AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53309


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53309.t1 MTR_4g428370 87.931 116 14 0 1 116 58 173 1.25e-69 206
MS.gene53309.t1 MTR_4g027840 86.957 115 15 0 1 115 1 115 1.35e-66 197
MS.gene53309.t1 MTR_4g027800 86.207 116 16 0 1 116 1 116 1.72e-66 196
MS.gene53309.t1 MTR_4g029390 66.667 117 36 2 1 115 1 116 1.03e-47 149
MS.gene53309.t1 MTR_4g029350 66.667 117 36 2 1 115 1 116 1.24e-46 146
MS.gene53309.t1 MTR_4g028190 48.246 114 57 2 1 112 5 118 5.72e-31 107
MS.gene53309.t1 MTR_4g029210 48.214 112 58 0 1 112 1 112 2.13e-30 105
MS.gene53309.t1 MTR_7g072930 47.321 112 56 2 4 113 7 117 1.07e-28 102
MS.gene53309.t1 MTR_4g028180 43.220 118 60 3 5 115 9 126 2.91e-27 97.4
MS.gene53309.t1 MTR_7g072830 40.351 114 66 1 4 115 7 120 4.63e-27 97.1
MS.gene53309.t1 MTR_7g073150 45.690 116 58 4 2 113 3 117 4.94e-27 97.1
MS.gene53309.t1 MTR_7g072730 41.071 112 64 2 4 113 7 118 6.40e-26 95.5
MS.gene53309.t1 MTR_4g028310 40.336 119 68 1 1 116 1 119 5.60e-25 92.0
MS.gene53309.t1 MTR_7g073170 41.593 113 62 3 4 114 7 117 5.81e-25 91.7
MS.gene53309.t1 MTR_2g062600 41.739 115 65 2 1 114 1 114 1.17e-24 90.5
MS.gene53309.t1 MTR_7g073120 37.168 113 69 1 1 111 5 117 3.61e-21 82.8
MS.gene53309.t1 MTR_4g028250 39.831 118 68 2 1 115 1 118 6.59e-21 81.3
MS.gene53309.t1 MTR_7g072900 43.750 112 58 4 4 112 7 116 1.22e-20 80.5
MS.gene53309.t1 MTR_7g072993 42.857 112 59 3 4 111 7 117 8.94e-20 79.0
MS.gene53309.t1 MTR_3g467100 36.607 112 70 1 5 115 3 114 4.05e-19 76.6
MS.gene53309.t1 MTR_4g028360 36.283 113 69 3 4 114 1 112 1.23e-17 73.2
MS.gene53309.t1 MTR_7g072960 39.252 107 49 3 9 113 11 103 1.90e-17 72.8
MS.gene53309.t1 MTR_7g451500 38.043 92 56 1 24 114 7 98 3.34e-17 71.2
MS.gene53309.t1 MTR_7g072980 37.500 112 66 3 4 112 7 117 8.24e-17 71.2
MS.gene53309.t1 MTR_7g073130 38.739 111 64 4 4 112 7 115 1.08e-16 70.5
MS.gene53309.t1 MTR_1g040335 41.071 112 63 2 5 114 8 118 2.76e-16 69.3
MS.gene53309.t1 MTR_7g073060 38.053 113 67 3 4 114 7 118 7.07e-16 68.2
MS.gene53309.t1 MTR_7g073100 37.168 113 64 2 4 112 7 116 7.86e-16 68.9
MS.gene53309.t1 MTR_7g072810 39.091 110 59 3 4 111 7 110 5.80e-15 66.2
MS.gene53309.t1 MTR_3g056640 34.821 112 67 3 9 115 12 122 1.57e-14 65.1
MS.gene53309.t1 MTR_3g046515 34.821 112 67 4 3 110 10 119 9.26e-14 62.8
MS.gene53309.t1 MTR_3g046530 30.769 117 75 3 4 115 7 122 2.36e-13 62.0
MS.gene53309.t1 MTR_7g073030 35.455 110 68 3 4 111 7 115 2.96e-13 62.4
MS.gene53309.t1 MTR_3g464130 37.778 90 51 3 25 110 18 106 6.57e-13 60.5
MS.gene53309.t1 MTR_3g046350 31.373 102 64 3 10 106 13 113 1.66e-12 59.7
MS.gene53309.t1 MTR_3g046540 33.043 115 67 5 4 110 7 119 1.94e-12 59.7
MS.gene53309.t1 MTR_3g464110 40.244 82 44 3 33 110 92 172 2.54e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53309.t1 AT5G59320 60.185 108 41 1 8 115 10 115 2.33e-39 127
MS.gene53309.t1 AT2G38540 63.793 116 36 6 4 115 5 118 2.80e-38 125
MS.gene53309.t1 AT5G59310 60.185 108 38 2 8 115 10 112 1.21e-37 123
MS.gene53309.t1 AT2G38530 61.739 115 40 4 4 115 5 118 1.46e-34 115
MS.gene53309.t1 AT3G51600 53.913 115 49 4 4 115 5 118 2.66e-30 105
MS.gene53309.t1 AT3G51590 47.273 110 55 3 6 114 8 115 7.40e-29 101
MS.gene53309.t1 AT2G15050 45.763 118 58 4 4 115 5 122 3.22e-28 100
MS.gene53309.t1 AT2G15050 45.690 116 57 4 4 113 5 120 8.99e-27 96.3
MS.gene53309.t1 AT2G15050 45.872 109 55 3 4 108 5 113 4.03e-26 94.4
MS.gene53309.t1 AT5G01870 44.737 114 55 4 9 115 4 116 7.80e-26 93.6
MS.gene53309.t1 AT4G33355 48.387 93 48 0 23 115 27 119 3.43e-24 89.7
MS.gene53309.t1 AT4G33355 49.438 89 45 0 23 111 27 115 1.37e-23 88.2
MS.gene53309.t1 AT3G08770 46.392 97 48 3 22 115 18 113 1.16e-21 83.2
MS.gene53309.t1 AT3G08770 46.316 95 47 3 22 113 18 111 9.52e-21 80.9
MS.gene53309.t1 AT2G18370 36.364 110 68 2 6 114 7 115 7.44e-19 75.9
MS.gene53309.t1 AT2G15325 35.165 91 56 2 27 115 31 120 2.26e-12 59.3

