Table 2

Coding regions, intron location and length of 57 PabHLH motifs
Family Gene name Genomic coding sequence(s) Intron (location,length) Group
Contig no. Frame Coding region(s)
ASCa PaAse1 AEAC01008798.1 +3 9033-9242 A
ASCa PaAse2 AEAC01008800.1 +2 11015-11191 A
E12/E47 PaDa AEAC01014068.1 +3 28419-28447 Basic: 805 bp A
+1 29253-29385
MyoD PaNau AEAC01019196.1 −2 74906-74862 Helix 1: 1290bp A
−2 73571-73461
Ngn PaTap(bp) AEAC01026729.1 −1 32156-31998 A
Mist PaMistr1 AEAC01003460.1 −2 3518-3456 Helix 1: 100bp A
−3 3355-3260
Mist PaMistr2 AEAC01025732.1 −1 1835-1773 Helix 1: 788bp A
−3 984-889
Beta3 PaOli AEAC01025379.1 +2 21989-22153 A
Atonal PaCato AEAC01014266.1 −1 26350-26192 A
Atonal PaAto AEAC01015400.1 +2 188-346 A
Atonal PaAmos AEAC01014265.1 −1 11834-11676 A
Net PaNet AEAC01000094.1 +1 43-201 A
MyoRa PaMyoR AEAC01020981.1 −1 91681-91523 A
Mesp PaSage AEAC01024430.1 −2 277-116 A
Paraxis PaPxs AEAC01022136.1 +3 27672-27715 Helix 1: 560bp A
+2 28276-28390
Twist PaTwi1 AEAC01021518.1 −3 26828-26673 A
Twist PaTwi2 AEAC01021518.1 −3 48350-48195 A
PTFa PaFer1 AEAC01026349.1 +1 45976-46134 A
PTFb PaFer2 AEAC01016863.1 −3 13162-13119 Helix 1: 410bp A
−2 12708-12594
PTFb PaFer3 AEAC01022136.1 +2 110825-110905 Helix 1: 2060bp A
+1 112966-113043
Hand PaHand AEAC01000415.1 +1 31600-31758 A
SCL PaSCL AEAC01013335.1 +2 41306-41445 Helix 2: 769bp A
+3 42215-42233
NSCL PaNSCL AEAC01011813.1 −1 35707-35685 Basic: 536bp A
−3 35148-34998
Mnt PaMnt1 AEAC01010687.1 +1 58000-58008 Helix 2: 2123bp B
+2 55730-55876
Mnt PaMnt2 AEAC01009610.1 +1 110044-110202 B
Max PaMax1 AEAC01023724.1 +3 2178-2336 B
Max PaMax2 AEAC01012273.1 +1 1648-1803 B
Myc PaDm AEAC01001866.1 −3 39047-38889 B
USF PaUSF1 AEAC01020973.1 −2 90699-90538 Loop: 88bp B
−3 90449-90399
USF PaUSF2 AEAC01025009.1 −1 32215-32075 Loop: 101bp B
−3 31973-31923
MITF PaMitf AEAC01022111.1 +2 23396-23417 Basic: 5715bp B
+2 29133-29208 Loop: 7943bp
+1 37152-37233
AP4 PaCrp1 AEAC01009287.1 +3 29454-29564 locate on two separate contigs B
AEAC01009292.1 +2 42008-42052
AP4 PaCrp2 AEAC01008415.1 +2 21659-21817 B
TF4 PaBmx AEAC01010529.1 −1 64180-64010 B
MLX PaMLX AEAC01022037.1 −1 166446-166282 B
SREBP PaSREBP AEAC01008623.1 −2 34731-34589 Helix 2: 82bp B
−3 34506-34497
SRC PaTai AEAC01016429.1 −3 7000-6993 Basic: 2799bp B
−3 4193-4040
Clock PaClk1 AEAC01024883.1 −3 2390-2386 Basic: 117bp C
−3 2268-2121
Clock PaClk2 AEAC01008322.1 +3 17766-17927 C
AHR PaDys1 AEAC01000476.1 −3 12657-12496 C
AHR PaDys2 AEAC01002106.1 −1 11804-11649 C
AHR PaSs AEAC01016399.1 +2 38537-38698 C
Sim PaSim AEAC01018973.1 +2 52010-52171 C
Trh PaTrh AEAC01014876.1 −3 10700-10539 C
HIF PaSima AEAC01025720.1 −1 31971-31810 C
ARNT PaTgo AEAC01022806.1 −1 23646-23485 C
Bmal PaCyc AEAC01003406.1 +3 16767-16771 Basic: 1814bp C
+2 18586-18742
Emc PaEmc AEAC01012314.1 +1 2998-3096 D
Hey PaHey AEAC01012628.1 +1 61852-62019 E
Hey PaStich1 AEAC01002103.1 +3 5010-5177 E
H/E(spl) PaH1 AEAC01020843.1 +1 70384-70389 Basic: 406bp E
Loop: 272bp
+2 70796-70891
+1 71164-71235
H/E(spl) PaH2 AEAC01020833.1 −2 8228-8223 Basic: 301bp E
−3 7921-7826 Loop: 3123bp
−3 4702-4631
H/E(spl) PaSide AEAC01019264.1 −1 1124-957 locate on two separate contigs E
AEAC01019265.1 −2 1044-1039
H/E(spl) PaE(spl)1 AEAC01003976.1 +1 4951-4956 Basic: 1338bp E
+1 6295-6384 Loop: 2233bp
+2 8618-8695
H/E(spl) PaE(spl)2 AEAC01003969.1 −2 11262-11257 Basic: 199bp E
−3 11057-10890
H/E(spl) PaE(spl)3 AEAC01003972.1 +2 36986-37159 E
COE Pakn(col) AEAC01019320.1 −3 1427-1427 Helix 1: 197bp F
−2 1229-1096

Liu et al.

Liu et al. BMC Evolutionary Biology 2012 12:165   doi:10.1186/1471-2148-12-165

Open Data