Gene detail

Detail information of MD03G1220300 Annotation

Gene ID	Annotation
MD03G1220300	LSD1-like2

Network

Network Category	Global Network	Conditional network (different tissues and developmental stages)
Coexpression Positive	Top300 PCC genelist	Top300 PCC genelist
Coexpression Negative	Top300 PCC genelist	Top300 PCC genelist

Functional module

Method	Module ID	Function Annotation
--	--	--

Gene structure and chromatin state

more details in UCSC

details of chromatin state

Location

Gene	Type	Chr	Start	End	Strand
MD03G1220300	mRNA	Chr03	30449337	30452592	-

Sequences

CDS:

MD03G1220300

TAACTCCTACTGGACAAACCCTTCCAAATCGTCCCGTTTCCGATTCAACTCGGTCCAACCAGGTGAGTCGCCCTTCACTTTCAATTTCCCTAAACATTTACACAAACTTCTAATGTATTTTACACCCACTGCTGAATTGAATTTTGGGTACAAAATTGGGGAAATTAGGACTCGTATTTAAATTAATTGTAGCTCGTACTGTCAGTCTGAGTGATATTAACAGTGACTTTCTTGGTTGAAATCCGTAGTTGGGGTTAGAAACAACATGGGATTTGAGGATATGGATTGATATATGTGAGTTTGCTGTTCAATTTGTGTGTAAAGATAATCAATGTCTCAATTCGAGAATCCGAAAACATGCTGTTAATGGGTCGTGAGGGAATTGCTTGAAATGAAATGCCAATATGGGGTGTTGTGTTTTTTATTTGTTTTTGAGCTGATTACTTGATTTGGGTTAAGAAGTTGTCGTGGAGAGGGCACGGTCTAGGGCAATGGAGACACCGGGTTCAGATGGTTCTGTTTCTAAGCGGTCTCTGAGGAAGAAAGCAAGTTTGCGCAATTATGATGAGAATTTGATGGATGATATAATAGAGAAGCATTTAGGTGGTACTTTTAAGAAAAGGAAGGGAACAAAGGTGGATTTGGAGAAAGAGACTGAAACAGAGGCCATGATAGCACTGTCCCTCGGGTTCCCCATTGATGAGCTGCTTGAGGAGGAAAAACAAGCTGGGGTGGTCACCGAGTTGGGTGGGAAGCAGCAGAATGATTACATTGTTGTGAGAAATCATATTTTAGTAAGATGGCGGAGTAATGTGCGAGTGTGGCTTTCAAAAGGGCAGATTAAAGAAACTGTGAGTGGTGATTATGAGCATTTGATATCTTCAGCTTATGATTTTCTTTTGTATAATGGATACATCAATTTTGGGGTTGCACCAGCATTTATGGCTAATATGCCAGAGGAGGTAACTGAAGGGTCTGTCATCATTGTTGGTGCGGGACTTGCTGGACTAGCGGCTGCAAGGCAGCTTATGCAATTGGGTTTCAAGGTGGCTGTTTTAGAAGGTAGGAATCGACCAGGTGGAAGAGTCTACACCCAAAAGATGGGGAAGGATGGAAAGTTTTCTGCTGTGGATCTTGGCGGCAGTGTCATTACTGGCATCCATGCTAACCCACTTGGAGTTCTGGCGAGGCAACTTTCTATTCCGCTTCATAAGGTCAGAGATAAGTGTCCTTTGTACAAACCTGATGGGACACCTGTTAATAAGGACATTGACTCTAACATTGAAATCATCTTTAATAAGTTGCTTGACAAAGTCATGGAACTCCGACAGACAATGGGTGGGTTTGGAAATGATATATCTCTGGGTTCAGTTTTGGAGAAACTGAGGCAGTTGTATTCTGTTGCTAGAAGCACTGACGAGAAGCAACTTCTTGATTGGCATCTTGCAAATTTGGAATATGCAAATGCTGGATGTCTATCAAATCTCTCAGCTGCCTACTGGGATCAGGATGATCCTTATGAAATGGGTGGGGACCACTGTTTTCTTGCTGGAGGTAATGGGAGATTGATCAGAGCACTGTGTGAAAGAGTTCCCATATTCTATGGAAAGACTGTCAATACTATTAGGTATGGAGATGAAGGGGTTGAAGTTATTGCAGGGGACCAAGTGTTTCGAGGGGACATGGTCCTATGCACTGTTCCTCTTGGAGTTCTGAAAAAGGGTTCCATCAGATTTGAACCCGAGTTGCCCCAAAGAAAGCTCGCAGCAATTGAAAGGTTGGGATTTGGTCTGCTGAACAAAGTAGCTATGGTTTTTCCTCATGTTTTCTGGGGTGAAGAACTAGATACTTTTGGATGTCTCAATGAACATAGCCATCAACGTGGAGAGTTCTTTTTGTTCTATGGATACCATACTGTATCTGGAGGTCCAGTTCTTATTGCACTGGTGGCGGGAGAAGCTGCAGAGACATTTGAGTGCACAGAGCCATCAATATTGCTCCATCGAGTTTTAAGCGTCCTCAGAGGTATATATACTCCTAAGGGCATTGATGTACCTAATCCAATTCAAACCATTTGTACAAGGTGGGGTGGTGATCCCCTTTCCTATGGTTCATATTCTCATGTTAGAGTACAGTCATCTGGCAGTGACTATGATTTGCTCGCAGAAAGTGTGGGAAACCGGCTGTTCTTTGCAGGTGAGGCCACAACCAGGCAACATCCAGCTACCATGCATGGGGCCTTTCTGAGTGGCCTAAGAGAGGCTTCGTGCATATATCGTGCCACAAGACGTAGTCAAAACTATTTGAGGAAAGTCATACAAAAGAATGTTGGATCAAGCACTGATATGCTGGAAGATCTATTTGAGAAGCCCGATTTGGAATTTGGGAACTTTTCATGTGTATTTGATCCTTCAATAGAAGACCCAAAATCAATAGGATTTATGAGAGTTGGTGTTGGGAGTAGTGAAAACAGTTATAAACAAGAGCTAACAAGCAGCTCCCAAAATGCCTTAACCATACCATTGCAGCTTTACACATTTATATCTCGTGAGCAAGCATGTGGGTTAGAACTGGTGACAGGAGGAGATGAAAGTAGGCTATCGTACTTGGTGAAAGTTTTCGGCTTGAAGCTGATGGGACCTAGTGCCATAGGAACTGTAGGTAACTCCTTGGCAGTTAGCATTGGTAATGCTCGAAGAGGAAGGGGAAGGAATCGCATGTCCGCCGGGCGGCAGTAGGTTGCTTGCAGTTTCAAAGACTTTTGTGCATCGTTTGGAGTTTCATGTTCAGGTGCACACTTCTGTATATCATTGAGCCATTTATGCAATTCATTTGGTTTAAGAGAAATTGATCTCTTGGAGTCGAACTGTGAAAACTCATTTTATGCATATCTGTAGAACATGTTTTAGTCTGACCTTGATTCAGGTAGTGGGTTGACTGAAGACTCATCAACCATTCATGCAGGTATGAAATTTTGATTAGGTTGAAGATCTTGTACACCTTCCCATATTAATAGGGAACAGAATATCGATAGACATTGAAAGTTAATCGAATATTTTTGAATGTCAAGTTCTTTGTCTTTGTTCATATTTCATCCTGAATAAGCA

