AlfalfaGEDB | MS.gene52844

M. sativa cultivar XinJiangDaYe / MS.gene52844

KEGG: -
GO: GO:0000271 GO:0003674 GO:0003824 GO:0005575 GO:0005975 GO:0005976 GO:0006073 GO:0008150 GO:0008152 GO:0008194 GO:0009058 GO:0009059 GO:0009250 GO:0009987 GO:0016020 GO:0016051 GO:0016740 GO:0016757 GO:0016758 GO:0016759 GO:0016760 GO:0030243 GO:0030244 GO:0033692 GO:0034637 GO:0034645 GO:0035251 GO:0043170 GO:0044042 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044262 GO:0044264 GO:0046527 GO:0051273 GO:0051274 GO:0071704 GO:0110165 GO:1901576
PFAM: PF03552.17

Nr:

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
MS.gene52844.t1	XP_003598036.1	100	65	0	0	1	65	192	256	4.20E-28	133.3

Swissprot:

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score

Trembl:

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
MS.gene52844.t1	G7IYF8	100.0	65	0	0	1	65	192	256	3.0e-28	133.3

TFs/TRs:

Gene ID	Type	Classification

Protein Kinases:

Gene ID	Type	Classification

Network:

Co-expression Network:

Gene1	Gene2	correlation coefficient	p_value	FDR
MS.gene053114	MS.gene52844	0.820712	5.93E-53	-1.69E-46

PPI:

Gene1	Gene2	Type

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
MS.gene52844.t1	MTR_3g005560	100.000	65	0	0	1	65	192	256	4.01e-41	141
MS.gene52844.t1	MTR_3g005560	100.000	65	0	0	1	65	192	256	8.14e-41	139
MS.gene52844.t1	MTR_3g005560	100.000	65	0	0	1	65	192	256	3.91e-40	135
MS.gene52844.t1	MTR_0011s0020	78.125	64	14	0	2	65	193	256	1.25e-30	112
MS.gene52844.t1	MTR_3g450800	78.125	64	14	0	2	65	144	207	7.58e-30	109
MS.gene52844.t1	MTR_2g037830	75.000	64	16	0	2	65	193	256	2.34e-29	108
MS.gene52844.t1	MTR_2g037830	75.000	64	16	0	2	65	193	256	3.21e-29	107
MS.gene52844.t1	MTR_1g073740	41.096	73	34	2	2	65	208	280	6.74e-11	55.8

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score

Find 14 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE

CRISPR-Local

CRISPR-Local
sgRNA_sequence	on_target_score	Position	Region
TAAACAACACGTGGAATTTC+TGG	0.175283	3.2:+259796	None:intergenic
ACAGGTCAAGTACGAGAAAA+TGG	0.301944	3.2:-260326	None:intergenic
TTTATGTGTCTCGTGAAAGA+AGG	0.493243	3.2:-259777	MS.gene52844:CDS
TGGTGACTGATAGACCTTCT+CGG	0.518496	3.2:-260258	MS.gene52844:CDS
TTGAATTTGTGAGGAAGTGA+TGG	0.541973	3.2:+259754	None:intergenic
AAGTACACACCAATGTATTG+AGG	0.543839	3.2:+259722	None:intergenic
AGTACACACCAATGTATTGA+GGG	0.544381	3.2:+259723	None:intergenic
GGATTTACCTCGATCCGAGA+AGG	0.587807	3.2:+260244	None:intergenic
TCACTTCCTCACAAATTCAA+AGG	0.597910	3.2:-259751	MS.gene52844:CDS
GCACCTCCTTTGAATTTGTG+AGG	0.599322	3.2:+259745	None:intergenic
CGAGACACATAAACAACACG+TGG	0.616062	3.2:+259787	None:intergenic
AGGAGGTGCCCTCAATACAT+TGG	0.621577	3.2:-259731	None:intergenic
TGATAGACCTTCTCGGATCG+AGG	0.649181	3.2:-260251	MS.gene52844:intron
CTTCCTCACAAATTCAAAGG+AGG	0.671490	3.2:-259748	MS.gene52844:CDS

