AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene027391

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027391.t1 MTR_3g103160 69.811 106 31 1 3 108 338 442 1.85e-44 150
MS.gene027391.t1 MTR_3g103120 60.000 120 38 2 1 120 732 841 1.33e-43 152
MS.gene027391.t1 MTR_3g103110 60.684 117 36 2 1 117 691 797 5.18e-41 144
MS.gene027391.t1 MTR_7g109640 59.829 117 37 2 1 117 687 793 3.53e-38 136
MS.gene027391.t1 MTR_5g024390 53.846 117 44 2 1 117 319 425 1.54e-35 126
MS.gene027391.t1 MTR_5g024500 52.137 117 46 2 1 117 319 425 6.63e-34 122
MS.gene027391.t1 MTR_5g071340 46.465 99 52 1 2 100 985 1082 2.98e-26 102
MS.gene027391.t1 MTR_3g464550 42.424 99 56 1 2 100 909 1006 4.67e-23 93.6
MS.gene027391.t1 MTR_2g078040 35.849 106 67 1 1 106 1066 1170 3.58e-15 71.2
MS.gene027391.t1 MTR_1g072130 31.068 103 70 1 2 104 1121 1222 1.24e-12 63.9
MS.gene027391.t1 MTR_7g095140 33.010 103 68 1 2 104 202 303 4.58e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027391.t1 AT5G58610 40.000 110 65 1 2 111 909 1017 8.44e-21 87.4
MS.gene027391.t1 AT5G58610 40.000 110 65 1 2 111 909 1017 8.44e-21 87.4
MS.gene027391.t1 AT5G58610 40.000 110 65 1 2 111 900 1008 9.90e-21 87.0
MS.gene027391.t1 AT5G58610 40.000 110 65 1 2 111 678 786 1.03e-20 87.0
MS.gene027391.t1 AT5G58610 40.000 110 65 1 2 111 874 982 1.06e-20 87.0
MS.gene027391.t1 AT5G58610 40.000 110 65 1 2 111 900 1008 1.06e-20 87.0
MS.gene027391.t1 AT5G58610 40.000 110 65 1 2 111 874 982 1.10e-20 87.0
MS.gene027391.t1 AT5G58610 40.000 110 65 1 2 111 909 1017 1.12e-20 87.0
MS.gene027391.t1 AT5G36740 37.143 105 65 1 2 106 707 810 6.45e-18 79.0
MS.gene027391.t1 AT5G36740 37.143 105 65 1 2 106 850 953 6.51e-18 79.0
MS.gene027391.t1 AT5G36740 37.143 105 65 1 2 106 850 953 6.51e-18 79.0
MS.gene027391.t1 AT5G63900 39.216 102 60 2 5 106 445 544 3.28e-17 77.0
MS.gene027391.t1 AT3G14980 38.750 80 48 1 2 81 924 1002 3.05e-13 65.9
MS.gene027391.t1 AT3G14980 38.750 80 48 1 2 81 924 1002 3.49e-13 65.5
MS.gene027391.t1 AT3G14980 38.750 80 48 1 2 81 924 1002 3.49e-13 65.5
MS.gene027391.t1 AT3G14980 38.750 80 48 1 2 81 924 1002 3.49e-13 65.5
MS.gene027391.t1 AT3G14980 38.750 80 48 1 2 81 879 957 3.55e-13 65.5
MS.gene027391.t1 AT1G05380 30.693 101 69 1 2 102 826 925 9.80e-12 61.2
MS.gene027391.t1 AT1G05380 30.693 101 69 1 2 102 826 925 9.80e-12 61.2
MS.gene027391.t1 AT1G05380 30.693 101 69 1 2 102 826 925 9.80e-12 61.2

