Gene detail

Detail information of MD08G1046300 Annotation

Gene ID	Annotation
MD08G1046300	dicer-like 3

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
Co-expression network	CFinderM0329	meristem initiation determination of bilateral symmetry double-stranded RNA binding

Gene structure and chromatin state

more details in UCSC

details of chromatin state

Location

Gene	Type	Chr	Start	End	Strand
MD08G1046300	mRNA	Chr08	3498742	3509945	+

Sequences

CDS:

MD08G1046300

AGCTCTCCACTCTCCGTTGCTGTGCAGAAGCAGTGAAGATAGAGCACCCAATCTCTCGGGCTCACGATTCTCGCGTTCTTCACCTTCCGCCATCTTCTTCCGGCGTCTCTCGCATTCCCGGCCGGAATCGGAATCAAAGGACGGAGCTTTCACGGCATGGAAGTAGAGGAATCCAATTCCAGCCCCCTCAATCATGCCGCCGATGATGATCAGTCACCGCAGTCGTCCAAGAAATTCAGTCCCAGACGGTATCAGTCGGAGGTGTATGAGGTTGCGCGGCGGAAGAACACGATAGCGGTGCTGGAAACCGGTTCCGGGAAGACGATGATAGCTGTGATGCTCATCAGAGACTACGAAGGCTGCCAAACTATAAATTCAAGTAGTGGTGCCAAAAAATTGATTATTTTCTTGGCTCCAACTGTTCATCTTGTTCACCAACAATTTAAGGTTATTAAAGAAAGCACAAATTGTAGTGTGGGAGAGTATTATGGAGCCTTGGGGGTGGACTCGTGGACCATGGAGCGCTGGGAAAAGGAAATAAATGAGCACGATGTGCTAGTTATGACCCCCCAAATTCTTTTGGATGCCTTAAGAAAGGCATTCTTGAGTTTGGAAGTGGTATGCTTGATGATTGTTGATGAGTGCCATCGGGCTAATGGGAACCATCCATATACAAAGATAATGAAGGAATTTTATCACAAGTCTAGTAAAAAGCCAAGGATTTTTGGCTTGACGGCATCACCTGTTATCAAAAAAGGTGTCTCATCCACAAAGGATTGTGAGGGCCAGTTATCAGAACTTGAAAGCACTTTAGATTCCCAGATTTATACTATTAAGGACATAACAGAGATGGAAGTATGTGTCCCCTCTGCAAAAGAAACATGTAGATTTTATGGCCAAGCATGGTTTCCATGTTCAGATTTGAAAGAAAAGATGAAAGCCTCTTGGTCCAAGGTTGATGCTTCATTGTCAAAGTTGCAAGAATCAGTAGAAAGTAATGTGAATGACATGGAGGATACAATTAAGACCTTGCGGAAACGAATGTCTAATGACTACACAAAGATCTTGTATTGCCTTGATGACCTTGGTCTCATATGTACTTACGAGGCTGTTAAGATCTGTTTAGAGAATGCTCCGAAGTGCAACGAGGTGATTGAACTTTATAGAGAAGGCTCTTTGCAGTGCAGATGTTTTCTTGAGGAAGTGTTTGGTATAATTAAGGAATCATTTCTGCATGGTTCTGAAAATTTTTTGGATTTCGGGTTTGACTATTTGAAGGCAGTAGATGTGGGCTATATATCTCCAAAATTAAATGAACTTGTTCAAATTTTTCATTCTTTTGGAAGATCTAGGGAAGTACGGTGCCTCATATTTGTTGATAAAATCATCACAGCTAAAGTGATTGAGAGATTCATTAAGAAGGTTACCTCCCTGTCTCATTTTACGGTTTCCTATTTGACTGGAAGCACTACATCAGTTGACGCTCTGGCGCCGAAAATACAAAAGGAGACATTGGAGTTATTCTGCTCTGGGGCGGTCAATTTATTATTTGCTACCGATGTAGTTGAGGAGGGAATTCATGTTCTGAGCTGCTCCTGTGTGGTACGTTTCGACTTGCCAAAGACAGTGCGTAGTTATGTCCAGTCAAGGGGACGAGCTCGGCAAGATAACTCTCAATTCATCACAATGCTGGAGAGGGGAAACAAAAAACAAAGGGATCAACTATATGAGATTGTCAAGAGTGAGTGTTTGCTGACAGATACAGCTGTCAAAAGAGATCCTGAAGCATGCATTTTGAAAGAATGTACTTTGGAGGAAACAAATATATATACTGTGGATTCCACCAGAGCATTAGTCACTGCAGATTCCAGTGTCAGTCTTATACATAAATATTGTGAAACGCTGCCTAGGGATAAGTACTTCACTCCAAACCCAACTTTTCATTTCTCATATCTTGGAGGGTCTTATGAGTGTAAGATTACATTGCCTCCAAATGCGGCTTTCCAAACTTTAGTTGGCCCTGCATGCAAGAAATCTTCTTTAGCAAAGCAGCTTGTCTGCTTGGAAGCATGTAAGCAGCTACATCAAATGGGTGCCCTGAATGACCATCTTCTCCCAGTCATTGATGTGCCCGATGTGAAAAGAAAAGAGGAAGCTTCTGGTGCAGGAACTACTAAAAGGAAGGAACTACATGGTACAACTGGCATTCGTATGCTATCTGGAACTTGGGGGGAGAAACTTGATGGTGCTATTTTTCAGGCATATAAGTTTGACTTCTCCTGTAATATTGCCAGTGAATTGTATTCTGGATTTGTTTTTCTCATTGAATCGAAGCTTGCTGATGATGTGGGGAATATCAAATTGGATCTTTACCTGCTTTCGAAGACAGTTAAGGCTTCTGTTTCTTCCTGTGGGGAGGTTCATTTGGACGGGGAACAGATGGAAAAAGCAAAGTGCTTCCAGGAATTTTTCTTTAATGGATTGTTTGGGAAATTGTATGGAACCAAATCGGCTAGAAAAAAGAGAGAACTTTTACTGGAGAAAGAAACAAGAAAACTGTGGACTCCATCATGCTTATATTTGCTTCTTCCGGTTGAGACATTGAATGATTCAAAAGATGAATCCTGGAGAATAAATTGGGCAGGGATCAACTCTTGTGTTTCTGTGGTAGAGTTCTTAAAGAGAAACTCGTCTTTGGGTAGTCACCAGTGTAACGTTGACACAGGGAGTTCAGTTCCAAGTAGAACTGTCTCATCTGAGACTGAGTGCAGCAGTGCGGGGATAGTTCACTTTGCTAATTGCTCTGTTGATGTAAAAAATCTCGAAGATACGGTGGTGGTGGCTATCCATACTGGAAGAATCTACTCAGTTTATGAGGTTATGAGTAACACTTCGGCTGAGAGTCCTTTTGATGGAAAGAAAGACAATGTACCATCACAATATACTTCATTTTCTGAGTACTTCAACAAAAAATATGGGATTGTGCTCCTATATCCTGGTCAGCCTCTGTTGCGACTGAAACAAAGTCATAATCCGCACAACCTTCTTGTGAACTTCAATGGTGAAGGTGGTAATGGTAAGACATTGCAATCTGGCGTTGTTATTGGAAAGCAGCGCATGTATGCTCACATGCCACCTGAGCTTCTAGTCACTATTGGTGTCCCAAGAGACGTTCTAAAGTCATGTTATTTACTACCATCGTTGATTCATCGCTTGGAGTCCCTGATGCTAGCCAGTCAACTTAGAGAAGATATTAATTATCATTGTAGCAGCTTTGGGATATCAAGCTCATTGATTCTAGAAGCACTTACAACACTAAGATGTAATGATGATTTTTCTATGGAGCGCCTGGAATTGCTTGGTGATTCAATTTTAAAATATACCGTGAGCTGCCACCTGTTTCTCAAATATCCCAAAAAGCATGAAGGACAGTTAACTAACTATCGCATGCTGACTATTTGTAACTCAAACCTACATAGATTGGGAATGAATCGCAAGTTACAGGGATATATCCGTGATGGTGCATTTGACCCATGTCGTTGGGTTGCTCCAGGGCAGATTTCTCTACGACCCGTTCCTTGTAATTGTGGAGTGGAGACTTTAGAAGTACCATTAGATAGCAAATTCCAAACTGAAGACCCGAAAGTTGTCGTTGGAAAGAGCTGTGATAAGGGCCATAGATGGATGTGTTCAAAAACAATCTCTGATTGTGTTGAAGCACTTATAGGAGCATACTATGTTGCTGGTGGATTGCCTGCTGCCTTGCATGTGATGAAGTGGCTCGATATTGATGTAGACCTTGAACCTTCCTTGGTTGCTGATGCAATTACTACGGCATCTCTTCATTTGTACACCCCGAAAGCTAATGAGATTGCAGTCTTGGAATCAAAGCTTCACTATGAATTTTCTACCAAGGGTCTGTTGCTGGAGGCCATGACACATGCATCTGACCAAGAATCAGGAGGTGGCTACTGTTATGAGCGACTTGAATTTCTAGGTGACTCTGTGTTGGACCTGCTTATCACAAGGCATCTCTATCATAGCCACACAGATATTGATCCAGGCGAGTTAACTGACTTGCGCTCAGCTTCTGTTAATAATGAAAGTTTTGCGCAAGTTGCTGTTAGACATGACCTCCAGCAGCATCTGCAACATGCATCGATGTTACTTCTAAGTCAGATAACAGAATATGTGAAGTCTCTTTCAGAACCTGACAATGGTACCACACTTCAAGGCACCAAAGGTCCTAAGGCTCTCGGAGACATGGTGGAAAGTATTGCAGGGGCTATTCTAATTGATACCAAACTTAATCTTGATGAAGTGTGGAGAATTTTTGAGCCACTATTATCTCCAATTGTGACTCCTGACAAACTTGAGCTGCCTCCACTACGGGAGCTGATTGAATTATGCGACTTGTTCGGGTACTATAAAAAAGAGAAGTGTACCAATAAGGGTGAAACAGTTCATGCGGAGCTTACTGTACAACTGAAAGATGTTCTGTTGACTGGAGATGGGTGCGATCGGACTAAAAAAGGTGCAAAAGGAGAAGCAGCTCGTCGTTTACTCAAGAAACTTGAGGAGAGAGGTATTTCATTTTCCAAGAAGAGGAAACTGGATGCTAACCAAGTAGGTGATTCCTCTTCCCTTGACATCAACCATAAGGTCAGCGACCAAGTAACCGTCAAAGATTCTTCAGCGTTAATGGTCTATAAAAGGCGAAAGACAACTGAAATGCCTCTAGCTGCTCCACCAACTGGAGTTTCTCCTTCAGTAATTGCCAGGAAAACCTCTAGCCCCAACAATGCCGCCCCAGTCATTAAAGCAATCAACATGAAGAAAGGAGGGCCTCGATCTGCTCTTTTTGCTCTGTGCATGAAACAACAGTGGCCAAAGCCGGGCTTTAAAATAACAGAAACTCAGTCAAGAACTCCATTCACATTTGGTGAAAGCTCAACCAAGTACTTCAACAGTTTTGTCGCACAAGTAATCCTGCACATACCCAACTCCGGCGTCATTGAATGCACAGGAGATGCTAGACCTGACAAGGGGAGTTCAGAAGATTCTGCAGCCGTCGTCTTGTTTCAAGAGCTTCAACGGCAGGGAAGAGTTGTAATTGCTGGGTGATAAGATAACATATCTTTTTCCGGCTAGTTTCATAATTTAAGAATCGGAGGGTTTAATAATTTCCGAATCCACCATCCCAGTTATCTTTGTTCATATGGAGCAGTTGGGATCTGGCATTGCCATGAATCCATGGAGCATGGTTAATCTCAATGCAAGTAGATTAACATCACCAGGAAAAAGAACTGTAAATTATGTGCTGCCTTCACCCCCTTTTACTCTCCTTTCTCTTACTCTTATGTACTTAGTTTTTATCTATGAATAAAGACGACAAAAGTTTCGACATCATGGTCTTGAAGAACTTTAGTTTGAGCTCCTTCAAGACTTTTC

