AlfalfaGEDB | Msa0906000

M. sativa cultivar zhongmu-4 / Msa0906000

KEGG: K02493|K02979|K07767|K08767
GO: GO:0000028 GO:0002181 GO:0003674 GO:0003676 GO:0003723 GO:0003729 GO:0003735 GO:0005198 GO:0005488 GO:0005575 GO:0005618 GO:0005622 GO:0005623 GO:0005737 GO:0005783 GO:0005789 GO:0005791 GO:0005829 GO:0005840 GO:0005844 GO:0005886 GO:0006139 GO:0006364 GO:0006396 GO:0006412 GO:0006518 GO:0006725 GO:0006807 GO:0006996 GO:0007275 GO:0007444 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009888 GO:0009987 GO:0010467 GO:0012505 GO:0015935 GO:0016020 GO:0016043 GO:0016070 GO:0016072 GO:0019538 GO:0022607 GO:0022613 GO:0022618 GO:0022626 GO:0022627 GO:0030312 GO:0030490 GO:0030867 GO:0031090 GO:0031984 GO:0032501 GO:0032502 GO:0032991 GO:0034470 GO:0034622 GO:0034641 GO:0034645 GO:0034660 GO:0035220 GO:0035295 GO:0042175 GO:0042254 GO:0042255 GO:0042274 GO:0042788 GO:0043043 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043603 GO:0043604 GO:0043933 GO:0044085 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044271 GO:0044391 GO:0044422 GO:0044424 GO:0044425 GO:0044432 GO:0044444 GO:0044445 GO:0044446 GO:0044464 GO:0046483 GO:0048513 GO:0048731 GO:0048856 GO:0060429 GO:0065003 GO:0070925 GO:0071704 GO:0071826 GO:0071840 GO:0071944 GO:0090304 GO:0097159 GO:0098552 GO:0098554 GO:0098556 GO:0098562 GO:0098588 GO:0098827 GO:1901360 GO:1901363 GO:1901564 GO:1901566 GO:1901576 GO:1990904
PFAM: PF01200.21

Nr:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0906000	ABD32519.1	94.030	67	4	0	16	82	6	72	7.72e-36	125

Swissprot:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0906000	sp\|Q9SR73\|RS281_ARATH	81.250	64	12	0	19	82	1	64	4.93e-31	106

Trembl:

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

TFs/TRs:

Gene ID	Type	Classification

Protein Kinases:

Gene ID	Type	Classification

Network:

Co-expression Network

Gene1	Gene2	correlation coefficient	p_value	FDR
Msa0619860	Msa0906000	0.804467	2.129824e-49	-8.615850e-47
Msa0683780	Msa0906000	0.822458	2.343110e-53	-8.615850e-47
Msa0699190	Msa0906000	0.805090	1.579116e-49	-8.615850e-47
Msa0490820	Msa0906000	0.802325	5.918054e-49	-8.615850e-47
Msa0534750	Msa0906000	0.815437	9.247534e-52	-8.615850e-47
Msa0906000	Msa1227690	0.803469	3.434693e-49	-8.615850e-47
Msa0906000	Msa1310690	0.807967	3.902269e-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
Msa0906000	MtrunA17_Chr6g0453911	96.875	64	2	0	19	82	1	64	3.49e-39	124
Msa0906000	MtrunA17_Chr6g0453811	83.077	65	10	1	19	82	1	65	1.39e-31	105
Msa0906000	MtrunA17_Chr4g0041861	76.923	65	14	1	19	82	1	65	3.36e-28	96.3
Msa0906000	MtrunA17_Chr8g0381481	71.429	49	13	1	19	66	1	49	5.24e-17	67.8

Query id	Subject id	identity %	alignment length	mismatches	q. start	q. end	s. start	s. end	e-value	bit score
Msa0906000	AT5G03850.1	81.250	64	12	19	82	1	64	5.01e-32	106
Msa0906000	AT3G10090.1	81.250	64	12	19	82	1	64	5.01e-32	106
Msa0906000	AT5G64140.1	81.250	64	12	19	82	1	64	6.74e-32	105

