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

From: RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H

Rfam prediction Annotation Primary Whole
Description Accession Starta
End
Gene Annotation Startb
Stopd
Startc
Stopd
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
  1. aPositions according to Rfam database were adjusted according to the updated genome reference [10]. European Nucleotide Archive accession number: PRJEB18739
  2. bPosition of the TSS
  3. cObserved by manual inspection
  4. dEnd of the 5´-UTRs