Gene detail

Detail information of MD13G1248200 Annotation

Gene ID	Annotation
MD13G1248200	lysyl-tRNA synthetase 1

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	CFinderM0163	pyrimidine ribonucleotide biosynthetic process

Gene structure and chromatin state

more details in UCSC

details of chromatin state

Location

Gene	Type	Chr	Start	End	Strand
MD13G1248200	mRNA	Chr13	26366651	26373733	-

Sequences

CDS:

MD13G1248200

TACTGTAAAAAACAAGAAAGTATATGAACTTATTCCGACCCTGCCCGCCCTATATAGCCGAAACGGATTGTAATCTTTTACTACCCCAGTTGGCAAACCCTAGCTCCACTGACACAAAAAACCCCAGAAAACCCCCTCTCTCACTTTCCACTCTCGTTCCGAATCGCTGCAATGGCGGGCACGTCCAACGAAACCCCGAAATCACTCGCAGATTCGACTCTGGAATCGGAAGGAGCTATGAGCAAAAATGCACGGAAGAAGGAGTTGAAGAACAAGCAGCGGGAAGAGGAGAGGCGCCGAAAAGAGGAGGATAAGGCTGCTGCCTTGGCAAGCTCGCAAGTTAAGAAAGATGTAGCAACTGAAGATGACGACATGGATCCAACGCAATACTATGAAAATAGACTGAAGTATCTTGCTACCCAGAAGGCAGATAAAAATCCATATCCTCATAAATTCTTTTGTTCAATCACCGTACATGAATATGTAGAGAAGTATGCAAGCTTAAACGATGGGGAGCATCTTGAGGATATCACTGTTTCATTGGCTGGGCGAATCATGAGTAAAAGATCTTCCAGCTCTAAGCTCTTCTTTTATGACTTGGATGGTGGCGGACCTGATGGTGAGAAGGTCCAAGTCATGGCTGATTTAAGAAAATCAGAGTTGGATGAATCTGAATTTTCTAAGTTTCATTCTAGTGTTAAGCGTGGTGATATTGTCGGTGTGACTGGGTTTCCAGGAAAGACTAAGAGGGGGGAGCTGAGCATTTTCCCAAGATCATTTATAGTCTTATCACATTGTCTTCATATGATGCCAAGACAGAAAGCTGGTCCTGCTTCTGATAATGCTAATGTCAAGAAAACGAATCGATGGATCCCAGGAAGTCCCCGGAATCCTGAAGCATACATTTTAAAAGACCAGGAAACTCGCTATCGTCAACGTTATCTGGATCTAATATTGACTAATGAGGTTCGGCAAATATTCAGGACCAGATATAAAGTCATTCAATATATTAGAAGGTTCCTGGACAATCTGGACTTCTTGGAGGTCGAAACTCCTATGATGAATATGATTCCTGGTGGAGCGGCTGCCCGTCCTTTTATGACTTTTCACAATGAACTTGACATGAAGCTTTTCATGCGCGTTGCACCAGAACTCTATCTCAAGCAGCTTGTTGTTGGTGGCCTGGATCGTGTTTATGAGATTGGAAAGCAATTTAGAAATGAGGGCATTGATTTGACTCATAATCCTGAATTCACTACCTGTGAATTCTACATGGCTTATGCAGACTACAATGATTTGATGACGCTGACTGAGGAAATGTTGAGTGGTATGGTCAAGGAGCTAACTGGTGGGTATAAAATCAAGTATCATTCAAATGGGCTCGACAAGGAACCAATTGAGATTGACTTTACTCCTCCTTTCAGAAGGATCGACATGGTTGAGGAATTAAATAAGATTGCAGGTCTCAACATAAATCCAGAGAATCTCTCCAGTGCAGAAGCTAACCAATATCTTAAGGATGCGTGCAAGAAGTTTGATGTCAAATGTTCCCCTCCTGAAACAACAACTCGTTTGTTGGACAAGCTTGTTGGGCACTTTTTGGAAGAGACGTGTGTAAATCCCACTTTCATCATTAACCATCCTGAGATAATGAGTCCTTTGGCTAAGTGGCATCGATCGAAACCTGGCTTGACTGAACGTTTTGAATTGTTTGTGAACAAACATGAACTTGCCAATGCATACACAGAGTTGAATGATCCTGTGGTACAACGGGAAAGATTTGCTGATCAACTCAAGGACCGACAATCAGGTGATGATGAAGCAATGGCTTTGGACGAATCATTCTGTAGAGCTCTTGAGTACGGGTTACCTCCAACTGGTGGTTGGGGTTTGGGCGTTGATCGGCTCTGTATGTGGTTAACCGATTCACAAAATATCAAGGAAGTTCTACTCTTCCCGGCTATGAAGCCACAGGATGAGACTTGTGCTAAAGCCACTTTGGGTGCTTGAGATTATCGGGACTCAGCCATCGATTTTTTGTAGCTGCATTGGACTTCAAGCGGTGGTCTTATTGATGGCGAGATGTAACTTTTTGGTTTGATTTTCACTGTTATATCTAAAGTATTTTAGGTAGATCTATAATTGTCTGAACTATTAATACAGTTACATGAGTGAATGCGACTAATATTTATCCGAATTGCCAAACTTTGTTATCCCTAACTCCTATGTGTTAGTTTGTTTGAATGGATCTCTTTCGTCTGAAAAGAAAAAGTTGCTCTGTCGTCTCGTCATGTACAAGTCTCATCTCATCC

