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Table 3 Annotation of 28 DIRS1-like retrotransposons

From: Eukaryote DIRS1-like retrotransposons: an overview

         

Termini

size

 

ICR

Element

Host

 

Size

start

end

circular

long ORF

lE

divergent

conserved

rE

size

      

junction

overlap

 

ITR

ITR

  

AcDIRS1

A. carolinensis

Sauropsida

5938

CTT

CAT

AAG

No

-

26

140

26

40-58

AcDIRS2

A. carolinensis

Sauropsida

5997

TTT

TGT

AAA

Yes

-

26

136

28

39-60

AcaDIRS1

A. californica

Mollusca

5222

ATT

ATT

AAT

No

-

36

32

48

45-88

AcaDIRS2

A. californica

Mollusca

5808

ATT

ATT

AAT

No

-

34

36

48

44-88

AcasDIRS1

A. castellanii

Amoebozoa

3974

GTT

CTT

AAG

No

12

22

84

-

52-36

AmDIRS1

A. macrogynus

Blastocladiomycota

4801

CGG

GCG

CG

Yes

64

33

123

-

110-39

AmDIRS2

A. macrogynus

Blastocladiomycota

5713

ATT

AAT

AAT

Yes

14

9

193

75

24-86

BfDIRS1

B. floridae

Cephalochordata

4949

TTG

TTG

CAA

Yes

-

23

118

45

60-83

BfDIRS2

B. floridae

Cephalochordata

5269

TTA

TTT

AA

Yes

-

19

103

40

33-71

BmDIRS1

B. mori

Hexapoda

4870

ATT

ATA

AAT

Yes

-

16

155

30

40-62

CaspDIRS1

Capitella sp.

Annelida

4994

ATT

ATT

AAT

Yes

nd

nd

nd

nd

nd

DIRS1-2

D. discoideum

Amoebozoa

3793

TTA

TTA

TAA

Yes

-

12

304

24

26-59

DpuDIRS3

D. pulex

Crustacea

5195

ATT

ATT

AAT

No

-

24

170

50

38-89

GaDIRS1

G. aculeatus

Actinopterygii

5322

GTT

GTT

AAC

Yes

-

19

148

27

46-56

GaDIRS2

G. aculeatus

Actinopterygii

5782

GTT

GTT

AAC

Yes

-

21

144

26

38-57

LgDIRS1

L. gigantea

Mollusca

4680

ATT

ATT

AAT

No

-

35

31

48

39-86

LgDIRS2

L. gigantea

Mollusca

5036

AAT

AAT

ATT

No

-

34

141

46

46-67

LgDIRS3

L. gigantea

Mollusca

5133

ATT

ATT

AAT

No

-

30

36

49

42-86

MciDIRS1

M. circinelloides

Mucoromycotina

4402

ATT

ATT

AAT

Yes

38

8

107

11

75-42

NvDIRS2

N. vitripennis

Hexapoda

4849

TAA

TAA

TTA

No

-

25

62

35

41-73

NveDIRS6b

N. vectensis

Cnidaria

4142

ATT

AAT

AAT

No

-

30

118

49

40-82

PblDIRS1

P. blakesleeanus

Mucoromycotina

4315

ATT

ATT

AAT

Yes

28

20

94

9

58-39

RoDIRS1

R. oryzae

Mucoromycotina

4274

ATT

ATT

AAT

Yes

28

14

102

9

59-44

SkoDIRS1

S. kowalevskii

Hemichordata

6052

ATT

ATT

AAT

No

-

16

202

30

67-63

SkoDIRS2

S. kowalevskii

Hemichordata

6283

GTT

GTT

AAC

No

-

15

142

27

63-65

TnDIRS1a

T. nigroviridis

Actinopterygii

5931

GTT

GAT

AAC

Yes

-

21

146

27

36-57

XtDIRS2

X. tropicalis

Amphibia

5571

TTT

TAT

AAA

Yes

-

20

102

30

43-61

XtDIRS3

X. tropicalis

Amphibia

6196

TTT

TTT

AAA

Yes

-

11

123

34

41-65

  1. The element size and trinucleotide sequences beginning and ending the element complementary to the circular junction are given for each manually annotated DIRS1-like element. Evidence of long ORF overlap is also indicated. The lengths of the different parts of the termini (the divergent and the conserved ITRs, lE and rE) as well as those of the ICRs are reported. nd: not determined because CaspDIRS1 corresponds to a chimeric sequence. Each newly identified element has been submitted to Repbase.