myRT
Top 15 domains that tend to co-occur with CRISPR-like RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with CRISPR-like RT.Note 2: X*2, if found in the table, either means one gene has two consecutive X domains or two adjacent genes both have X domain.
Note 3: If two instances of a domain X are found in the neighborhood of a particular RT R, it will be counted as 2 occurences of domain X, but 1 co-occurance of X and R).
Note 4: click on 'link' to retrieve all genomes that contain the domain, and 'piechart' to see this domain's distribution among different RTs (including CRISPR-like).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-CRISPR | 75 (100%) | 1 (142/142) | link | piechart |
| YHI9 (COG0384) | 9 (12%) | 0.281 (9/32) | link | piechart |
| RnaI (COG3719) | 9 (12%) | 0.9 (9/10) | link | piechart |
| RVT-GII | 6 (8%) | 0 (2/18858) | link | piechart |
| RNase_T2_prok (cd01062) | 5 (7%) | 1 (5/5) | link | piechart |
| HTH_17 (pfam12728) | 5 (7%) | 0.066 (5/76) | link | piechart |
| GIIM (pfam08388) | 5 (7%) | 0.001 (8/11414) | link | piechart |
| DarT | 4 (5%) | 0.444 (4/9) | link | piechart |
| RVT-CRISPR*2 | 3 (4%) | 1 (7/7) | link | piechart |
| Macro_Poa1p_like | 3 (4%) | 0.176 (3/17) | link | piechart |
| HTH_Tnp_1 (pfam01527) | 3 (4%) | 0.003 (1/292) | link | piechart |
| DUF45 (pfam01863) | 3 (4%) | 0.053 (1/19) | link | piechart |
| DDE_Tnp_1_assoc (pfam13808) | 3 (4%) | 0.085 (4/47) | link | piechart |
| DDE_Tnp_1 (pfam01609) | 3 (4%) | 0.007 (4/566) | link | piechart |
| COG4584 (Transposase ) | 3 (4%) | 0.013 (3/239) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-CRISPR | 1968 (100%) | 1 (2021/2021) | link | piechart |
| GIIM (pfam08388) | 97 (5%) | 0.001 (44/84110) | link | piechart |
| L1-EN (cd09076) | 53 (3%) | 0.171 (54/316) | link | piechart |
| RVT-GII | 51 (3%) | 0 (7/162823) | link | piechart |
| RVT-CRISPR*2 | 47 (2%) | 1 (86/86) | link | piechart |
| R1-I-EN (cd09077) | 46 (2%) | 0.439 (47/107) | link | piechart |
| YfmG (COG1262) | 45 (2%) | 0.001 (2/1659) | link | piechart |
| RnaI (COG3719) | 42 (2%) | 0.75 (3/4) | link | piechart |
| NrdG (TIGR02491) | 34 (2%) | 0.453 (34/75) | link | piechart |
| PTPS (pfam01242) | 33 (2%) | 0.717 (33/46) | link | piechart |
| GT4_PimA-like (cd03801) | 33 (2%) | 0.158 (21/133) | link | piechart |
| YHI9 (COG0384) | 28 (1%) | 0.151 (28/185) | link | piechart |
| queuosine biosynthesis protein QueC (PRK11106) | 28 (1%) | 0.384 (28/73) | link | piechart |
| group_II_RT_mat (TIGR04416) | 26 (1%) | 0.003 (12/3757) | link | piechart |
| RT_nLTR_like (cd01650) | 25 (1%) | 0.439 (25/57) | link | piechart |