AlfalfaGEDB | Msa0539000

M. sativa cultivar zhongmu-4 / Msa0539000

KEGG: -
GO: GO:0000151 GO:0000278 GO:0000281 GO:0000819 GO:0000910 GO:0000911 GO:0001568 GO:0001570 GO:0001932 GO:0001934 GO:0001944 GO:0002682 GO:0002683 GO:0002761 GO:0002762 GO:0003674 GO:0003700 GO:0003824 GO:0004842 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005739 GO:0005783 GO:0005794 GO:0005886 GO:0006275 GO:0006355 GO:0006464 GO:0006508 GO:0006511 GO:0006807 GO:0006950 GO:0006974 GO:0006996 GO:0007049 GO:0007059 GO:0007062 GO:0007154 GO:0007165 GO:0007166 GO:0007176 GO:0007219 GO:0007275 GO:0008150 GO:0008152 GO:0008156 GO:0009056 GO:0009057 GO:0009314 GO:0009411 GO:0009416 GO:0009628 GO:0009653 GO:0009791 GO:0009825 GO:0009888 GO:0009889 GO:0009890 GO:0009892 GO:0009893 GO:0009894 GO:0009896 GO:0009966 GO:0009967 GO:0009987 GO:0010235 GO:0010374 GO:0010440 GO:0010468 GO:0010469 GO:0010498 GO:0010506 GO:0010556 GO:0010558 GO:0010562 GO:0010564 GO:0010594 GO:0010604 GO:0010605 GO:0010632 GO:0010638 GO:0010646 GO:0010647 GO:0010721 GO:0010821 GO:0010822 GO:0010941 GO:0010942 GO:0010948 GO:0012505 GO:0016020 GO:0016021 GO:0016043 GO:0016049 GO:0016567 GO:0016740 GO:0019005 GO:0019219 GO:0019220 GO:0019222 GO:0019538 GO:0019787 GO:0019899 GO:0019941 GO:0022402 GO:0022603 GO:0023051 GO:0023052 GO:0023056 GO:0030135 GO:0030136 GO:0030154 GO:0030162 GO:0030163 GO:0030234 GO:0030323 GO:0030324 GO:0030332 GO:0030334 GO:0030674 GO:0031146 GO:0031224 GO:0031323 GO:0031324 GO:0031325 GO:0031326 GO:0031327 GO:0031329 GO:0031331 GO:0031347 GO:0031348 GO:0031396 GO:0031398 GO:0031399 GO:0031401 GO:0031410 GO:0031461 GO:0031625 GO:0031647 GO:0031648 GO:0031974 GO:0031981 GO:0031982 GO:0032268 GO:0032270 GO:0032386 GO:0032388 GO:0032446 GO:0032501 GO:0032502 GO:0032506 GO:0032875 GO:0032876 GO:0032879 GO:0032880 GO:0032991 GO:0033043 GO:0033157 GO:0033554 GO:0033674 GO:0034644 GO:0035239 GO:0035295 GO:0036211 GO:0040007 GO:0040012 GO:0042058 GO:0042176 GO:0042325 GO:0042327 GO:0042802 GO:0042981 GO:0043065 GO:0043067 GO:0043068 GO:0043085 GO:0043161 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043392 GO:0043408 GO:0043410 GO:0043412 GO:0043523 GO:0043525 GO:0043535 GO:0043549 GO:0043632 GO:0044092 GO:0044093 GO:0044237 GO:0044238 GO:0044248 GO:0044257 GO:0044260 GO:0044265 GO:0044267 GO:0044389 GO:0044422 GO:0044424 GO:0044425 GO:0044428 GO:0044444 GO:0044446 GO:0044464 GO:0045088 GO:0045309 GO:0045595 GO:0045596 GO:0045637 GO:0045638 GO:0045670 GO:0045671 GO:0045732 GO:0045741 GO:0045742 GO:0045765 GO:0045786 GO:0045824 GO:0045859 GO:0045860 GO:0045862 GO:0045934 GO:0045937 GO:0048471 GO:0048513 GO:0048514 GO:0048518 GO:0048519 GO:0048522 GO:0048523 GO:0048583 GO:0048584 GO:0048585 GO:0048731 GO:0048856 GO:0048869 GO:0050730 GO:0050731 GO:0050776 GO:0050777 GO:0050789 GO:0050790 GO:0050793 GO:0050794 GO:0050816 GO:0050821 GO:0050896 GO:0051049 GO:0051050 GO:0051052 GO:0051053 GO:0051093 GO:0051098 GO:0051100 GO:0051101 GO:0051128 GO:0051130 GO:0051171 GO:0051172 GO:0051173 GO:0051174 GO:0051219 GO:0051222 GO:0051223 GO:0051239 GO:0051241 GO:0051246 GO:0051247 GO:0051252 GO:0051270 GO:0051276 GO:0051301 GO:0051338 GO:0051347 GO:0051438 GO:0051443 GO:0051603 GO:0051716 GO:0051726 GO:0055106 GO:0060090 GO:0060255 GO:0060284 GO:0060341 GO:0060541 GO:0061097 GO:0061098 GO:0061136 GO:0061640 GO:0065007 GO:0065008 GO:0065009 GO:0070013 GO:0070201 GO:0070372 GO:0070374 GO:0070647 GO:0071214 GO:0071478 GO:0071482 GO:0071704 GO:0071840 GO:0071944 GO:0072358 GO:0072359 GO:0080008 GO:0080090 GO:0080134 GO:0080135 GO:0090049 GO:0090087 GO:0090316 GO:0090329 GO:0090558 GO:0097027 GO:0097708 GO:0098772 GO:0098813 GO:0104004 GO:0140096 GO:0140110 GO:1900407 GO:1900409 GO:1901184 GO:1901186 GO:1901214 GO:1901216 GO:1901342 GO:1901564 GO:1901565 GO:1901575 GO:1901800 GO:1902105 GO:1902106 GO:1902175 GO:1902177 GO:1902410 GO:1902494 GO:1902531 GO:1902533 GO:1902882 GO:1902884 GO:1903010 GO:1903011 GO:1903025 GO:1903026 GO:1903047 GO:1903050 GO:1903052 GO:1903146 GO:1903201 GO:1903203 GO:1903209 GO:1903214 GO:1903223 GO:1903320 GO:1903322 GO:1903362 GO:1903364 GO:1903376 GO:1903378 GO:1903506 GO:1903533 GO:1903670 GO:1903706 GO:1903707 GO:1903747 GO:1903749 GO:1903827 GO:1903829 GO:1903955 GO:1904951 GO:1990234 GO:1990452 GO:2000026 GO:2000058 GO:2000060 GO:2000104 GO:2000112 GO:2000113 GO:2000145 GO:2000273 GO:2000677 GO:2000678 GO:2001141 GO:2001204 GO:2001205 GO:2001233 GO:2001235 GO:2001242 GO:2001244
PFAM: PF02141.24

