Plant Transcription factor database - Universität Potsdam
version: 3.0

Physcomitrella patens bHLH Family


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:


There are 101 gene models in this family

Gene modelDescriptionDomains
113607 e_gw1.7.385.1 HLH
114892 e_gw1.11.52.1 HLH
118546 e_gw1.25.105.1 HLH
119981 e_gw1.31.140.1 HLH
120233 e_gw1.31.270.1 HLH
121037 e_gw1.34.393.1 HLH
128346 e_gw1.69.179.1 HLH
130556 e_gw1.83.237.1 HLH
130842 e_gw1.84.236.1 HLH
136623 e_gw1.130.107.1 HLH
140422 e_gw1.167.42.1 HLH
141013 e_gw1.173.38.1 HLH
143875 e_gw1.209.40.1 HLH
145569 e_gw1.229.33.1 HLH
148152 e_gw1.272.41.1 HLH
148201 e_gw1.273.42.1 HLH
148564 e_gw1.280.47.1 HLH
156270 e_gw1.519.9.1 HLH
158731 estExt_fgenesh1_pg.C_50104 HLH
160137 estExt_fgenesh1_pg.C_190036 HLH
161207 estExt_fgenesh1_pg.C_300202 HLH
161304 estExt_fgenesh1_pg.C_310143 HLH
161497 estExt_fgenesh1_pg.C_330151 HLH
161996 estExt_fgenesh1_pg.C_380067 HLH
162363 estExt_fgenesh1_pg.C_420092 HLH
162880 estExt_fgenesh1_pg.C_480124 HLH
163362 estExt_fgenesh1_pg.C_550008 HLH
163809 estExt_fgenesh1_pg.C_600113 HLH
164347 estExt_fgenesh1_pg.C_680048 HLH
164436 estExt_fgenesh1_pg.C_690022 HLH
164645 estExt_fgenesh1_pg.C_740025 HLH
164647 estExt_fgenesh1_pg.C_740028 HLH
165193 estExt_fgenesh1_pg.C_840011 HLH
165670 estExt_fgenesh1_pg.C_930064 HLH
165916 estExt_fgenesh1_pg.C_980121 HLH
166219 estExt_fgenesh1_pg.C_1050039 HLH
166279 estExt_fgenesh1_pg.C_1070108 HLH
166411 estExt_fgenesh1_pg.C_1140117 HLH
166708 estExt_fgenesh1_pg.C_1230002 HLH
166769 estExt_fgenesh1_pg.C_1240014 HLH
166771 estExt_fgenesh1_pg.C_1240017 HLH
167103 estExt_fgenesh1_pg.C_1360017 HLH
167487 estExt_fgenesh1_pg.C_1470079 HLH
167852 estExt_fgenesh1_pg.C_1590022 HLH
168015 estExt_fgenesh1_pg.C_1630065 HLH
169502 estExt_fgenesh1_pg.C_2110039 HLH
169585 estExt_fgenesh1_pg.C_2130035 HLH
170100 estExt_fgenesh1_pg.C_2310009 HLH
170794 estExt_fgenesh1_pg.C_2620021 HLH
171257 estExt_fgenesh1_pg.C_2820040 HLH
171589 estExt_fgenesh1_pg.C_3000052 ACT HLH
171809 estExt_fgenesh1_pg.C_3120001 HLH
172669 estExt_fgenesh1_pg.C_3710032 HLH
18085 gw1.90.96.1 HLH
184221 estExt_gwp_gw1.C_710125 HLH
192553 estExt_gwp_gw1.C_1820005 HLH
195760 estExt_gwp_gw1.C_2460032 HLH
209063 estExt_Genewise1.C_510113 HLH
229640 fgenesh2_pg.scaffold_77000085 HLH
229808 fgenesh2_pg.scaffold_82000048 HLH
229964 fgenesh2_pg.scaffold_89000062 HLH
230424 fgenesh2_pg.scaffold_105000066 HLH
231364 fgenesh2_pg.scaffold_130000004 HLH
231841 fgenesh2_pg.scaffold_140000014 HLH
233706 estExt_fgenesh2_pg.C_970074 HLH
27712 gw1.28.196.1 HLH
28478 gw1.257.54.1 HLH
34992 gw1.90.123.1 HLH
36721 gw1.377.16.1 HLH
47728 gw1.67.189.1 HLH
48139 gw1.194.125.1 HLH
48206 gw1.145.145.1 HLH
48248 gw1.226.91.1 HLH
48267 gw1.270.82.1 HLH
49107 gw1.57.119.1 HLH
49171 gw1.185.89.1 HLH
49174 gw1.68.283.1 HLH
49175 gw1.69.191.1 HLH
49470 gw1.31.360.1 HLH
49637 gw1.147.92.1 HLH
63900 fgenesh1_pg.scaffold_1000274 HLH
64936 fgenesh1_pg.scaffold_4000051 HLH
64941 fgenesh1_pg.scaffold_4000056 HLH
65387 fgenesh1_pg.scaffold_6000069 HLH
67124 fgenesh1_pg.scaffold_13000185 HLH
71136 fgenesh1_pg.scaffold_31000088 HLH
72483 fgenesh1_pg.scaffold_37000071 HLH
76229 fgenesh1_pg.scaffold_57000137 HLH
78099 fgenesh1_pg.scaffold_69000055 HLH
78495 fgenesh1_pg.scaffold_72000001 HLH
79459 fgenesh1_pg.scaffold_79000057 HLH
80954 fgenesh1_pg.scaffold_90000096 HLH
81303 fgenesh1_pg.scaffold_93000105 HLH
81393 fgenesh1_pg.scaffold_94000090 HLH
85769 fgenesh1_pg.scaffold_138000041 HLH
87230 fgenesh1_pg.scaffold_155000050 HLH
88041 fgenesh1_pg.scaffold_164000047 HLH
95064 fgenesh1_pg.scaffold_273000011 HLH
95182 fgenesh1_pg.scaffold_275000043 HLH
98910 fgenesh1_pg.scaffold_371000022 ACT HLH
99319 fgenesh1_pg.scaffold_386000005 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