Table 2

Sequence and binding-site conservation in pCRMs between D. melanogaster and D. pseudoobscura

pCRM
 Name
 CRM activity
 pCRM length (D. melanogaster)
 pCRM length (D. pseudoobscura)
 Percent identity
 D. melanogaster sites
 D. pseudoobscura sites
 Conserved sites
 Fraction conserved


















A
 A+P
 A
 A+P
1
 PCE7001
 runt stripe 3
 +
 1,089
 1,504
 71%
 27
 20
 11
 20
 41%
 74%
2
 PCE7002
 eve stripes 3/7
 +
 1,278
 1,114
 61%
 28
 25
 21
 25
 75%
 89%
3
 PCE7003
 eve stripe 2
 +
 587
 771
 67%
 14
 10
 9
 10
 64%
 71%
4
 PCE7004
 eve stripes 4/6
 +
 799
 1,003
 70%
 20
 18
 13
 17
 65%
 85%
5
 PCE7005
 hairy stripe 7
 +
 895
 869
 66%
 20
 16
 12
 16
 60%
 80%
6
 PCE7006
 hairy stripe 6
 +
 868
 952
 62%
 23
 19
 11
 19
 48%
 83%
7
 PCE7007
 hairy stripes 1,5
 +
 787
 723
 56%
 16
 15
 9
 13
 56%
 81%
8
 PCE7008
 kni upstream
 +
 1,356
 1,654
 68%
 33
 31
 24
 30
 73%
 91%
9
 PCE7009
 hb HZ1.4
 +
 1,207
 1,383
 69%
 24
 23
 17
 21
 71%
 88%













10
 PCE8001
 gt posterior domain
 +
 944
 1,092
 64%
 23
 19
 15
 18
 65%
 78%
11
 PCE8010
 odd stripes 3/6
 +
 760
 825
 70%
 17
 19
 12
 16
 71%
 94%
12
 PCE8011
 nub blastoderm
 +
 695
 894
 70%
 18
 13
 10
 12
 56%
 67%
13
 PCE8024
 ftz stripes 1/5
 +
 693
 744
 77%
 14
 10
 10
 10
 71%
 71%
14
 PCE8012
 pdm2 neurogenic
 +
 723
 723
 72%
 14
 8
 4
 8
 29%
 57%
15
 PCE8027
 sqz neurogenic
 +
 810
 818
 69%
 16
 17
 11
 14
 69%
 88%













16
 PCE8005
 cluster_at_7A
 amb.
 548
 819
 54%
 13
 4
 2
 2
 15%
 15%
17
 PCE8016
 cluster_at_55C
 amb.
 703
 1,617
 55%
 16
 6
 3
 6
 19%
 38%
18
 PCE8020
 cluster_at_70F
 amb.
 710
 538
 47%
 14
 2
 2
 2
 14%
 14%













19
 PCE8006
 cluster_at_7B
 -
 639
 663
 69%
 15
 9
 8
 8
 53%
 53%
20
 PCE8008
 cluster_at_8F
 -
 745
 716
 58%
 14
 2
 1
 2
 7%
 14%
21
 PCE8013
 cluster_at_34E
 -
 850
 919
 61%
 17
 8
 6
 8
 35%
 47%
22
 PCE8014
 cluster_at_36F
 -
 701
 596
 53%
 15
 6
 5
 6
 33%
 40%
23
 PCE8015
 cluster_at_47A
 -
 655
 652
 66%
 16
 3
 3
 3
 19%
 19%
24
 PCE8017
 cluster_at_56B
 -
 633
 331
 33%
 15
 9
 4
 8
 27%
 53%
25
 PCE8018
 cluster_at_59B
 -
 716
 960
 59%
 16
 4
 3
 4
 19%
 25%
26
 PCE8019
 cluster_at_67B
 -
 667
 675
 62%
 15
 7
 5
 6
 33%
 40%
27
 PCE8021
 cluster_at_75C
 -
 752
 640
 59%
 19
 13
 10
 12
 53%
 63%
28
 PCE8022
 cluster_at_76C
 -
 704
 725
 67%
 15
 9
 7
 9
 47%
 60%
29
 PCE8023
 cluster_at_84A
 -
 765
 1,001
 55%
 16
 7
 5
 7
 31%
 44%
30
 PCE8025
 cluster_at_85C
 -
 838
 827
 54%
 16
 6
 1
 5
 6%
 31%
31
 PCE8026
 cluster_at_88F
 -
 682
 1,096
 62%
 16
 6
 5
 5
 31%
 31%
32
 PCE8028
 cluster_at_95C
 -
 624
 723
 60%
 15
 6
 4
 6
 27%
 40%













33
 PCE8003
 cluster_at_5C.1
 -
 628
 None
15




34
 PCE8004
 cluster_at_5C.2
 -
 694
 None
15




35
 PCE8009
 cluster_at_12E
 -
 663
 None
15




36
 PCE8002
 cluster_at_4B
 -
 1,341
 None
28




37
 PCE8007
 cluster_at_7F
 Unknown
 658
 None
15


















Mean (pCRMs 1-15)
899
 1,005
 67%
 20
 18
 13
 17
 61%
 80%

Mean (pCRMs 19-32)
712
 752
 58%
 16
 7
 5
 6
 30%
 40%

Conservation properties are listed for the pCRMs described in Table 1. The number and fraction of conserved sites are shown under two conditions - aligned sites only (A), or aligned + preserved sites (A+P) (see Materials and methods). D. pseudoobscura sequences used to determine these properties are available as supplemental material at [42].

Berman et al. Genome Biology 2004 5:R61   doi:10.1186/gb-2004-5-9-r61

Open Data