AlfalfaGEDB | Msa0289620

M. sativa cultivar zhongmu-4 / Msa0289620

KEGG: K15083|K15173
GO: GO:0000228 GO:0000278 GO:0000724 GO:0000725 GO:0000785 GO:0000790 GO:0003674 GO:0003678 GO:0003824 GO:0004003 GO:0004386 GO:0004842 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005694 GO:0005737 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006281 GO:0006302 GO:0006310 GO:0006464 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0006996 GO:0007049 GO:0007154 GO:0008026 GO:0008094 GO:0008150 GO:0008152 GO:0008270 GO:0009058 GO:0009059 GO:0009605 GO:0009892 GO:0009894 GO:0009895 GO:0009987 GO:0009991 GO:0010605 GO:0016043 GO:0016462 GO:0016567 GO:0016740 GO:0016787 GO:0016817 GO:0016818 GO:0016887 GO:0017111 GO:0019222 GO:0019538 GO:0019787 GO:0022402 GO:0030162 GO:0031323 GO:0031324 GO:0031329 GO:0031330 GO:0031668 GO:0031974 GO:0031981 GO:0032268 GO:0032269 GO:0032392 GO:0032434 GO:0032435 GO:0032446 GO:0032508 GO:0033260 GO:0033554 GO:0034641 GO:0034645 GO:0036211 GO:0042176 GO:0042177 GO:0042262 GO:0042623 GO:0043167 GO:0043169 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043412 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044454 GO:0044464 GO:0044786 GO:0045005 GO:0045861 GO:0046483 GO:0046872 GO:0046914 GO:0048519 GO:0048523 GO:0050789 GO:0050794 GO:0050896 GO:0051171 GO:0051172 GO:0051246 GO:0051248 GO:0051276 GO:0051716 GO:0060255 GO:0061136 GO:0061630 GO:0061659 GO:0065007 GO:0070013 GO:0070035 GO:0070647 GO:0071103 GO:0071496 GO:0071704 GO:0071840 GO:0080090 GO:0090304 GO:0140083 GO:0140096 GO:0140097 GO:1901360 GO:1901564 GO:1901576 GO:1901799 GO:1902298 GO:1902969 GO:1903047 GO:1903050 GO:1903051 GO:1903362 GO:1903363 GO:1990505 GO:2000058 GO:2000059
PFAM: PF00176.26

Nr:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0289620	XP_013470409.1	99.074	108	1	0	2	109	295	402	1.62e-64	221

Swissprot:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0289620	sp\|Q94BR5\|CHR28_ARATH	52.632	114	47	3	2	109	231	343	9.42e-25	100

Trembl:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0289620	A0A072VRQ7	99.074	108	1	0	2	109	295	402	7.72e-65	221

TFs/TRs:

Gene ID	Type	Classification
Msa0289620	TR	SNF2

Protein Kinases:

Gene ID	Type	Classification

Network:

Co-expression Network

Gene1	Gene2	correlation coefficient	p_value	FDR
Msa0289620	Msa0484780	0.801772	7.691212e-49	-8.615850e-47
Msa0289620	Msa1172670	0.800352	1.500542e-48	-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
Msa0289620	MtrunA17_Chr1g0212331	99.074	108	1	0	2	109	295	402	1.49e-68	221
Msa0289620	MtrunA17_Chr2g0281601	41.818	110	56	3	2	109	559	662	1.74e-17	76.3

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0289620	AT1G50410.4	52.632	114	47	3	2	109	231	343	8.80e-26	100
Msa0289620	AT1G50410.2	52.632	114	47	3	2	109	231	343	9.58e-26	100
Msa0289620	AT1G50410.1	52.632	114	47	3	2	109	231	343	9.58e-26	100
Msa0289620	AT1G50410.3	52.632	114	47	3	2	109	231	343	9.58e-26	100
Msa0289620	AT3G20010.3	47.328	131	44	6	2	109	20	148	7.05e-19	80.9
Msa0289620	AT3G20010.1	61.429	70	24	2	2	70	286	353	1.13e-18	80.1
Msa0289620	AT3G20010.5	61.429	70	24	2	2	70	286	353	1.13e-18	80.1
Msa0289620	AT3G20010.7	61.429	70	24	2	2	70	286	353	1.13e-18	80.1
Msa0289620	AT3G20010.4	45.038	131	47	4	2	109	286	414	1.23e-17	77.4
Msa0289620	AT3G20010.6	45.038	131	47	4	2	109	286	414	1.23e-17	77.4
Msa0289620	AT3G20010.8	45.038	131	47	4	2	109	286	414	1.23e-17	77.4
Msa0289620	AT3G16600.1	66.071	56	18	1	2	56	58	113	7.36e-16	72.0
Msa0289620	AT3G20010.2	44.800	125	44	6	8	109	1	123	2.31e-14	67.8
Msa0289620	AT1G11100.5	56.364	55	24	0	2	56	404	458	7.24e-13	63.5
Msa0289620	AT1G11100.1	56.364	55	24	0	2	56	547	601	8.19e-13	63.5
Msa0289620	AT1G11100.3	56.364	55	24	0	2	56	404	458	8.81e-13	63.5
Msa0289620	AT1G11100.4	56.364	55	24	0	2	56	547	601	9.77e-13	63.2
Msa0289620	AT1G11100.2	56.364	55	24	0	2	56	546	600	9.86e-13	63.2
Msa0289620	AT1G61140.2	69.048	42	13	0	2	43	568	609	1.75e-12	62.4
Msa0289620	AT1G61140.3	69.048	42	13	0	2	43	403	444	2.57e-12	62.0
Msa0289620	AT1G61140.1	69.048	42	13	0	2	43	561	602	3.96e-12	61.6

