Gene detail

Detail information of MD08G1243800 Annotation

Gene ID	Annotation
MD08G1243800	Smg-4/UPF3 family protein

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	CFinderM0796	regulator of nonsense transcripts 3 phosphoenolpyruvate carboxykinase (ATP) [EC:4.1.1.49] magnesium ion transmembrane transporter activity phosphoenolpyruvate carboxykinase (ATP) activity

Gene structure and chromatin state

more details in UCSC

details of chromatin state

Location

Gene	Type	Chr	Start	End	Strand
MD08G1243800	mRNA	Chr08	30907325	30915677	-

Sequences

CDS:

MD08G1243800

AGAACTACAGAGGAGGGGGAGAAGACCTGAAGGCGCAAAACGCAACCGTTTCAACTCACTCTTGCGTCTGTAGCATTTTCGTGCATGGCGATTGGTGAATTAGGGGTTTCAGATCGACCTCGATCGATGATTTTCAGAAGCCAAGAAGATGTAATTTAGCGGAGATTTTTCGTGTATTTCCGAAGCAATTTCCGAAAACCGTTCGATTCTGCGGAGCTTTTAGTTGGTTTTTCTAGGGTTTTTGTTTTTGGATTGGGGAGATGATGAAGGGCCAGTTGGATCGAACCAAGGTGGTGCTTCGACACTTGCCGCCTTCGATTTCGCAAGCTGCGCTTGTGGAGCAAATCGACGTTTTCTTTGCTGGCCGCTACAACTGGGTTGCTTTTCGTCCTGGCAAGAGGAAGAGGAGCCAAAAGAATCAGTCATATTCAAGAGCCTACATTGATTTGAAGAGGCCAGAGGATGTATTCGACTTTGCTGAATTCTTTGACGGTCATCTGTTTGTTAATGAAAAGGGCAGTCAATTTAAAGTTATTGTTGAGTATGCTCCTTCACAACGTGTTCCAAAACATTGGTCTAAGAAGGATGGTCGTGAAGGAACCATATTCAAAGATCCCGAGTATTTGGAGTTTCTTGAATTCATTGCAAAGCCTGCTGAGAATCTTCCAAGTGCAGAGACACAATTGGAGAGAAGAGAAGCAGAACGATCTGGTGCTGGAAAGGACGTTCCTATAGTTACACCATTAATGGACTTTGTTCGTCAAAAAAGGGCTGCCAAGGCTGGATCTCGGAGGTTACTGCCTAATGGTAAAACAAGTAGAAGAGCTGGTGCATCATCTGCTCGAAGTCCTACTTTACCTATGACCAAACAGGGTTCTGAGAGGAAAAAGAATTCTGCCTCAATGTATGTTGTGAGGGATGTTAGAAAGAACACGAGTGCCAAAGACAAGTCAACATATACATTGGTACCCAAGCGCGATGATCAGCAACCTTCCGAGAAGTCTTCCATTTTGGCATCTCCAGTTGGAACTCAATTGTTTGAAGAGGAGAGTGGAGTTTCAGGTGCTGATGCTGGGAAAAAGAAAGTCTTGCTTGTGAAAAGGAAAGAGAAGGAGATATCTCATGTGCCGGCGAACATGTCACAGCAGCATAGTACATATTCTAAAAACATGGGTGGTTCAGTTGCACTTAAACAGAACCTGCGTCATCATGATAATGGAAGGATTATAAAAAGCATACTTCTAAACAAGGATGCATGTCAAAGTCAGTCTTCTGGGACTCACTCCGAGCAGCAAATCCAGAGTTCAAGTTCAGATAGGGACAAAAGACTTCCTCGGTCGCAACATGTGCAATTGATTTTAAAGGATACAAATGGAGCTCCAGATCATAAGATAGTTGGGAATGACTTGCATGGTAGTTATAGTGAGAAGCAGGGGAAACGGACGAGGAATAAGGACAGACCTGATCGTGGTGTATGGACTCCTCTTAATCGTTTAGATGGATCATCTGCAAGCAATGAGTCTTTGTCGTCTGCTTTTCAACCTGATCATTCACTCCTAGATTCTTCAGAAGGCTCCCATAAACATCATGGTCGCCGTGGAGCAACACATGGTGTTAAGGATCTTGATGGCTCTCCAGTTGCCGGTGAAGGAAAACATTCGAAGAGAGGCTATGGCTCCCATGAGAAACAAGTGTGGGTTCAGAAGTCAAGTTCTGGTTCCTGAGGATTTTCTTTTTGTTAAATTGTGTGATGTTTGGCTACTTCAACCTTGAGAGTGAATTACCAAAAAGAAAAAAAAAAGAACCTTCAGAGTGAGCATGTACCAGTGCCCTGAAGCTGTCTGTTTTTTTCCGGACAGATTACAGAGTTGTAAACAAAGCGTCGGCAGCATTGAAAGATGTTCCTTTTGGAAAGCCATACGGAGTGATGGAGACACAGGTATATAAACATAGCATGGGTTTGAAGAAATTTCCAAGTTTGCTGGTGTCGGCATGGAAATAGGAGGGGAAAGGAAGAATAGTAAAAGACATCAGCATCATTAAGGTATGTAACAGTTTTTATCAGAGTGCCCCCCAACAATGCGCTCCTCGCAGAAGGGTTACGCACATTCCTTCTTGTCCTTCACTGGTTATCGGGATATTTAGGTATTTATGTTATAGATGGTTGTCGTCCATTAGTATAACTGTAAATATGAAGGCGGAGCACTATGTGCGGCTTCACGGTTTATTTCTTGTGTATCTACGCCCTGTTGCGAGCAGTGTAGCATCTGCAACCAGTTTGTATTGTAAGGCCCTGGAGTTTTCTCAGATACTCTGATTGCTGGCTTGTTTCGAGTAGAAAAGACAGCTCGAGCCATTTTGCAGTTGATGCCCGGGTGAGTGACTGAATGATTGGGTCTATGTCTTGGCAGTGTTTCACCTTGTATTAACGGAAGGAGACATTGTTCTGAGTGGAGATTGCCGGAATATAGTTTGGTCGTTTGCTCTCTTTCTCTGTCTGTCTCTCTCTGGAAAAATGGCTTCCGACGAATCTTGCCACGGCGAGTGGGAGGGCCACATGAAGCCCGACCATCGGGCCGAGGAGCCTCTAGGGCATACGTCATGACACAGAGTTGGAATGCAATGTTGATGATTGGAATTGTATATTTCGAATTCTATATGTGCTTGTTATGGCTATAGGTTTTTCGAGGTAGCGGAACTGTATAGGAAACACAAAATGGAAACACTAACGCTCGTTTGGTGGTGTGAACGTATATTTGATGAACTGCTTAAAGTTTTTACCAATCGGACTTTTTGTTTTCTGCCATCGTAAGACAGCTAAAGTAAGATGAGAGAAAAACGGTTAAGGT

