AlfalfaGEDB | Msa0235840

M. sativa cultivar zhongmu-4 / Msa0235840

KEGG: -
GO: GO:0003674 GO:0005102 GO:0005179 GO:0005488 GO:0005515 GO:0005575 GO:0005576 GO:0006810 GO:0006811 GO:0006820 GO:0006950 GO:0006970 GO:0008150 GO:0009628 GO:0009966 GO:0010033 GO:0010037 GO:0010469 GO:0010646 GO:0015698 GO:0015706 GO:0023051 GO:0030545 GO:0042221 GO:0042493 GO:0048018 GO:0048046 GO:0048583 GO:0050789 GO:0050793 GO:0050794 GO:0050896 GO:0051179 GO:0051234 GO:0051239 GO:0065007 GO:0065009 GO:0071705 GO:0072347 GO:0098772 GO:1901700 GO:1902025 GO:2000026 GO:2000280
PFAM: -

Nr:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0235840	XP_013462611.1	95.098	102	5	0	1	102	1	102	8.24e-64	198

Swissprot:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0235840	sp\|Q52K95\|PCP14_ARATH	40.187	107	51	3	4	102	6	107	2.16e-11	58.5

Trembl:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0235840	I3S8D3	95.098	102	5	0	1	102	1	102	3.93e-64	198

TFs/TRs:

Gene ID	Type	Classification

Protein Kinases:

Gene ID	Type	Classification

Network:

Co-expression Network

Gene1	Gene2	correlation coefficient	p_value	FDR
Msa0129640	Msa0235840	0.800684	1.284326e-48	-8.615850e-47
Msa0147790	Msa0235840	0.846470	2.128161e-59	-8.615850e-47
Msa0193970	Msa0235840	0.861085	1.313829e-63	-8.615850e-47
Msa0212710	Msa0235840	0.801120	1.045933e-48	-8.615850e-47
Msa0235840	Msa0262360	0.826862	2.148859e-54	-8.615850e-47
Msa0235840	Msa0300140	0.830488	2.855366e-55	-8.615850e-47
Msa0235840	Msa0303240	0.802045	6.757122e-49	-8.615850e-47
Msa0235840	Msa0332360	0.846786	1.744775e-59	-8.615850e-47
Msa0235840	Msa0393100	0.823227	1.551490e-53	-8.615850e-47
Msa0235840	Msa0402800	0.816636	4.994066e-52	-8.615850e-47
Msa0235840	Msa0459640	0.823059	1.697756e-53	-8.615850e-47
Msa0235840	Msa0488580	0.825376	4.848383e-54	-8.615850e-47
Msa0235840	Msa0497860	0.817125	3.878115e-52	-8.615850e-47
Msa0235840	Msa0737430	0.801525	8.641433e-49	-8.615850e-47
Msa0235840	Msa0816630	0.839241	1.783018e-57	-8.615850e-47
Msa0235840	Msa0863940	0.833062	6.614754e-56	-8.615850e-47
Msa0235840	Msa1025750	0.816883	4.396155e-52	-8.615850e-47
Msa0235840	Msa1212470	0.810309	1.229084e-50	-8.615850e-47
Msa0235840	Msa1221220	0.813365	2.655925e-51	-8.615850e-47
Msa0235840	Msa1344330	0.815692	8.113862e-52	-8.615850e-47
Msa0235840	Msa1369320	0.822092	2.849513e-53	-8.615850e-47
Msa0235840	Msa1401110	0.851703	7.466699e-61	-8.615850e-47
Msa0235840	Msa1422230	0.808186	3.504791e-50	-8.615850e-47

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
Msa0235840	MtrunA17_Chr2g0284361	95.098	102	5	0	1	102	1	102	7.58e-68	198
Msa0235840	MtrunA17_Chr8g0379531	56.190	105	38	3	1	102	1	100	2.20e-33	111

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0235840	AT1G29290.1	40.187	107	51	3	4	102	6	107	2.20e-12	58.5

Find 23 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE

CRISPR-Local

CRISPR-Local
sgRNA_sequence	on_target_score	Position	Region
CTCTTGCTTGGTGCAGAATA+TGG	0.235499	2_2:-8681069	None:intergenic
AATATGGAACTTTGCCTTTA+GGG	0.239595	2_2:-8681053	None:intergenic
GAATATGGAACTTTGCCTTT+AGG	0.290280	2_2:-8681054	None:intergenic
TCTCTTTCAATGGGTCGTAT+TGG	0.361579	2_2:+8680889	None:intergenic
TCCCTTTGTTCATGTCTAGA+AGG	0.367085	2_2:+8680949	Msa0235840:CDS
GAAGGAAGAAAGCTTCATAT+TGG	0.368317	2_2:+8680967	Msa0235840:CDS
AACAAATTGTCCCTTGAAGA+TGG	0.411417	2_2:-8681018	None:intergenic
CTTCGATCTGTTCCTAGTCC+TGG	0.413490	2_2:+8681171	Msa0235840:CDS
CAGCAGGTTCGGTGCTTATG+AGG	0.439064	2_2:-8681134	None:intergenic
AATCCGTACTTCAGCAGGTT+CGG	0.461110	2_2:-8681145	None:intergenic
ACAGAGTTACCTCTCTTGCT+TGG	0.463840	2_2:-8681081	None:intergenic
TTCTTGACTTCACTCCCTAA+AGG	0.479462	2_2:+8681039	Msa0235840:CDS
AGAAGAATCCGTACTTCAGC+AGG	0.481211	2_2:-8681150	None:intergenic
TCCTTCTAGACATGAACAAA+GGG	0.484605	2_2:-8680950	None:intergenic
AGAAAATTGACCCATCTTCA+AGG	0.491293	2_2:+8681007	Msa0235840:CDS
TCTGTTCCTAGTCCTGGTGC+TGG	0.534087	2_2:+8681177	Msa0235840:CDS
TTCCTTCTAGACATGAACAA+AGG	0.543888	2_2:-8680951	None:intergenic
ATCATTCAATGTCCAGCACC+AGG	0.555598	2_2:-8681189	None:intergenic
CAATGTCCAGCACCAGGACT+AGG	0.555682	2_2:-8681183	None:intergenic
ACAAATTGTCCCTTGAAGAT+GGG	0.568936	2_2:-8681017	None:intergenic
GCACCGAACCTGCTGAAGTA+CGG	0.569118	2_2:+8681142	Msa0235840:CDS
GAAAATTGACCCATCTTCAA+GGG	0.591769	2_2:+8681008	Msa0235840:CDS
TATTCTGCACCAAGCAAGAG+AGG	0.618318	2_2:+8681072	Msa0235840:CDS