Find 31 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTGCTGCTGGTGCTATTTC+TGG 0.136175 4.3:+70973147 MS.gene53309:CDS
CCATGCATTGCATATCTTAG+AGG 0.320070 4.3:+70973024 MS.gene53309:CDS
AATGTTAACACCGCATTTGC+CGG 0.346833 4.3:-70973199 None:intergenic
CCATCTCCAGCATGCTGTGC+TGG 0.375274 4.3:+70973057 MS.gene53309:CDS
AACACAGCTGCTGGTCTTCC+CGG 0.392611 4.3:+70973180 MS.gene53309:CDS
TTGCAAGCAGCCTGACGGTC+AGG 0.421711 4.3:-70973114 None:intergenic
ATCTCATGTGGAACAGTAAC+TGG 0.426922 4.3:+70972991 MS.gene53309:CDS
GGTAGAGGTACTGATCTTGT+AGG 0.430936 4.3:-70973223 None:intergenic
CACCACCACGCCTGACCGTC+AGG 0.443141 4.3:+70973104 MS.gene53309:CDS
ACGGTCAGGCGTGGTGGTGG+CGG 0.445777 4.3:-70973100 None:intergenic
GTCAGGCGTGGTGGTGGCGG+CGG 0.446691 4.3:-70973097 None:intergenic
GTGCATGATTGTTGCACCTA+TGG 0.467928 4.3:+70972957 MS.gene53309:CDS
TTCACTCCAGCACAGCATGC+TGG 0.485039 4.3:-70973063 None:intergenic
AACTGCTTGAAAAGTGCTGC+TGG 0.486030 4.3:+70973135 MS.gene53309:CDS
ATGTTAACACCGCATTTGCC+GGG 0.493990 4.3:-70973198 None:intergenic
GCATATCTTAGAGGTGGTGC+TGG 0.504129 4.3:+70973033 MS.gene53309:CDS
CTGACGGTCAGGCGTGGTGG+TGG 0.517462 4.3:-70973103 None:intergenic
CCAGCACAGCATGCTGGAGA+TGG 0.550113 4.3:-70973057 None:intergenic
TTGAATGCTAACACAGCTGC+TGG 0.551046 4.3:+70973171 MS.gene53309:CDS
GTAGAGGTACTGATCTTGTA+GGG 0.565695 4.3:-70973222 None:intergenic
AGCAGCCTGACGGTCAGGCG+TGG 0.565783 4.3:-70973109 None:intergenic
TGGTTATATTTACAGCATCA+GGG 0.568642 4.3:+70973702 MS.gene53309:intron
AGCCTGACGGTCAGGCGTGG+TGG 0.576862 4.3:-70973106 None:intergenic
GAGATTGCAGCATCTGCCAT+AGG 0.577723 4.3:-70972973 None:intergenic
AAGAACTTACGTAGCACAGT+TGG 0.585095 4.3:-70973244 None:intergenic
CCTCTAAGATATGCAATGCA+TGG 0.588805 4.3:-70973024 None:intergenic
GCTGGTCTTCCCGGCAAATG+CGG 0.592170 4.3:+70973189 MS.gene53309:CDS
TTACGTAGCACAGTTGGTAG+AGG 0.599761 4.3:-70973238 None:intergenic
TGCATTGCATATCTTAGAGG+TGG 0.623803 4.3:+70973027 MS.gene53309:CDS
AGCAGTTGCAAGCAGCCTGA+CGG 0.624471 4.3:-70973119 None:intergenic
GCAGATGCTGCAATCTCATG+TGG 0.654132 4.3:+70972979 MS.gene53309:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTGGTTATTTATTTTT+TGG + chr4.3:70973607-70973626 MS.gene53309:intron 10.0%
!!! AAACATTTTTGTGAATTTTT+TGG + chr4.3:70973525-70973544 MS.gene53309:intron 15.0%
!!! ACTAGTTTTTTTTTTTTGTT+TGG + chr4.3:70973682-70973701 MS.gene53309:intron 15.0%
!!! TTATTTTTTGGTGTTATTAT+TGG + chr4.3:70973619-70973638 MS.gene53309:intron 15.0%
!!! TTTTTCTTACTTCTAAAATT+TGG - chr4.3:70973463-70973482 None:intergenic 15.0%
!!! TTATTGGTTAATATTCAAGT+CGG + chr4.3:70973635-70973654 MS.gene53309:intron 20.0%
! GAAAAATATAGTAAGAGTGA+AGG - chr4.3:70973280-70973299 None:intergenic 25.0%
TGGTTATATTTACAGCATCA+GGG + chr4.3:70973702-70973721 MS.gene53309:intron 30.0%
TTAAGAAACGCTGTATAAAG+AGG + chr4.3:70973311-70973330 MS.gene53309:intron 30.0%
TTGGTTATATTTACAGCATC+AGG + chr4.3:70973701-70973720 MS.gene53309:intron 30.0%
CTGATCTACTGCTTCTTTAT+TGG + chr4.3:70973592-70973611 MS.gene53309:intron 35.0%