Protein:

Gene family

Gene family	Subfamily
--	--

Orthologous genes

Species	Gene ID	Score of Inparanoid	Annotation
Prunus persica	Prupe.1G581100.5.p	1	Smg-4/UPF3 family protein
Prunus persica	Prupe.1G581100.1.p	1	Smg-4/UPF3 family protein
Prunus persica	Prupe.1G581100.2.p	0.871	Smg-4/UPF3 family protein
Pyrus communis	PCP022656.1	1	-
Vitis vinifera	GSVIVT01023232001	1	Smg-4/UPF3 family protein
Solanum lycopersicum	Solyc01g103420.2.1	1	Smg-4/UPF3 family protein
Populus trichocarpa	Potri.004G225800.1	1	Smg-4/UPF3 family protein
Nicotiana benthamiana	Niben101Scf05032g02004.1	1	Regulator of nonsense transcripts UPF3
Nicotiana benthamiana	Niben101Scf02892g02004.1	0.839	Regulator of nonsense transcripts UPF3
Oryza sativa	LOC_Os04g35920.2	1	"nonsense-mediated decay UPF3, putative, expressed"

Gene Ontology

GO term	Description	Category
GO:0000166	nucleotide binding	molecular_function

KEGG

KO	Description	Enzyme
K14328	regulator of nonsense transcripts 3	-

Pfam domain

Pfam accession	Pfam name	Alignment start	Alignment end	E-value
--	--	--	--	--

Expression pattern

SRA Experiment	Tissue	Stress	Stage	FPKM
SRR768136	whole seedling	no	seedling	3.56615
SRR5252888	dormant buds	no	dormant buds(0 month)	16.8006
SRR5252889	dormant buds	no	dormant buds(0 month)	17.5163
SRR5252886	dormant buds	no	dormant buds(1 months)	16.86
SRR5252887	dormant buds	no	dormant buds(1 months)	13.9495
SRR5252884	dormant buds	no	dormant buds(2 months)	20.4058
SRR5252882	dormant buds	no	dormant buds(3 months)	16.8329
SRR5252883	dormant buds	no	dormant buds(3 months)	14.3836
SRR5252880	dormant buds	no	dormant buds(4 months)	18.5518
SRR5252881	dormant buds	no	dormant buds(4 months)	16.7015
SRR5252878	bud break	no	bud break	13.9038
SRR5252879	bud break	no	bud break	9.94481
SRR3744766	flower	no	mature	10.0261
SRR3744767	flower	no	mature	9.65491
SRR3744768	flower	no	mature	10.3589
SRR6308190	stigmas	no	open flowers	6.83425
SRR6308181	styles	no	open flowers	6.13591
SRR6308188	filaments	no	open flowers	4.87822
SRR6308187	anthers	no	buds 1-3 days prior to flower opening	5.43173
SRR6308192	pollen	no	open flowers	3.30055
SRR6308191	petals	no	open flowers	4.28306
SRR6308194	sepals	no	open flowers	7.05557
SRR6308193	receptacles	no	open flowers	6.82754
SRR6308189	ovaries	no	open flowers	6.05618
SRR3384922	fruit	no	1 week after full bloom	3.76927
SRR3384921	fruit	no	2 week after full bloom	3.46647
SRR3384920	fruit	no	3 week after full bloom	2.75516
SRR3384919	fruit	no	4 week after full bloom	4.11749
SRR3384923	fruit	no	5 week after full bloom	4.27168
SRR3384918	fruit	no	6 week after full bloom	4.54391
SRR3384917	fruit	no	8 week after full bloom	5.64486
SRR3384916	fruit	no	10 week after full bloom	4.7814
