Gene detail

Detail information of MD16G1178600 Annotation

Gene ID	Annotation
MD16G1178600	DNA topoisomerase 1 beta

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	CFinderM0131	intracellular transport ubiquitin conjugation factor E4 B [EC:2.3.2.27] nuclear pore complex protein Nup50 DNA topoisomerase I [EC:5.99.1.2] anaphase-promoting complex subunit 3

Gene structure and chromatin state

more details in UCSC

details of chromatin state

Location

Gene	Type	Chr	Start	End	Strand
MD16G1178600	mRNA	Chr16	15262809	15270090	-

Sequences

CDS:

MD16G1178600

TTCACCTACATTCCACAAATCCGATATCACATTACCGAAGCTCGCCCTCTCTCTCTCTCACTTAAAACGGTAACTGTGGTGGCCATCTTTTCCCAAATATCAATTCAATCAGCTCAATAAGACTTTCGAATTTGCCCTAATTTAAGAGATCAGAAGCTGCAAACTCAATTTATTCTTTGACGAACAAGTGATTTACATGCCACCTGAGTATATTGTTGGATGATGGCTGTTCAGACTTCTACTAAACTGAATTTATGTGAAGACGAGGATGATGAACCTTTAGTTTTCAAACGGTACAGCACAAAATCTAAACCGAATCAATTAAATGCTGAAGCAAATAAATTATCAGCTGAGAGGCAAGTTGGACAACCAGGGAAGCAGTTATCTGAGCACCGTTATTCCAATGGTCTAAACTCGAGTGTTCAAAAGGTTAAGATGGTTCCATCAACCAAATCACCACCAGTAAAATCTCCGCTAGCAAGCCCAAAAGCTTCAACTTCATCTGCTGGGGCATCACCAGTATCAAATTCAAAAGCTTCAACTTCATCTAGGGCATCACCAGTTTCCAAATCACCACCGTCGACTACATTAGATGATCAGTCAAAGCGGTTGTCAGAACAGAATAAGTCTACCACGATTAAGGAGGAAATTAATTCTATTGAACATCTTGCTCAAGGAAATAGTGATTCTGAAGATGAAAAACCGATAGGTGCCAGACTGGGGAAAGTGAAACCTTCTGAAGATTCGGATGATGATAAACCTTTATCATCAAGGATTGCACCAAAGTCCAAGGTGGGAACATCAGGCAGTTGGCCTTATGATTCTAACAAAAGGAAGCCCGTTGTTTCAAAAGTTCAGAAGAATGGTTCCAGCACAATAGATAAAGGCAAAGCTTCATCTGTGGTCTCTAGTAAGAGGCCTCTAGATAAGGTCAATTCTTCTGAGAACTCTTCAGCTAAAAGGCCAAAAGTTTCAGATTCTTCTACATCTGCAAAGAATAAGCAGGCATCAGCCAAAAAAGAACCAAAGGAAGAAGATGATGATGATGATGATGACTTCGTTCCAATTTCCCAGAGGAGTAAGAAAGTTACATCTGATAGTAAACCATCTCTGACAAAGCAAACGGTAACCAAAGTTGGTTCATCCTCAATCACGAAAACAATCAAGAAGGGCCAAAAAGCTTCAAAATTTTCAAAGTATTCTAAGTCGACAACAAAGCCACCGGGCTCTAATGATGGGCAGATAAAATGGACTACTTTAAAACACAATGGTGTCATTTTCCCGCCTCCTTACAACCCTCATGGGGTAAAGATGCTCTATAATGGGAAGCCAGTCACCTTGACTCCTGAACAAGAGGAGGTTGCAACAATGTATGCAGTGATGAAAGATACTGATTATGTGCAGAAAGAAACATTCAGAAACAATTTCTGGGCTGATTGGCATAAGTTGCTTGGGAAGAACCATGTAATTCAGAAATTGGATGCTTGTGATTTTACGCCAATATATGACTGGTATCAGAATGAAAAGGAAAAGAAGAAACAAATGAGCACGGAAGAGAAGAAGGCCTTGAAGGAGGAGAAACTGAAACAAGAGGAGAAGTATATGTGGGCTGAGGTTGATGGTGATAAGGAGAAGGTTGGAAACTTCAGAGTTGAACCACCTGGGTTATTTCGAGGCCGTGGAGAGCATCCAAAGTCGGGAAAGCTGAAAAGACGGATTCGTCCAAGTGATGTTACAATTAATATAGGAAAGGATGCCCCAATTCCAGAATGTCCCATCCCTGGTGAAAGCTGGAAAGAAGTAAGACATGACAATACGGTTACATGGTTAGCTTTCTGGAATGATCCAATTAATCAAAAGGAATTCAAATACGTATTTCTGGCACCTAGTAGTTCCTTGAAGGGGAAAAGTGACGAGCTGAAATATGATAAAGCAAGGAGATTGACGGACTGCATAGGAAAAATCAGGGCTTCATACACCAAGGATTTTACTAGTAAAGATGTATCTAAGCGCCAGATTGCGGTTGCTACCTATCTCATTGATAAACTTGCCCTCAGGGCGGGCAATGAGAAGGATGATGATGAAGCCGATACTGTTGGTTGCTGCACTTTAAAAGTAGAGAATGTAAAAGCAATCCCCCCTAACTCGTTGGAGTTCAACTTCCTTGGTAAAGATTCAATCAGATATGAAAATACTGTTGAAGTTGAGATTCCTGTTTACAAGGCAATTATGCAGTTCCAGTCTGGGAAAAGTGGCAGTGATGATCTCTTTGACTTGTTGGATACCAGTAGATTGAATGCTCATCTAAAGGAAAAAATGGATGGCCTTACAGCGAAAGTGTTTCGTACCTACAATGCATCTGTCACATTGGATAACATATTGAACAAGGAAACCAAAGATGGAGATCTTTCAGAGAAACTCGTTGTTTATCAGCATGCAAACAAAGAGGTCGCCATTATTTGTAATCATCAGCGTACTGTCTCAAAGTCTCACAGTGCACAAATGTCTAAGTTAACGGAGAAGATTGCTGAACTTCAGGGCAACCTGAAAGAGCTGAAAGTAGATTTGGACAGGGCCAAAAAAGGAAAGCCCCCACTGAAAGATGCTGATGGAAAGCAAAAGAAAAATTTGACCCCGGAAGCGTTGGAGAGGAAGATAGCTCAAACAAATGCAAAGATAGAAAAAATGGAACTGGATATGAGAATTAAAGAGGATCTGAAAACAGTGGCATTGGGAACGTCGAAAATCAACTATCTTGACCCTAGGATCACCGTTGCTTGGTGCAAGCGACATGAAGTTCCCATCGAGAAGATATTCAACAAGTCGCTCCTCGCAAAGTTTTCTTGGGCAATGCGAGTGGAGCCTGACTTCAGATTCTGATACTCGGAAATGTTGCTCGGCCATCCCCTCTATTTCAAATTGAGAAAAAAAAATAGCGAAAACAGACCCGACTTCCCTTCTTTGTTCGGTTATAGAACTGGACATTTTTATTCTTTTTTCTCATCGTGTTTTTCTCATTCGGCGGAAAATTCTTCTGGTGTGTTAATCTAATCTAATCTGACTGGCTGAGTAGCCTTGCCACCTTCTTGACATTCCATTTGTGTTTCCTTTTCCTTGGATCCCAGCAATTGTTTTATTTGAACTCTGAGAACCTCTTTATACTGATTCTAAAGATAGTTATGTTACATTCAACAGGCAGCGTAAGGTTGTAAGGTTGTATTGTTTACTTTTTGGTCATTGTTCTCTACGATCCAATCCTGTATTGCTACTTGATGTAAAGATTTTCTTCTCTAATATTCCCCATTCTTGAATCCTGATACCGTTGATTTATGGAGATGTAAATGTGTATGGGTAGTGATTTTCATCTCCTGCACTCCTCTTGTTGATTCTAAGGACTTGGGAAAAAAAAGGGTGGAGTGTGGCGGAAGAAAAGTAGAGTGCGGAAATCATTTCTTAGTATATTTTTACTATTTCCTTGTTTTACAAGATTGTATCTTTTCCACGAATTGTTATATAGCACTTGGGGCCTTCATC

