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Table 1 Characteristics of probes used in chicken chromosome mapping of MDV integrations.

From: Chromosomal integration of an avian oncogenic herpesvirus reveals telomeric preferences and evidence for lymphoma clonality

Chromosome¶

Clone Identity

Insert Size (Kb)

Features (NCBI Accession)

Marker Position (Mb)*

References

6

CH261-169D14

226†

SCD (AJ297918/X60465)

18.5

[50]

7

CH261-95H15

158†

SP5 (NM_001044684)

19.7

 

8

CH261-84K8

235†

ZNF326 (NM_001006533)

15.6

 

9

TAM31-29A21

-

TR (AY312571)

21.5

[37]

10

TAM33-42N22

179‡

NEO1 (U07644)

1.30

 

11

TAM32-22B17

181‡

ADL210 (G01630)

12.8

 

12

TAM32-43M12

118‡

MCW198 (G31980)

12.7

 

13

TAM32-5E13

173‡

MCW322 (G32078)

16.3

 

14

TAM32-2I7

225 ‡

ADL200 (G01621)

39.8

 

15

TAM32-87J1

-

MCW226 (G31998)

2.4

 

16

ETS rDNA

3

NOR

q arm

[26, 51]

17

TAM31-22I10

-

GSN (AF042795)

9.1

 

18

TAM32-14L7

78‡

SFRS2 (X62446)

4.2

 

19

TAM32-21A11

164‡

ACACA (X77240)

8.5

 

20

TAM32-13H1

-

BMP7 (AF223970)

11.6

 

21

TAM32-12A6

-

TUS0022 (AI979776)

2.5

 

22

TAM32-13C2

202‡

CRMP62 (U17277)

0.5

 

23

TAM32-27O5

-

ADL299 (G01708)

17.8

 

24

TAM32-54P15

219‡

APOA1 (M96012)

5.2

 

25

TAM32-49A10

149‡

LEI0345 (AJ240692)

1.7

 

26

TAM32-40J16

152‡

MCW209 (G31986)

2.1

 

27

TAM32-76B6

169‡

MCW233 (G31915)

1.9

 

28

TAM32-4G3

167‡

ADL299 (G01751)

4.3

 

W

TAM32-55E18

-

CW01 (D85614)

q arm

[24, 52]

LG E50C23

TAM32-2A12

-

LEI0336 (AJ240683)

N/A

 
 

MDV: Md11gDc1.2

178§

N/A

N/A

[18]

 

MDV: P89

43

N/A

N/A

[29]

 

MDV: SN16

42

N/A

N/A

[29]

  1. CH = Children's Hospital Oakland Research Institute, CH261 = EcoRI BAC library.
  2. TAM = Texas A&M University, TAM31 = BamHI, TAM32 = EcoRI, TAM33 = HindIII BAC libraries [26, 31].
  3. ETS = external transcribed spacer of the 18S-5.8S-28 S rRNA gene repeat (rDNA).
  4. BAC locations and features were obtained from US Poultry Genome Project 'Database of BACs Assigned to Chicken Genes and Markers' (http://poultry.mph.msu.edu/resources/resources.htm, May 2006 version) and/or UCSC Genome Browser (http://genome.ucsc.edu, Chicken May 2006 assembly).
  5. Features = Genes/Markers and Genbank accession numbers (in parentheses).
  6. ¶ Probes for GGA 1-5 and the Z were not needed because these chromosomes are easily identified by their morphological features
  7. *Position refers to the start position of the BAC or gene/marker on the chromosome in the May 2006 chicken assembly (UCSC Genome Browser). In two cases the chromosomal coordinates are unknown, but the chromosome arm location is indicated.
  8. †Obtained from the UCSC Genome Browser.
  9. ‡Insert size was estimated using the UCSC Genome Browser and Chicken FPC http://www.bioinformatics.nl/gbrowse/cgi-bin/gbrowse/ChickFPC as described in O'Hare and Delany 2009.
  10. §Based on the Md5 strain (GenBank accession no. AF243438) [17].
  11. "-" = unknown
  12. N/A = not applicable