Nr:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0539000	KAG5014724.1	89.189	37	4	0	3	39	205	241	4.72e-13	73.2

Swissprot:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0539000	sp\|Q8RXA7\|SCD1_ARATH	77.143	35	8	0	3	37	205	239	4.13e-12	62.4

Trembl:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0539000	A0A2Z6NYQ0	84.615	39	6	0	1	39	203	241	3.24e-13	72.8

TFs/TRs:

Gene ID	Type	Classification

Protein Kinases:

Gene ID	Type	Classification

Network:

Co-expression Network

Gene1	Gene2	correlation coefficient	p_value	FDR
Msa0539000	Msa0585000	0.804886	1.741900e-49	-8.615850e-47
Msa0539000	Msa0661190	0.825806	3.833471e-54	-8.615850e-47
Msa0539000	Msa1201430	0.804444	2.153587e-49	-8.615850e-47
Msa0539000	Msa1249640	0.807628	4.605461e-50	-8.615850e-47
Msa0539000	Msa1254370	0.809853	1.541120e-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
Msa0539000	MtrunA17_Chr8g0390861	89.189	37	4	0	1	37	203	239	1.03e-16	72.0

Query id	Subject id	identity %	alignment length	mismatches	q. start	q. end	s. start	s. end	e-value	bit score
Msa0539000	AT1G49040.1	77.143	35	8	3	37	205	239	4.20e-13	62.4
Msa0539000	AT1G49040.3	77.143	35	8	3	37	205	239	5.50e-13	62.0
Msa0539000	AT1G49040.2	77.143	35	8	3	37	205	239	4.19e-12	59.3
Msa0539000	AT1G49040.4	77.143	35	8	3	37	205	239	4.19e-12	59.3

Find 14 sgRNAs with CRISPR-Local

Find 19 sgRNAs with CRISPR-GE

CRISPR-Local

CRISPR-Local
sgRNA_sequence	on_target_score	Position	Region
TATGCTTCATACTGATGAAA+TGG	0.337886	4_1:-19096048	Msa0539000:CDS
CATCCCCAGTGGCAATGATC+TGG	0.428659	4_1:-19096140	Msa0539000:intron
TAGACTACATAAATATTAAC+GGG	0.449403	4_1:+19096012	None:intergenic
ATGCTTCATACTGATGAAAT+GGG	0.482734	4_1:-19096047	Msa0539000:CDS
GCAGATATCATTCCAGCCTC+TGG	0.492433	4_1:-19096288	Msa0539000:CDS
CGGCGGTGCTGCTTGAGAGA+AGG	0.509850	4_1:-19096226	Msa0539000:CDS
ATGAAGCATAGAGAAAATAC+AGG	0.519895	4_1:+19096061	None:intergenic
CTAAACACTGTACCAGAGGC+TGG	0.524706	4_1:+19096276	None:intergenic
AGAAACCAGATCATTGCCAC+TGG	0.537134	4_1:+19096135	None:intergenic
GAAACCAGATCATTGCCACT+GGG	0.610206	4_1:+19096136	None:intergenic
AAGCATAGAGAAAATACAGG+TGG	0.653782	4_1:+19096064	None:intergenic
ACATCTAAACACTGTACCAG+AGG	0.659497	4_1:+19096272	None:intergenic
AAACCAGATCATTGCCACTG+GGG	0.701072	4_1:+19096137	None:intergenic
AGTCACATTGACATCCCCAG+TGG	0.779303	4_1:-19096151	Msa0539000:CDS

