International Journal of Genomics

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
A	Mesp	Mesp1	hmm11657	Mesp2	n/m	n/m	NW_001471429.1
A	Mesp	Mesp2	NP_989897.1	Mesp1	n/m	n/m	NW_001471429.1
A	Mesp	Mesp2	NP_989897.1	Mesp2	n/m	n/m	NW_001471429.1
A	Mesp	pMesp1	hmm17962	pMesp1	n/m	n/m	NW_001471429.1
A	Mesp	pMesp1	hmm17962	pMesp2	n/m	n/m	NW_001471429.1
A	Mesp	pMesp2	XP_001231219.1	pMesp1	n/m	n/m	NW_001471429.1
A	Mesp	pMesp2	XP_001231219.1	pMesp2	n/m	n/m	NW_001471429.1
A	Mesp	pMespo1	NP_990015.1	pMesp1	n/m	n/m	NW_001471673.1
A	Mesp	pMespo1	NP_990015.1	pMesp2	n/m	n/m	NW_001471673.1
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%.