RNAhub
U6-0c44b443 (U6)
The raw output files for each step of the pipeline can be found here.
Input: sequence:
>u6 human GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUGCGCAAGGAUGACACG CAAAUUCGUGAAGCGUUCCAUAUUUUUDatabase: metazoa
PDB hits:
>u6 human GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUGCGCAAGGAUGACACG time blastn -num_threads 6 -db /home/rnahub/db/pdbnt/pdbnt -query /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq.fa -outfmt=5 -out /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq.xml gi|2258077654|pdb|7W5B|F Chain F, U6 snRNA gi|2258077599|pdb|7W5A|F Chain F, U6 snRNA gi|2258077563|pdb|7W59|F Chain F, U6 snRNA gi|1979407700|pdb|6AHD|F Chain F, U6snRNA gi|1890525250|pdb|5Z57|F Chain F, U6 snRNA gi|1890525191|pdb|5Z56|F Chain F, U6 snRNA gi|1890525129|pdb|5YZG|F Chain F, U6 snRNA gi|1890524963|pdb|5XJC|F Chain F, U6 snRNA gi|1595430737|pdb|6ID1|F Chain F, U6snRNA gi|1595430689|pdb|6ID0|F Chain F, U6snRNA gi|1595430635|pdb|6ICZ|F Chain F, U6snRNA gi|1595430362|pdb|6FF7|6 Chain 6, U6 snRNA gi|1540347645|pdb|6FF4|6 Chain 6, U6 snRNA gi|1516608147|pdb|6AH0|F Chain F, U6snRNA gi|1482416893|pdb|5Z58|F Chain F, U6 snRNA gi|1979440414|pdb|6QX9|6 Chain 6, U6 snRNA gi|1917925253|pdb|7A5P|6 Chain 6, U6 snRNA gi|1004171286|pdb|3JCR|N Chain N, U6 snRNA gi|1983831652|pdb|7ABI|6 Chain 6, U6 snRNA gi|1979406317|pdb|7ABG|6 Chain 6, U6 snRNA gi|1979406270|pdb|7ABF|6 Chain 6, U6 small nuclear RNA gi|1951686208|pdb|7AAV|6 Chain 6, U6 snRNA gi|1890522053|pdb|6QDV|6 Chain 6, U6 snRNA gi|1233034096|pdb|5O9Z|6 Chain 6, Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNA gi|1169077292|pdb|5MQF|6 Chain 6, Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNA gi|1979440390|pdb|6QW6|6 Chain 6, U6 snRNA gi|1917925130|pdb|6ZYM|6 Chain 6, U6 snRNA gi|929984519|pdb|3JB9|N Chain N, U6 snRNA gi|1991455749|pdb|7D58|R Chain R, Non-template DNA
Rfam hits:
rank E-value score bias modelname start end mdl trunc gc description (1) ! 6.3e-29 109.4 0.0 U6 1 107 + cm no 0.46 U6 spliceosomal RNA Rfam accession for U6: RF00026 saved to /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq+RF00026_seed.fa >u6 human GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUGCGCAAGGAUGACACG CAAAUUCGUGAAGCGUUCCAUAUUUUU >AB010698.1/46416-46518 GUCCCUUCGGGGACAUCUGAUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUG CGCAAGGAUGACACGCAUAAAUCGAGAAAUGGUCCAAAUUUUU >AARH01001853.1/272694-272592 GUCUCUUCGGAGACAUCUGAUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUG CGCAAGGAUGACACGCACAAAUCGAGAAAUGGUCCAAAUUUUU >X60506.1/390-492 GUCCCUUCGGGGACAUCCGAUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUG CGCAAGGAUGACACGCACAAAUCGAGAAAUGGUCCAAAUUUUU >AC146705.11/15272-15374 GUCCCUUCGGGGACAUCCGAUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUG CGCAAGGAUGACACGCACAAAUCGAGAAAUGGUCCAAAUUUUU [...] cmalign RF00026.cm /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq+RF00026_seed.fa > /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq+RF00026_seed.sto /home/rnahub/opt/hmmer/hmmer-3.3.2/bin//esl-alistat /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq+RF00026_seed.sto > /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/rfam_stats.txt cmd: /home/rnahub/opt/hmmer/hmmer-3.3.2/bin//esl-alistat /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq+RF00026_seed.sto > /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/rfam_stats.txt Rscape DONE Query u6 length 107 in the alignment seq+RF00026_seed.sto number of columns with low coverage (<50%) for the query sequence 1; coverge for the query: 99%
R-scape on rfam alignment:
The final alignment (*cacofold.sto) can be found here.
List of covarying basepairs (#3)
| In given structure | Left Position | Right Position | Score | E-value | p-value | Substitutions | Power |
|---|---|---|---|---|---|---|---|
| * | 2 | 50 | 272.77949 | 4.86652e-07 | 8.42249e-11 | 49 | 0.86 |
| * | 3 | 49 | 258.80373 | 1.66548e-06 | 2.88245e-10 | 59 | 0.89 |
| * | 5 | 45 | 214.78797 | 8.08633e-05 | 1.3995e-08 | 56 | 0.88 |
BPAIRS 19 avg substitutions per BP 23.2 BPAIRS expected to covary 10.1 +/- 1.9 BPAIRS observed to covary 3
Alignment statistics:
Alignment number: 1 Format: Stockholm Number of sequences: 189 Alignment length: 225 Total # residues: 20223 Smallest: 85 Largest: 167 Average length: 107.0 Average identity: 70%
There is no statistically significant covariation in the final alignment
R-scape on nhmmer alignment:
The final nhmmer alignment can be found here.
Alignments from each iteration: iteration 1, iteration 2, iteration 3.Alignment statistics:
Alignment number: 1 Alignment name: u6 Format: Stockholm Number of sequences: 178 Alignment length: 1238 Total # residues: 18148 Smallest: 62 Largest: 106 Average length: 102.0 Average identity: 94%
Job log: