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Clan: TD (CL00124)


TD (Treponema denticola) motifs

Clan TD include two Treponema dentricola motifs, TD-1 and TD-2, in some cases TD-1 motif overlap reverse complements of TD-2 motif. TD-1 is usually in 5' regulatory region and it has been proposed as a cis-regulatory element while TD-2 is not in 5' regulatory regions and has been propose as a non-coding RNA

This clan contains 2 families and the total number of sequence regions in the clan is 345.

Literature references

  1. Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR, Nucleic Acids Res. 2007;35:4809-4819.: Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. 17621584


This clan contains the following 2 member families:

TD-1 TD-2

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.


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
TD-2 (RF03162) 236 (68.4%) View
TD-1 (RF03155) 109 (31.6%) View