Find 32 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE

CRISPR-Local

CRISPR-Local
sgRNA_sequence	on_target_score	Position	Region
TATATTATGTTTGGAGTTCT+TGG	0.223464	6_2:-4461853	Msa0906000:three_prime_UTR
TTAGTAAATAATTGAATATA+TGG	0.244948	6_2:+4461693	None:intergenic
GTTTGACTCTATATTATGTT+TGG	0.286542	6_2:-4461862	Msa0906000:three_prime_UTR
ATGACATCTCCTTCTCTAAT+GGG	0.349028	6_2:+4462094	None:intergenic
AATAGGTCATAGGTGCAAAA+TGG	0.363522	6_2:+4461933	None:intergenic
TCAAAACTCAGCCAAATAAA+AGG	0.363604	6_2:+4461897	None:intergenic
AATGACATCTCCTTCTCTAA+TGG	0.375631	6_2:+4462093	None:intergenic
CGCTCAAGTTGAGAAAGTTA+TGG	0.416411	6_2:-4462203	Msa0906000:CDS
TGGATATTCAGATTGACTTC+AGG	0.443679	6_2:-4462400	Msa0906000:CDS
AAGGTCTAGTAATAATAAAT+AGG	0.443893	6_2:+4461916	None:intergenic
AGTAATAATAAATAGGTCAT+AGG	0.445981	6_2:+4461923	None:intergenic
AACCTGAGTGACCTGTCCTC+TGG	0.457012	6_2:+4462168	None:intergenic
GCTCAAGTTGAGAAAGTTAT+GGG	0.472061	6_2:-4462202	Msa0906000:CDS
ACCGGCCAAGTTAGACCTTA+CGG	0.482887	6_2:+4461666	None:intergenic
GAGAAAGTTATGGGTCGTAC+TGG	0.491245	6_2:-4462193	Msa0906000:CDS
CTTCTCTCTCAGACTCAAGT+AGG	0.493446	6_2:+4462068	None:intergenic
TAGTAAATAATTGAATATAT+GGG	0.497460	6_2:+4461694	None:intergenic
AAGATATAATAAAGCAATGC+TGG	0.501496	6_2:-4461999	Msa0906000:three_prime_UTR
GAGAAAATCTACTCTTCTAT+CGG	0.520920	6_2:+4462035	None:intergenic
ATCACAGCATTTGACTCTCA+TGG	0.535820	6_2:+4462366	None:intergenic
TTATTTACTAAGTGTCCGTA+AGG	0.572475	6_2:-4461681	Msa0906000:three_prime_UTR
TACAAAATAGCTTTCAGACA+AGG	0.591169	6_2:-4461766	Msa0906000:three_prime_UTR
ATGAGAATCGCTACATCATG+AGG	0.591990	6_2:-4462129	Msa0906000:CDS
TCGTACTGGATCCAGAGGAC+AGG	0.601747	6_2:-4462179	Msa0906000:CDS
ATCCAGAGGACAGGTCACTC+AGG	0.602839	6_2:-4462170	Msa0906000:CDS
GTGAAGGGCCCCATTAGAGA+AGG	0.605680	6_2:-4462103	Msa0906000:CDS
TTCTCTCTCAGACTCAAGTA+GGG	0.606054	6_2:+4462069	None:intergenic
CTACATCATGAGGAATGTGA+AGG	0.633338	6_2:-4462119	Msa0906000:CDS
TGACATCTCCTTCTCTAATG+GGG	0.633980	6_2:+4462095	None:intergenic
ATTCAGATTGACTTCAGGCA+CGG	0.639783	6_2:-4462395	Msa0906000:CDS
TACATCATGAGGAATGTGAA+GGG	0.640443	6_2:-4462118	Msa0906000:CDS
ATGGGTCGTACTGGATCCAG+AGG	0.663896	6_2:-4462184	Msa0906000:CDS

