |
Chlre3_1_ESTcluster.cr.210 | mRNA transcripts | JGI2 | gmap6 |
Chlamy ESTs | mRNA (202044 EST sequences from Genbank) | PlantGDB4 | gmap6 |
Chlamy ESTcontigs | mRNA (50380 EST assembly sequences) | PlantGDB4 | gmap6 |
| Â | RNA data | Â | Â |
microRNAs | RNA (microRNAs) | MirBase10 | GFF (from JGI) |
Cresi-RNAdb | RNA (small RNAs) | cresi-RNA11 | razerS12 |
Chlamydomonas_reinhardtii.scRNA.PLN | RNA (1 scRNA from Genbank) | Genbank | razerS12 |
Chlamydomonas_reinhardtii.snRNA.PLN | RNA (5 snRNAs from Genbank) | Genbank | razerS12 |
Chlamydomonas_reinhardtii.tRNA.PLN | RNA (7 tRNA sequences from Genbank) | Genbank | razerS12 |
Chlamydomonas_reinhardtii.RNA.PLN | RNA (4182 RNA sequences from PLN nucleotides) | Genbank | razerS12 |
| Â | Protein sequence data | Â | Â |
Chlre3_1.GeneCatalog_2007_09_13.proteins | Protein (Frozen gene catalog 3.1) | JGI2 | GFF (from JGI) |
Chlamy Chlre3.1M.pep | Protein (Science Paper) | JGI2 | GFF (from JGI) |
allChlre3.proteins | Proteins (alternative gene models) | JGI2 | GFF (from JGI) |
Chlamy cp aa | Proteins (chloroplast) | Genbank | Genbank |
Chlamy mt aa | Proteins (mitochondrion) | Genbank | Genbank |
Chlamy peptides | Proteins (experimental identified peptides) | JGI3 | JGI |