AlfalfaGEDB | Msa0078280

M. sativa cultivar zhongmu-4 / Msa0078280

KEGG: -
GO: GO:0003674 GO:0003676 GO:0003677 GO:0003700 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006355 GO:0008150 GO:0009889 GO:0010468 GO:0010556 GO:0019219 GO:0019222 GO:0031323 GO:0031326 GO:0043076 GO:0043078 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043565 GO:0044424 GO:0044464 GO:0050789 GO:0050794 GO:0051171 GO:0051252 GO:0060255 GO:0065007 GO:0080090 GO:0097159 GO:0140110 GO:1901363 GO:1903506 GO:2000112 GO:2001141
PFAM: PF00319.21

Nr:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0078280	XP_013468828.1	89.172	157	17	0	1	157	1	157	3.84e-87	261

Swissprot:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0078280	sp\|Q9FJK3\|AGL80_ARATH	45.161	155	78	3	1	150	1	153	2.68e-29	112

Trembl:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0078280	A0A072VXU8	89.172	157	17	0	1	157	1	157	1.83e-87	261

TFs/TRs:

Gene ID	Type	Classification
Msa0078280	TF	MADS-M-type

Protein Kinases:

Gene ID	Type	Classification

Network:

Co-expression Network

Gene1	Gene2	correlation coefficient	p_value	FDR

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
Msa0078280	MtrunA17_Chr1g0188651	89.172	157	17	0	1	157	1	157	3.53e-91	261
Msa0078280	MtrunA17_Chr1g0188661	77.987	159	33	1	1	157	1	159	5.85e-82	238
Msa0078280	MtrunA17_Chr4g0012761	77.358	159	34	1	1	157	1	159	1.71e-79	232
Msa0078280	MtrunA17_Chr7g0218151	76.730	159	35	1	1	157	1	159	1.13e-78	230
Msa0078280	MtrunA17_Chr1g0193311	78.205	156	32	1	1	154	1	156	2.49e-75	221
Msa0078280	MtrunA17_Chr5g0420351	71.795	156	42	1	1	154	1	156	6.90e-75	220
Msa0078280	MtrunA17_Chr1g0188681	70.064	157	45	1	1	155	1	157	9.08e-75	220
Msa0078280	MtrunA17_Chr1g0197261	55.769	156	67	1	1	154	1	156	5.63e-56	172
Msa0078280	MtrunA17_Chr1g0197461	57.143	154	64	1	2	153	1	154	1.12e-55	172
Msa0078280	MtrunA17_Chr1g0197321	52.229	157	72	1	1	154	1	157	7.15e-53	165
Msa0078280	MtrunA17_Chr5g0432691	37.821	156	94	2	1	153	1	156	2.49e-35	120
Msa0078280	MtrunA17_Chr3g0107381	41.830	153	86	2	1	150	1	153	8.50e-35	120
Msa0078280	MtrunA17_Chr4g0014321	37.013	154	93	2	1	150	1	154	6.60e-34	119
Msa0078280	MtrunA17_Chr3g0110131	43.949	157	85	2	1	154	1	157	3.15e-32	115
Msa0078280	MtrunA17_Chr3g0107331	41.772	158	89	2	2	156	1	158	1.01e-31	111
Msa0078280	MtrunA17_Chr4g0013041	37.342	158	87	4	1	151	1	153	3.43e-31	111
Msa0078280	MtrunA17_Chr3g0107461	36.646	161	98	2	1	157	1	161	3.23e-30	107
Msa0078280	MtrunA17_Chr3g0107351	40.252	159	92	2	2	157	1	159	4.93e-30	107
Msa0078280	MtrunA17_Chr3g0107361	39.623	159	93	2	2	157	1	159	1.33e-29	105
Msa0078280	MtrunA17_Chr8g0351751	38.125	160	93	2	1	154	1	160	3.83e-29	107
Msa0078280	MtrunA17_Chr4g0014031	39.130	161	94	2	1	157	1	161	6.29e-29	106
Msa0078280	MtrunA17_Chr4g0014131	39.130	161	94	2	1	157	1	161	3.36e-27	101
Msa0078280	MtrunA17_Chr3g0107341	37.107	159	97	2	2	157	1	159	9.53e-27	98.6
Msa0078280	MtrunA17_Chr2g0283941	37.013	154	93	2	1	150	1	154	1.32e-26	100
Msa0078280	MtrunA17_Chr4g0014121	38.509	161	93	3	1	156	29	188	9.15e-26	97.1
Msa0078280	MtrunA17_Chr2g0296831	43.478	115	64	1	1	114	1	115	2.08e-25	94.0
Msa0078280	MtrunA17_Chr3g0105791	36.090	133	81	2	29	157	1	133	2.51e-22	86.7
Msa0078280	MtrunA17_Chr4g0031421	36.090	133	81	2	29	157	1	133	2.91e-22	86.7
Msa0078280	MtrunA17_Chr2g0296861	37.013	154	92	3	1	150	1	153	2.81e-20	82.0
Msa0078280	MtrunA17_Chr4g0008701	33.600	125	78	2	3	126	6	126	4.05e-20	85.9
Msa0078280	MtrunA17_Chr7g0267601	36.111	108	68	1	3	109	6	113	3.18e-19	83.2
Msa0078280	MtrunA17_Chr3g0106501	34.351	131	82	2	29	155	1	131	7.53e-19	78.2
Msa0078280	MtrunA17_Chr3g0106421	34.921	126	78	3	29	150	1	126	1.27e-18	79.0
Msa0078280	MtrunA17_Chr3g0128721	31.579	133	83	3	3	132	6	133	3.03e-15	72.0
Msa0078280	MtrunA17_Chr1g0162261	41.000	100	54	2	62	157	20	118	1.33e-14	66.2
Msa0078280	MtrunA17_Chr1g0162181	41.414	99	55	1	62	157	20	118	1.42e-14	66.2
Msa0078280	MtrunA17_Chr1g0161931	39.362	94	54	1	64	154	28	121	2.73e-14	65.5
Msa0078280	MtrunA17_Chr6g0449861	30.357	112	72	3	1	106	9	120	8.38e-11	58.9

