Plastid-ndhA-ndhB group II-D5 intron clan

Plastid ndhA-ndhB clan include non-coding RNAs (ncRNA) recognised in plastids [1]. They were recognised in the group II D5 intronic region of ndhA and ndhB genes.

This clan contains 3 families and the total number of sequence regions in the clan is 10,359.

Literature references

1. Richter AS, Nagele T, Grimm B, Kaufmann K, Schroda M, Leister D, Kleine T, Plant Commun. 2023;4:100511.: Retrograde signaling in plants: A critical review focusing on the GUN pathway and beyond. 36575799
2. Stern DB, Gruissem W, Cell. 1987;51:1145-1157.: Control of plastid gene expression: 3' inverted repeats act as mRNA processing and stabilizing elements, but do not terminate transcription. 3690662
3. Zandueta-Criado A, Bock R, Nucleic Acids Res. 2004;32:542-550.: Surprising features of plastid ndhD transcripts: addition of non-encoded nucleotides and polysome association of mRNAs with an unedited start codon. 14744979

Members

This clan contains the following 3 member families:

Plastid-ndhA-ndhB-1 Plastid-ndhA-ndhB-2 Plastid-ndhA-ndhB-3

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
Plastid-ndhA-ndhB-3 (RF04358)	1,681 (16.2%)	View
Plastid-ndhA-ndhB-2 (RF04357)	6,909 (66.7%)	View
Plastid-ndhA-ndhB-1 (RF04356)	1,769 (17.1%)	View