Protein:

Gene family

Gene family	Subfamily
--	--

Orthologous genes

Species	Gene ID	Score of Inparanoid	Annotation
Arabidopsis thaliana	AT3G11710.1	1	ATKRS-1\|lysyl-tRNA synthetase 1
Pyrus communis	PCP018837.1	1	-
Pyrus x bretschneideri	Pbr035249.1	1	-
Rosa multiflora	Rmu_sc0001909.1_g000026.1	1	-
Rubus occidentalis	Ro04_G16381	1	-
Fragaria vesca	mrna17007.1	1	lysyl-tRNA synthetase 1
Vitis vinifera	GSVIVT01019319001	1	lysyl-tRNA synthetase 1
Solanum lycopersicum	Solyc06g073330.2.1	1	lysyl-tRNA synthetase 1
Populus trichocarpa	Potri.018G090400.1	1	lysyl-tRNA synthetase 1
Populus trichocarpa	Potri.018G090600.1	0.895	lysyl-tRNA synthetase 1
Populus trichocarpa	Potri.006G166000.1	0.696	lysyl-tRNA synthetase 1
Nicotiana benthamiana	Niben101Scf00182g04001.1	1	Lysine--tRNA ligase
Nicotiana benthamiana	Niben101Scf01673g01007.1	0.652	Lysine--tRNA ligase
Oryza sativa	LOC_Os03g38980.2	1	"tRNA synthetases class II domain containing protein, expressed"
Zea mays	GRMZM2G386714_P01	1	Lysine--tRNA ligase
Zea mays	GRMZM2G146589_P01	0.603	-

Gene Ontology

GO term	Description	Category
GO:0003676	nucleic acid binding	molecular_function
GO:0005737	cytoplasm	cellular component
GO:0005524	ATP binding	molecular_function
GO:0004824	lysine-tRNA ligase activity	molecular_function
GO:0006430	lysyl-tRNA aminoacylation	biological_process

KEGG

KO	Description	Enzyme
K04567	"lysyl-tRNA synthetase, class II"	EC:6.1.1.6

Pfam domain

Pfam accession	Pfam name	Alignment start	Alignment end	E-value
PF01336.21	tRNA_anti-codon	122	202	3.70E-12
PF00152.16	tRNA-synt_2	248	598	8.00E-79

