AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene00393

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00393.t1 MTR_2g035580 91.139 158 14 0 1 158 1 158 2.63e-93 267
MS.gene00393.t1 MTR_3g466980 46.203 158 85 0 1 158 1 158 2.70e-46 150
MS.gene00393.t1 MTR_3g467080 49.351 154 77 1 1 153 1 154 5.89e-46 147
MS.gene00393.t1 MTR_4g063790 46.753 154 81 1 1 153 1 154 5.33e-43 140
MS.gene00393.t1 MTR_3g065100 44.156 154 86 0 1 154 1 154 5.25e-38 130
MS.gene00393.t1 MTR_3g031100 42.138 159 91 1 1 158 1 159 7.59e-37 127
MS.gene00393.t1 MTR_4g032620 37.662 154 95 1 1 153 1 154 8.58e-35 121
MS.gene00393.t1 MTR_3g465410 47.541 122 63 1 30 150 2 123 1.36e-33 115
MS.gene00393.t1 MTR_2g016210 38.750 160 93 2 1 157 1 158 6.85e-33 117
MS.gene00393.t1 MTR_3g466830 39.597 149 90 0 4 152 3 151 8.01e-33 114
MS.gene00393.t1 MTR_3g031240 38.462 156 95 1 1 155 1 156 5.24e-31 110
MS.gene00393.t1 MTR_5g075380 33.333 153 102 0 1 153 1 153 1.46e-30 108
MS.gene00393.t1 MTR_4g031910 37.179 156 97 1 1 155 1 156 2.69e-29 107
MS.gene00393.t1 MTR_8g036130 37.975 158 95 2 1 155 1 158 3.05e-29 107
MS.gene00393.t1 MTR_1g090783 33.333 153 101 1 6 158 5 156 1.79e-28 103
MS.gene00393.t1 MTR_5g047580 34.194 155 101 1 1 155 1 154 4.95e-28 102
MS.gene00393.t1 MTR_4g032260 36.943 157 98 1 1 156 1 157 2.64e-27 100
MS.gene00393.t1 MTR_1g077390 33.987 153 100 1 1 153 1 152 5.48e-27 99.4
MS.gene00393.t1 MTR_3g466890 35.417 144 93 0 6 149 5 148 2.82e-26 97.8
MS.gene00393.t1 MTR_1g090697 30.968 155 106 1 1 155 1 154 1.18e-23 90.9
MS.gene00393.t1 MTR_2g035610 36.752 117 74 0 1 117 1 117 2.34e-23 89.0
MS.gene00393.t1 MTR_4g032290 35.032 157 101 1 1 156 1 157 1.08e-22 90.1
MS.gene00393.t1 MTR_4g028720 35.897 156 97 3 1 155 1 154 5.85e-22 86.7
MS.gene00393.t1 MTR_3g466930 36.885 122 77 0 32 153 2 123 1.05e-21 85.1
MS.gene00393.t1 MTR_1g090710 31.210 157 104 3 1 155 1 155 1.18e-21 85.9
MS.gene00393.t1 MTR_7g011950 32.903 155 103 1 1 155 1 154 1.60e-21 85.5
MS.gene00393.t1 MTR_1g084950 34.194 155 101 1 1 155 1 154 2.90e-21 84.7
MS.gene00393.t1 MTR_3g466900 35.246 122 79 0 32 153 2 123 1.01e-20 82.8
MS.gene00393.t1 MTR_1g077320 30.323 155 107 1 1 155 1 154 6.20e-20 81.3
MS.gene00393.t1 MTR_1g077300 36.129 155 92 4 1 153 1 150 5.37e-18 76.3
MS.gene00393.t1 MTR_4g028800 41.096 73 41 1 1 73 1 71 7.90e-18 73.6
MS.gene00393.t1 MTR_5g047560 25.806 155 98 2 1 155 1 138 1.13e-13 64.7
MS.gene00393.t1 MTR_4g019670 28.814 118 80 1 11 128 14 127 5.26e-11 60.1
MS.gene00393.t1 MTR_7g106510 27.273 121 78 2 11 128 14 127 6.76e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00393.t1 AT5G48670 41.667 156 87 2 1 154 1 154 6.84e-32 116
MS.gene00393.t1 AT3G05860 36.913 149 94 0 1 149 1 149 2.48e-29 107
MS.gene00393.t1 AT1G65300 37.086 151 95 0 4 154 3 153 3.03e-29 108
MS.gene00393.t1 AT1G65330 39.333 150 89 2 6 154 5 153 3.43e-29 108
MS.gene00393.t1 AT3G05860 39.103 156 81 3 1 149 1 149 1.32e-28 106
MS.gene00393.t1 AT3G05860 39.103 156 81 3 1 149 1 149 1.47e-28 106
MS.gene00393.t1 AT1G31630 33.333 153 91 3 6 153 5 151 6.79e-24 95.5
MS.gene00393.t1 AT1G31640 35.915 142 90 1 11 152 10 150 1.98e-23 95.5
MS.gene00393.t1 AT5G27810 43.182 88 50 0 30 117 2 89 7.43e-23 87.8
MS.gene00393.t1 AT5G26650 32.237 152 103 0 4 155 2 153 1.68e-22 92.0
MS.gene00393.t1 AT5G27960 31.579 152 104 0 4 155 2 153 1.35e-21 89.0
MS.gene00393.t1 AT1G22590 36.111 108 69 0 11 118 11 118 5.07e-21 84.3
MS.gene00393.t1 AT2G28700 32.680 153 95 3 1 149 1 149 5.85e-20 84.7
MS.gene00393.t1 AT2G40210 32.479 117 79 0 1 117 1 117 9.34e-15 70.5
MS.gene00393.t1 AT5G26580 28.571 154 96 3 1 154 1 140 2.89e-14 69.3
MS.gene00393.t1 AT5G26630 26.623 154 113 0 1 154 1 154 3.26e-14 67.8
MS.gene00393.t1 AT5G06500 28.182 110 75 1 1 110 1 106 4.28e-13 65.1

Find 28 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGATCTATCATTGCTTAT+TGG 0.201999 2.2:-51021038 MS.gene00393:CDS
CTTCTCCTTCGATTTCATTA+TGG 0.221424 2.2:+51021166 None:intergenic
ATTCATACGGGTGAATTTGA+TGG 0.333961 2.2:-51021083 MS.gene00393:CDS
AGATGGTGTTGGACAAGTTT+AGG 0.350542 2.2:-51021250 MS.gene00393:CDS
GTTTAGGAGCTTTCCTGAAT+CGG 0.417309 2.2:-51021234 MS.gene00393:CDS
TAAACTTGTCCAACACCATC+TGG 0.418271 2.2:+51021252 None:intergenic
AGTGAAATCACCACACTTTG+TGG 0.451943 2.2:-51021347 MS.gene00393:CDS
GGAAGACAACATTCAACAAA+AGG 0.464060 2.2:-51021779 MS.gene00393:CDS
ATCTATGATGAAAACAATGA+TGG 0.489972 2.2:-51021305 MS.gene00393:CDS
ACTTGGTGAATTCATTCATA+CGG 0.496749 2.2:-51021096 MS.gene00393:CDS
GGAGAAGTTGAAGAAACAAA+AGG 0.500916 2.2:-51021150 MS.gene00393:CDS
CCTGAATCGGAACAAAGAAA+AGG 0.516491 2.2:-51021221 MS.gene00393:CDS
GGAACAAAGAAAAGGAAAGC+TGG 0.520124 2.2:-51021213 MS.gene00393:CDS
AGTTGAAGAAACAAAAGGAC+AGG 0.532305 2.2:-51021145 MS.gene00393:CDS
AAAAGGAAAGCTGGATCATG+AGG 0.532487 2.2:-51021204 MS.gene00393:CDS
CTTGGTGAATTCATTCATAC+GGG 0.535817 2.2:-51021095 MS.gene00393:CDS
AAGAAAATGAATGATCTACT+TGG 0.551967 2.2:-51021113 MS.gene00393:CDS
