Plant Transcription factor database - Universität Potsdam
version: 3.0

Oryza sativa subsp. indica bHLH Family

Description

Buck & Atchley. 2003: The basic helix-loop-helix (bHLH) family of proteins is a group of functionally diverse transcription factors found in both plants and animals. These proteins evolved early in eukaryotic cells before the split of animals and plants, but appear to function in lsquoplant-specificrsquo or lsquoanimal-specificrsquo processes. In animals bHLH proteins are involved in regulation of a wide variety of essential developmental processes. On the contrary, bHLH proteins have not been extensively studied in plants. Those that have been characterized function in anthocyanin biosynthesis, phytochrome signaling, globulin expression, fruit dehiscence, carpel and epidermal development.

Members of this family
  SHOULD possess HLH domain

Domain alignments

Benchmark against A. thaliana

The Sensitivity and Positive Predictive Value (PPV) were assessed for this family. The data reported by Bailey et al. 2003 for A. thaliana were taken as gold standard.

The gold standard reported 154 members for this family, 122 of which are present in ArabTFDB, giving a PPV of 0.92. Thirty-two additional members not present in ArabTFDB might be false negatives, giving a Sensitivity of 0.80.

This family is also present in:

References

There are 143 gene models in this family



Gene modelDescriptionDomains
OsIBCD000069 Chr01_108,675,,,1,675, HLH
OsIBCD000070 Chr01_109,468,,,1,468, HLH
OsIBCD000087 Chr01_133,867,,,1,867, HLH
OsIBCD000413 Chr01_640,777,,,1,777, HLH
OsIBCD000621 Chr01_927,861,,,1,861, HLH
OsIBCD000622 Chr01_928,1962,,,1,1962, HLH
OsIBCD000624 Chr01_933,1425,,,1,1425, HLH
OsIBCD000748 Chr01_1121,627,,,1,627, HLH
OsIBCD001217 Chr01_1786,2100,,,1,2100, HLH
OsIBCD001266 Chr01_1853,1053,,,1,1053, HLH
OsIBCD002015 Chr01_3190,534,,,1,534, ACT HLH
OsIBCD002018 Chr01_3194,534,,,1,534, ACT HLH
OsIBCD002382 Chr01_3798,1332,,,1,1332, HLH
OsIBCD002389 Chr01_3812,1497,,,1,1497, HLH
OsIBCD002471 Chr01_3929,1470,,,1,1470, HLH
OsIBCD003461 Chr01_5351,783,,,1,783, HLH
OsIBCD003462 Chr01_5355,1878,,,1,1878, DUF295 F-box HLH
OsIBCD004193 Chr01_6427,1134,,,1,1134, HLH
OsIBCD004276 Chr01_6552,1446,,,1,1446, HLH
OsIBCD004373 Chr01_6681,1239,,,1,1239, HLH
OsIBCD004527 Chr01_6899,546,,,1,546, HLH
OsIBCD004536 Chr01_6909,747,,,1,747, HLH
OsIBCD004828 Chr02_163,711,,,1,711, HLH
OsIBCD004866 Chr02_210,1659,,,1,1659, HLH
OsIBCD005555 Chr02_1203,1992,,,1,1992, HLH
OsIBCD005756 Chr02_1510,1248,,,1,1248, HLH
OsIBCD006799 Chr02_3400,951,,,1,951, HLH
OsIBCD006895 Chr02_3537,1575,,,1,1575, HLH
OsIBCD007128 Chr02_3889,573,,,1,573, HLH
OsIBCD007620 Chr02_4634,1122,,,1,1122, HLH
OsIBCD007702 Chr02_4751,1056,,,1,1056, HLH
