Table 1.

Top-ranking loci (> 90-fold enrichment) that were identified in mTERF2 RIP-Seq experiments.

Gene ID	Fold Enrichment	Gene model Description	Gene Symbol	Intron Classification	IGV
ATCG01200	1487	tRNA-Ile	trnI.3	group IIA	Maybe not informative 1, therefore Northern performed
ATCG00940	826	tRNA-Ala	trnA.1	group IIA	Maybe not informative 1, therefore Northern performed
ATCG00960	233	4.5S ribosomal RNA	rrn4.5S.1	/	Maybe not informative 2, therefore Northern performed
ATCG01230	223	30S RIBOSOMAL PROTEIN S12B.	rps12B	group IIA/group IIB	Higher accumulation, especially first intron and upstream (intron 1b), splicing of groupII A intron OK
ATCG01310	194	50S RIBOSOMAL PROTEIN L2	rpl2.2	group IIA	Higher accumulation, splicing OK
ATCG00065	182	30S RIBOSOMAL PROTEIN S12A.	rps12A	group IIB	Higher accumulation downstream (intron 1a), trans-splicing defect?
ATCG00400	159	tRNA-Leu	trnL.1	group I	Higher accumulation
ATCG01190	154	tRNA-Ala	trnA.2	group IIA	1
ATCG01150	142	tRNA-Arg	trnR.3	/	/
ATCG01100	133	NADH dehydrogenase ND1	ndhA	group IIB	Splicing defect
ATCG00360	132	Encodes a protein required for PSI assembly and stability	ycf3	group IIB	First intron splicing defect
ATCG00750	131	30S RIBOSOMAL PROTEIN S11	rps11	/	/
ATCG00830	106	50S RIBOSOMAL PROTEIN L2	rpl2.1	group IIA	Higher accumulation, splicing seems to be OK
ATCG00670	91	PLASTID-ENCODED CLP P.	pclpP	group IIA	Splicing OK, but carefully look downstream (ATCG0065, RPS12A)

Highlighted in bold are those loci which show a splicing defect in RNA-Seq data (see Figure 4). ¹ Because of the large number of modifications found in tRNAs, their structure, and their small size, the RNA library preparation method used for genome-wide RNA-Seq analysis does not allow them to be mapped in a representative – and informative – manner. ²Of limited relevance, since rRNA depletion was performed prior to library preparation of immunoprecipitated RNAs. IGV, Integrated Genomics Viewer (http://software.broadinstitute.org/software/igv/).