AAGAACTTACGTAGCACAGT+TGG - chr4.3:70973247-70973266 None:intergenic 40.0%
AATGTTAACACCGCATTTGC+CGG - chr4.3:70973202-70973221 None:intergenic 40.0%
ATCTCATGTGGAACAGTAAC+TGG + chr4.3:70972991-70973010 MS.gene53309:CDS 40.0%
CCATGCATTGCATATCTTAG+AGG + chr4.3:70973024-70973043 MS.gene53309:CDS 40.0%
TATTCAAGTCGGTCGAAAAG+TGG + chr4.3:70973646-70973665 MS.gene53309:intron 40.0%
TGCATTGCATATCTTAGAGG+TGG + chr4.3:70973027-70973046 MS.gene53309:CDS 40.0%
!! CCTCTAAGATATGCAATGCA+TGG - chr4.3:70973027-70973046 None:intergenic 40.0%
!! GTAGAGGTACTGATCTTGTA+GGG - chr4.3:70973225-70973244 None:intergenic 40.0%
ATGTTAACACCGCATTTGCC+GGG - chr4.3:70973201-70973220 None:intergenic 45.0%
GTGCATGATTGTTGCACCTA+TGG + chr4.3:70972957-70972976 MS.gene53309:CDS 45.0%
TTGAATGCTAACACAGCTGC+TGG + chr4.3:70973171-70973190 MS.gene53309:CDS 45.0%
!! AACTGCTTGAAAAGTGCTGC+TGG + chr4.3:70973135-70973154 MS.gene53309:CDS 45.0%
!! GGTAGAGGTACTGATCTTGT+AGG - chr4.3:70973226-70973245 None:intergenic 45.0%
!! TTACGTAGCACAGTTGGTAG+AGG - chr4.3:70973241-70973260 None:intergenic 45.0%
!!! AAAAATTATAATATTTTTAG+AGG + chr4.3:70973478-70973497 MS.gene53309:intron 5.0%
!!! CTTTATAATAATTTTTTTTT+AGG + chr4.3:70973554-70973573 MS.gene53309:intron 5.0%
GAGATTGCAGCATCTGCCAT+AGG - chr4.3:70972976-70972995 None:intergenic 50.0%
GCAGATGCTGCAATCTCATG+TGG + chr4.3:70972979-70972998 MS.gene53309:CDS 50.0%
GCATATCTTAGAGGTGGTGC+TGG + chr4.3:70973033-70973052 MS.gene53309:CDS 50.0%
!! AGTGCTGCTGGTGCTATTTC+TGG + chr4.3:70973147-70973166 MS.gene53309:CDS 50.0%
AGCAGTTGCAAGCAGCCTGA+CGG - chr4.3:70973122-70973141 None:intergenic 55.0%
TTCACTCCAGCACAGCATGC+TGG - chr4.3:70973066-70973085 None:intergenic 55.0%
!! AACACAGCTGCTGGTCTTCC+CGG + chr4.3:70973180-70973199 MS.gene53309:CDS 55.0%
CCAGCACAGCATGCTGGAGA+TGG - chr4.3:70973060-70973079 None:intergenic 60.0%
CCATCTCCAGCATGCTGTGC+TGG + chr4.3:70973057-70973076 MS.gene53309:CDS 60.0%
TTGCAAGCAGCCTGACGGTC+AGG - chr4.3:70973117-70973136 None:intergenic 60.0%
!! GCTGGTCTTCCCGGCAAATG+CGG + chr4.3:70973189-70973208 MS.gene53309:CDS 60.0%
AGCAGCCTGACGGTCAGGCG+TGG - chr4.3:70973112-70973131 None:intergenic 70.0%
AGCCTGACGGTCAGGCGTGG+TGG - chr4.3:70973109-70973128 None:intergenic 70.0%
CACCACCACGCCTGACCGTC+AGG + chr4.3:70973104-70973123 MS.gene53309:CDS 70.0%
CTGACGGTCAGGCGTGGTGG+TGG - chr4.3:70973106-70973125 None:intergenic 70.0%
!! ACGGTCAGGCGTGGTGGTGG+CGG - chr4.3:70973103-70973122 None:intergenic 70.0%
!! GTCAGGCGTGGTGGTGGCGG+CGG - chr4.3:70973100-70973119 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 70972919 70973729 70972919 ID=MS.gene53309
chr4.3 mRNA 70972919 70973729 70972919 ID=MS.gene53309.t1;Parent=MS.gene53309
chr4.3 exon 70972919 70973256 70972919 ID=MS.gene53309.t1.exon1;Parent=MS.gene53309.t1
chr4.3 CDS 70972919 70973256 70972919 ID=cds.MS.gene53309.t1;Parent=MS.gene53309.t1
chr4.3 exon 70973717 70973729 70973717 ID=MS.gene53309.t1.exon2;Parent=MS.gene53309.t1
chr4.3 CDS 70973717 70973729 70973717 ID=cds.MS.gene53309.t1;Parent=MS.gene53309.t1
Gene Sequence