SRR3384915	fruit	no	12 week after full bloom	4.27962
SRR3384914	fruit	no	14 week after full bloom	5.60049
SRR3384913	fruit	no	16 week after full bloom	6.09418
SRR3384912	fruit	no	18 week after full bloom	4.99633
SRR3384911	fruit	no	19 week after full bloom	7.77581
SRR3384910	fruit	no	20 week after full bloom	6.79618
SRR768128	whole fruit	no	25 days post anthesis	5.4004
SRR768129	whole fruit	no	35 days post anthesis	2.70248
SRR768130	whole fruit	no	60 days post anthesis	4.59389
SRR768131	whole fruit	no	87 days post anthesis	9.85253
SRR7343308	immature fruit flesh	no	immature	6.8592
SRR7343309	immature fruit flesh	no	immature	6.84076
SRR6320494	ripe fruit flesh	no	mature	14.4748
SRR5405143	ripe fruit peel	no	mature	11.3624
SRR6320572	ripe fruit peel	no	mature	10.099
SRR7403504	fruit	uninfected	mature	11.488
SRR7403506	fruit	uninfected	mature	10.9534
SRR7403507	fruit	uninfected	mature	10.6731
SRR7403500	fruit	infected with penicillium expansum	mature	4.31724
SRR7403501	fruit	infected with penicillium expansum	mature	4.10995
SRR7403508	fruit	infected with penicillium expansum	mature	3.35497
SRR7403502	fruit	infected with penicillium expansum	mature	3.33499
SRR7403503	fruit	infected with penicillium expansum	mature	4.32692
SRR7403505	fruit	infected with penicillium expansum	mature	3.41589
SRR1613973	Central seeds	no	20DAPF	4.744
SRR1613974	Central seeds	no	20DAPF	5.31157
SRR1613975	Central seeds	no	20DAPF	4.59116
SRR1613976	Lateral seeds	no	20DAPF	4.25895
SRR1613977	Lateral seeds	no	20DAPF	4.42506
SRR1613978	Lateral seeds	no	20DAPF	4.56311
SRR3744786	stem	no	mature	15.7363
SRR3744787	stem	no	mature	15.5602
SRR3744772	stem	no	mature	15.7744
SRX765691	seedling shoot apex	no	4-6 week old seedling	7.12016
SRX765683	tree shoot apex	no	Adult (tree), new shoot has 10-12 visible leaves	6.88924
SRR1089478	leaf	Virus-free	plantlets	1.85861
SRR1089477	leaf	ASGV-infected	plantlets	2.92581
SRR767660	leaf	uninfected	fully developed	1.99717
SRR767669	leaf	2 days post infection by Venturia inaequalis	fully developed	1.93322
SRR767670	leaf	4 days post infection by Venturia inaequalis	fully developed	2.09511
SRR767671	leaf	6 days post infection by Venturia inaequalis	fully developed	0
SRR767672	leaf	8 days post infection by Venturia inaequalis	fully developed	0
SRR767673	leaf	10 days post infection by Venturia inaequalis	fully developed	3.47325
SRR767674	leaf	12 days post infection by Venturia inaequalis	fully developed	2.44286
SRR768127	leaf	14 days post infection by Venturia inaequalis	fully developed	1.48519
SRR6308182	young leaf	no	immature leaves	5.73573
SRR3744769	leaf	no	mature	12.5281
SRR3744770	leaf	no	mature	11.6839
SRR3744771	leaf	no	mature	13.2083
SRR5405145	leaf	no	mature	7.38115
SRR6320561	leaf	no	mature	4.52594