AlfalfaGEDB | Msa0903960

M. sativa cultivar zhongmu-4 / Msa0903960

KEGG: K02937
GO: GO:0000463 GO:0000470 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:0005773 GO:0005774 GO:0005829 GO:0005840 GO:0005844 GO:0005886 GO:0006139 GO:0006364 GO:0006396 GO:0006412 GO:0006518 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009507 GO:0009536 GO:0009987 GO:0010467 GO:0015934 GO:0016020 GO:0016070 GO:0016072 GO:0019538 GO:0022613 GO:0022625 GO:0022626 GO:0030312 GO:0031090 GO:0032991 GO:0034470 GO:0034641 GO:0034645 GO:0034660 GO:0042254 GO:0042273 GO:0042788 GO:0043043 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043603 GO:0043604 GO:0044085 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044271 GO:0044391 GO:0044422 GO:0044424 GO:0044437 GO:0044444 GO:0044445 GO:0044446 GO:0044464 GO:0046483 GO:0071704 GO:0071840 GO:0071944 GO:0090304 GO:0097159 GO:0098588 GO:0098805 GO:1901360 GO:1901363 GO:1901564 GO:1901566 GO:1901576 GO:1990904
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
Msa0903960	AFK47155.1	98.039	102	2	0	4	105	47	148	3.56e-67	208

Swissprot:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0903960	sp\|P60040\|RL72_ARATH	87.255	102	13	0	4	105	141	242	1.66e-63	195

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
Msa0757320	Msa0903960	0.832468	9.292263e-56	-8.615850e-47
Msa0903960	Msa1231890	0.811807	5.819503e-51	-8.615850e-47

PPI

Gene1	Gene2	Type

Query id	Subject id	identity %	alignment length	mismatches	q. start	q. end	s. start	s. end	e-value	bit score
Msa0903960	MtrunA17_Chr1g0155331	98.039	102	2	4	105	143	244	5.66e-71	211
Msa0903960	MtrunA17_Chr2g0298841	98.039	102	2	4	105	143	244	6.74e-71	211
Msa0903960	MtrunA17_Chr4g0002321	89.216	102	11	4	105	142	243	3.09e-65	197
Msa0903960	MtrunA17_Chr7g0237701	54.902	102	46	4	105	145	246	4.36e-41	135
Msa0903960	MtrunA17_Chr1g0155311	95.082	61	3	35	95	2	62	3.90e-39	124

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0903960	AT2G01250.1	87.255	102	13	0	4	105	141	242	1.69e-64	195
Msa0903960	AT2G44120.1	85.294	102	15	0	4	105	141	242	6.07e-64	194
Msa0903960	AT2G44120.2	85.294	102	15	0	4	105	146	247	8.05e-64	194
Msa0903960	AT3G13580.5	84.314	102	16	0	4	105	143	244	8.48e-63	191
Msa0903960	AT3G13580.4	84.314	102	16	0	4	105	143	244	8.48e-63	191
Msa0903960	AT3G13580.2	84.314	102	16	0	4	105	143	244	8.48e-63	191
Msa0903960	AT3G13580.3	84.314	102	16	0	4	105	143	244	8.48e-63	191
Msa0903960	AT3G13580.1	84.314	102	16	0	4	105	143	244	8.48e-63	191
Msa0903960	AT3G13580.7	84.314	102	16	0	4	105	143	244	8.48e-63	191
Msa0903960	AT3G13580.8	84.314	102	16	0	4	105	143	244	8.48e-63	191
Msa0903960	AT3G13580.6	84.314	102	16	0	4	105	143	244	8.48e-63	191
Msa0903960	AT3G13580.9	84.314	102	16	0	4	105	143	244	8.48e-63	191
Msa0903960	AT1G80750.1	50.980	102	49	1	5	105	146	247	4.53e-29	105
Msa0903960	AT2G01250.2	72.973	37	10	0	4	40	141	177	2.76e-11	57.4