Protein:

Gene family

Gene family	Subfamily
Transcription Factors Family	SWI/SNF-SWI3
Epigenetic Regulators	HDMA

Orthologous genes

Species	Gene ID	Score of Inparanoid	Annotation
Arabidopsis thaliana	AT3G13682.1	1	LDL2\|LSD1-like2
Prunus persica	Prupe.4G188600.1.p	1	LSD1-like2
Pyrus communis	PCP002413.1	1	-
Pyrus x bretschneideri	Pbr024850.1	1	-
Pyrus x bretschneideri	Pbr001009.1	1	-
Rosa multiflora	Rmu_sc0000879.1_g000007.1	1	-
Rubus occidentalis	Ro03_G16046	1	-
Fragaria vesca	mrna25010.1	1	LSD1-like2
Vitis vinifera	GSVIVT01014417001	1	LSD1-like2
Solanum lycopersicum	Solyc07g063450.1.1	1	LSD1-like2
Populus trichocarpa	Potri.011G127600.1	1	LSD1-like2
Nicotiana benthamiana	Niben101Scf01976g00017.1	1	Lysine-specific histone demethylase 1 homolog 2
Nicotiana benthamiana	Niben101Scf01992g01012.1	0.76	Lysine-specific histone demethylase 1 homolog 2
Oryza sativa	LOC_Os08g04780.1	1	"amine oxidase, putative, expressed"
Zea mays	GRMZM2G149786_P01	1	LSD1-like2

Gene Ontology

GO term	Description	Category
GO:0005515	protein binding	molecular_function
GO:0055114	oxidation-reduction process	biological_process
GO:0003677	DNA binding	molecular_function
GO:0016491	oxidoreductase activity	molecular_function

KEGG

KO	Description	Enzyme
K11450	lysine-specific histone demethylase 1A	EC:1.-.-.-

Pfam domain

Pfam accession	Pfam name	Alignment start	Alignment end	E-value
PF04433.13	SWIRM	61	144	1.40E-16
PF01593.20	Amino_oxidase	170	594	6.50E-87