CRISPR-GE

badsite warning	sgRNA_sequence	Strand	Position	Region	GC_content
!!!	TTTATTTTAGATTATAAATG+AGG	-	chr3.2:260233-260252	MS.gene52844:intron	10.0%
!!	TACAATTTACAATTTACATT+CGG	+	chr3.2:260090-260109	None:intergenic	15.0%
!!	ATTAACCAACTTATTACAAA+TGG	+	chr3.2:259969-259988	None:intergenic	20.0%
!!	GAGAAAAATATTGAGAAATT+CGG	-	chr3.2:259750-259769	MS.gene52844:CDS	20.0%
!!!	ATTATTCAATGTAATTTGTG+AGG	+	chr3.2:259877-259896	None:intergenic	20.0%
!!!	GATTGACTATTTTTTAAATG+TGG	-	chr3.2:260010-260029	MS.gene52844:intron	20.0%
!!!	GTTTATTTGTTAATTAGTTG+AGG	+	chr3.2:260149-260168	None:intergenic	20.0%
!	AGTAAATTGTAAACTGTAAG+TGG	-	chr3.2:260037-260056	MS.gene52844:intron	25.0%
!	GTTAACCATTTGTAATAAGT+TGG	-	chr3.2:259961-259980	MS.gene52844:intron	25.0%
	AATCCAATAAAGGATCGCAA+TGG	-	chr3.2:259828-259847	MS.gene52844:intron	35.0%
	AATCCATTGCGATCCTTTAT+TGG	+	chr3.2:259834-259853	None:intergenic	35.0%
	GATCGAGGTAAATCCAATAA+AGG	-	chr3.2:259818-259837	MS.gene52844:intron	35.0%
	TAAACAACACGTGGAATTTC+TGG	+	chr3.2:260261-260280	None:intergenic	35.0%
	TCACTTCCTCACAAATTCAA+AGG	-	chr3.2:260303-260322	MS.gene52844:CDS	35.0%
	TTGAATTTGTGAGGAAGTGA+TGG	+	chr3.2:260303-260322	None:intergenic	35.0%
	TTTATGTGTCTCGTGAAAGA+AGG	-	chr3.2:260277-260296	MS.gene52844:CDS	35.0%
!	AGTCACCATACGAAGATTTT+TGG	+	chr3.2:259784-259803	None:intergenic	35.0%
!	GTCACCATACGAAGATTTTT+GGG	+	chr3.2:259783-259802	None:intergenic	35.0%
!	TCACCATACGAAGATTTTTG+GGG	+	chr3.2:259782-259801	None:intergenic	35.0%
	CTTCCTCACAAATTCAAAGG+AGG	-	chr3.2:260306-260325	MS.gene52844:CDS	40.0%
!!!	CATACGAAGATTTTTGGGGT+CGG	+	chr3.2:259778-259797	None:intergenic	40.0%
	CGACCCCAAAAATCTTCGTA+TGG	-	chr3.2:259776-259795	MS.gene52844:CDS	45.0%
	CGAGACACATAAACAACACG+TGG	+	chr3.2:260270-260289	None:intergenic	45.0%
	GCACCTCCTTTGAATTTGTG+AGG	+	chr3.2:260312-260331	None:intergenic	45.0%
	TGGTGACTGATAGACCTTCT+CGG	-	chr3.2:259796-259815	MS.gene52844:CDS	45.0%
	GGATTTACCTCGATCCGAGA+AGG	+	chr3.2:259813-259832	None:intergenic	50.0%
	TGATAGACCTTCTCGGATCG+AGG	-	chr3.2:259803-259822	MS.gene52844:CDS	50.0%
!!	AGGAGGTGCCCTCAATACAT+TGG	-	chr3.2:260323-260342	MS.gene52844:CDS	50.0%

Chromosome	Type	Strat	End	Strand	Name
chr3.2	gene	259732	260344	259732	ID=MS.gene52844
chr3.2	mRNA	259732	260344	259732	ID=MS.gene52844.t1;Parent=MS.gene52844
chr3.2	exon	260252	260344	260252	ID=MS.gene52844.t1.exon1;Parent=MS.gene52844.t1
chr3.2	CDS	260252	260344	260252	ID=cds.MS.gene52844.t1;Parent=MS.gene52844.t1
chr3.2	exon	259732	259833	259732	ID=MS.gene52844.t1.exon2;Parent=MS.gene52844.t1
chr3.2	CDS	259732	259833	259732	ID=cds.MS.gene52844.t1;Parent=MS.gene52844.t1

Gene Sequence

>MS.gene52844

GTCAAGTACGAGAAAATGGAGAAAAATATTGAGAAATTCGGTTCCGACCCCAAAAATCTTCGTATGGTGACTGATAGACCTTCTCGGATCGAGGTAAATCCAATAAAGGATCGCAATGGATTATGACTAATAATCATTATATCCTCACAAATTACATTGAATAATTTAGTTTAATGAATAAAAATATGTTTTTGTTAATATATCTTATGTGTTAATATTCACACTAGTAGTTAACCATTTGTAATAAGTTGGTTAATTGTTTTTTTTTTTACTAAAGTGATTGACTATTTTTTAAATGTGGTCTAAGTAAATTGTAAACTGTAAGTGGTTAGTATATTTCAATTTTCTTTGACAACCGAATGTAAATTGTAAATTGTATCTGATTTGACAATACAAAATGTGCATTTCATAATTCCTCAACTAATTAACAAATAAACTTTTATTGTTTGTTAAAGATGAAAAAATGTTTTCATTTATAATGTTTTATTCATATTTGTTTATTTTATTTTAGATTATAAATGAGGAACCAGAAATTCCACGTGTTGTTTATGTGTCTCGTGAAAGAAGGCCATCACTTCCTCACAAATTCAAAGGAGGTGCCCTCAATACATTG

Protein sequence

>MS.gene52844.t1

VKYEKMEKNIEKFGSDPKNLRMVTDRPSRIEIINEEPEIPRVVYVSRERRPSLPHKFKGGALNTL