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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.
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Mobile DNA

ISSN: 1759-8753