Expression pattern

SRA Experiment	Tissue	Stress	Stage	FPKM
SRR768136	whole seedling	no	seedling	20.6748
SRR5252888	dormant buds	no	dormant buds(0 month)	47.689
SRR5252889	dormant buds	no	dormant buds(0 month)	46.1598
SRR5252886	dormant buds	no	dormant buds(1 months)	41.101
SRR5252887	dormant buds	no	dormant buds(1 months)	32.0495
SRR5252884	dormant buds	no	dormant buds(2 months)	39.1267
SRR5252882	dormant buds	no	dormant buds(3 months)	37.5688
SRR5252883	dormant buds	no	dormant buds(3 months)	36.1312
SRR5252880	dormant buds	no	dormant buds(4 months)	59.2769
SRR5252881	dormant buds	no	dormant buds(4 months)	57.2441
SRR5252878	bud break	no	bud break	45.2072
SRR5252879	bud break	no	bud break	44.2618
SRR3744766	flower	no	mature	20.4523
SRR3744767	flower	no	mature	20.2068
SRR3744768	flower	no	mature	19.01
SRR6308190	stigmas	no	open flowers	13.6031
SRR6308181	styles	no	open flowers	15.2645
SRR6308188	filaments	no	open flowers	21.32
SRR6308187	anthers	no	buds 1-3 days prior to flower opening	8.74648
SRR6308192	pollen	no	open flowers	2.75842
SRR6308191	petals	no	open flowers	18.5099
SRR6308194	sepals	no	open flowers	16.1175
SRR6308193	receptacles	no	open flowers	31.7744
SRR6308189	ovaries	no	open flowers	21.0699
SRR3384922	fruit	no	1 week after full bloom	16.5522
SRR3384921	fruit	no	2 week after full bloom	16.4141
SRR3384920	fruit	no	3 week after full bloom	13.7065
SRR3384919	fruit	no	4 week after full bloom	13.4463
SRR3384923	fruit	no	5 week after full bloom	16.2748
SRR3384918	fruit	no	6 week after full bloom	14.0027
SRR3384917	fruit	no	8 week after full bloom	16.8629
SRR3384916	fruit	no	10 week after full bloom	18.2034
SRR3384915	fruit	no	12 week after full bloom	18.5558
SRR3384914	fruit	no	14 week after full bloom	17.8537
SRR3384913	fruit	no	16 week after full bloom	14.6359
SRR3384912	fruit	no	18 week after full bloom	16.9715
SRR3384911	fruit	no	19 week after full bloom	14.877
SRR3384910	fruit	no	20 week after full bloom	18.2579
SRR768128	whole fruit	no	25 days post anthesis	21.624
SRR768129	whole fruit	no	35 days post anthesis	22.6627
SRR768130	whole fruit	no	60 days post anthesis	19.5115
SRR768131	whole fruit	no	87 days post anthesis	26.4
SRR7343308	immature fruit flesh	no	immature	27.3232
SRR7343309	immature fruit flesh	no	immature	24.9482
SRR6320494	ripe fruit flesh	no	mature	20.9827
SRR5405143	ripe fruit peel	no	mature	24.9426
SRR6320572	ripe fruit peel	no	mature	16.1603
SRR7403504	fruit	uninfected	mature	18.5777
SRR7403506	fruit	uninfected	mature	15.8
SRR7403507	fruit	uninfected	mature	18.5861
SRR7403500	fruit	infected with penicillium expansum	mature	8.13033
SRR7403501	fruit	infected with penicillium expansum	mature	9.48524
SRR7403508	fruit	infected with penicillium expansum	mature	9.35416
SRR7403502	fruit	infected with penicillium expansum	mature	9.60054
SRR7403503	fruit	infected with penicillium expansum	mature	9.49484
SRR7403505	fruit	infected with penicillium expansum	mature	9.2141
SRR1613973	Central seeds	no	20DAPF	37.0354
SRR1613974	Central seeds	no	20DAPF	39.4246
SRR1613975	Central seeds	no	20DAPF	33.6307
SRR1613976	Lateral seeds	no	20DAPF	33.0192
SRR1613977	Lateral seeds	no	20DAPF	33.9018
SRR1613978	Lateral seeds	no	20DAPF	34.6315
SRR3744786	stem	no	mature	26.5045
SRR3744787	stem	no	mature	27.2896
SRR3744772	stem	no	mature	29.2876
SRX765691	seedling shoot apex	no	4-6 week old seedling	34.4764
SRX765683	tree shoot apex	no	Adult (tree), new shoot has 10-12 visible leaves	31.6716
SRR1089478	leaf	Virus-free	plantlets	18.8621
SRR1089477	leaf	ASGV-infected	plantlets	19.5792
SRR767660	leaf	uninfected	fully developed	14.198
SRR767669	leaf	2 days post infection by Venturia inaequalis	fully developed	12.545
SRR767670	leaf	4 days post infection by Venturia inaequalis	fully developed	17.1134
SRR767671	leaf	6 days post infection by Venturia inaequalis	fully developed	1.79794
SRR767672	leaf	8 days post infection by Venturia inaequalis	fully developed	8.73414
SRR767673	leaf	10 days post infection by Venturia inaequalis	fully developed	11.6109
SRR767674	leaf	12 days post infection by Venturia inaequalis	fully developed	21.9561
SRR768127	leaf	14 days post infection by Venturia inaequalis	fully developed	12.2447
SRR6308182	young leaf	no	immature leaves	30.3049
SRR3744769	leaf	no	mature	24.0249
SRR3744770	leaf	no	mature	22.3765
SRR3744771	leaf	no	mature	24.4562
SRR5405145	leaf	no	mature	9.75478
SRR6320561	leaf	no	mature	15.5808