International Journal of Genomics / 2010 / Article / Tab 1 / Research Article
Genome-Wide Identification and Analysis of the Chicken Basic Helix-Loop-Helix Factors Table 1 A complete list of 104 bHLH genes from chicken (Gallus gallus ) with the corresponding human homologue information.
Group Family Gallus gallus Protein ID (GenBank Accession number) Homo sapiens BI posterior probability
ML Bootstrap value
Genome contig link A ASCa CASH1 NP_989743.1 Hash1 83 71 NW_001471698.1 A ASCa CASH2 NP_990280.1 Hash2 93 n/m* NW_001471698.1 A ASCb CASH3a XP_001232099.1 (ASCL3 transcript variant 1); XP_420985.2 (ASCL3 transcript variant 2) Hash3a 100 89 NW_001471698.1 A ASCb CASH3c XP_425485.1 Hash3c 51 89 NW_001471513.1 A MyoD MYF3 NP_989545.1 MYF3 88 95 NW_001471698.1 A MyoD MYF4 NP_989515.1 MYF4 100 94 NW_001471608.1 A MyoD MYF5 NP_001025534.1 MYF5 75 96 NW_001471512.1 A MyoD MYF6 NP_001025917.1 MYF6 93 99 NW_001471512.1 A E12/E47 TF12a NP_990706.2 TF12 54 78 NW_001471425.1 A E12/E47 TF12b hmm39106 TF12 54 78 NW_001471425.1 A E12/E47 E2A hmm9164 E2A 96 98 NW_001471627.1 A E12/E47 TCF3 NP_989817.2 TCF3 98 97 NW_001471627.1 A E12/E47 TCF4 Q90683.1 TCF4 55 n/m* NW_001488824.1 A Ngn CATH4a NP_990127.1 HATH4a 99 94 NW_001471685.1 A Ngn CATH4c NP_990214.1 HATH4c 100 90 NW_001471449.1 A NeuroD NDF1 NP_990251.1 NDF1 55 n/m* NW_001471729.1 A NeuroD CATH2 XP_418852.1 HATH2 97 89 NW_001471633.1 A NeuroD CATH3 NP_990407.1 HATH3 99 94 NW_001471747.1 A Atonal CATH1a hmm54472 HATH1 100 87 NW_001471683.1 A Atonal CATH1b XR_026796.1 HATH1 100 87 NW_001471683.1 A Atonal CATH5 NP_989999.1 HATH5 99 91 NW_001471715.1 A Mist Mist1 XP_425228.1 Mist1 100 98 NW_001471454.1 A Beta3 Beta3a NP_989835.1 Beta3a 57 62 NW_001471567.1 A Beta3 Beta3b NP_989834.1 Beta3b 95 76 NW_001471646.1 A Oligo Oligo2 NP_001026697.1 Oligo2 67 62 NW_001471669.1 A Oligo Oligo3 XP_001232806.1 Oligo3 84 76 NW_001471669.1 A Net CATH6 XP_001234980.1 HATH6 96 98 NW_001471687.1 A Mesp Mesp1 hmm11657 Mesp1 n/m n/m NW_001471429.1 Mesp2 A Mesp Mesp2 NP_989897.1 Mesp1 n/m n/m NW_001471429.1 Mesp2 A Mesp pMesp1 hmm17962 pMesp1 n/m n/m NW_001471429.1 pMesp2 A Mesp pMesp2 XP_001231219.1 pMesp1 n/m n/m NW_001471429.1 pMesp2 A Mesp pMespo1 NP_990015.1 pMesp1 n/m n/m NW_001471673.1 pMesp2 A Twist Twist1 NP_990070.1 Twist1 96 82 NW_001471633.1 A Twist Dermo-1a NP_990010.1 Twist2 98 92 NW_001471728.1 A Twist Dermo-1b NP_001096684.1 Twist2 100 98 NW_001471747.1 A Twist Dermo-1c XP_424492.1 Twist2 100 98 NW_001471747.1 A Paraxis Paraxis NP_990277.1 Paraxis 79 74 NW_001471567.1 A Paraxis Scleraxis1 NP_989584.1 Scleraxis 95 92 NW_001471733.1 A Paraxis Scleraxis2 XP_001234790.1 Scleraxis 91 97 NW_001471733.1 A MyoRa MyoRa1 XP_418293.2 MyoRa1 80 79 NW_001471650.1 A MyoRa MyoRa2 XP_419734.1 MyoRa2 100 n/m* NW_001471669.1 A MyoRb MyoRb2 XP_427081.2 MyoRb2 85 n/m* NW_001471649.1 A Hand Hand1 NP_990296.1 Hand1 99 91 NW_001471449.1 A Hand Hand2 NP_990297.1 Hand2 100 98 NW_001471685.1 A PTFa PTFa XP_425989.1 PTFa 100 98 NW_001471633.1 A PTFb PTFb XP_001234487.1 PTFb 99 95 NW_001471728.1 A SCL TAL1 NP_990683.1 TAL1 60 62 NW_001471740.1 A SCL TAL2 XP_424886.1 TAL2 99 82 NW_001488876.1 A NSCL NSCL1 NP_989452.1 NSCL1 100 99 NW_001471598.1 A NSCL NSCL2 NP_990128.1 NSCL2 72 85 NW_001471526.1 B SRC SRC1 NP_001012900.1 SRC1 91 98 NW_001471673.1 B SRC SRC2 XP_001231617.1 SRC2 100 98 NW_001471649.1 B SRC SRC3 XP_417385.2 SRC3 99 86 NW_001471567 B MYC v-MYC NP_001026262.1 v-MYC 100 89 NW_001471673.1 B MYC c-MYC NP_001026123.1 c-MYC 100 56 NW_001471654.1 B MYC L-MYC XP_425790.1 