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Searching for conserved non-coding sequences by comparative genomics is a valuable tool …

Biology Articles » Evolutionary Biology » Comparative Genomics » Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes » Tables

Tables
- Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes

Table 1
Pairwise sequence comparison of the coding and the 5'-flanking sequence of mammalian HL genes.

upstream regulatory sequence
cDNA sequence
 81
53
 53
 61
 57
 56
 hedgehoga

79
 76
86
 64
 55
 59
 mouse

79
 76
 92
63
 57
 57
 rat

85
 82
 79
 79
94
 94
 rhesusa

85
 82
 80
 80
 96
98
 chimp

85
 82
 79
 79
 96
 99
human

rabbitb
 hedgehog
 mouse
 rat
 rhesus
 chimp
 human
Sequence identity (%) was determined by pairwise alignment using the DNAMAN software package (optimal alignment; gap open penalty 10.0, gap extension penalty 5.0). cDNA sequence was from the translation start ATG up till the stopcodon; the upstream regulatory region was from -1400 up till the translation start ATG.
a: Because of a gap in upstream regulatory region of the public sequence of the rhesus monkey and hedgehog HL gene (Ensembl e!42: Dec 2006), alignments with the rhesus and hedgehog sequence were done with the sequence from -900 and -1000 up till the start ATG, respectively.
b:the rabbit HL cDNA sequence was taken from [38].
Table 2
Oligonucleotides used to generate serial 5'-deletions of the rat and human HL promoter region.
Name
 species and orientationa
 positionb
 5'→3' sequencec
3F
 r
 F
 -1697/-1675
 cggaagc TTA GCA GAC AGC GAT TGG C
4F
 r
 F
 -1048/-1030
 cggaag CTT GCC TCC TCC TGA GTG C
5F
 r
 F
 -754/-736
 cggaagc TTG TCC AGG GCG TCC ATA C
9F
 r
 F
 -211/-196
 cggaagctt AGC TTG GCT CAA AAG G
8F
 r
 F
 -86/-71
 cggaagctt GTG TTC AAA TAC TGG G
7F
 r
 F
 -75/-58
 cggaagct TGG GTA ACA TGT TTT AGG
6F
 r
 F
 -39/-22
 cggaag CTT CCA CAA CTA AAT ACC
11F
 r
 F
 -23/-8
 cggaagctt CCA AGA AGC ATT CTG G
HHL-685Sac
 h
 F
 -685/-667
 ccgagctc TGG TCG CCT TTT CCC TAC C
HHL-306Nhe
 h
 F
 -306/-291
 gcatgctagc GAA GCC ACC TAC CCC G
HHL-79Kpn
 h
 F
 -79/-55
 ggggtacc TAA CAT GTT GAG AGG
HHL-36Kpn
 h
 F
 -36/-20
 ggggtac CAA AGT ATC TAA TAG GC
HHL+13Xba
 h
 R
 +13/-6
 gctctaga CTT GGT AAT TTC TGA AGC C
HHL-10Kfw
 h
 F
 -10457/-10437
 gtcgac GAA GGA TCA GGT GAG GGA TGG
HHL-10Krev
 h
 R
 -9956/-9975
 ggatcc GCT TCA AGG GCA ATG AAA GC
HHL-14Kfw
 h
 F
 -14202/-14183
 gtcgac GAC TTG GGG ATA TCC ACA TC
HHL-14Krev
 h
 R
 -13524/-13549
 ggatc CTG GTA AAA GGA CAT GAA CAA TAT GG
HHL-22Kfw
 h
 F
 -21929/-21909
 gtcgac GAT GGG AAA TGG ACC TAC AGC
HHL-22Krev
 h
 R
 -21543/-21562
 ggatcc GAT GAG GAC TGA TTC TCA GC
CATREV2d
 -
 R
gca act gac tga aat gcc tc
T3primere
 -
 R
att aac cct cac taa ag
a: r and h: rat and human, respectively; F and R: forward and reverse orientation.
b: numbering of the rat and human sequence according to [35] and Ensembl e!42 [26], respectively.
c: rat and human HL specific parts of the primer sequences are given in capitals.
d: oligonucleotide specific for pCAT-Basic.
e: oligonucleotide specific for pBluescript.

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