AlfalfaGEDB | Msa0012540

M. sativa cultivar zhongmu-4 / Msa0012540

KEGG: K11699
GO: GO:0001101 GO:0006139 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009605 GO:0009607 GO:0009615 GO:0009719 GO:0009725 GO:0009751 GO:0009892 GO:0009987 GO:0010025 GO:0010033 GO:0010166 GO:0010467 GO:0010468 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016070 GO:0016246 GO:0016441 GO:0016458 GO:0019222 GO:0030422 GO:0031047 GO:0031050 GO:0034641 GO:0035194 GO:0040029 GO:0042221 GO:0042493 GO:0043170 GO:0043207 GO:0043331 GO:0044237 GO:0044238 GO:0046483 GO:0046677 GO:0048518 GO:0048519 GO:0048522 GO:0050789 GO:0050794 GO:0050896 GO:0051704 GO:0051707 GO:0051716 GO:0060147 GO:0060148 GO:0060255 GO:0060968 GO:0065007 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:1901360 GO:1901568 GO:1901570 GO:1901576 GO:1901698 GO:1901699 GO:1901700
PFAM: -

Nr:

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

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Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0012540	sp\|Q9LQV2\|RDR1_ARATH	46.269	67	36	0	35	101	108	174	6.83e-13	68.2

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Trembl:

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

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Gene ID	Type	Classification
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Protein Kinases:

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Network:

Co-expression Network

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Gene1	Gene2	correlation coefficient	p_value	FDR
Msa0012540	Msa0117910	0.805589	1.241263e-49	-8.615850e-47
Msa0012540	Msa0123300	0.808260	3.379691e-50	-8.615850e-47
Msa0012540	Msa0152400	0.805558	1.259840e-49	-8.615850e-47
Msa0012540	Msa0322690	0.806835	6.780870e-50	-8.615850e-47
Msa0012540	Msa0333920	0.805393	1.364401e-49	-8.615850e-47
Msa0012540	Msa0334040	0.808618	2.835485e-50	-8.615850e-47
Msa0012540	Msa0369850	0.800223	1.594046e-48	-8.615850e-47
Msa0012540	Msa0403850	0.812024	5.220214e-51	-8.615850e-47
Msa0012540	Msa0440530	0.816527	5.282668e-52	-8.615850e-47
Msa0012540	Msa0484780	0.815168	1.061703e-51	-8.615850e-47

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PPI

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Gene1	Gene2	Type
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Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0012540	MtrunA17_Chr1g0161491	79.104	67	13	1	35	101	125	190	1.18e-27	107
Msa0012540	MtrunA17_Chr1g0161471	70.149	67	20	0	35	101	113	179	6.28e-27	105
Msa0012540	MtrunA17_Chr1g0161471	80.556	36	7	0	1	36	1	36	7.20e-13	65.1
Msa0012540	MtrunA17_Chr1g0161511	73.134	67	18	0	35	101	113	179	1.67e-26	103
Msa0012540	MtrunA17_Chr1g0161521	73.134	67	18	0	35	101	113	179	1.31e-25	101

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Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0012540	AT1G14790.1	46.269	67	36	0	35	101	108	174	6.94e-14	68.2

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Find 28 sgRNAs with CRISPR-Local

Find 864 sgRNAs with CRISPR-GE

CRISPR-Local

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CRISPR-Local
sgRNA_sequence	on_target_score	Position	Region
AAAAGAGTTGGCATTGAAGA+TGG	0.454789	1_1:-18780394	Msa0012540:exon
AAATGTCTTTACGTCAGGCA+CGG	0.661308	1_1:+18780326	None:intergenic
ACATTTGTAGAGCAGTATAC+TGG	0.461229	1_1:-18780309	Msa0012540:CDS
AGATTGAACTGCATCAACCA+TGG	0.634369	1_1:-18779876	Msa0012540:CDS
AGCTTTCATATGAGAATATT+TGG	0.191630	1_1:-18779900	Msa0012540:CDS
AGGAAAGATTCTCTGTATTA+TGG	0.218992	1_1:-18780011	Msa0012540:CDS
AGGAAGGTTCTCTGTTGTAC+TGG	0.464188	1_1:-18770434	Msa0012540:CDS
AGTAAAACAATTAAGTTGCA+TGG	0.485965	1_1:-18780366	Msa0012540:CDS
ATGAAGCTCGATGGGTGTGA+CGG	0.597981	1_1:+18770886	None:intergenic
ATGGATGCTAGTGTAGATTT+TGG	0.197478	1_1:-18779982	Msa0012540:CDS

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CRISPR-GE

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sgRNA_sequence	Strand	Position	Region	GC_content
TTAATACATGGGTGTTTGTT+TGG	-	chr1_1:18771301-18771320	Msa0012540:intron	30.0%
TAATACATGGGTGTTTGTTT+GGG	-	chr1_1:18771302-18771321	Msa0012540:intron	30.0%
CAATAGTTGCAGGATTTATT+TGG	-	chr1_1:18771560-18771579	Msa0012540:intron	30.0%
TTACTTAATAGCTCATAGAC+TGG	+	chr1_1:18771589-18771608	None:intergenic	30.0%
TATACGAATATCTTGCCAAT+AGG	-	chr1_1:18771995-18772014	Msa0012540:intron	30.0%
TCGCTTATTTAAGTAACACA+AGG	+	chr1_1:18772539-18772558	None:intergenic	30.0%
TGCAACAGTGTTAACAAAAT+TGG	+	chr1_1:18772572-18772591	None:intergenic	30.0%
ACGCTAGTAATTTATACAAG+GGG	+	chr1_1:18772663-18772682	None:intergenic	30.0%
CACGCTAGTAATTTATACAA+GGG	+	chr1_1:18772664-18772683	None:intergenic	30.0%
TCACGCTAGTAATTTATACA+AGG	+	chr1_1:18772665-18772684	None:intergenic	30.0%