L-MYC1, L-MYC2 98 98 NW_001471589.1 B Mad Mad1a NP_001034399.1 Mad1 (Mxi1) 98 96 NW_001471581.1 B Mad Mad1c NP_001012929.1 Mad1 (Mxi1) 98 74 NW_001471720.1 B Mad Mad4 NP_001006460.1 Mad4 100 85 NW_001471687.1 B Mnt Mnt XP_425414.2 Mnt 98 68 NW_001471508.1 B MAX MAX P52162.1 MAX 100 91 NW_001471508.1 B USF USF1 NP_001007486.1 USF1 92 82 NW_001474499.1 B MITF MITF NP_990360.1 MITF 100 64 NW_001471443.1 B MITF TFEB NP_001026093.1 TFEB 100 96 NW_001471610.1 B MITF TFEC NP_001006229.1 TFEC 100 71 NW_001471512.1 B SREBP1 SREBP1 NP_989457.1 SREBP1 100 96 NW_001471454.1 B SREBP2 SREBP2 XP_416222.2 SREBP2 100 99 NW_001471513.1 B Mlx Mlx1 NP_001104311.1 Mlx 96 n/m* NW_001471508.1 B Mlx Mlx2 hmm20496 Mlx 96 n/m* NW_001471508.1 B Mlx MondoA hmm54830 MondoA 100 91 NW_001471459.1 B TF4 TF4 NP_001026101.1 TF4 100 83 NW_001471622.1 C Clock Clock NP_989505.2 Clock 98 87 NW_001471686.1 C Clock NPAS2a NP_001025713.1 NPAS2 100 97 NW_001471545.1 C Clock NPAS2b XP_420353.2 NPAS2 100 99 NW_001471681.1 C ARNT ARNT1 NP_989531.1 ARNT1 100 100 NW_001471606.1 C ARNT ARNT2 XP_413854.2 ARNT2 100 100 NW_001471428.1 C Bmal Bmal1 NP_001001463.1 Bmal1 71 85 NW_001471698.1 C Bmal Bmal2 NP_989464.1 Bmal2 100 n/m* NW_001471513.1 C AHR AHR1a hmm34307 AHR1 68 94 NW_001471728.1 C AHR AHR1b hmm34113 AHR1 68 94 NW_001471728.1 C AHR AHR2 hmm46108 AHR2 70 90 NW_001471639.1 C Sim Sim1 XP_419817.2 Sim1 74 n/m* NW_001471671.1 C Sim Sim2 XP_416724.2 Sim2 93 88 NW_001471534.1 C Trh NPAS3 XP_421232.2 NPAS3 73 n/m* NW_001471710.1 C HIF Hif1α NP_989628.1 Hif1α 100 92 NW_001471710.1 C HIF EPAS1 NP_990138.1 EPAS1 100 91 NW_001471679.1 D Emc Id1 NP_989921.1 Id1 69 n/m* NW_001471567.1 D Emc Id2 NP_990333.1 Id2 98 89 NW_001471673.1 D Emc Id3 NP_989920.1 Id3 100 96 No clear D Emc Id4 NP_989613.1 Id4 91 86 NW_001471637.1 E Hey Herp1 XP_425926.2 Herp1 97 89 NW_001471651.1 E Hey Herp2 XP_419754.2 Herp2 66 73 NW_001471671.1 E H/E(spl) Dec1 hmm32419 Dec1 82 80 NW_001471443.1 E H/E(spl) Dec3a XP_422641.2 ? n/m n/m NW_001471743.1 E H/E(spl) Dec3b XP_416543.2 ? n/m n/m NW_001471526.1 E H/E(spl) Hes5a NP_001012713.1 Hes5 75 78 NW_001471571.1 E H/E(spl) Hes5b XP_417552.2 Hes5 n/m 97 NW_001471571.1 E H/E(spl) Hes5c XP_417553.2 Hes5 n/m 97 NW_001471571.1 F Coe EBF1 NP_990083.1 EBF1 52 n/m* NW_001471449.1 F Coe EBF2 XP_417675.2 EBF2 94 90 NW_001471575.1 F Coe EBF3 XP_421824.2 EBF3 67 n/m* NW_001471723.1 ? Orphan Orphan2 XP_422318.1 ? n/m n/m NW_001471740.1 ? Orphan Orphan3 XP_001234727.1 Orphan3 100 93 NW_001471567.1 ? Orphan Orphan4 XP_001235101.1 ? n/m n/m NW_001471508.1
Chicken bHLH genes were named according to their human homologues. Bootstrap values were from phylogenetic analyses with human bHLH sequences using Bayesian inference and ML algorithm, respectively. BI posterior probability (note a) refers the result from Bayesian inference in phylogenetic analysis, and ML bootstrap value (note b) refers the result from maximum likelihood estimate in phylogenetic analysis. The numbers in the phylogenetic trees are converted into percentages. All bHLH members are in the order of bHLH families manifested in Ledent et al. [5 , Table
]. All protein sequences were retrieved in NCBI website except those numbered beginning with “hmm” which were from database of “Ab initio protein”. The question mark means no matching, mark n/m means none monophyletic group with another single bHLH sequence of a known family, but formed a monophyletic group with two or more homologue sequences of the same family; n/m* denotes cases of lower bootstrap value estimated less than 50%.