Table 1.
B. floridae bHLH-PAS gene models and identified cDNA clones
| Family name | Protein ID (Expect value) | cDNA cluster ID (Expect value) | Accession number | cDNA length (nt) | Full length coding sequence | Best hit human protein | Name given after phylogenetic analyses | Related reports a |
|---|---|---|---|---|---|---|---|---|
| NCOA (SRC) |
212110 (1.42e-62) |
N/A |
KC305624 |
3,004b |
Yes (1911 nt) |
NCOA2 (Q15596.2) |
BfNcoa |
Bb, NCOA (JN831351.1) [58] |
| ARNT |
124387 (4.79e-179) |
01670 (1e-63) |
KC305625 |
3,418b |
Yes (2139 nt) |
ARNT2 (AAG15310.1) |
BfArnt |
|
| orphanc |
117200; 125569 |
16184 |
KC305626 |
2,659b |
Yes (2418 nt) |
BMAL1e (BAA19938.1) |
BfbHLHPAS-orphan |
|
| Clock |
63636 (3.72e-137); 63642 (6.95e-109) |
N/A |
KC305627 |
2,425b |
No (2343 nt) |
CLOCK (O15516.1) |
BfClock |
|
| Bmal/cycle |
110703 (0e0); 96140 (8.13e-77) |
N/A |
KC305628 |
1,782b |
No (1782 nt) |
MOP3 (BMAL1) (AAC51213.1) |
BfBmal |
Bl, amphiBmal[60] |
| AHR |
235977 (4.04e-79); 98840 (5.68e-14) |
N/A |
KC305629 |
1,047b |
No (915 nt) |
AHR (BAA03857.1) |
BfAhr |
|
| NPAS4/dysfusion |
121518 (3.54e-66) |
N/A |
KC305630 |
2,529 |
No (2526 nt) |
NPAS4 (NP_849195.2) |
BfNpas4 |
|
| Sim |
265033 (0e0) |
N/A |
KC305631 |
999 |
No (996 nt) |
SIM1 (P81133.2) |
BfSim |
Bf, AmphiSim (AJ506161.1) [55] |
| Trh |
220692 (1.75e-53); 220681 (4.62e-48); 163191 (1.73e-24); 220639 (4.06e-23) and others |
N/A |
KC305632 |
1,176b |
No (1104 nt) |
NPAS3 transcript variant 1 (AAO17043.1) |
BfNpas1/3 |
|
| HIF |
208339 (5.04e-114); 208408 (1.73e-105) |
13696 (5e-55); 04181 (4e-51); 00128 (3e-46) |
KC305633 |
4,514b,d; |
Yes (2676 nt) |
HIF1A (NP_851397.1) |
BfHifα |
Bj, Hifα (HM188448- HM188451) [59] |
| KC305634 | 2,809b,d | Yes (2589 nt) | HIF1A (NP_851397.1) | BfHifα |
aExpressions in amphioxus reported. Bb, Branchiostoma belcheri; Bl, B. lanceolatum; Bf, B. floridae; Bj, B. japonicum (B. belcheri tsingtauense in their article). bObtained cDNA sequences do not agree with Joint Genome Institute gene models. cSee Results for its obtainment. dThe long isoform (KC305633) was from cDNA cluster 00128; the short isoform (KC305634) was from 13696. These two forms correspond to the same Joint Genome Institute gene model and may be different products of the same gene. See Results for detail. N/A, not applicable; nt, nucleotides.