AlfalfaGEDB | Msa0661840

M. sativa cultivar zhongmu-4 / Msa0661840

KEGG: -
GO: -
PFAM: PF00249.34

Nr:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0661840	XP_024633411.1	100.000	81	0	0	1	81	1	81	1.75e-52	169

Swissprot:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0661840	sp\|Q1A173\|RADL6_ARATH	67.500	80	22	1	1	80	1	76	4.92e-34	115

Trembl:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0661840	G7J732	100.000	81	0	0	1	81	1	81	8.38e-53	169

TFs/TRs:

Gene ID	Type	Classification
Msa0661840	TF	MYB-related

Protein Kinases:

Gene ID	Type	Classification

Network:

Co-expression Network

Gene1	Gene2	correlation coefficient	p_value	FDR
Msa0661840	Msa1418060	0.928767	1.811490e-92	-8.615850e-47
Msa0386790	Msa0661840	0.921148	5.188168e-88	-8.615850e-47
Msa0523830	Msa0661840	0.951270	2.909994e-109	-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
Msa0661840	MtrunA17_Chr3g0144631	100.000	81	0	0	1	81	1	81	1.61e-56	169
Msa0661840	MtrunA17_Chr1g0155181	71.014	69	20	0	14	82	5	73	1.80e-34	113
Msa0661840	MtrunA17_Chr3g0141601	69.565	69	21	0	14	82	5	73	7.05e-32	107
Msa0661840	MtrunA17_Chr7g0255841	72.308	65	18	0	19	83	15	79	1.70e-30	103
Msa0661840	MtrunA17_Chr3g0081631	62.963	81	23	2	1	80	1	75	6.13e-29	99.8
Msa0661840	MtrunA17_Chr8g0373131	62.687	67	24	1	16	82	5	70	2.39e-27	95.1
Msa0661840	MtrunA17_Chr8g0373111	62.687	67	24	1	16	82	5	70	2.43e-27	95.1
Msa0661840	MtrunA17_Chr8g0373121	62.687	67	24	1	16	82	5	70	2.43e-27	95.1
Msa0661840	MtrunA17_Chr5g0404101	60.938	64	25	0	16	79	19	82	7.98e-26	92.0
Msa0661840	MtrunA17_Chr6g0449111	60.000	65	26	0	14	78	8	72	1.71e-25	90.5
Msa0661840	MtrunA17_Chr5g0404301	68.852	61	18	1	16	76	4	63	2.05e-25	89.7
Msa0661840	MtrunA17_Chr8g0373101	63.492	63	22	1	14	76	3	64	3.83e-25	89.4
Msa0661840	MtrunA17_Chr3g0141641	52.239	67	32	0	16	82	3	69	8.41e-22	81.6
Msa0661840	MtrunA17_Chr8g0364741	45.122	82	39	1	16	91	10	91	2.68e-21	81.3
Msa0661840	MtrunA17_Chr5g0429521	53.623	69	32	0	16	84	29	97	6.49e-21	84.3
Msa0661840	MtrunA17_Chr8g0365011	52.239	67	32	0	14	80	6	72	2.33e-20	82.4
Msa0661840	MtrunA17_Chr3g0104071	56.522	69	30	0	16	84	43	111	1.56e-19	80.5
Msa0661840	MtrunA17_Chr7g0241761	50.000	70	35	0	14	83	33	102	2.66e-18	77.0
Msa0661840	MtrunA17_Chr5g0436501	50.000	68	34	0	16	83	27	94	4.44e-18	76.3
Msa0661840	MtrunA17_Chr1g0162081	45.455	77	42	0	14	90	10	86	8.36e-18	75.9
Msa0661840	MtrunA17_Chr7g0270711	50.000	80	33	2	16	88	11	90	1.69e-16	68.2
Msa0661840	MtrunA17_Chr1g0194071	59.649	57	22	1	16	71	11	67	7.93e-16	66.6
Msa0661840	MtrunA17_Chr1g0210471	47.619	63	33	0	16	78	24	86	1.14e-15	69.3
Msa0661840	MtrunA17_Chr4g0062741	40.000	70	39	1	12	78	4	73	2.70e-13	63.5