Protein:

Gene family

Gene family	Subfamily
--	--

Orthologous genes

Species	Gene ID	Score of Inparanoid	Annotation
Arabidopsis thaliana	AT5G55300.1	1	MGO1;TOP1;TOP1ALPHA\|MGOUN 1;TOPOISOMERASE 1;DNA topoisomerase I alpha
Arabidopsis thaliana	AT5G55300.2	0.985	MGO1;TOP1;TOP1ALPHA\|MGOUN 1;TOPOISOMERASE 1;DNA topoisomerase I alpha
Prunus persica	Prupe.8G003200.2.p	1	DNA topoisomerase 1 beta
Prunus persica	Prupe.8G003200.5.p	1	DNA topoisomerase 1 beta
Prunus persica	Prupe.8G003200.3.p	1	DNA topoisomerase 1 beta
Prunus persica	Prupe.8G003200.4.p	1	DNA topoisomerase 1 beta
Prunus persica	Prupe.8G003200.1.p	1	DNA topoisomerase 1 beta
Pyrus communis	PCP013406.1	1	-
Pyrus x bretschneideri	Pbr031096.1	1	-
Pyrus x bretschneideri	Pbr011175.1	0.944	-
Rosa multiflora	Rmu_sc0001767.1_g000005.1	1	-
Rubus occidentalis	Ro02_G02309	1	-
Fragaria vesca	mrna06650.1	1	DNA topoisomerase 1 beta
Vitis vinifera	GSVIVT01020301001	1	DNA topoisomerase I alpha
Populus trichocarpa	Potri.001G359700.2	1	DNA topoisomerase 1 beta
Populus trichocarpa	Potri.011G092700.1	0.622	DNA topoisomerase 1 beta
Oryza sativa	LOC_Os08g05840.1	1	"DNA topoisomerase 1, putative, expressed"

Gene Ontology

GO term	Description	Category
GO:0003677	DNA binding	molecular_function
GO:0003918	DNA topoisomerase type II (ATP-hydrolyzing) activity	molecular_function
GO:0006265	DNA topological change	biological_process
GO:0005694	chromosome	cellular component
GO:0003917	DNA topoisomerase type I activity	molecular_function

KEGG

KO	Description	Enzyme
K03163	DNA topoisomerase I	EC:5.99.1.2

Pfam domain

Pfam accession	Pfam name	Alignment start	Alignment end	E-value
PF01028.16	Topoisom_I	557	781	1.80E-91

