Skip to main content

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
  Genomic sequence data   
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
  Transcript sequence data   
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
  RNA data   
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
  Protein sequence data   
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
  1. 1Assembly v.3.1 scaffolds and scaffolds excluded from v.3.1 assembly file based on blast hits or manual examination
  2. 2 http://genome.jgi-psf.org/Chlre3/Chlre3.download.ftp.html
  3. 3Personal communication
  4. 4 http://www.ncbi.nlm.nih.gov/dbGSS/
  5. 5 http://www.plantgdb.org/search/misc/plantlistconstruction.php?mySpecies=Chlamydomonas%20reinhardtii
  6. 6 http://www.gene.com/share/gmap/
  7. 7 http://www.ncbi.nlm.nih.gov/dbSTS/
  8. 8 http://www.ncbi.nlm.nih.gov/HTGS/
  9. 9 http://www.ncbi.nlm.nih.gov/dbEST/
  10. 10 http://microrna.sanger.ac.uk/
  11. 11 http://cresirna.cmp.uea.ac.uk/
  12. 12 http://www.seqan.de/projects/razers.html