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0661840	AT1G75250.1	67.500	80	22	1	1	80	1	76	3.36e-35	117
Msa0661840	AT1G75250.2	67.500	80	22	1	1	80	1	76	5.01e-35	115
Msa0661840	AT4G39250.1	69.697	66	20	0	16	81	14	79	1.46e-33	112
Msa0661840	AT2G21650.1	65.672	67	23	0	16	82	14	80	2.14e-30	103
Msa0661840	AT1G19510.1	71.429	63	18	0	19	81	15	77	1.68e-29	101
Msa0661840	AT2G18328.1	69.841	63	19	0	19	81	14	76	9.69e-29	99.0
Msa0661840	AT4G36570.1	77.273	44	10	0	16	59	12	55	3.13e-21	79.3
Msa0661840	AT5G05790.2	52.941	68	32	0	14	81	29	96	6.05e-18	76.3
Msa0661840	AT5G05790.1	52.941	68	32	0	14	81	29	96	6.05e-18	76.3
Msa0661840	AT2G38090.1	53.846	65	30	0	16	80	29	93	1.46e-17	75.5
Msa0661840	AT5G58900.1	49.231	65	33	0	14	78	32	96	2.53e-17	74.7
Msa0661840	AT3G11280.2	47.826	69	36	0	16	84	33	101	4.83e-17	73.6
Msa0661840	AT3G11280.1	47.826	69	36	0	16	84	33	101	4.83e-17	73.6
Msa0661840	AT5G08520.1	49.254	67	34	0	14	80	10	76	3.80e-16	71.6
Msa0661840	AT5G04760.1	41.791	67	38	1	12	78	2	67	3.23e-13	62.8
Msa0661840	AT1G49010.1	42.647	68	36	1	14	78	6	73	1.58e-12	61.6
Msa0661840	AT5G01200.1	43.284	67	37	1	13	78	27	93	3.84e-12	60.5
Msa0661840	AT5G23650.1	39.189	74	45	0	5	78	2	75	3.52e-11	58.2

Find 23 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE

CRISPR-Local

CRISPR-Local
sgRNA_sequence	on_target_score	Position	Region
CTTCACGTGGATTTGTAATT+TGG	0.099924	4_3:+73402166	None:intergenic
ACAAGCCTTGTGATTCAATT+TGG	0.187124	4_3:-73402366	Msa0661840:CDS
TCAAAATTACAAAATCTGAT+AGG	0.347322	4_3:+73401892	None:intergenic
GTGGATTTGTAATTTGGAAT+AGG	0.364725	4_3:+73402172	None:intergenic
CTTATATAGATGCTTGCCTC+AGG	0.419615	4_3:-73401983	Msa0661840:intron
AGCACTTGCAAAATTTGATA+AGG	0.422428	4_3:-73402314	Msa0661840:CDS
CTGAAGTATCTAAAGTTGAA+TGG	0.424280	4_3:-73401957	Msa0661840:CDS
CAAAATTACAAAATCTGATA+GGG	0.464530	4_3:+73401893	None:intergenic
CACAAGGCTTGTGTTTGCTA+AGG	0.474591	4_3:+73402377	None:intergenic
GATCTCAAACACATTGAGTC+TGG	0.498892	4_3:-73402202	Msa0661840:CDS
AGACAGATGGAGGAACAAAC+AGG	0.503947	4_3:+73401916	None:intergenic
GAGACACTATGAGCTACTCT+TGG	0.504426	4_3:-73402227	Msa0661840:CDS
ACAAGGCTTGTGTTTGCTAA+GGG	0.544579	4_3:+73402378	None:intergenic
ACACTATGAGCTACTCTTGG+AGG	0.567606	4_3:-73402224	Msa0661840:CDS
GTGTTTGCTAAGGGAACTTG+AGG	0.586339	4_3:+73402387	None:intergenic
AATGTAGCAAAAGCAGTTGG+TGG	0.597235	4_3:-73402271	Msa0661840:CDS
CAAAATGTAGCAAAAGCAGT+TGG	0.599555	4_3:-73402274	Msa0661840:CDS
GGAGTCCAAATTGAATCACA+AGG	0.603739	4_3:+73402361	None:intergenic
ATAAGGATACCCCTGACCGT+TGG	0.605106	4_3:-73402297	Msa0661840:CDS
AAATCTGATAGGGAGACAGA+TGG	0.611076	4_3:+73401903	None:intergenic
AGTTGGTGGTAAATCAGTTG+AGG	0.635333	4_3:-73402257	Msa0661840:CDS
TTAGATACTTCAGAAGCCTG+AGG	0.659984	4_3:+73401967	None:intergenic
TCTGATAGGGAGACAGATGG+AGG	0.662436	4_3:+73401906	None:intergenic