ACGGTTTATCCATCAAAAGA+AGG 0.566324 2.2:-51021278 MS.gene00393:CDS
ACAATCCATAATGAAATCGA+AGG 0.573214 2.2:-51021171 MS.gene00393:CDS
ACATAACTGATGACTTGAAG+AGG 0.573872 2.2:-51021800 MS.gene00393:CDS
AGAAGGAGTCCAGATGGTGT+TGG 0.590630 2.2:-51021261 MS.gene00393:CDS
ACCGAAAAGAAGTCGATGAG+AGG 0.615793 2.2:-51021010 MS.gene00393:CDS
ATCAAAAGAAGGAGTCCAGA+TGG 0.615817 2.2:-51021267 MS.gene00393:CDS
TGCATCAATTCCACAAAGTG+TGG 0.616904 2.2:+51021337 None:intergenic
TGAAAACAATGATGGAGCAA+CGG 0.627126 2.2:-51021297 MS.gene00393:CDS
ACATTCAACAAAAGGAAGCA+TGG 0.630577 2.2:-51021771 MS.gene00393:intron
AAAGGAAAGCTGGATCATGA+GGG 0.661580 2.2:-51021203 MS.gene00393:CDS
CTTTGTGGAATTGATGCATG+TGG 0.684212 2.2:-51021332 MS.gene00393:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAAATAACAATAATTTCAA+AGG + chr2.2:51021339-51021358 None:intergenic 15.0%
!! ACATAACTGATATGTTATTA+TGG + chr2.2:51021313-51021332 None:intergenic 20.0%
!! AGTGTTCTTTATAGAAATAA+AGG + chr2.2:51021089-51021108 None:intergenic 20.0%
!! TCATATTGATAAATTCCTAA+TGG + chr2.2:51021213-51021232 None:intergenic 20.0%
!!! ACAATATTTTAAGATCATGT+CGG - chr2.2:51021359-51021378 MS.gene00393:CDS 20.0%
!!! TTTCATATTTTTAGTATCCA+TGG + chr2.2:51021177-51021196 None:intergenic 20.0%
! AAGAAAATGAATGATCTACT+TGG - chr2.2:51021704-51021723 MS.gene00393:intron 25.0%
! ATCTATGATGAAAACAATGA+TGG - chr2.2:51021512-51021531 MS.gene00393:intron 25.0%
!! ATCATTCATTTTCTTCTTCT+TGG + chr2.2:51021699-51021718 None:intergenic 25.0%
!!! GTTTTTTTTTATCACTACCA+TGG - chr2.2:51021157-51021176 MS.gene00393:CDS 25.0%
ACAATCCATAATGAAATCGA+AGG - chr2.2:51021646-51021665 MS.gene00393:intron 30.0%
GAAGATCTATCATTGCTTAT+TGG - chr2.2:51021779-51021798 MS.gene00393:CDS 30.0%
! ACTTGGTGAATTCATTCATA+CGG - chr2.2:51021721-51021740 MS.gene00393:intron 30.0%
!! GTTTTGTTGTGTTTTTCAAC+AGG - chr2.2:51021431-51021450 MS.gene00393:intron 30.0%
AAGTTGACTGCATAACCATT+AGG - chr2.2:51021195-51021214 MS.gene00393:CDS 35.0%
ACATAACTGATGACTTGAAG+AGG - chr2.2:51021017-51021036 MS.gene00393:CDS 35.0%
ACATTCAACAAAAGGAAGCA+TGG - chr2.2:51021046-51021065 MS.gene00393:CDS 35.0%
ACGGTTTATCCATCAAAAGA+AGG - chr2.2:51021539-51021558 MS.gene00393:intron 35.0%
AGTTGAAGAAACAAAAGGAC+AGG - chr2.2:51021672-51021691 MS.gene00393:intron 35.0%
ATTCATACGGGTGAATTTGA+TGG - chr2.2:51021734-51021753 MS.gene00393:intron 35.0%
CTTCTCCTTCGATTTCATTA+TGG + chr2.2:51021654-51021673 None:intergenic 35.0%
CTTGGTGAATTCATTCATAC+GGG - chr2.2:51021722-51021741 MS.gene00393:intron 35.0%