Protein:

Gene family

Gene family	Subfamily
Epigenetic Regulators	DCL

Orthologous genes

Species	Gene ID	Score of Inparanoid	Annotation
Arabidopsis thaliana	AT3G43920.2	1	ATDCL3;DCL3\|DICER-LIKE 3
Arabidopsis thaliana	AT3G43920.3	0.984	ATDCL3;DCL3\|DICER-LIKE 3
Arabidopsis thaliana	AT3G43920.1	0.928	ATDCL3;DCL3\|DICER-LIKE 3
Prunus persica	Prupe.1G401900.1.p	1	dicer-like 3
Prunus persica	Prupe.1G401900.2.p	0.979	dicer-like 3
Pyrus communis	PCP026425.1	1	-
Pyrus x bretschneideri	Pbr036439.1	1	-
Rosa multiflora	Rmu_sc0004065.1_g000007.1	1	-
Rubus occidentalis	Ro02_G04571	1	-
Fragaria vesca	mrna15481.1	1	dicer-like 3
Vitis vinifera	GSVIVT01035494001	1	dicer-like 3
Solanum lycopersicum	Solyc08g067210.2.1	1	dicer-like 3
Populus trichocarpa	Potri.018G047500.1	1	dicer-like 3
Nicotiana benthamiana	Niben101Scf06666g01011.1	1	MADS-box transcription factor 6
Oryza sativa	LOC_Os01g68120.1	1	"DCL3, putative, expressed"
Oryza sativa	LOC_Os10g34430.1	1	"Dicer, putative, expressed"
Zea mays	GRMZM2G413853_P01	1	dicer-like 3

Gene Ontology

GO term	Description	Category
GO:0008026	ATP-dependent helicase activity	molecular_function
GO:0004525	ribonuclease III activity	molecular_function
GO:0006396	RNA processing	biological_process
GO:0005524	ATP binding	molecular_function
GO:0003723	RNA binding	molecular_function
GO:0005515	protein binding	molecular_function

KEGG

KO	Description	Enzyme
K11592	endoribonuclease Dicer	EC:3.1.26.-

Pfam domain

Pfam accession	Pfam name	Alignment start	Alignment end	E-value
PF03368.10	Dicer_dimer	572	655	7.40E-25