CRISPR-GE

badsite warning	sgRNA_sequence	Strand	Position	Region	GC_content
!!	AATATCATTGTATATTATAT+AGG	-	chr4_1:19096228-19096247	Msa0539000:CDS	10.0%
!!!	CAACTTAATAAATCTTTTTA+CGG	-	chr4_1:19096071-19096090	Msa0539000:intron	15.0%
!!	CTAATAGTCATAAATAAGAA+AGG	+	chr4_1:19096140-19096159	None:intergenic	20.0%
!!	CTTAATAAATCTTTTTACGG+CGG	-	chr4_1:19096074-19096093	Msa0539000:intron	25.0%
!	TTGAGAGAAGGATTTTACTT+CGG	-	chr4_1:19096103-19096122	Msa0539000:intron	30.0%
	ATGAAGCATAGAGAAAATAC+AGG	+	chr4_1:19096259-19096278	None:intergenic	30.0%
	TATGCTTCATACTGATGAAA+TGG	-	chr4_1:19096269-19096288	Msa0539000:CDS	30.0%
	ATGCTTCATACTGATGAAAT+GGG	-	chr4_1:19096270-19096289	Msa0539000:CDS	30.0%
!	TGAGAGAAGGATTTTACTTC+GGG	-	chr4_1:19096104-19096123	Msa0539000:intron	35.0%
	AAGCATAGAGAAAATACAGG+TGG	+	chr4_1:19096256-19096275	None:intergenic	35.0%
	ACATCTAAACACTGTACCAG+AGG	+	chr4_1:19096048-19096067	None:intergenic	40.0%
	AAACCAGATCATTGCCACTG+GGG	+	chr4_1:19096183-19096202	None:intergenic	45.0%
	GAAACCAGATCATTGCCACT+GGG	+	chr4_1:19096184-19096203	None:intergenic	45.0%
	AGAAACCAGATCATTGCCAC+TGG	+	chr4_1:19096185-19096204	None:intergenic	45.0%
	GCAGATATCATTCCAGCCTC+TGG	-	chr4_1:19096029-19096048	Msa0539000:CDS	50.0%
	CTAAACACTGTACCAGAGGC+TGG	+	chr4_1:19096044-19096063	None:intergenic	50.0%
	AGTCACATTGACATCCCCAG+TGG	-	chr4_1:19096166-19096185	Msa0539000:intron	50.0%
	CATCCCCAGTGGCAATGATC+TGG	-	chr4_1:19096177-19096196	Msa0539000:intron	55.0%
!!	CGGCGGTGCTGCTTGAGAGA+AGG	-	chr4_1:19096091-19096110	Msa0539000:intron	65.0%

Chromosome	Type	Strat	End	Strand	Name
chr4_1	gene	19096027	19096312	19096027	ID=Msa0539000;Name=Msa0539000
chr4_1	mRNA	19096027	19096312	19096027	ID=Msa0539000-mRNA-1;Parent=Msa0539000;Name=Msa0539000-mRNA-1;_AED=0.73;_eAED=0.73;_QI=0\|0\|0\|0.33\|0\|0\|3\|0\|66
chr4_1	exon	19096206	19096312	19096206	ID=Msa0539000-mRNA-1:exon:5648;Parent=Msa0539000-mRNA-1
chr4_1	exon	19096141	19096171	19096141	ID=Msa0539000-mRNA-1:exon:5647;Parent=Msa0539000-mRNA-1
chr4_1	exon	19096027	19096089	19096027	ID=Msa0539000-mRNA-1:exon:5646;Parent=Msa0539000-mRNA-1
chr4_1	CDS	19096206	19096312	19096206	ID=Msa0539000-mRNA-1:cds;Parent=Msa0539000-mRNA-1
chr4_1	CDS	19096141	19096171	19096141	ID=Msa0539000-mRNA-1:cds;Parent=Msa0539000-mRNA-1
chr4_1	CDS	19096027	19096089	19096027	ID=Msa0539000-mRNA-1:cds;Parent=Msa0539000-mRNA-1

Gene Sequence	>Msa0539000 ATGCAGATATCATTCCAGCCTCTGGTACAGTGTTTAGATGTTGACAACTTAATAAATCTTTTTACGGCGGTGCTGCTTGAGAGAAGGATTTTACTTCGGGCTAACAATCACATTGACATCCCCAGTGGCAATGATCTGGTTCCACCTGTATTTTCTCTATGCTTCATACTGATGAAATGGGAGAGTTTGTTTTCCCGTTAA
Protein sequence	>Msa0539000 MQISFQPLVQCLDVDNLINLFTAVLLERRILLRANNHIDIPSGNDLVPPVFSLCFILMKWESLFSR*