Table 1 The reference collection of 14 gene pairs and 40 verified transcription-factor-binding sites used for testing
From: Identification of conserved regulatory elements by comparative genome analysis
Gene name | Human sequence | Rodent sequence | Transcription factors | Binding sequence | Location | MEDLINE ID [49] |
|---|---|---|---|---|---|---|
Skeletal muscle actin | AF182035* | M12347 | SP1 | GCGGGGTGGCGCG | -64/-51 | 11017083 |
SRF | ACCCAAATATGGCT | -100/ -86 | 1922033 | |||
TEF-1 | GACATTCCTGCG | -73/-51 | 11017083 | |||
Aldolase A α B crystallin | X12447* | J05517 | MEF2 | CCTAAATATAGGTC | -125/-111 | 8413246 |
M28638* | U04320 | SP1 | AGGAGGAGGGGCA | -343/-330 | 11017083 | |
SRF | GCCCAAGATAGTTG | -393/-379 | 11017083 | |||
Cardiac α myosin heavy chain | Z20656 | U71441 and M62404* | MEF2 | TTAAAAATAACTGA | -327/-313 | 8366095 |
TEF-1 | AGGAGGAATGTGC | -239/-226 | 7961957 | |||
SRF | CTCCAAATTTAGGC | -62/-48 | 8782063 | |||
CEBPα | U34070* | M62362 | AP2 α | GGCCGGGGGCGGA | -243/-232 | 9520389 |
TBP | TATAAAA | -30/-24 | 96003748 | |||
Cell division cycle protein 2 | L06298 and | U69555 | E2F | TCTTTCGCGC | -131/-119 | 94094909 |
X66172* | cETS | GGGAAG | -109/-104 | 951721551 | ||
Cholesterol 7 α hydroxylase | L13460 | U01962* | HNF3 β | TCTGTTTGTTCT | -175/-166 | 9799805 |
cEBP | ATGTTATGTCA | -227/-217 | 28182075 | |||
Early growth response protein 1 | AJ243425 | M22326* | SRF | TGCTTCCCATATATGGCCATGT | -88/-67 | 90097904 |
SRF | CCAGCGCCTTATATGGAGTGGC | -358/-337 | 90097904 | |||
SRF | GAAACGCCATATAAGGAGCAGG | -412/-391 | 90097904 | |||
Glucose-6-phosphatase | AF051355* | U57552 | HNF3 β | CCAAAGA | -72/-66 | 9369482 |
HNF3 β | ACAAACG | -91/-85 | 9369482 | |||
HNF3 β | GTTTTTGAG | -82/-74 | 9369482 | |||
HNF3 β | TGTGTGC | -180/-174 | 9369482 | |||
HNF3 β | TGTTTGC | -139/-133 | 9369482 | |||
HNF1 | AGTTAATCATTGGCC | -226/-212 | 9369482 | |||
Leptin | U43589 | U36238* | SP1 | GGGCGG | -100/-95 | 9492033 |
cEBP | GTTGCGCAAG | -58/-49 | 9492033 | |||
TBP | TATAAG | -33/-28 | 9492033 | |||
Lipoprotein lipase | M29549* | M63335 | NFY | CAAT | -65/-61 | 1918010 |
cEBP | TAGCCAAT | -68/-61 | 1918010 | |||
TBP | TATAA | -27/-23 | 1918010 | |||
Muscle creatine kinase | M21487 | AF188002 and M21390* | SRF | CCATGTAAGG | -1236/-1227 | 93233638 |
AP2 α | GGCCTGGGGA | -1220/-1211 | 93233638 | |||
MEF2 | TCTAAAAATAAC | -1078/-1067 | 93233638 | |||
MYF | GGGCCAGCTGTCCC | -253/-240 | 96347575 | |||
MYF | CCAACACCTGCTGC | -1157/-1144 | 96347575 | |||
P53 | ATACAAGGCC | -176/-167 | 96047120 | |||
P53 | ATACAAGGCC | -158/-149 | 96047120 | |||
Rb susceptibility gene | L11910* | M86180 U49920 and S66110 | SP1 | GGGCGG | -202/-188 | 1881452 |
Troponin I | L21905* | MEF2 | AGACTATAATAGCC | -976/-962 | 9774679 | |
MYF | TAAACAGGTGCAGC | -879/-865 | 9774679 |