Find 29 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE

CRISPR-Local

CRISPR-Local
sgRNA_sequence	on_target_score	Position	Region
ACTCATTAGAAGGATGAATT+AGG	0.270598	6_2:-1405415	None:intergenic
TTTCAAGCTCAAAGCTCCTT+TGG	0.284641	6_2:-1405511	Msa0903960:CDS
AGTGTTCAATTGCAGGTTCT+TGG	0.317764	6_2:-1405624	Msa0903960:intron
TTCAAGCTCAAAGCTCCTTT+GGG	0.329811	6_2:-1405510	Msa0903960:CDS
TTGATCTACAAGCGCGGTTA+TGG	0.337108	6_2:-1405972	Msa0903960:CDS
TCAATTCTCTAACACTCTTC+AGG	0.373375	6_2:+1405991	None:intergenic
GTGTTCAATTGCAGGTTCTT+GGG	0.403327	6_2:-1405623	Msa0903960:intron
ACATCAATGAACTCATTAGA+AGG	0.462677	6_2:-1405425	Msa0903960:CDS
TGAAGTGAGGTCCAACAGTC+AGG	0.464367	6_2:+1405559	None:intergenic
AGATAACTCTATCATTGAAC+AGG	0.482014	6_2:-1405919	Msa0903960:intron
AAGAGAAATCACTATGTTGA+AGG	0.489111	6_2:-1405474	Msa0903960:CDS
AAAGGAGCTTTGAGCTTGAA+AGG	0.504831	6_2:+1405513	None:intergenic
GAGAGGCAAACAACTTCCTA+TGG	0.504947	6_2:-1405536	Msa0903960:CDS
TATGTTGAAGGTGGTGATGC+TGG	0.533299	6_2:-1405462	Msa0903960:CDS
TTGCAGGTTCTTGGGAAACA+TGG	0.547799	6_2:-1405615	Msa0903960:intron
GCGGTTATGGAAAGGTTGAT+AGG	0.549876	6_2:-1405959	Msa0903960:CDS
TTCTTCTTCATGCCACCCAA+AGG	0.554983	6_2:+1405495	None:intergenic
ATCCACGAGATCCTGACTGT+TGG	0.556683	6_2:-1405570	Msa0903960:CDS
AGGTGGTGATGCTGGTAAGA+GGG	0.564495	6_2:-1405454	Msa0903960:CDS
CTTTGAGCTTGAAAGGCCAT+AGG	0.568033	6_2:+1405520	None:intergenic
AAGCTCAAAGCTCCTTTGGG+TGG	0.570830	6_2:-1405507	Msa0903960:CDS
TTGTTTGCCTCTCTGAAGTG+AGG	0.573961	6_2:+1405546	None:intergenic
GTCCAACAGTCAGGATCTCG+TGG	0.575620	6_2:+1405568	None:intergenic
AAGGTGGTGATGCTGGTAAG+AGG	0.583947	6_2:-1405455	Msa0903960:CDS
CTACAAGCGCGGTTATGGAA+AGG	0.599869	6_2:-1405967	Msa0903960:CDS
TGGTGATGCTGGTAAGAGGG+AGG	0.608332	6_2:-1405451	Msa0903960:CDS
AGAAATCACTATGTTGAAGG+TGG	0.637998	6_2:-1405471	Msa0903960:CDS
AGAGAATTGATCTACAAGCG+CGG	0.721136	6_2:-1405978	Msa0903960:CDS
TGTTGGACCTCACTTCAGAG+AGG	0.737396	6_2:-1405553	Msa0903960:CDS