CRISPR-GE

badsite warning	sgRNA_sequence	Strand	Position	Region	GC_content
!!	AAAGAAAAAAAAATATCATA+AGG	-	chr4_3:73402174-73402193	Msa0661840:CDS	10.0%
!!!	TCAAACAACTTGTTTTGTTT+TGG	+	chr4_3:73401955-73401974	None:intergenic	25.0%
!	GAAACATGAACAAAAAATAG+TGG	+	chr4_3:73402245-73402264	None:intergenic	25.0%
	AGCACTTGCAAAATTTGATA+AGG	-	chr4_3:73401978-73401997	Msa0661840:intron	30.0%
!	GTGGATTTGTAATTTGGAAT+AGG	+	chr4_3:73402123-73402142	None:intergenic	30.0%
	ATGAACAAAAAATAGTGGCA+TGG	+	chr4_3:73402240-73402259	None:intergenic	30.0%
!	CTGAAGTATCTAAAGTTGAA+TGG	-	chr4_3:73402335-73402354	Msa0661840:CDS	30.0%
!	ACAAGCCTTGTGATTCAATT+TGG	-	chr4_3:73401926-73401945	Msa0661840:three_prime_UTR	35.0%
!	CTTTTGCTACATTTTGCCAA+CGG	+	chr4_3:73402014-73402033	None:intergenic	35.0%
	CAAAATGTAGCAAAAGCAGT+TGG	-	chr4_3:73402018-73402037	Msa0661840:intron	35.0%
	CTTCACGTGGATTTGTAATT+TGG	+	chr4_3:73402129-73402148	None:intergenic	35.0%
	TAGTGGCATGGTACATAATT+TGG	+	chr4_3:73402228-73402247	None:intergenic	35.0%
!	ACAAGGCTTGTGTTTGCTAA+GGG	+	chr4_3:73401917-73401936	None:intergenic	40.0%
	GGAGTCCAAATTGAATCACA+AGG	+	chr4_3:73401934-73401953	None:intergenic	40.0%
	AATGTAGCAAAAGCAGTTGG+TGG	-	chr4_3:73402021-73402040	Msa0661840:intron	40.0%
!!	AGTTGGTGGTAAATCAGTTG+AGG	-	chr4_3:73402035-73402054	Msa0661840:intron	40.0%
	GATCTCAAACACATTGAGTC+TGG	-	chr4_3:73402090-73402109	Msa0661840:intron	40.0%
!!	CTAATTTGCTACACTTCACG+TGG	+	chr4_3:73402142-73402161	None:intergenic	40.0%
	CTTATATAGATGCTTGCCTC+AGG	-	chr4_3:73402309-73402328	Msa0661840:CDS	40.0%
	TTAGATACTTCAGAAGCCTG+AGG	+	chr4_3:73402328-73402347	None:intergenic	40.0%
	AAATCTGATAGGGAGACAGA+TGG	+	chr4_3:73402392-73402411	None:intergenic	40.0%
!	GTGTTTGCTAAGGGAACTTG+AGG	+	chr4_3:73401908-73401927	None:intergenic	45.0%
!	CACAAGGCTTGTGTTTGCTA+AGG	+	chr4_3:73401918-73401937	None:intergenic	45.0%
!	TACATTTTGCCAACGGTCAG+GGG	+	chr4_3:73402007-73402026	None:intergenic	45.0%
!	CTACATTTTGCCAACGGTCA+GGG	+	chr4_3:73402008-73402027	None:intergenic	45.0%
	GAGACACTATGAGCTACTCT+TGG	-	chr4_3:73402065-73402084	Msa0661840:intron	45.0%
	ACACTATGAGCTACTCTTGG+AGG	-	chr4_3:73402068-73402087	Msa0661840:intron	45.0%
	AGACAGATGGAGGAACAAAC+AGG	+	chr4_3:73402379-73402398	None:intergenic	45.0%
	ATAAGGATACCCCTGACCGT+TGG	-	chr4_3:73401995-73402014	Msa0661840:intron	50.0%
!	GCTACATTTTGCCAACGGTC+AGG	+	chr4_3:73402009-73402028	None:intergenic	50.0%
	TCTGATAGGGAGACAGATGG+AGG	+	chr4_3:73402389-73402408	None:intergenic	50.0%

Chromosome	Type	Strat	End	Strand	Name
chr4_3	gene	73401901	73402413	73401901	ID=Msa0661840;Name=Msa0661840
chr4_3	mRNA	73401901	73402413	73401901	ID=Msa0661840-mRNA-1;Parent=Msa0661840;Name=Msa0661840-mRNA-1;_AED=0.16;_eAED=0.16;_QI=0\|0\|0.5\|1\|1\|1\|2\|50\|95
chr4_3	exon	73401901	73401996	73401901	ID=Msa0661840-mRNA-1:exon:22191;Parent=Msa0661840-mRNA-1
chr4_3	exon	73402172	73402413	73402172	ID=Msa0661840-mRNA-1:exon:22190;Parent=Msa0661840-mRNA-1
chr4_3	CDS	73402172	73402413	73402172	ID=Msa0661840-mRNA-1:cds;Parent=Msa0661840-mRNA-1
chr4_3	CDS	73401951	73401996	73401951	ID=Msa0661840-mRNA-1:cds;Parent=Msa0661840-mRNA-1
chr4_3	three_prime_UTR	73401901	73401950	73401901	ID=Msa0661840-mRNA-1:three_prime_utr;Parent=Msa0661840-mRNA-1

Gene Sequence	>Msa0661840 ATGGCCTCAAGTTCCCTTAGCAAACACAAGCCTTGTGATTCAATTTGGACTCCAAAACAAAACAAGTTGTTTGAAAAAGCACTTGCAAAATTTGATAAGGATACCCCTGACCGTTGGCAAAATGTAGCAAAAGCAGTTGGTGGTAAATCAGTTGAGGAAGTTAAGAGACACTATGAGCTACTCTTGGAGGATCTCAAACACATTGAGTCTGGTCATGTTCCTATTCCAAATTACAAATCCACATGCTTGCCTCAGGCTTCTGAAGTATCTAAAGTTGAATGGATTTGA
Protein sequence	>Msa0661840 MASSSLSKHKPCDSIWTPKQNKLFEKALAKFDKDTPDRWQNVAKAVGGKSVEEVKRHYELLLEDLKHIESGHVPIPNYKSTCLPQASEVSKVEWI*