Find 23 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTATACTTTCATTGAATTTC+AGG 0.198303 4.2:-52171731 MS.gene027391:CDS
TTGTCTTCGATGTTCTTTCT+TGG 0.292807 4.2:+52171915 None:intergenic
GTGGCAACCGTAAGGATTTA+TGG 0.295747 4.2:-52171970 MS.gene027391:CDS
AGCCACTGAATGGACCAATA+TGG 0.415003 4.2:-52171663 MS.gene027391:CDS
TGACTTAGGAGTTCGGAGTT+TGG 0.415135 4.2:-52171845 MS.gene027391:CDS
CTGCCACTGTAAGGCCATAT+TGG 0.419368 4.2:+52171649 None:intergenic
TCTTCGATGTTCTTTCTTGG+TGG 0.446230 4.2:+52171918 None:intergenic
GGTGTCTATAACATCTTTAG+AGG 0.451179 4.2:+52171813 None:intergenic
TTGGTCCATTCAGTGGCTTA+AGG 0.459226 4.2:+52171668 None:intergenic
CTCTTGACCATAAATCCTTA+CGG 0.483392 4.2:+52171963 None:intergenic
AAGTGCCTTAAGCCACTGAA+TGG 0.500912 4.2:-52171673 MS.gene027391:CDS
GAGAATCGGTTGAATGACTT+AGG 0.503980 4.2:-52171859 MS.gene027391:CDS
GGTTGAATGACTTAGGAGTT+CGG 0.519650 4.2:-52171852 MS.gene027391:CDS
AAAATGAAATGCATTTGTCC+AGG 0.546196 4.2:+52171792 None:intergenic
TGATATATGTGGCAACCGTA+AGG 0.563661 4.2:-52171978 MS.gene027391:CDS
CTAAAGATGTTATAGACACC+TGG 0.565432 4.2:-52171810 MS.gene027391:CDS
CGTAAGGATTTATGGTCAAG+AGG 0.572874 4.2:-52171962 MS.gene027391:CDS
GGCCATATTGGTCCATTCAG+TGG 0.575479 4.2:+52171661 None:intergenic
GGTTGTTGAGATAGTTGTCA+TGG 0.576253 4.2:-52171941 MS.gene027391:CDS
TGAGTAGTGTGCTTGAGAAT+CGG 0.582605 4.2:-52171873 MS.gene027391:CDS
AATGGATAAAGTGATATATG+TGG 0.588383 4.2:-52171989 MS.gene027391:CDS
AAGAAAGAACATCGAAGACA+AGG 0.618287 4.2:-52171913 MS.gene027391:CDS
GGACCAATATGGCCTTACAG+TGG 0.705054 4.2:-52171652 MS.gene027391:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATACTTTCATTGAATTTC+AGG - chr4.2:52171869-52171888 MS.gene027391:CDS 20.0%
!!! TTTTTTTGTTAATTGGCTTA+AGG + chr4.2:52171908-52171927 None:intergenic 20.0%
!! GTAAAAATATCTTTTGTTGG+TGG - chr4.2:52171976-52171995 MS.gene027391:CDS 25.0%
!! GTCGTAAAAATATCTTTTGT+TGG - chr4.2:52171973-52171992 MS.gene027391:CDS 25.0%
!!! AGGCACTTTTTTTTGTTAAT+TGG + chr4.2:52171915-52171934 None:intergenic 25.0%
!!! ATTTCATTTTGCTATGATGA+CGG - chr4.2:52171821-52171840 MS.gene027391:CDS 25.0%
AAAATGAAATGCATTTGTCC+AGG + chr4.2:52171811-52171830 None:intergenic 30.0%
AAGAAAGAACATCGAAGACA+AGG - chr4.2:52171687-52171706 MS.gene027391:CDS 35.0%
CTAAAGATGTTATAGACACC+TGG - chr4.2:52171790-52171809 MS.gene027391:CDS 35.0%