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0078280	AT5G48670.1	45.161	155	78	3	1	150	1	153	2.72e-30	112
Msa0078280	AT3G05860.2	40.909	132	77	1	1	131	1	132	4.08e-30	108
Msa0078280	AT3G05860.3	46.018	113	60	1	1	112	1	113	1.60e-29	108
Msa0078280	AT3G05860.1	46.018	113	60	1	1	112	1	113	1.98e-29	108
Msa0078280	AT5G26630.1	41.176	153	87	2	1	150	1	153	2.30e-29	107
Msa0078280	AT1G65330.1	39.189	148	87	2	2	146	1	148	3.69e-28	105
Msa0078280	AT1G65300.1	36.184	152	94	2	2	150	1	152	7.52e-28	104
Msa0078280	AT5G26650.1	40.260	154	81	4	4	150	2	151	2.09e-26	102
Msa0078280	AT5G27960.1	46.729	107	56	1	4	109	2	108	2.76e-25	99.0
Msa0078280	AT1G22590.2	35.976	164	83	4	1	153	1	153	9.20e-24	91.3
Msa0078280	AT1G31630.1	31.847	157	99	4	2	153	1	154	3.26e-23	93.6
Msa0078280	AT1G31640.1	41.964	112	63	2	2	112	1	111	3.46e-21	89.4
Msa0078280	AT2G28700.1	36.885	122	73	2	1	118	1	122	6.06e-21	87.4
Msa0078280	AT5G27810.1	42.000	100	53	3	29	123	1	100	5.39e-19	77.8
Msa0078280	AT5G26580.1	40.367	109	52	1	1	109	1	96	5.41e-18	79.3
Msa0078280	AT2G40210.1	37.864	103	59	2	1	100	1	101	1.03e-11	62.0

