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Table 2 Full-length endogenous betaretroviruses identified in the Illumina sequenced transcriptome of P. alecto and the Sanger sequenced genomes of P. vampyrus and M. lucifugus

From: Identification of diverse full-length endogenous betaretroviruses in megabats and microbats

       

Extra

LTR

  
  

Genome

gag b

pro c

pol

env

ORFsd

Lengthe

PBSf

Additional notes

  

Sizea(nt)

    

≥ 300 nt

(nt)

  

P. vampyrus

          
 

PvERV-βA

7,705

Defective

Defective

Defective

Defective

0

407*

Unknown

100 nt NSR overlapping 5' LTR and beginning of gag gene

 

PvERV-βB

9,257

Defective

Intact

Intact

Defective

1

1265

Lys 3

102 nt NSR within gag gene

 

PvERV-βC

7,126

Defective

Defective

Defective

Intact

0

366*

Lys 3

Short env gene may indicate in-frame deletion

 

PvERV-βD

7,928

Defective

Defective

Defective

Defective

1

398

Lys 1,2

NSRs overlapping 5' LTR and pro-pol junction

 

PvERV-βE

7,879

Intact

Defective

Intact

Intact

1

371*

Lys 3

A single stop mutation in pro prevents this ERV being intact

 

PvERV-βF

7,804

Intact

Defective

Defective

Defective

1

370

Lys 3

41 nt NSR at extreme 5' end of the 5′ LTR

 

PvERV-βG

7,631

Defective

Intact

Defective

Defective

0

387*

Lys 3

Appears to contain a deletion that overlaps PPT and 3'LTR

 

PvERV-βH

7,843

Defective

Intact

Defective

Defective

1

361

Lys 3

 
 

PvERV-βI

7,809

Defective

Defective

Defective

Defective

0

371*

Lys 3

 
 

PvERV-βJ

8,773

Defective

Intact

Intact

Intact

2

427*

Lys 1,2

 
 

PvERV-βK

8,611

Defective

Defective

Intact

Intact

1

425*

Lys 1,2

3' LTR appears truncated

P. alecto

          
 

PaERV-βA

>8,103§

Defective

Defective

Defective

Defective

2

Unknown

Unknown

Contains artifact ORF (denoted as ORF* in Figure 1)

M. lucifugus

          
 

MlERV-βA

9,866

Defective

Intact

Defective

Defective

0

422*

Lys 1,2

Large foreign insertion in 5' LTR

 

MlERV-βB

8,121

Unknown

Defective

Intact

Defective

0

480

Lys 3

669 nt NSR within gag gene

 

MlERV-βC

8,102

Intact

Intact

Intact

Intact

0

479*

Lys 3

Completely intact

 

MlERV-βD

9,007

Defective

Defective

Defective

Intact

0

479*

Lys 3

Contains short foreign insertions in pro and pol genes

 

MlERV-βE

7,890

Defective

Defective

Defective

Defective

1

440

Lys†

 
 

MlERV-βF

8,235

Intact

Intact

Defective

Defective

1

470

Lys 3

Small ~45nt deletion overlapping pol and env genes

  1. a The genome size is given for the proviral version of the βERVs. § The genome size of PaERV-βA is uncertain as the known sequence begins 25nt upstream of the gag gene and does not include the (unique 5') region.
  2. b The core retroviral genes gag, pro, pol, and env that contain frameshift or premature stop mutations are described as ‘defective’, those that contain neither of these are described as ‘intact’ in bold font.
  3. c The pro open reading frame (ORF) of each βERV was found to encode a betaretroviral dUTPase protein domain.
  4. d The number of ORFs that do not code for the core genes and are 300 nucleotides or greater in length.
  5. e The length of the long terminal repeats (LTRs). * For those βERVs whose 5′ and 3′ LTR lengths differ, the value of the 5′ LTR is given.
  6. f The specific lysine (Lys) tRNA complementary to the primer binding site (PBS) for each βERV is given. † The specific identity of the PBS of MlERV-βE is uncertain. NSR: non-sequenced region.