Find 32 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE

CRISPR-Local

CRISPR-Local
sgRNA_sequence	on_target_score	Position	Region
AATTCAAGGCTTCAGCTTTA+TGG	0.156810	2_3:-35831074	None:intergenic
TAAAGCTGAAGCCTTGAATT+TGG	0.196050	2_3:+35831077	Msa0289620:CDS
GAACTACTCGGTTCAATAAT+AGG	0.220766	2_3:-35831177	None:intergenic
AAAGGCAATCACAGATAAAA+TGG	0.318808	2_3:+35831031	Msa0289620:CDS
AAACAGGAGTTTGCATTGCT+TGG	0.345698	2_3:+35830852	Msa0289620:CDS
TCTGTGATTGCCTTTGCATT+AGG	0.354321	2_3:-35831023	None:intergenic
AACAGGAGTTTGCATTGCTT+GGG	0.374896	2_3:+35830853	Msa0289620:CDS
ACCTTGTTCAAACAGGGTCT+TGG	0.402982	2_3:+35830973	Msa0289620:intron
TCCAGAAAATTGCACTGGCT+TGG	0.406949	2_3:+35830815	Msa0289620:intron
CATATGGAAATGTAGAATCT+TGG	0.416297	2_3:-35830707	None:intergenic
ATCATCATCATCCAAATTCA+AGG	0.426949	2_3:-35831088	None:intergenic
TGGTAGTATTGATGTGGAAA+AGG	0.445155	2_3:+35831116	Msa0289620:CDS
CAAGATTCTACATTTCCATA+TGG	0.451268	2_3:+35830708	Msa0289620:exon
GGATGCTTCAGAGGGAAAAC+AGG	0.455159	2_3:+35830836	Msa0289620:CDS
CACTGGCTTGGATGCTTCAG+AGG	0.473005	2_3:+35830827	Msa0289620:CDS
CACAGGCCCCAGGTAGGAAA+AGG	0.493320	2_3:+35831202	Msa0289620:CDS
ACCTTTCCAGAAAATTGCAC+TGG	0.497114	2_3:+35830810	Msa0289620:intron
AGGAGTTTGCATTGCTTGGG+GGG	0.512503	2_3:+35830856	Msa0289620:CDS
ACAGGAGTTTGCATTGCTTG+GGG	0.528297	2_3:+35830854	Msa0289620:CDS
ACAACCAGTGTACCAGCAGC+TGG	0.551867	2_3:-35831225	None:intergenic
GGAGTTTGCATTGCTTGGGG+GGG	0.561095	2_3:+35830857	Msa0289620:CDS
GGTAGGAAAAGGCCAGCTGC+TGG	0.562826	2_3:+35831213	Msa0289620:CDS
CAGGAGTTTGCATTGCTTGG+GGG	0.563404	2_3:+35830855	Msa0289620:CDS
ACTGGCTTGGATGCTTCAGA+GGG	0.591785	2_3:+35830828	Msa0289620:CDS
AGTAGTTCAACACAGGCCCC+AGG	0.608515	2_3:+35831192	Msa0289620:CDS
TTGGATGATGATGATGAGAA+TGG	0.612698	2_3:+35831096	Msa0289620:CDS
TTGCTCTCATCCTAATGCAA+AGG	0.614230	2_3:+35831013	Msa0289620:CDS
GCTTCAGCTTTATGGTTGCG+TGG	0.616461	2_3:-35831066	None:intergenic
GGGGCCTGTGTTGAACTACT+CGG	0.619233	2_3:-35831189	None:intergenic
TGAGAATGGTAGTATTGATG+TGG	0.651173	2_3:+35831110	Msa0289620:CDS
TGAACCGAGTAGTTCAACAC+AGG	0.685975	2_3:+35831185	Msa0289620:CDS
GTTCAACACAGGCCCCAGGT+AGG	0.695205	2_3:+35831196	Msa0289620:CDS