CRISPR-GE

badsite warning	sgRNA_sequence	Strand	Position	Region	GC_content
!!	TAGTAAATAATTGAATATAT+GGG	+	chr6_2:4462390-4462409	None:intergenic	10.0%
!!	TTAGTAAATAATTGAATATA+TGG	+	chr6_2:4462391-4462410	None:intergenic	10.0%
!!	AGTAATAATAAATAGGTCAT+AGG	+	chr6_2:4462161-4462180	None:intergenic	20.0%
!!	AAGGTCTAGTAATAATAAAT+AGG	+	chr6_2:4462168-4462187	None:intergenic	20.0%
!!!	TTATTACTAGACCTTTTATT+TGG	-	chr6_2:4462173-4462192	Msa0906000:CDS	20.0%
!	AAGATATAATAAAGCAATGC+TGG	-	chr6_2:4462082-4462101	Msa0906000:CDS	25.0%
!!!	TGAGTTTTGAGTAAAGATTT+TGG	-	chr6_2:4462197-4462216	Msa0906000:CDS	25.0%
!	GTTTGACTCTATATTATGTT+TGG	-	chr6_2:4462219-4462238	Msa0906000:CDS	25.0%
!!	TATATTATGTTTGGAGTTCT+TGG	-	chr6_2:4462228-4462247	Msa0906000:intron	25.0%
!!!	TGCAAATGCTTTTGATTATT+AGG	-	chr6_2:4462268-4462287	Msa0906000:intron	25.0%
	ATAATCTATGTGACAGAGTA+AGG	+	chr6_2:4461777-4461796	None:intergenic	30.0%
	GAGAAAATCTACTCTTCTAT+CGG	+	chr6_2:4462049-4462068	None:intergenic	30.0%
!	AGAAGAGTAGATTTTCTCAA+TGG	-	chr6_2:4462051-4462070	Msa0906000:CDS	30.0%
!	AGTAGATTTTCTCAATGGTT+TGG	-	chr6_2:4462056-4462075	Msa0906000:CDS	30.0%
	TCAAAACTCAGCCAAATAAA+AGG	+	chr6_2:4462187-4462206	None:intergenic	30.0%
	TACAAAATAGCTTTCAGACA+AGG	-	chr6_2:4462315-4462334	Msa0906000:intron	30.0%
	TTATTTACTAAGTGTCCGTA+AGG	-	chr6_2:4462400-4462419	Msa0906000:CDS	30.0%
!	TGGATATTCAGATTGACTTC+AGG	-	chr6_2:4461681-4461700	Msa0906000:three_prime_UTR	35.0%
	GAATGTGTTTGTGTTTGAGT+AGG	-	chr6_2:4461835-4461854	Msa0906000:three_prime_UTR	35.0%
!!	GCTCAAGTTGAGAAAGTTAT+GGG	-	chr6_2:4461879-4461898	Msa0906000:three_prime_UTR	35.0%
	TACATCATGAGGAATGTGAA+GGG	-	chr6_2:4461963-4461982	Msa0906000:three_prime_UTR	35.0%
	ATGACATCTCCTTCTCTAAT+GGG	+	chr6_2:4461990-4462009	None:intergenic	35.0%
	AATGACATCTCCTTCTCTAA+TGG	+	chr6_2:4461991-4462010	None:intergenic	35.0%
	AATAGGTCATAGGTGCAAAA+TGG	+	chr6_2:4462151-4462170	None:intergenic	35.0%
!	ATTCAGATTGACTTCAGGCA+CGG	-	chr6_2:4461686-4461705	Msa0906000:three_prime_UTR	40.0%
	ATCACAGCATTTGACTCTCA+TGG	+	chr6_2:4461718-4461737	None:intergenic	40.0%
	GTGTTTGTGTTTGAGTAGGA+TGG	-	chr6_2:4461839-4461858	Msa0906000:three_prime_UTR	40.0%
!!	CGCTCAAGTTGAGAAAGTTA+TGG	-	chr6_2:4461878-4461897	Msa0906000:three_prime_UTR	40.0%
	ATGAGAATCGCTACATCATG+AGG	-	chr6_2:4461952-4461971	Msa0906000:three_prime_UTR	40.0%
	CTACATCATGAGGAATGTGA+AGG	-	chr6_2:4461962-4461981	Msa0906000:three_prime_UTR	40.0%
	TGACATCTCCTTCTCTAATG+GGG	+	chr6_2:4461989-4462008	None:intergenic	40.0%
	TTCTCTCTCAGACTCAAGTA+GGG	+	chr6_2:4462015-4462034	None:intergenic	40.0%
	GAGAAAGTTATGGGTCGTAC+TGG	-	chr6_2:4461888-4461907	Msa0906000:three_prime_UTR	45.0%
	CTTCTCTCTCAGACTCAAGT+AGG	+	chr6_2:4462016-4462035	None:intergenic	45.0%
	ATGGGTCGTACTGGATCCAG+AGG	-	chr6_2:4461897-4461916	Msa0906000:three_prime_UTR	55.0%
	TCGTACTGGATCCAGAGGAC+AGG	-	chr6_2:4461902-4461921	Msa0906000:three_prime_UTR	55.0%
	ATCCAGAGGACAGGTCACTC+AGG	-	chr6_2:4461911-4461930	Msa0906000:three_prime_UTR	55.0%
	AACCTGAGTGACCTGTCCTC+TGG	+	chr6_2:4461916-4461935	None:intergenic	55.0%
	GTGAAGGGCCCCATTAGAGA+AGG	-	chr6_2:4461978-4461997	Msa0906000:three_prime_UTR	55.0%