OsIBCD007729 Chr02_4787,900,,,1,900, HLH
OsIBCD007973 Chr02_5123,267,,,1,267, HLH
OsIBCD008036 Chr02_5213,1005,,,1,1005, HLH
OsIBCD008250 Chr02_5520,1038,,,1,1038, HLH
OsIBCD008304 Chr02_5594,1023,,,1,1023, HLH
OsIBCD008678 Chr03_210,879,,,1,879, HLH
OsIBCD008779 Chr03_338,1071,,,1,1071, HLH
OsIBCD009108 Chr03_806,990,,,1,990, HLH
OsIBCD009219 Chr03_949,1026,,,1,1026, HLH
OsIBCD009361 Chr03_1144,1059,,,1,1059, HLH
OsIBCD009375 Chr03_1159,900,,,1,900, HLH
OsIBCD009532 Chr03_1399,1407,,,1,1407, HLH
OsIBCD009670 Chr03_1602,1833,,,1,1833, HLH
OsIBCD009671 Chr03_1604,1113,,,1,1113, HLH
OsIBCD010356 Chr03_2569,789,,,1,789, HLH
OsIBCD011005 Chr03_3836,930,,,1,930, HLH
OsIBCD011050 Chr03_3933,984,,,1,984, HLH
OsIBCD011191 Chr03_4182,933,,,1,933, HLH
OsIBCD011332 Chr03_4376,1443,,,1,1443, HLH
OsIBCD011517 Chr03_4683,927,,,1,927, HLH
OsIBCD011522 Chr03_4690,1143,,,1,1143, HLH
OsIBCD011850 Chr03_5194,1080,,,1,1080, HLH
OsIBCD011931 Chr03_5313,882,,,1,882, HLH
OsIBCD012047 Chr03_5468,954,,,1,954, HLH
OsIBCD012156 Chr03_5630,1623,,,1,1623, HLH
OsIBCD012263 Chr03_5779,834,,,1,834, HLH
OsIBCD012304 Chr03_5833,792,,,1,792, HLH
OsIBCD012376 Chr03_5916,942,,,1,942, HLH
OsIBCD013466 Chr04_1276,1284,,,1,1284, HLH
OsIBCD013691 Chr04_1721,828,,,1,828, HLH
OsIBCD013912 Chr04_2129,1221,,,1,1221, HLH
OsIBCD014090 Chr04_2440,1152,,,1,1152, HLH
OsIBCD014352 Chr04_2833,1053,,,1,1053, HLH
OsIBCD014792 Chr04_3440,726,,,1,726, HLH
OsIBCD015225 Chr04_4066,1647,,,1,1647, HLH
OsIBCD015227 Chr04_4071,1332,,,1,1332, HLH
OsIBCD015228 Chr04_4072,2925,,,1,2925, HLH Peptidase_C48
OsIBCD015412 Chr04_4361,954,,,1,954, HLH
OsIBCD015458 Chr04_4432,1395,,,1,1395, HLH
OsIBCD015618 Chr04_4632,546,,,1,546, HLH
OsIBCD016146 Chr05_23,918,,,1,918, HLH
OsIBCD016391 Chr05_366,1212,,,1,1212, HLH
OsIBCD016554 Chr05_591,942,,,1,942, ACT HLH
OsIBCD019035 Chr05_4722,1347,,,1,1347, HLH
OsIBCD019531 Chr06_654,948,,,1,948, HLH
OsIBCD019636 Chr06_796,1212,,,1,1212, HLH
OsIBCD019692 Chr06_882,1434,,,1,1434, HLH
OsIBCD019896 Chr06_1199,264,,,1,264, HLH
OsIBCD020764 Chr06_2780,885,,,1,885, HLH
OsIBCD020918 Chr06_3059,1188,,,1,1188, HLH
OsIBCD021128 Chr06_3431,1692,,,1,1692, HLH
OsIBCD021387 Chr06_3824,990,,,1,990, HLH
OsIBCD022050 Chr06_4805,1047,,,1,1047, HLH
OsIBCD022327 Chr07_365,1794,,,1,1794, HLH
OsIBCD022549 Chr07_675,882,,,1,882, HLH
OsIBCD022628 Chr07_795,771,,,1,771, HLH
OsIBCD023792 Chr07_2945,711,,,1,711, HLH
OsIBCD023828 Chr07_3002,684,,,1,684, HLH
OsIBCD024060 Chr07_3346,840,,,1,840, HLH
OsIBCD024273 Chr07_3673,798,,,1,798, HLH
OsIBCD024767 Chr08_86,1029,,,1,1029, HLH
OsIBCD024939 Chr08_345,744,,,1,744, HLH
OsIBCD026606 Chr08_3301,1059,,,1,1059, HLH
OsIBCD026856 Chr08_3721,1050,,,1,1050, HLH
OsIBCD026888 Chr08_3772,909,,,1,909, HLH
OsIBCD026898 Chr08_3783,543,,,1,543, HLH
