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