RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H

BMC Genomics

Table 2 Predicted cis-regulatory elements in G. oxydans 621H according to the Rfam database compared to RNAseq results

Rfam prediction			Annotation		Primary	Whole
Description	Accession	Start^a End	Gene	Annotation	Start^b Stop^d	Start^c Stop^d
FMN riboswitch	RF00050	1,075,971 1,076,128	GOX_RS06030	Riboflavin biosynthesis protein RibD	1,075,965 1,076,281	1,075,974 1,076,281
Glycine riboswitch	RF00504	1,200,190 1,200,279	GOX_RS06635	Glycine cleavage system, amino methyl-transferase T	1,200,192 1,200,436	1,200,201 1,200,436
SAM-II riboswitch	RF00521	1,829,621 1,829,542	GOX_RS09595	O-succinyl-homoserine sulfhydrylase	1,829,638 1,829,484	1,829,625 1,829,484
TPP riboswitch	RF00059	2,443,346 2,443,480	GOX_RS12420	Phosphomethyl-pyrimidine synthase	2,443,351 2,443,615	2,443,363 2,443,615
Cobalamin riboswitch	RF00174	1,111,882 1,111,673	GOX_RS06220	TonB-dependent receptor	–	1,111,858 1,111,529
ROSE element	RF00435	1,450,717 1,450,634	GOX_RS07835	Molecular chaperone Hsp20	–	1,450,712 1,450,641
Fluoride riboswitch	RF01734	152,387 152,452	GOX_RS00740	Camphor resistance protein CrcB	–	152,404 152,966

^aPositions according to Rfam database were adjusted according to the updated genome reference [10]. European Nucleotide Archive accession number: PRJEB18739
^bPosition of the TSS
^cObserved by manual inspection
^dEnd of the 5´-UTRs

ISSN: 1471-2164