CRISPR-GE

badsite warning	sgRNA_sequence	Strand	Position	Region	GC_content
	AATATGGAACTTTGCCTTTA+GGG	-	chr2_2:8681056-8681075	None:intergenic	30.0%
	TCCTTCTAGACATGAACAAA+GGG	-	chr2_2:8680953-8680972	None:intergenic	35.0%
	TTCCTTCTAGACATGAACAA+AGG	-	chr2_2:8680954-8680973	None:intergenic	35.0%
	GAAGGAAGAAAGCTTCATAT+TGG	+	chr2_2:8680967-8680986	Msa0235840:CDS	35.0%
!	TGAAGATGGGTCAATTTTCT+TGG	-	chr2_2:8681007-8681026	None:intergenic	35.0%
	AGAAAATTGACCCATCTTCA+AGG	+	chr2_2:8681007-8681026	Msa0235840:CDS	35.0%
	GAAAATTGACCCATCTTCAA+GGG	+	chr2_2:8681008-8681027	Msa0235840:CDS	35.0%
	ACAAATTGTCCCTTGAAGAT+GGG	-	chr2_2:8681020-8681039	None:intergenic	35.0%
	AACAAATTGTCCCTTGAAGA+TGG	-	chr2_2:8681021-8681040	None:intergenic	35.0%
	GAATATGGAACTTTGCCTTT+AGG	-	chr2_2:8681057-8681076	None:intergenic	35.0%
	TCCCTTTGTTCATGTCTAGA+AGG	+	chr2_2:8680949-8680968	Msa0235840:CDS	40.0%
	TTCTTGACTTCACTCCCTAA+AGG	+	chr2_2:8681039-8681058	Msa0235840:CDS	40.0%
!!	CTCTTGCTTGGTGCAGAATA+TGG	-	chr2_2:8681072-8681091	None:intergenic	45.0%
	TATTCTGCACCAAGCAAGAG+AGG	+	chr2_2:8681072-8681091	Msa0235840:CDS	45.0%
	ACAGAGTTACCTCTCTTGCT+TGG	-	chr2_2:8681084-8681103	None:intergenic	45.0%
	AATCCGTACTTCAGCAGGTT+CGG	-	chr2_2:8681148-8681167	None:intergenic	45.0%
	AGAAGAATCCGTACTTCAGC+AGG	-	chr2_2:8681153-8681172	None:intergenic	45.0%
	CTTCGATCTGTTCCTAGTCC+TGG	+	chr2_2:8681171-8681190	Msa0235840:CDS	50.0%
!!	CAGCAGGTTCGGTGCTTATG+AGG	-	chr2_2:8681137-8681156	None:intergenic	55.0%
	GCACCGAACCTGCTGAAGTA+CGG	+	chr2_2:8681142-8681161	Msa0235840:CDS	55.0%
	TCTGTTCCTAGTCCTGGTGC+TGG	+	chr2_2:8681177-8681196	Msa0235840:CDS	55.0%
	CAATGTCCAGCACCAGGACT+AGG	-	chr2_2:8681186-8681205	None:intergenic	55.0%

Chromosome	Type	Strat	End	Strand	Name
chr2_2	gene	8680898	8681206	8680898	ID=Msa0235840;Name=Msa0235840
chr2_2	mRNA	8680898	8681206	8680898	ID=Msa0235840-mRNA-1;Parent=Msa0235840;Name=Msa0235840-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0\|-1\|0\|1\|-1\|1\|1\|0\|102
chr2_2	exon	8680898	8681206	8680898	ID=Msa0235840-mRNA-1:exon:3729;Parent=Msa0235840-mRNA-1
chr2_2	CDS	8680898	8681206	8680898	ID=Msa0235840-mRNA-1:cds;Parent=Msa0235840-mRNA-1

Gene Sequence	>Msa0235840 ATGGGTCGTATTGGAACTATGCAACTAGTTATATTCTTTATTCTCTTTGTTTCCCTTTGTTCATGTCTAGAAGGAAGAAAGCTTCATATTGGTTCAAGCAAAGAAACCAAGAAAATTGACCCATCTTCAAGGGACAATTTGTTCTTGACTTCACTCCCTAAAGGCAAAGTTCCATATTCTGCACCAAGCAAGAGAGGTAACTCTGTTGAAGTTGATGAGAAGCTTGTTGCACGTCACCTCATAAGCACCGAACCTGCTGAAGTACGGATTCTTCTTCGATCTGTTCCTAGTCCTGGTGCTGGACATTGA
Protein sequence	>Msa0235840 MGRIGTMQLVIFFILFVSLCSCLEGRKLHIGSSKETKKIDPSSRDNLFLTSLPKGKVPYSAPSKRGNSVEVDEKLVARHLISTEPAEVRILLRSVPSPGAGH*