OsIBCD026915 Chr08_3810,1098,,,1,1098, HLH
OsIBCD026926 Chr08_3825,1527,,,1,1527, HLH
OsIBCD027022 Chr08_3976,1212,,,1,1212, HLH
OsIBCD027145 Chr08_4170,1188,,,1,1188, HLH
OsIBCD027229 Chr08_4276,876,,,1,876, HLH
OsIBCD028524 Chr09_1943,1092,,,1,1092, HLH
OsIBCD028564 Chr09_1995,1209,,,1,1209, HLH
OsIBCD028747 Chr09_2277,684,,,1,684, HLH
OsIBCD028824 Chr09_2408,648,,,1,648, HLH
OsIBCD028851 Chr09_2455,1059,,,1,1059, HLH
OsIBCD028884 Chr09_2503,1308,,,1,1308, HLH
OsIBCD028891 Chr09_2514,3357,,,1,3357, HLH PPR
OsIBCD028951 Chr09_2625,1293,,,1,1293, HLH
OsIBCD029018 Chr09_2714,1101,,,1,1101, HLH
OsIBCD029082 Chr09_2793,711,,,1,711, HLH
OsIBCD030347 Chr10_1567,990,,,1,990, HLH
OsIBCD031356 Chr10_3128,1158,,,1,1158, HLH
OsIBCD031553 Chr10_3397,1995,,,1,1995, HLH
OsIBCD033005 Chr11_2401,1575,,,1,1575, HLH
OsIBCD033336 Chr11_2907,303,,,1,303, HLH
OsIBCD033350 Chr11_2936,807,,,1,807, HLH
OsIBCD033464 Chr11_3083,777,,,1,777, HLH
OsIBCD035037 Chr12_2231,780,,,1,780, HLH
OsIBCD035099 Chr12_2309,597,,,1,597, HLH
OsIBCD035512 Chr12_2923,915,,,1,915, HLH
OsIBCD035561 Chr12_2994,798,,,1,798, HLH
OsIBCD035562 Chr12_2999,1050,,,1,1050, HLH
OsIBCD035564 Chr12_3002,1053,,,1,1053, HLH
OsIBCD035565 Chr12_3007,1461,,,1,1461, HLH
OsIBCD035622 Chr12_3109,1338,,,1,1338, HLH
OsIBCD035626 Chr12_3116,1827,,,1,1827, HLH
OsIBCD035757 Chr12_3303,930,,,1,930, HLH
OsIBCD036534 Chr01_3716,1395,,,1,1395, HLH
OsIBCD036758 Chr01_4784,1422,,,1,1422, HLH
OsIBCD036761 Chr01_4799,1185,,,1,1185, HLH
OsIBCD036993 Chr01_5815,672,,,1,672, HLH
OsIBCD039134 Chr03_3837,792,,,1,792, HLH
OsIBCD039747 Chr04_641,1842,,,1,1842, HLH
OsIBCD040720 Chr05_537,333,,,1,333, HLH
OsIBCD041429 Chr05_4322,1248,,,1,1248, HLH
OsIBCD041792 Chr06_1042,606,,,1,606, HLH
OsIBCD044034 Chr08_3658,741,,,1,741, HLH
OsIBCD044185 Chr08_4354,792,,,1,792, HLH
OsIBCD044660 Chr09_2346,711,,,1,711, HLH
OsIBCD044779 Chr09_2874,855,,,1,855, HLH
OsIBSD048791 Supscaffold300_1,1314,,,1,1314, HLH

General references

Buck, MJ; Atchley, WR. 2003. Phylogenetic analysis of plant basic helix-loop-helix proteins. J. Mol. Evol. 56(6):742-50 PUBMEDID:12911037
Heim, MA; Jakoby, M; Werber, M; Martin, C; Weisshaar, B; Bailey, PC. 2003. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol. 20(5):735-47 PUBMEDID:12679534
Littlewood, TD; Evan, GI. 1995. Transcription factors 2: helix-loop-helix. Protein Profile 2(6):621-702 PUBMEDID:7553065
Massari, ME; Murre, C. 2000. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol. Cell. Biol. 20(2):429-40 PUBMEDID:10611221
Quattrocchio, F; Wing, JF; van der Woude, K; Mol, JN; Koes, R. 1998. Analysis of bHLH and MYB domain proteins: species-specific regulatory differences are caused by divergent evolution of target anthocyanin genes. Plant J. 13(4):475-88 PUBMEDID:9680994