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Table 2 Rfam predictions for regulatory regions in C. glutamicum compared to RNAseq data

From: Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique

Rfampredictiona

 

RNAseq identificationb

Name

ID

Start

End

Bit Score

Strand

RNAseq

Start

End

Gene

FMN riboswitch

RF00050

66,442

66,279

111.60

-

observed

66,438

66,198

cg0083

cspA mRNA 5′-UTR

RF01766

186,399

186,766

60.19

+

observed

186,328

186,508

cg0215 (cspA)

TPP riboswitch

RF00059

742,654

742,547

63.54

-

observed

742,651

742,490

cg0825

ydaO-yuaA leader

RF00379

870,027

869,859

69.93

-

observed

870,047

869,853

cg0936 (rpf1)

TPP riboswitch

RF00059

1,127,774

1,127,883

51.03

+

observed

1,127,765

1,127,874

cg1227

mini-ykkC RNA motif

RF01068

1,131,047

1,131,094

33.52

+

not observed

-

-

-

TPP riboswitch

RF00059

1,373,213

1,373,103

55.87

-

observed

1,373,210

1,373,105

cg1476 (thiC)

SAM-IV riboswitch

RF00634

1,374,007

1,374,123

70.47

+

observed

1,374,005

1,374,139

cg1478

TPP riboswitch

RF00059

1,544,490

1,544,383

52.11

-

observed

1,544,485

1,544,390

cg1655 (thiM)

yybP-ykoY leader

RF00080

1,550,030

1,550,196

43.71

+

not observed

-

-

-

yybP-ykoY leader

RF00080

2,043,157

2,042,989

49.13

-

observed

2,043,151

2,042,955

cg2157 (terC)

TPP riboswitch

RF00059

2,120,271

2,120,383

62.55

+

observed

2,120,271

2,120,384

cg2236 (thiE)

mraW RNA motif

RF01746

2,267,021

2,266,916

56.64

-

observed

2,266,932

2,266,800

cg2377 (mraW)

ydaO-yuaA leader

RF00379

2,292,467

2,292,279

59.37

-

observed

2,292,509

2,292,267

cg2402

msiK RNA motif

RF01747

2,582,375

2,582,317

52.13

-

observed

2,582,404

2,582,315

cg2708 (msiK1)

yybP-ykoY leader

RF00080

2,649,004

2,648,890

49.90

-

not observed

-

-

-

  1. aName, ID, coordinates, and bit score of predicted regulatory 5′-UTRs for C. glutamicum were taken from the Rfam database [50].
  2. bRefers to detected TSSs and RNAseq ends relate to the last position of the 5′-UTR. The secondary structures of the verified regulatory regions are shown in Additional file 3: Figure S2.
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BMC Genomics

ISSN: 1471-2164

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