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Clan: SL (CL00020)

Summary

SL clan

The SL clan contains the RNA families SL1 and SL2. Homology between these families has been established in the published literature [1]. The following bioinformatic methods were used to confirm the relationship between these families: HMMER3 and PRC [2,3].

This clan contains 2 families and the total number of sequence regions in the clan is 1,216.

Literature references

  1. Dassanayake RS, Chandrasekharan NV, Karunanayake EH, Gene 2001;269:185-193.: Trans-spliced leader RNA, 5S-rRNA genes and novel variant orphan spliced-leader of the lymphatic filarial nematode Wuchereria bancrofti, and a sensitive polymerase chain reaction based detection assay. 11376950
  2. Eddy SR, PLoS Comput Biol. 2008;4:e1000069.: A probabilistic model of local sequence alignment that simplifies statistical significance estimation. 18516236
  3. 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 2 member families:

SL1 SL2

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
SL2 (RF00199) 306 (25.2%) View
SL1 (RF00198) 910 (74.8%) View