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Chromosome	Type	Strat	End	Strand	Name
chr1_1	gene	18770404	18784633	18770404	ID=Msa0012540;Name=Msa0012540
chr1_1	mRNA	18770404	18784633	18770404	ID=Msa0012540-mRNA-1;Parent=Msa0012540;Name=Msa0012540-mRNA-1;_AED=0.57;_eAED=0.57;_QI=52\|0\|0\|0.12\|0.42\|0.75\|8\|0\|151
chr1_1	exon	18784627	18784633	18784627	ID=Msa0012540-mRNA-1:exon:6975;Parent=Msa0012540-mRNA-1
chr1_1	exon	18784599	18784604	18784599	ID=Msa0012540-mRNA-1:exon:6974;Parent=Msa0012540-mRNA-1
chr1_1	exon	18784551	18784556	18784551	ID=Msa0012540-mRNA-1:exon:6973;Parent=Msa0012540-mRNA-1
chr1_1	exon	18784498	18784504	18784498	ID=Msa0012540-mRNA-1:exon:6972;Parent=Msa0012540-mRNA-1
chr1_1	exon	18780296	18780423	18780296	ID=Msa0012540-mRNA-1:exon:6971;Parent=Msa0012540-mRNA-1
chr1_1	exon	18779862	18780040	18779862	ID=Msa0012540-mRNA-1:exon:6970;Parent=Msa0012540-mRNA-1
chr1_1	exon	18770844	18770940	18770844	ID=Msa0012540-mRNA-1:exon:6969;Parent=Msa0012540-mRNA-1
chr1_1	exon	18770404	18770478	18770404	ID=Msa0012540-mRNA-1:exon:6968;Parent=Msa0012540-mRNA-1
chr1_1	five_prime_UTR	18784627	18784633	18784627	ID=Msa0012540-mRNA-1:five_prime_utr;Parent=Msa0012540-mRNA-1
chr1_1	five_prime_UTR	18784599	18784604	18784599	ID=Msa0012540-mRNA-1:five_prime_utr;Parent=Msa0012540-mRNA-1
chr1_1	five_prime_UTR	18784551	18784556	18784551	ID=Msa0012540-mRNA-1:five_prime_utr;Parent=Msa0012540-mRNA-1
chr1_1	five_prime_UTR	18784498	18784504	18784498	ID=Msa0012540-mRNA-1:five_prime_utr;Parent=Msa0012540-mRNA-1
chr1_1	five_prime_UTR	18780398	18780423	18780398	ID=Msa0012540-mRNA-1:five_prime_utr;Parent=Msa0012540-mRNA-1
chr1_1	CDS	18780296	18780397	18780296	ID=Msa0012540-mRNA-1:cds;Parent=Msa0012540-mRNA-1
chr1_1	CDS	18779862	18780040	18779862	ID=Msa0012540-mRNA-1:cds;Parent=Msa0012540-mRNA-1
chr1_1	CDS	18770844	18770940	18770844	ID=Msa0012540-mRNA-1:cds;Parent=Msa0012540-mRNA-1
chr1_1	CDS	18770404	18770478	18770404	ID=Msa0012540-mRNA-1:cds;Parent=Msa0012540-mRNA-1

Gene Sequence

>Msa0012540

ATGGTTAAAAGTAAAACAATTAAGTTGCATGGATTCCCTCATCATGTGACCGTGCCTGACGTAAAGACATTTGTAGAGCAGTATACTGGTGAAGAAAGTGTGATCTCAAAGGAAAGATTCTCTGTATTATGGGGAAAGATGGATGCTAGTGTAGATTTTGGGATTGGATTGAGAAAGTGGCGATTCTCTATGTGCCATGACGATAAGAAGTTCAAACTTGAGCTTTCATATGAGAATATTTGGAAGATTGAACTGCATCAACCATGGTTTAAAACTGCAAAGTTATATTGTATTCTCATAATCACTTTTGTCGCCGTCACACCCATCGAGCTTCATGCCGTCGAGTTTACTCTTTCTTCATCTTACAGTCGCACAAAGATTTTATCTCAATTTATAGAGCAGGAAGGTTCTCTGTTGTACTGGTGTTCCAGTGTTGTCTTTGTTAGACAATAT

Protein sequence

>Msa0012540

MVKSKTIKLHGFPHHVTVPDVKTFVEQYTGEESVISKERFSVLWGKMDASVDFGIGLRKWRFSMCHDDKKFKLELSYENIWKIELHQPWFKTAKLYCILIITFVAVTPIELHAVEFTLSSSYSRTKILSQFIEQEGSLLYWCSSVVFVRQY