CRISPR-GE

badsite warning	sgRNA_sequence	Strand	Position	Region	GC_content
!	TTTATAACCTTGTTCAAACA+GGG	+	chr2_3:35830967-35830986	Msa0289620:intron	25.0%
!!	AATAATAGGTTTTGCATCAT+TGG	-	chr2_3:35831166-35831185	None:intergenic	25.0%
	CATATGGAAATGTAGAATCT+TGG	-	chr2_3:35830710-35830729	None:intergenic	30.0%
	CAAGATTCTACATTTCCATA+TGG	+	chr2_3:35830708-35830727	Msa0289620:exon	30.0%
	TACATTTCCATATGGTATTG+CGG	+	chr2_3:35830716-35830735	Msa0289620:intron	30.0%
	TAAGAGCAGTTATAATAGAC+AGG	-	chr2_3:35830742-35830761	None:intergenic	30.0%
	CTTTATAACCTTGTTCAAAC+AGG	+	chr2_3:35830966-35830985	Msa0289620:intron	30.0%
	AAAGGCAATCACAGATAAAA+TGG	+	chr2_3:35831031-35831050	Msa0289620:CDS	30.0%
	ATCATCATCATCCAAATTCA+AGG	-	chr2_3:35831091-35831110	None:intergenic	30.0%
	AATTCAAGGCTTCAGCTTTA+TGG	-	chr2_3:35831077-35831096	None:intergenic	35.0%
	TAAAGCTGAAGCCTTGAATT+TGG	+	chr2_3:35831077-35831096	Msa0289620:CDS	35.0%
!	TTGGATGATGATGATGAGAA+TGG	+	chr2_3:35831096-35831115	Msa0289620:CDS	35.0%
!!	TGAGAATGGTAGTATTGATG+TGG	+	chr2_3:35831110-35831129	Msa0289620:CDS	35.0%
!!	TGGTAGTATTGATGTGGAAA+AGG	+	chr2_3:35831116-35831135	Msa0289620:CDS	35.0%
	GAACTACTCGGTTCAATAAT+AGG	-	chr2_3:35831180-35831199	None:intergenic	35.0%
	ACCTTTCCAGAAAATTGCAC+TGG	+	chr2_3:35830810-35830829	Msa0289620:intron	40.0%
	AAACAGGAGTTTGCATTGCT+TGG	+	chr2_3:35830852-35830871	Msa0289620:CDS	40.0%
	AACAGGAGTTTGCATTGCTT+GGG	+	chr2_3:35830853-35830872	Msa0289620:CDS	40.0%
	TTGCTCTCATCCTAATGCAA+AGG	+	chr2_3:35831013-35831032	Msa0289620:CDS	40.0%
	TCTGTGATTGCCTTTGCATT+AGG	-	chr2_3:35831026-35831045	None:intergenic	40.0%
!!	GCCAGTGCAATTTTCTGGAA+AGG	-	chr2_3:35830814-35830833	None:intergenic	45.0%
!!	TCCAGAAAATTGCACTGGCT+TGG	+	chr2_3:35830815-35830834	Msa0289620:intron	45.0%
!	TCCAAGCCAGTGCAATTTTC+TGG	-	chr2_3:35830819-35830838	None:intergenic	45.0%
	ACAGGAGTTTGCATTGCTTG+GGG	+	chr2_3:35830854-35830873	Msa0289620:CDS	45.0%
	ACCTTGTTCAAACAGGGTCT+TGG	+	chr2_3:35830973-35830992	Msa0289620:intron	45.0%
	TCCAAGACCCTGTTTGAACA+AGG	-	chr2_3:35830977-35830996	None:intergenic	45.0%
	TGAACCGAGTAGTTCAACAC+AGG	+	chr2_3:35831185-35831204	Msa0289620:CDS	45.0%
!!!	TACTATTATTATTATTATTT+TGG	+	chr2_3:35830770-35830789	Msa0289620:intron	5.0%
	AGACAGGCCGCAATACCATA+TGG	-	chr2_3:35830726-35830745	None:intergenic	50.0%
!!	ACTGGCTTGGATGCTTCAGA+GGG	+	chr2_3:35830828-35830847	Msa0289620:CDS	50.0%
	GGATGCTTCAGAGGGAAAAC+AGG	+	chr2_3:35830836-35830855	Msa0289620:CDS	50.0%
	CAGGAGTTTGCATTGCTTGG+GGG	+	chr2_3:35830855-35830874	Msa0289620:CDS	50.0%
	AGGAGTTTGCATTGCTTGGG+GGG	+	chr2_3:35830856-35830875	Msa0289620:CDS	50.0%
!!!	GGGGATTTTGGCTGATGATC+AGG	+	chr2_3:35830876-35830895	Msa0289620:CDS	50.0%
!	GCTTCAGCTTTATGGTTGCG+TGG	-	chr2_3:35831069-35831088	None:intergenic	50.0%
!!	CACTGGCTTGGATGCTTCAG+AGG	+	chr2_3:35830827-35830846	Msa0289620:CDS	55.0%
	GGAGTTTGCATTGCTTGGGG+GGG	+	chr2_3:35830857-35830876	Msa0289620:CDS	55.0%
!	GCATTGCTTGGGGGGGATTT+TGG	+	chr2_3:35830864-35830883	Msa0289620:CDS	55.0%
	GGGGCCTGTGTTGAACTACT+CGG	-	chr2_3:35831192-35831211	None:intergenic	55.0%
	AGTAGTTCAACACAGGCCCC+AGG	+	chr2_3:35831192-35831211	Msa0289620:CDS	55.0%
!!!	AGCTGGCCTTTTCCTACCTG+GGG	-	chr2_3:35831211-35831230	None:intergenic	55.0%
!!!	CAGCTGGCCTTTTCCTACCT+GGG	-	chr2_3:35831212-35831231	None:intergenic	55.0%
	GTTCAACACAGGCCCCAGGT+AGG	+	chr2_3:35831196-35831215	Msa0289620:CDS	60.0%
	CACAGGCCCCAGGTAGGAAA+AGG	+	chr2_3:35831202-35831221	Msa0289620:CDS	60.0%
!!!	GCAGCTGGCCTTTTCCTACC+TGG	-	chr2_3:35831213-35831232	None:intergenic	60.0%

