Summary
CRISPR-1 clan
The CRISPR-1 clan contains the RNA families CRISPR-DR2, CRISPR-DR4, CRISPR-DR14, CRISPR-DR17, CRISPR-DR25, CRISPR-DR43 and CRISPR-DR66. The following bioinformatic methods were used to confirm the relationship between these families: CMSEARCH, HMMER3 and PRC [1,2,3].
This clan contains 7 families and the total number of sequence regions in the clan is 31,777.
Literature references
- Nawrocki EP, Kolbe DL, Eddy SR, Bioinformatics. 2009;25:1335-7.: Infernal 1.0: inference of RNA alignments. 19307242
- Eddy SR, PLoS Comput Biol. 2008;4:e1000069.: A probabilistic model of local sequence alignment that simplifies statistical significance estimation. 18516236
- Madera M, Bioinformatics. 2008;24:2630-2631.: Profile Comparer: a program for scoring and aligning profile hidden Markov models. 18845584
Members
This clan contains the following 7 member families:
CRISPR-DR2 CRISPR-DR4 CRISPR-DR14 CRISPR-DR17 CRISPR-DR25 CRISPR-DR43 CRISPR-DR66Structures
For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the mapping between the Rfam families in this clan, the corresponding EMBL entries, and the region of the three-dimensional structures that are available for that sequence.
Loading structure mapping...
Secondary structures
This tool allows you to view the secondary structure images of two clan members side-by-side. Choose the family structures using the two drop-down menus below.
Alignments
The table below shows the number of occurrences of each family throughout the sequence database. In brackets beside each number is the percentage of the total number of sequence hits for the clan that are represented by this family. The rightmost column provides a link to the alignments tab for each family.
| Rfam family | Num. regions | Alignment |
|---|---|---|
| CRISPR-DR66 (RF01379) | 0 (0.0%) | View |
| CRISPR-DR43 (RF01352) | 1,277 (4.0%) | View |
| CRISPR-DR25 (RF01338) | 313 (1.0%) | View |
| CRISPR-DR17 (RF01328) | 45 (0.1%) | View |
| CRISPR-DR14 (RF01327) | 448 (1.4%) | View |
| CRISPR-DR4 (RF01317) | 15,411 (48.5%) | View |
| CRISPR-DR2 (RF01315) | 14,283 (44.9%) | View |
