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Table 1 ALVEs of the Hy-Line elite layer lines

From: Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data

Name

Location

TSD

Gene

Length

WL1

WL2

WL3

WL4

WL5

WPR1

WPR2

RIR

ALVEB5

1:10,637,460

GGTGGT

 

7530

(F)

     

AD

✓

✓

ALVE1

1:65,993,542

ACGGTT

SOX5 int1

7530

(F)

✓

✓

✓

✓

✓

   

ALVE_ros001

(COTW55)

1:101,668,931

GTTGTG

 

7531

(F)

       

✓

ALVE_ros002

(COTW69)

1:158,775,708

ATAAGT

 

–

       

✓

ALVE_ros003

(SGT-24)

1:163,248,553

CCTACT

 

7528

(F)

       

✓

ALVE-TYR

1:187,921,213

ACACTG

TYR int4

7534

(F)

     

✓

✓

 

ALVE-NSAC1

2:120,868,843

CCTGTT

 

4838

(P-E-3 L)

     

✓

✓

✓

ALVE_ros004

2:124,432,997

CTTGAC

 

7530

(F)

     

NSI

NSI

✓

ALVE_ros005

(New11)

2:142,480,536

TTGATA

 

280

(SL)

     

NSI

 

✓

ALVE-NSAC3

3:53,639,776

ATAAAA

 

–

     

✓

✓

 

ALVE_ros006

(N4)

3:57,337,987

GGACTC

 

–

       

✓

ALVE15

3:70,384,294

GTTTAT

GRIK2 int16

280

(SL)

✓

✓

  

✓

   

ALVE_ros007

4:59,843,015

AATAGA

 

1400

(E-3 L)

       

✓

ALVE_ros008

(BK-59)

4:62,680,158

CTGTAG

 

7529

(F)

   

✓

    

ALVE_ros009

4:71,095,932

GTCCAG

 

–

      

✓

 

ALVE9

6:33,153,441

CTCAAA

DOCK1 int35

5077

(P-E-3 L)

  

✓

     

ALVE-NSAC7

9:11,714,130

CTTCTC

 

7531

(F)

     

✓

✓

 

ALVE_ros010

9:11,871,576

TCGGAT

 

–

     

NSI

 

✓

ALVE3

20:10,309,347

AACCAC

HCK int6

5848

(F, RT-)

 

✓

✓

✓

   

AD

ALVE21

Z:10,681,671

GGGTAG

 

7529

(F)

   

✓

 

✓

✓

 
  1. Identified ALVEs are shown with Galgal5 location, target site duplication (TSD), overlap with annotated gene, sequence integrity, and presence in each of the eight analysed lines. Ambiguous prior names are shown. ALVE integrity is shown under length where: F = full, P = polymerase, E = envelope, 3 L = 3’LTR, RT- = missing reverse transcriptase, SL = solo LTR. Five ALVEs were not sequenced. ALVE detection: tick indicates detection by obsERVer; AD shows allelic dropout in the sequencing data, NSI shows that ALVE was present in the line, but not in the sequenced individuals.