Chromosome	Type	Strat	End	Strand	Name
chr2_3	gene	35830698	35831233	35830698	ID=Msa0289620;Name=Msa0289620
chr2_3	mRNA	35830698	35831233	35830698	ID=Msa0289620-mRNA-1;Parent=Msa0289620;Name=Msa0289620-mRNA-1;_AED=0.11;_eAED=0.11;_QI=29\|1\|0.66\|1\|0.5\|0.33\|3\|0\|109
chr2_3	exon	35830698	35830729	35830698	ID=Msa0289620-mRNA-1:exon:11725;Parent=Msa0289620-mRNA-1
chr2_3	exon	35830820	35830897	35830820	ID=Msa0289620-mRNA-1:exon:11726;Parent=Msa0289620-mRNA-1
chr2_3	exon	35830988	35831233	35830988	ID=Msa0289620-mRNA-1:exon:11727;Parent=Msa0289620-mRNA-1
chr2_3	five_prime_UTR	35830698	35830726	35830698	ID=Msa0289620-mRNA-1:five_prime_utr;Parent=Msa0289620-mRNA-1
chr2_3	CDS	35830727	35830729	35830727	ID=Msa0289620-mRNA-1:cds;Parent=Msa0289620-mRNA-1
chr2_3	CDS	35830820	35830897	35830820	ID=Msa0289620-mRNA-1:cds;Parent=Msa0289620-mRNA-1
chr2_3	CDS	35830988	35831233	35830988	ID=Msa0289620-mRNA-1:cds;Parent=Msa0289620-mRNA-1

Gene Sequence	>Msa0289620 ATGAAAATTGCACTGGCTTGGATGCTTCAGAGGGAAAACAGGAGTTTGCATTGCTTGGGGGGGATTTTGGCTGATGATCAGGGTCTTGGAAAGACAATTTCAACGATTGCTCTCATCCTAATGCAAAGGCAATCACAGATAAAATGGAAAACAGATGATCCACGCAACCATAAAGCTGAAGCCTTGAATTTGGATGATGATGATGAGAATGGTAGTATTGATGTGGAAAAGGAAAAGCTTAAAAATGATGAAGAATCCAATGATGCAAAACCTATTATTGAACCGAGTAGTTCAACACAGGCCCCAGGTAGGAAAAGGCCAGCTGCT
Protein sequence	>Msa0289620 MKIALAWMLQRENRSLHCLGGILADDQGLGKTISTIALILMQRQSQIKWKTDDPRNHKAEALNLDDDDENGSIDVEKEKLKNDEESNDAKPIIEPSSSTQAPGRKRPAA