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BIOINF 09-020: Nematode sbRNAs: homologs of vertebrate Y RNAs
Ilenia Boria, Andreas R. Gruber, Andrea Tanzer, Stephan Bernhart, Ronny Lorenz, Michael M. Mueller, Ivo L. Hofacker, Peter F. Stadler
Detected sbRNAs/Y RNAs
- Full list of detected sbRNAs/Y RNAs [HTML|CSV]
- all sbRNAs [FASTA]
- sbRNAs with verified promoter regions [FASTA]
- Loop motifs of sbRNAs with verified promoter regions (+ Hits from A. caninum) [FASTA]
Genomes/Sequences used in this anlysis
- C. elegans (ftp://ftp.wormbase.org/pub/wormbase/genomes/c_elegans/sequences/dna/c_elegans.WS198.dna.fa.gz)
- C. briggsae (ftp://ftp.wormbase.org/pub/wormbase/genomes/c_briggsae/assembly/cb3)
- C. remanei (ftp://ftp.wormbase.org/pub/wormbase/genomes/c_remanei/assembly/Caenorhabditis_remanei-15.0.1/output/supercontigs.fa.gz)
- C. brenneri (ftp://ftp.wormbase.org/pub/wormbase/genomes/c_brenneri/sequences/dna/c_brenneri.WS198.dna.fa.gz)
- C. japonica (ftp://ftp.wormbase.org/pub/wormbase/genomes/c_japonica/sequences/dna/c_japonica.WS198.dna.fa.gz)
- P. pacificus (ftp://ftp.wormbase.org/pub/wormbase/genomes/p_pacificus/sequences/dna/p_pacificus.WS198.dna.fa.gz)
- H. contortus (ftp://ftp.sanger.ac.uk/pub/pathogens/Haemonchus/contortus/genome/contigs/combined_worms_supercontigs200808.fasta)
- M. incognita (http://meloidogyne.toulouse.inra.fr/Mi/MiV1A1/img/Mincognita_scaffold_v1.fasta.gz)
- M. hapla (http://www.hapla.org/Mh10g200708.Contigs.fas)
Upstream sequences and Position Weight Matrices of other Pol III transcripts than sbRNAs/Y RNAs
- Upstream sequences of U6 RNAs, RNAseP, RNAseMRP and tRNA-Sec used to build PWMs for TATA box, PSE A and PSE B [FASTA]
- TATA box used for all species in clade V [Alignment|PWM]
- C. elegans [Alignment|PWM PSE A|PWM PSE B]
- C. briggsae [Alignment|PWM PSE A|PWM PSE B]
- C. remanei [Alignment|PWM PSE A|PWM PSE B]
- C. brenneri [Alignment|PWM PSE A|PWM PSE B]
- C. japonica [Alignment|PWM PSE A|PWM PSE B]
- P. pacificus [Alignment|PWM PSE A|PWM PSE B]
- H. contortus [Alignment|PWM PSE A|PWM PSE B]
- M. incognita [Alignment]
- M. hapla [Alignment]