Introduction

These are motifs that we would like to agree on definitions for.

Motifs

A minor RNA motif (SO:0000022)

SO def: "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]

hammerhead ribozyme (SO:0000380)

SO def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." http://rnaworld.bio.ku.edu/class/RNA/RNA00/RNA_World_3.html

asymmetric RNA internal loop (SO:0000021)

SO def: "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]

K turn RNA motif (SO:0000023)

SO def: "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]

also in FR3D: cWW-tSH-tWH-tHS-cWW_kink-turn

also in FR3D: cWW-tSH-tSH-tHS-cWW_kink-turn

sarcin like RNA motif (SO:0000024)

SO def: "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." http:////proton.chem.yale.edu/pdf/7897662.pdf

also in FR3D: cWW-tSH-tHW-tHH-cWW_sarcin-like

symmetric RNA internal loop (SO:0000025)

SO def: "An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]

RNA junction loop (SO:0000026)

no SO def.

RNA hook turn (SO:0000027)

no SO def.

C-loop

cWW-tHW-cSW-cWW

sarcin/ricin motif

(contrast sarcin like RNA motif above (SO:0000024))

cWW-tSH-tHW-cSH-tHH-tHS-cWW

cWW-tWH-insertion-tHS-cWW

GAAA-receptor

cWW-tWH-cWW

cWW-(cWW-cSW)-(tWH-cWW)-cWW-cWW

cWW-tSH-tWH-tHS-cWW

cWW-tHS-cWW

cWW-tSH-tHS-cWW

cWW-tSH-tSH-tHS-cWW

cWW-tSH-tSH-tHS-tHS-cWW

cWW-tWH-tSH-tHS-cWW

cWW-cWS-cWW

cWW-(cWH-cWW)-(tHW-cWW)-cWW

cWW-cSH-cWW-tHS-cWW

insertion-c

cWW-tSH-tHH-cSH-tWH-tHS

GNRA tetraloop

UNCG tetraloop

T-loop

cWW-tSH-tSW (hairpin loop)

CUCAA (hairpin loop)