>MS.gene53309

ATGGCAAGCATGAAGGTAGCATGTGTTGTTTTGATGATGTGCATGATTGTTGCACCTATGGCAGATGCTGCAATCTCATGTGGAACAGTAACTGGTGCTCTTTCTCCATGCATTGCATATCTTAGAGGTGGTGCTGGTCCATCTCCAGCATGCTGTGCTGGAGTGAAGAGACTTAACGCCGCCGCCACCACCACGCCTGACCGTCAGGCTGCTTGCAACTGCTTGAAAAGTGCTGCTGGTGCTATTTCTGGTTTGAATGCTAACACAGCTGCTGGTCTTCCCGGCAAATGCGGTGTTAACATTCCCTACAAGATCAGTACCTCTACCAACTGTGCTACGTAAGTTCTTCTAATTTTTACCTTCACTCTTACTATATTTTTCATGTCAAATATTTAAGAAACGCTGTATAAAGAGGTCTAGATTGCAAATCTTGACTATTAAAATAACACACTATTATCTGTTTAGAAAAAAAATGAAGCAACTCTATTTAAGCATCACAATAATAAACATACAAAAATTATTAACATAAAAGACTAATTTGCCAAATTTTAGAAGTAAGAAAAATTATAATATTTTTAGAGGATATTTTTATATATTTTTTTAAATAAACATTTTTGTGAATTTTTTGGAATATACTTTATAATAATTTTTTTTTAGGATTAATTAGTCGCTTCTGATCTACTGCTTCTTTATTGGTTATTTATTTTTTGGTGTTATTATTGGTTAATATTCAAGTCGGTCGAAAAGTGGAATTTAATTATTGACTAGTTTTTTTTTTTTGTTTGGTTATATTTACAGCATCAGGGCTTGA

Protein sequence

>MS.gene53309.t1

MASMKVACVVLMMCMIVAPMADAAISCGTVTGALSPCIAYLRGGAGPSPACCAGVKRLNAAATTTPDRQAACNCLKSAAGAISGLNANTAAGLPGKCGVNIPYKISTSTNCATIRA