Expression pattern

SRA Experiment	Tissue	Stress	Stage	FPKM
SRR768136	whole seedling	no	seedling	2.07254
SRR5252888	dormant buds	no	dormant buds(0 month)	5.35576
SRR5252889	dormant buds	no	dormant buds(0 month)	4.5794
SRR5252886	dormant buds	no	dormant buds(1 months)	4.73
SRR5252887	dormant buds	no	dormant buds(1 months)	2.78899
SRR5252884	dormant buds	no	dormant buds(2 months)	5.11386
SRR5252882	dormant buds	no	dormant buds(3 months)	5.45983
SRR5252883	dormant buds	no	dormant buds(3 months)	1.98314
SRR5252880	dormant buds	no	dormant buds(4 months)	6.54974
SRR5252881	dormant buds	no	dormant buds(4 months)	6.53684
SRR5252878	bud break	no	bud break	6.96231
SRR5252879	bud break	no	bud break	9.24022
SRR3744766	flower	no	mature	2.37492
SRR3744767	flower	no	mature	2.32294
SRR3744768	flower	no	mature	2.34227
SRR6308190	stigmas	no	open flowers	1.59065
SRR6308181	styles	no	open flowers	1.71253
SRR6308188	filaments	no	open flowers	1.71018
SRR6308187	anthers	no	buds 1-3 days prior to flower opening	1.47387
SRR6308192	pollen	no	open flowers	2.00544
SRR6308191	petals	no	open flowers	1.41544
SRR6308194	sepals	no	open flowers	1.51345
SRR6308193	receptacles	no	open flowers	1.32032
SRR6308189	ovaries	no	open flowers	1.65643
SRR3384922	fruit	no	1 week after full bloom	1.98756
SRR3384921	fruit	no	2 week after full bloom	1.5926
SRR3384920	fruit	no	3 week after full bloom	1.32851
SRR3384919	fruit	no	4 week after full bloom	1.45463
SRR3384923	fruit	no	5 week after full bloom	1.08074
SRR3384918	fruit	no	6 week after full bloom	1.41964
SRR3384917	fruit	no	8 week after full bloom	1.2506
SRR3384916	fruit	no	10 week after full bloom	1.42155
SRR3384915	fruit	no	12 week after full bloom	1.04122
SRR3384914	fruit	no	14 week after full bloom	1.29466
SRR3384913	fruit	no	16 week after full bloom	0.853937
SRR3384912	fruit	no	18 week after full bloom	0.629653
SRR3384911	fruit	no	19 week after full bloom	0.933317
SRR3384910	fruit	no	20 week after full bloom	0.773747
SRR768128	whole fruit	no	25 days post anthesis	2.39759
SRR768129	whole fruit	no	35 days post anthesis	1.29936
SRR768130	whole fruit	no	60 days post anthesis	1.66254
SRR768131	whole fruit	no	87 days post anthesis	1.72607
SRR7343308	immature fruit flesh	no	immature	2.4378
SRR7343309	immature fruit flesh	no	immature	3.34277
SRR6320494	ripe fruit flesh	no	mature	0.879294
SRR5405143	ripe fruit peel	no	mature	1.52634
SRR6320572	ripe fruit peel	no	mature	1.02307
SRR7403504	fruit	uninfected	mature	1.09098
SRR7403506	fruit	uninfected	mature	0.970498
SRR7403507	fruit	uninfected	mature	1.09829
SRR7403500	fruit	infected with penicillium expansum	mature	0.445217
SRR7403501	fruit	infected with penicillium expansum	mature	0.991037
SRR7403508	fruit	infected with penicillium expansum	mature	0.714431
SRR7403502	fruit	infected with penicillium expansum	mature	0.490986
SRR7403503	fruit	infected with penicillium expansum	mature	0.788313
SRR7403505	fruit	infected with penicillium expansum	mature	0.739407
SRR1613973	Central seeds	no	20DAPF	1.95629
SRR1613974	Central seeds	no	20DAPF	2.25773
SRR1613975	Central seeds	no	20DAPF	2.10599
SRR1613976	Lateral seeds	no	20DAPF	1.76384
SRR1613977	Lateral seeds	no	20DAPF	1.77381
SRR1613978	Lateral seeds	no	20DAPF	1.94739
SRR3744786	stem	no	mature	2.9835
SRR3744787	stem	no	mature	3.26354
SRR3744772	stem	no	mature	3.53309
SRX765691	seedling shoot apex	no	4-6 week old seedling	4.07152
SRX765683	tree shoot apex	no	Adult (tree), new shoot has 10-12 visible leaves	4.27641
SRR1089478	leaf	Virus-free	plantlets	1.89266
SRR1089477	leaf	ASGV-infected	plantlets	1.23631
SRR767660	leaf	uninfected	fully developed	1.36483
SRR767669	leaf	2 days post infection by Venturia inaequalis	fully developed	0
SRR767670	leaf	4 days post infection by Venturia inaequalis	fully developed	3.67283
SRR767671	leaf	6 days post infection by Venturia inaequalis	fully developed	1.30577
SRR767672	leaf	8 days post infection by Venturia inaequalis	fully developed	0
SRR767673	leaf	10 days post infection by Venturia inaequalis	fully developed	1.71468
SRR767674	leaf	12 days post infection by Venturia inaequalis	fully developed	2.07319
SRR768127	leaf	14 days post infection by Venturia inaequalis	fully developed	2.0621
SRR6308182	young leaf	no	immature leaves	5.4193
SRR3744769	leaf	no	mature	3.09085
SRR3744770	leaf	no	mature	3.13955
SRR3744771	leaf	no	mature	3.43439
SRR5405145	leaf	no	mature	2.03482
SRR6320561	leaf	no	mature	1.37499