Chromosome	Type	Strat	End	Strand	Name
chr6_2	gene	4461680	4462423	4461680	ID=Msa0906000;Name=Msa0906000
chr6_2	mRNA	4461680	4462423	4461680	ID=Msa0906000-mRNA-1;Parent=Msa0906000;Name=Msa0906000-mRNA-1;_AED=0.12;_eAED=0.12;_QI=0\|0\|0.5\|0.5\|1\|1\|2\|371\|82
chr6_2	exon	4461680	4462246	4461680	ID=Msa0906000-mRNA-1:exon:1293;Parent=Msa0906000-mRNA-1
chr6_2	exon	4462371	4462423	4462371	ID=Msa0906000-mRNA-1:exon:1292;Parent=Msa0906000-mRNA-1
chr6_2	CDS	4462371	4462423	4462371	ID=Msa0906000-mRNA-1:cds;Parent=Msa0906000-mRNA-1
chr6_2	CDS	4462051	4462246	4462051	ID=Msa0906000-mRNA-1:cds;Parent=Msa0906000-mRNA-1
chr6_2	three_prime_UTR	4461680	4462050	4461680	ID=Msa0906000-mRNA-1:three_prime_utr;Parent=Msa0906000-mRNA-1

Gene Sequence	>Msa0906000 ATGGATATTCAGATTGACTTCAGGCACGGTTTCAACCATGAGAGTCAAATGCTGATGGAATCACAGATTAAGCACGCTCAAGTTGAGAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTCACTCAGGTTAGAGTCAAGATTCTTTATGAGAATCGCTACATCATGAGGAATGTGAAGGGCCCCATTAGAGAAGGAGATGTCATTGCCCTACTTGAGTCTGAGAGAGAAGCAAGAAGACTCCGATAG
Protein sequence	>Msa0906000 MDIQIDFRHGFNHESQMLMESQIKHAQVEKVMGRTGSRGQVTQVRVKILYENRYIMRNVKGPIREGDVIALLESEREARRLR*