Find 21 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE

CRISPR-Local

CRISPR-Local
sgRNA_sequence	on_target_score	Position	Region
GAGCTAAATATTCGTATAAT+TGG	0.249166	1_2:+55669383	Msa0078280:CDS
GCTGCAAGAGAAAAGTTTCT+TGG	0.265401	1_2:-55669304	None:intergenic
CTCCTTTCTTCTTGAAGCAT+TGG	0.353516	1_2:-55669087	None:intergenic
TCTGAAACAGTCAAATCATC+TGG	0.455315	1_2:-55669422	None:intergenic
CTCCAATGCTTCAAGAAGAA+AGG	0.468651	1_2:+55669085	Msa0078280:CDS
CAAGGCCATGGTTCGGAAGA+AGG	0.471800	1_2:+55669046	None:intergenic
TACATTGCAAGGCCATGGTT+CGG	0.507534	1_2:+55669039	None:intergenic
GACATACAGAAAGAGAAAGA+AGG	0.512113	1_2:+55669109	Msa0078280:CDS
AGAGAACTCACTATTCTTTG+TGG	0.526508	1_2:+55669149	Msa0078280:CDS
ACATACAGAAAGAGAAAGAA+GGG	0.541098	1_2:+55669110	Msa0078280:CDS
TGCAGCAGATTACTAAAGCT+AGG	0.546331	1_2:+55669321	Msa0078280:CDS
AAACAGTCAAATCATCTGGC+AGG	0.548613	1_2:-55669418	None:intergenic
AGGATCGGAAATTATAGCAC+AGG	0.559456	1_2:-55669180	None:intergenic
AGAGGTGTGGCCAAATCTGA+AGG	0.570010	1_2:+55669217	Msa0078280:CDS
TCGGAAATTATAGCACAGGC+TGG	0.570119	1_2:-55669176	None:intergenic
AAAGAAGGGTATCATCAAGA+AGG	0.577075	1_2:+55669124	Msa0078280:CDS
CTTCACCTTCTTCCGAACCA+TGG	0.581108	1_2:-55669051	None:intergenic
GCAGCAGATTACTAAAGCTA+GGG	0.592338	1_2:+55669322	Msa0078280:CDS
AAGCAAAACAAGTGATTGAG+AGG	0.592587	1_2:+55669240	Msa0078280:CDS
GAAACAAGACAATCGTGAGA+AGG	0.628912	1_2:+55669361	Msa0078280:CDS
TTGATTCTAAAACAGAGGTG+TGG	0.633348	1_2:+55669204	Msa0078280:CDS

CRISPR-GE

badsite warning	sgRNA_sequence	Strand	Position	Region	GC_content
!!	GATAATTGAGAAAAATATGA+AGG	+	chr1_2:55669463-55669482	Msa0078280:CDS	20.0%
!!!	TGTTTTAGAATCAAAAGGAT+CGG	-	chr1_2:55669198-55669217	None:intergenic	25.0%
!	GAGCTAAATATTCGTATAAT+TGG	+	chr1_2:55669383-55669402	Msa0078280:CDS	25.0%
	ACATACAGAAAGAGAAAGAA+GGG	+	chr1_2:55669110-55669129	Msa0078280:CDS	30.0%
!!!	TCCTTTTGATTCTAAAACAG+AGG	+	chr1_2:55669199-55669218	Msa0078280:CDS	30.0%
!!!	ACCTCTGTTTTAGAATCAAA+AGG	-	chr1_2:55669203-55669222	None:intergenic	30.0%
	GACATACAGAAAGAGAAAGA+AGG	+	chr1_2:55669109-55669128	Msa0078280:CDS	35.0%
!!	AAAGAAGGGTATCATCAAGA+AGG	+	chr1_2:55669124-55669143	Msa0078280:CDS	35.0%
	AGAGAACTCACTATTCTTTG+TGG	+	chr1_2:55669149-55669168	Msa0078280:CDS	35.0%
!!	TTGATTCTAAAACAGAGGTG+TGG	+	chr1_2:55669204-55669223	Msa0078280:CDS	35.0%
!	TGTTTTGCTTCCTTCAGATT+TGG	-	chr1_2:55669230-55669249	None:intergenic	35.0%
	AAGCAAAACAAGTGATTGAG+AGG	+	chr1_2:55669240-55669259	Msa0078280:CDS	35.0%
!	TCTGAAACAGTCAAATCATC+TGG	-	chr1_2:55669425-55669444	None:intergenic	35.0%
	CTCCAATGCTTCAAGAAGAA+AGG	+	chr1_2:55669085-55669104	Msa0078280:CDS	40.0%
	CTCCTTTCTTCTTGAAGCAT+TGG	-	chr1_2:55669090-55669109	None:intergenic	40.0%
	AGGATCGGAAATTATAGCAC+AGG	-	chr1_2:55669183-55669202	None:intergenic	40.0%
	GCTGCAAGAGAAAAGTTTCT+TGG	-	chr1_2:55669307-55669326	None:intergenic	40.0%
	TGCAGCAGATTACTAAAGCT+AGG	+	chr1_2:55669321-55669340	Msa0078280:CDS	40.0%
	GCAGCAGATTACTAAAGCTA+GGG	+	chr1_2:55669322-55669341	Msa0078280:CDS	40.0%
	GAAACAAGACAATCGTGAGA+AGG	+	chr1_2:55669361-55669380	Msa0078280:CDS	40.0%
	AAACAGTCAAATCATCTGGC+AGG	-	chr1_2:55669421-55669440	None:intergenic	40.0%
	TCGGAAATTATAGCACAGGC+TGG	-	chr1_2:55669179-55669198	None:intergenic	45.0%
!	AGAGGTGTGGCCAAATCTGA+AGG	+	chr1_2:55669217-55669236	Msa0078280:CDS	50.0%

Chromosome	Type	Strat	End	Strand	Name
chr1_2	gene	55669053	55669526	55669053	ID=Msa0078280;Name=Msa0078280
chr1_2	mRNA	55669053	55669526	55669053	ID=Msa0078280-mRNA-1;Parent=Msa0078280;Name=Msa0078280-mRNA-1;_AED=0.22;_eAED=0.22;_QI=0\|-1\|0\|1\|-1\|1\|1\|0\|157
chr1_2	exon	55669053	55669526	55669053	ID=Msa0078280-mRNA-1:exon:17336;Parent=Msa0078280-mRNA-1
chr1_2	CDS	55669053	55669526	55669053	ID=Msa0078280-mRNA-1:cds;Parent=Msa0078280-mRNA-1

Gene Sequence

>Msa0078280

ATGGTTCGGAAGAAGGTGAAGCTTGCTTTTATCTCCAATGCTTCAAGAAGAAAGGAGACATACAGAAAGAGAAAGAAGGGTATCATCAAGAAGGTGAGAGAACTCACTATTCTTTGTGGTATTCCAGCCTGTGCTATAATTTCCGATCCTTTTGATTCTAAAACAGAGGTGTGGCCAAATCTGAAGGAAGCAAAACAAGTGATTGAGAGGTATCAGAACTCATATATGAAAGATGATAAAAAGAATGTGAACCAAGAAACTTTTCTCTTGCAGCAGATTACTAAAGCTAGGGAACAACTGAAAAAGCTGAAACAAGACAATCGTGAGAAGGAGCTAAATATTCGTATAATTGGATACATGCAAAACCTGCCAGATGATTTGACTGTTTCAGATTTGAAAGAACTTGATACGATAATTGAGAAAAATATGAAGGAAATTGATGAAAAGATTGTCGCACTCAATTTATCAGATTGA

Protein sequence

>Msa0078280

MVRKKVKLAFISNASRRKETYRKRKKGIIKKVRELTILCGIPACAIISDPFDSKTEVWPNLKEAKQVIERYQNSYMKDDKKNVNQETFLLQQITKAREQLKKLKQDNREKELNIRIIGYMQNLPDDLTVSDLKELDTIIEKNMKEIDEKIVALNLSD*