CRISPR-GE

badsite warning	sgRNA_sequence	Strand	Position	Region	GC_content
!!	GAAAAATAGAAAAATTTAAC+TGG	+	chr6_2:1405762-1405781	None:intergenic	15.0%
	AGATAACTCTATCATTGAAC+AGG	-	chr6_2:1405496-1405515	Msa0903960:CDS	30.0%
!!	GGTGCTATTATTATTGTTGA+AGG	-	chr6_2:1405728-1405747	Msa0903960:intron	30.0%
	AAGAGAAATCACTATGTTGA+AGG	-	chr6_2:1405941-1405960	Msa0903960:CDS	30.0%
	ACATCAATGAACTCATTAGA+AGG	-	chr6_2:1405990-1406009	Msa0903960:CDS	30.0%
	TCAATTCTCTAACACTCTTC+AGG	+	chr6_2:1405427-1405446	None:intergenic	35.0%
	TCTGAACTGTATGACATAGA+TGG	-	chr6_2:1405569-1405588	Msa0903960:CDS	35.0%
	CTGAACTGTATGACATAGAT+GGG	-	chr6_2:1405570-1405589	Msa0903960:CDS	35.0%
	AAATTGGGTAAAGTACAGAG+CGG	+	chr6_2:1405609-1405628	None:intergenic	35.0%
	CATTCTGACTTTGGCAAATT+GGG	+	chr6_2:1405624-1405643	None:intergenic	35.0%
	ACATTCTGACTTTGGCAAAT+TGG	+	chr6_2:1405625-1405644	None:intergenic	35.0%
	AACAACTCACATTCTGACTT+TGG	+	chr6_2:1405633-1405652	None:intergenic	35.0%
	AATAATAGCACCACCATACA+GGG	+	chr6_2:1405720-1405739	None:intergenic	35.0%
	TAATAATAGCACCACCATAC+AGG	+	chr6_2:1405721-1405740	None:intergenic	35.0%
	AGAAATCACTATGTTGAAGG+TGG	-	chr6_2:1405944-1405963	Msa0903960:CDS	35.0%
	AGAGAATTGATCTACAAGCG+CGG	-	chr6_2:1405437-1405456	Msa0903960:CDS	40.0%
	TGTGTGATCGAATGAAAGCA+GGG	+	chr6_2:1405541-1405560	None:intergenic	40.0%
	ATAATAGCACCACCATACAG+GGG	+	chr6_2:1405719-1405738	None:intergenic	40.0%
	CTGACATAGTGTTCAATTGC+AGG	-	chr6_2:1405784-1405803	Msa0903960:intron	40.0%
	AGTGTTCAATTGCAGGTTCT+TGG	-	chr6_2:1405791-1405810	Msa0903960:intron	40.0%
	GTGTTCAATTGCAGGTTCTT+GGG	-	chr6_2:1405792-1405811	Msa0903960:intron	40.0%
!!	AAAGGAGCTTTGAGCTTGAA+AGG	+	chr6_2:1405905-1405924	None:intergenic	40.0%
	TTTCAAGCTCAAAGCTCCTT+TGG	-	chr6_2:1405904-1405923	Msa0903960:intron	40.0%
	TTCAAGCTCAAAGCTCCTTT+GGG	-	chr6_2:1405905-1405924	Msa0903960:intron	40.0%
	TTGATCTACAAGCGCGGTTA+TGG	-	chr6_2:1405443-1405462	Msa0903960:CDS	45.0%
!	GCGGTTATGGAAAGGTTGAT+AGG	-	chr6_2:1405456-1405475	Msa0903960:CDS	45.0%
	CTGTGTGATCGAATGAAAGC+AGG	+	chr6_2:1405542-1405561	None:intergenic	45.0%
	TTGCAGGTTCTTGGGAAACA+TGG	-	chr6_2:1405800-1405819	Msa0903960:intron	45.0%
!!	TTGTTTGCCTCTCTGAAGTG+AGG	+	chr6_2:1405872-1405891	None:intergenic	45.0%
	GAGAGGCAAACAACTTCCTA+TGG	-	chr6_2:1405879-1405898	Msa0903960:intron	45.0%
	CTTTGAGCTTGAAAGGCCAT+AGG	+	chr6_2:1405898-1405917	None:intergenic	45.0%
	TTCTTCTTCATGCCACCCAA+AGG	+	chr6_2:1405923-1405942	None:intergenic	45.0%
!	TATGTTGAAGGTGGTGATGC+TGG	-	chr6_2:1405953-1405972	Msa0903960:CDS	45.0%
	CTACAAGCGCGGTTATGGAA+AGG	-	chr6_2:1405448-1405467	Msa0903960:CDS	50.0%
	CTTGACCAATGTCCCCTGTA+TGG	-	chr6_2:1405704-1405723	Msa0903960:intron	50.0%
	ATCCACGAGATCCTGACTGT+TGG	-	chr6_2:1405845-1405864	Msa0903960:intron	50.0%
	TGAAGTGAGGTCCAACAGTC+AGG	+	chr6_2:1405859-1405878	None:intergenic	50.0%
	TGTTGGACCTCACTTCAGAG+AGG	-	chr6_2:1405862-1405881	Msa0903960:intron	50.0%
	AAGCTCAAAGCTCCTTTGGG+TGG	-	chr6_2:1405908-1405927	Msa0903960:intron	50.0%
!	AAGGTGGTGATGCTGGTAAG+AGG	-	chr6_2:1405960-1405979	Msa0903960:CDS	50.0%
!	AGGTGGTGATGCTGGTAAGA+GGG	-	chr6_2:1405961-1405980	Msa0903960:CDS	50.0%
	GACCAATGTCCCCTGTATGG+TGG	-	chr6_2:1405707-1405726	Msa0903960:intron	55.0%
	CACCACCATACAGGGGACAT+TGG	+	chr6_2:1405712-1405731	None:intergenic	55.0%
	GTCCAACAGTCAGGATCTCG+TGG	+	chr6_2:1405850-1405869	None:intergenic	55.0%
!	TGGTGATGCTGGTAAGAGGG+AGG	-	chr6_2:1405964-1405983	Msa0903960:CDS	55.0%