Expression pattern

SRA Experiment	Tissue	Stress	Stage	FPKM
SRR768136	whole seedling	no	seedling	5.90176
SRR5252888	dormant buds	no	dormant buds(0 month)	18.1342
SRR5252889	dormant buds	no	dormant buds(0 month)	19.1538
SRR5252886	dormant buds	no	dormant buds(1 months)	20.0434
SRR5252887	dormant buds	no	dormant buds(1 months)	20.4922
SRR5252884	dormant buds	no	dormant buds(2 months)	25.0117
SRR5252882	dormant buds	no	dormant buds(3 months)	18.4055
SRR5252883	dormant buds	no	dormant buds(3 months)	22.648
SRR5252880	dormant buds	no	dormant buds(4 months)	21.5342
SRR5252881	dormant buds	no	dormant buds(4 months)	20.1757
SRR5252878	bud break	no	bud break	18.6781
SRR5252879	bud break	no	bud break	18.4871
SRR3744766	flower	no	mature	9.94631
SRR3744767	flower	no	mature	10.6773
SRR3744768	flower	no	mature	9.51498
SRR6308190	stigmas	no	open flowers	10.0217
SRR6308181	styles	no	open flowers	9.39703
SRR6308188	filaments	no	open flowers	5.2706
SRR6308187	anthers	no	buds 1-3 days prior to flower opening	13.4255
SRR6308192	pollen	no	open flowers	17.1985
SRR6308191	petals	no	open flowers	8.85713
SRR6308194	sepals	no	open flowers	8.16973
SRR6308193	receptacles	no	open flowers	9.47841
SRR6308189	ovaries	no	open flowers	7.62764
SRR3384922	fruit	no	1 week after full bloom	3.32883
SRR3384921	fruit	no	2 week after full bloom	4.45537
SRR3384920	fruit	no	3 week after full bloom	3.06554
SRR3384919	fruit	no	4 week after full bloom	3.30743
SRR3384923	fruit	no	5 week after full bloom	2.93816
SRR3384918	fruit	no	6 week after full bloom	3.37561
SRR3384917	fruit	no	8 week after full bloom	3.11783
SRR3384916	fruit	no	10 week after full bloom	3.3425
SRR3384915	fruit	no	12 week after full bloom	4.76904
SRR3384914	fruit	no	14 week after full bloom	4.69297
SRR3384913	fruit	no	16 week after full bloom	4.33167
SRR3384912	fruit	no	18 week after full bloom	4.18975
SRR3384911	fruit	no	19 week after full bloom	3.73143
SRR3384910	fruit	no	20 week after full bloom	4.43859
SRR768128	whole fruit	no	25 days post anthesis	5.91643
SRR768129	whole fruit	no	35 days post anthesis	5.09636
SRR768130	whole fruit	no	60 days post anthesis	5.14671
SRR768131	whole fruit	no	87 days post anthesis	5.90498
SRR7343308	immature fruit flesh	no	immature	6.63747
SRR7343309	immature fruit flesh	no	immature	6.22161
SRR6320494	ripe fruit flesh	no	mature	8.68839
SRR5405143	ripe fruit peel	no	mature	6.05598
SRR6320572	ripe fruit peel	no	mature	2.45486
SRR7403504	fruit	uninfected	mature	7.1938
SRR7403506	fruit	uninfected	mature	6.83268
SRR7403507	fruit	uninfected	mature	7.0613
SRR7403500	fruit	infected with penicillium expansum	mature	18.7868
SRR7403501	fruit	infected with penicillium expansum	mature	16.6987
SRR7403508	fruit	infected with penicillium expansum	mature	18.6796
SRR7403502	fruit	infected with penicillium expansum	mature	17.8386
SRR7403503	fruit	infected with penicillium expansum	mature	16.7878
SRR7403505	fruit	infected with penicillium expansum	mature	16.9429
SRR1613973	Central seeds	no	20DAPF	4.42874
SRR1613974	Central seeds	no	20DAPF	5.30727
SRR1613975	Central seeds	no	20DAPF	3.72219
SRR1613976	Lateral seeds	no	20DAPF	4.64275
SRR1613977	Lateral seeds	no	20DAPF	3.97526
SRR1613978	Lateral seeds	no	20DAPF	4.61722
SRR3744786	stem	no	mature	8.78054
SRR3744787	stem	no	mature	8.71154
SRR3744772	stem	no	mature	9.74736
SRX765691	seedling shoot apex	no	4-6 week old seedling	10.0814
SRX765683	tree shoot apex	no	Adult (tree), new shoot has 10-12 visible leaves	11.3949
SRR1089478	leaf	Virus-free	plantlets	5.47099
SRR1089477	leaf	ASGV-infected	plantlets	5.59103
SRR767660	leaf	uninfected	fully developed	3.43753
SRR767669	leaf	2 days post infection by Venturia inaequalis	fully developed	1.67778
SRR767670	leaf	4 days post infection by Venturia inaequalis	fully developed	4.45353
SRR767671	leaf	6 days post infection by Venturia inaequalis	fully developed	2.27679
SRR767672	leaf	8 days post infection by Venturia inaequalis	fully developed	0
SRR767673	leaf	10 days post infection by Venturia inaequalis	fully developed	2.58825
SRR767674	leaf	12 days post infection by Venturia inaequalis	fully developed	5.15736
SRR768127	leaf	14 days post infection by Venturia inaequalis	fully developed	3.31465
SRR6308182	young leaf	no	immature leaves	8.8757
SRR3744769	leaf	no	mature	7.49534
SRR3744770	leaf	no	mature	8.28205
SRR3744771	leaf	no	mature	8.04548
SRR5405145	leaf	no	mature	9.09835
SRR6320561	leaf	no	mature	6.50971