CTCTTGACCATAAATCCTTA+CGG + chr4.2:52171640-52171659 None:intergenic 35.0%
GGTGTCTATAACATCTTTAG+AGG + chr4.2:52171790-52171809 None:intergenic 35.0%
TTGTCTTCGATGTTCTTTCT+TGG + chr4.2:52171688-52171707 None:intergenic 35.0%
CGTAAGGATTTATGGTCAAG+AGG - chr4.2:52171638-52171657 MS.gene027391:CDS 40.0%
GAGAATCGGTTGAATGACTT+AGG - chr4.2:52171741-52171760 MS.gene027391:CDS 40.0%
GGTTGAATGACTTAGGAGTT+CGG - chr4.2:52171748-52171767 MS.gene027391:CDS 40.0%
GGTTGTTGAGATAGTTGTCA+TGG - chr4.2:52171659-52171678 MS.gene027391:CDS 40.0%
TCTTCGATGTTCTTTCTTGG+TGG + chr4.2:52171685-52171704 None:intergenic 40.0%
TGAGTAGTGTGCTTGAGAAT+CGG - chr4.2:52171727-52171746 MS.gene027391:CDS 40.0%
TGATATATGTGGCAACCGTA+AGG - chr4.2:52171622-52171641 MS.gene027391:CDS 40.0%
! TTTTTACGACTGCCACTGTA+AGG + chr4.2:52171963-52171982 None:intergenic 40.0%
AAGTGCCTTAAGCCACTGAA+TGG - chr4.2:52171927-52171946 MS.gene027391:CDS 45.0%
AGCCACTGAATGGACCAATA+TGG - chr4.2:52171937-52171956 MS.gene027391:CDS 45.0%
GTGGCAACCGTAAGGATTTA+TGG - chr4.2:52171630-52171649 MS.gene027391:CDS 45.0%
TGACTTAGGAGTTCGGAGTT+TGG - chr4.2:52171755-52171774 MS.gene027391:CDS 45.0%
TTGGTCCATTCAGTGGCTTA+AGG + chr4.2:52171935-52171954 None:intergenic 45.0%
CTGCCACTGTAAGGCCATAT+TGG + chr4.2:52171954-52171973 None:intergenic 50.0%
GGCCATATTGGTCCATTCAG+TGG + chr4.2:52171942-52171961 None:intergenic 50.0%
! GGACCAATATGGCCTTACAG+TGG - chr4.2:52171948-52171967 MS.gene027391:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 52171612 52172010 52171612 ID=MS.gene027391
chr4.2 mRNA 52171612 52172010 52171612 ID=MS.gene027391.t1;Parent=MS.gene027391
chr4.2 exon 52171612 52172010 52171612 ID=MS.gene027391.t1.exon1;Parent=MS.gene027391.t1
chr4.2 CDS 52171612 52172010 52171612 ID=cds.MS.gene027391.t1;Parent=MS.gene027391.t1
Gene Sequence

>MS.gene027391

ATGGATAAAGTGATATATGTGGCAACCGTAAGGATTTATGGTCAAGAGGTTGTTGAGATAGTTGTCATGGCCACCAAGAAAGAACATCGAAGACAAGGAATGTGTCGTTTGTTGATGAGTAGTGTGCTTGAGAATCGGTTGAATGACTTAGGAGTTCGGAGTTTGGTTTTGCATTCCTCTAAAGATGTTATAGACACCTGGACAAATGCATTTCATTTTGCTATGATGACGGATGAAGACAAGCGTAAATTTATTGATTATACTTTCATTGAATTTCAGGACATTATCATGTGCCTTAAGCCAATTAACAAAAAAAAGTGCCTTAAGCCACTGAATGGACCAATATGGCCTTACAGTGGCAGTCGTAAAAATATCTTTTGTTGGTGGAATTTTGTTTGA
Protein sequence

>MS.gene027391.t1

MDKVIYVATVRIYGQEVVEIVVMATKKEHRRQGMCRLLMSSVLENRLNDLGVRSLVLHSSKDVIDTWTNAFHFAMMTDEDKRKFIDYTFIEFQDIIMCLKPINKKKCLKPLNGPIWPYSGSRKNIFCWWNFV