Chromosome	Type	Strat	End	Strand	Name
chr6_2	gene	1405416	1406021	1405416	ID=Msa0903960;Name=Msa0903960
chr6_2	mRNA	1405416	1406021	1405416	ID=Msa0903960-mRNA-1;Parent=Msa0903960;Name=Msa0903960-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0\|0\|0\|0.5\|1\|1\|2\|0\|105
chr6_2	exon	1405920	1406021	1405920	ID=Msa0903960-mRNA-1:exon:559;Parent=Msa0903960-mRNA-1
chr6_2	exon	1405416	1405631	1405416	ID=Msa0903960-mRNA-1:exon:558;Parent=Msa0903960-mRNA-1
chr6_2	CDS	1405920	1406021	1405920	ID=Msa0903960-mRNA-1:cds;Parent=Msa0903960-mRNA-1
chr6_2	CDS	1405416	1405631	1405416	ID=Msa0903960-mRNA-1:cds;Parent=Msa0903960-mRNA-1

Gene Sequence	>Msa0903960 ATGTTGATCCTGAAGAGTGTTAGAGAATTGATCTACAAGCGCGGTTATGGAAAGGTTGATAGGCAGAGAATTGCTTTGACAGATAACTCTATCATTGAACAGGTTCTTGGGAAACATGGTATCATTTGCGTTGAAGATCTCATCCACGAGATCCTGACTGTTGGACCTCACTTCAGAGAGGCAAACAACTTCCTATGGCCTTTCAAGCTCAAAGCTCCTTTGGGTGGCATGAAGAAGAAGAGAAATCACTATGTTGAAGGTGGTGATGCTGGTAAGAGGGAGGATTACATCAATGAACTCATTAGAAGGATGAATTAG
Protein sequence	>Msa0903960 MLILKSVRELIYKRGYGKVDRQRIALTDNSIIEQVLGKHGIICVEDLIHEILTVGPHFREANNFLWPFKLKAPLGGMKKKRNHYVEGGDAGKREDYINELIRRMN*