Expression pattern

SRA Experiment	Tissue	Stress	Stage	FPKM
SRR768136	whole seedling	no	seedling	4.3474
SRR5252888	dormant buds	no	dormant buds(0 month)	11.4536
SRR5252889	dormant buds	no	dormant buds(0 month)	13.35
SRR5252886	dormant buds	no	dormant buds(1 months)	9.77126
SRR5252887	dormant buds	no	dormant buds(1 months)	6.0864
SRR5252884	dormant buds	no	dormant buds(2 months)	6.56099
SRR5252882	dormant buds	no	dormant buds(3 months)	8.77376
SRR5252883	dormant buds	no	dormant buds(3 months)	4.63087
SRR5252880	dormant buds	no	dormant buds(4 months)	11.1582
SRR5252881	dormant buds	no	dormant buds(4 months)	12.4695
SRR5252878	bud break	no	bud break	15.4443
SRR5252879	bud break	no	bud break	14.1374
SRR3744766	flower	no	mature	0.885311
SRR3744767	flower	no	mature	1.18309
SRR3744768	flower	no	mature	0.967001
SRR6308190	stigmas	no	open flowers	3.47949
SRR6308181	styles	no	open flowers	3.97036
SRR6308188	filaments	no	open flowers	3.53899
SRR6308187	anthers	no	buds 1-3 days prior to flower opening	1.01416
SRR6308192	pollen	no	open flowers	0
SRR6308191	petals	no	open flowers	2.89716
SRR6308194	sepals	no	open flowers	1.75773
SRR6308193	receptacles	no	open flowers	4.56198
SRR6308189	ovaries	no	open flowers	5.31049
SRR3384922	fruit	no	1 week after full bloom	3.23658
SRR3384921	fruit	no	2 week after full bloom	5.58691
SRR3384920	fruit	no	3 week after full bloom	3.54684
SRR3384919	fruit	no	4 week after full bloom	3.01311
SRR3384923	fruit	no	5 week after full bloom	2.50726
SRR3384918	fruit	no	6 week after full bloom	1.82086
SRR3384917	fruit	no	8 week after full bloom	1.41996
SRR3384916	fruit	no	10 week after full bloom	1.76987
SRR3384915	fruit	no	12 week after full bloom	1.38623
SRR3384914	fruit	no	14 week after full bloom	1.6448
SRR3384913	fruit	no	16 week after full bloom	1.65091
SRR3384912	fruit	no	18 week after full bloom	1.70739
SRR3384911	fruit	no	19 week after full bloom	1.51628
SRR3384910	fruit	no	20 week after full bloom	1.36529
SRR768128	whole fruit	no	25 days post anthesis	5.69846
SRR768129	whole fruit	no	35 days post anthesis	3.23286
SRR768130	whole fruit	no	60 days post anthesis	2.56746
SRR768131	whole fruit	no	87 days post anthesis	4.12754
SRR7343308	immature fruit flesh	no	immature	4.12234
SRR7343309	immature fruit flesh	no	immature	5.53581
SRR6320494	ripe fruit flesh	no	mature	0.24333
SRR5405143	ripe fruit peel	no	mature	1.4496
SRR6320572	ripe fruit peel	no	mature	1.27752
SRR7403504	fruit	uninfected	mature	0.531628
SRR7403506	fruit	uninfected	mature	0.502914
SRR7403507	fruit	uninfected	mature	0.646886
SRR7403500	fruit	infected with penicillium expansum	mature	0.0205078
SRR7403501	fruit	infected with penicillium expansum	mature	0
SRR7403508	fruit	infected with penicillium expansum	mature	0.021939
SRR7403502	fruit	infected with penicillium expansum	mature	0.08481
SRR7403503	fruit	infected with penicillium expansum	mature	0.0568356
SRR7403505	fruit	infected with penicillium expansum	mature	0.119206
SRR1613973	Central seeds	no	20DAPF	4.47059
SRR1613974	Central seeds	no	20DAPF	5.20228
SRR1613975	Central seeds	no	20DAPF	4.21779
SRR1613976	Lateral seeds	no	20DAPF	4.14905
SRR1613977	Lateral seeds	no	20DAPF	4.09118
SRR1613978	Lateral seeds	no	20DAPF	4.51104
SRR3744786	stem	no	mature	1.91185
SRR3744787	stem	no	mature	2.23467
SRR3744772	stem	no	mature	2.31805
SRX765691	seedling shoot apex	no	4-6 week old seedling	9.72574
SRX765683	tree shoot apex	no	Adult (tree), new shoot has 10-12 visible leaves	10.8944
SRR1089478	leaf	Virus-free	plantlets	2.92107
SRR1089477	leaf	ASGV-infected	plantlets	2.73611
SRR767660	leaf	uninfected	fully developed	0.839244
SRR767669	leaf	2 days post infection by Venturia inaequalis	fully developed	5.78056
SRR767670	leaf	4 days post infection by Venturia inaequalis	fully developed	1.40535
SRR767671	leaf	6 days post infection by Venturia inaequalis	fully developed	1.44515
SRR767672	leaf	8 days post infection by Venturia inaequalis	fully developed	0
SRR767673	leaf	10 days post infection by Venturia inaequalis	fully developed	0.62119
SRR767674	leaf	12 days post infection by Venturia inaequalis	fully developed	1.06427
SRR768127	leaf	14 days post infection by Venturia inaequalis	fully developed	0.499234
SRR6308182	young leaf	no	immature leaves	8.72122
SRR3744769	leaf	no	mature	0.853776
SRR3744770	leaf	no	mature	0.99749
SRR3744771	leaf	no	mature	1.17765
SRR5405145	leaf	no	mature	4.10767
SRR6320561	leaf	no	mature	3.33742