GGAAGACAACATTCAACAAA+AGG - chr2.2:51021038-51021057 MS.gene00393:CDS 35.0%
GGAGAAGTTGAAGAAACAAA+AGG - chr2.2:51021667-51021686 MS.gene00393:intron 35.0%
! TGAAAACAATGATGGAGCAA+CGG - chr2.2:51021520-51021539 MS.gene00393:intron 35.0%
AAAAGGAAAGCTGGATCATG+AGG - chr2.2:51021613-51021632 MS.gene00393:intron 40.0%
AAAGGAAAGCTGGATCATGA+GGG - chr2.2:51021614-51021633 MS.gene00393:intron 40.0%
AGTGAAATCACCACACTTTG+TGG - chr2.2:51021470-51021489 MS.gene00393:intron 40.0%
ATCAAAAGAAGGAGTCCAGA+TGG - chr2.2:51021550-51021569 MS.gene00393:intron 40.0%
ATTTCTCTCAACTCTCTCAC+GGG - chr2.2:51021409-51021428 MS.gene00393:intron 40.0%
CATTTCTCTCAACTCTCTCA+CGG - chr2.2:51021408-51021427 MS.gene00393:intron 40.0%
CCTGAATCGGAACAAAGAAA+AGG - chr2.2:51021596-51021615 MS.gene00393:intron 40.0%
CTTTGTGGAATTGATGCATG+TGG - chr2.2:51021485-51021504 MS.gene00393:intron 40.0%
GGAACAAAGAAAAGGAAAGC+TGG - chr2.2:51021604-51021623 MS.gene00393:intron 40.0%
GTTTAGGAGCTTTCCTGAAT+CGG - chr2.2:51021583-51021602 MS.gene00393:intron 40.0%
TAAACTTGTCCAACACCATC+TGG + chr2.2:51021568-51021587 None:intergenic 40.0%
TGCATCAATTCCACAAAGTG+TGG + chr2.2:51021483-51021502 None:intergenic 40.0%
! AGATGGTGTTGGACAAGTTT+AGG - chr2.2:51021567-51021586 MS.gene00393:intron 40.0%
! ATCTGGACTCCTTCTTTTGA+TGG + chr2.2:51021551-51021570 None:intergenic 40.0%
! CCTTTTCTTTGTTCCGATTC+AGG + chr2.2:51021599-51021618 None:intergenic 40.0%
!!! TCCTCTCATCGACTTCTTTT+CGG + chr2.2:51021811-51021830 None:intergenic 40.0%
ACCGAAAAGAAGTCGATGAG+AGG - chr2.2:51021807-51021826 MS.gene00393:CDS 45.0%
AGAAGGAGTCCAGATGGTGT+TGG - chr2.2:51021556-51021575 MS.gene00393:intron 50.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 51020989 51021850 51020989 ID=MS.gene00393
chr2.2 mRNA 51020989 51021850 51020989 ID=MS.gene00393.t1;Parent=MS.gene00393
chr2.2 exon 51021772 51021850 51021772 ID=MS.gene00393.t1.exon1;Parent=MS.gene00393.t1
chr2.2 CDS 51021772 51021850 51021772 ID=cds.MS.gene00393.t1;Parent=MS.gene00393.t1
chr2.2 exon 51020989 51021386 51020989 ID=MS.gene00393.t1.exon2;Parent=MS.gene00393.t1
chr2.2 CDS 51020989 51021386 51020989 ID=cds.MS.gene00393.t1;Parent=MS.gene00393.t1
Gene Sequence

>MS.gene00393

ATGGCTGATAAAAATATGAGAGTTGACTACATAACTGATGACTTGAAGAGGAAGACAACATTCAACAAAAGGAAGCATGGTTAGATACTAAATTTCTCCTTTATTTCTATAAAGAACACTCATATCATACAAATTTATTATGAATTTTTTTCTTGTTCATTTCTTTCAGTTTTTTTTTATCACTACCATGGATACTAAAAATATGAAAGTTGACTGCATAACCATTAGGAATTTATCAATATGAATATAGTTATTTGATGTTTGTTATTTTTTTTGTTGTTGTTGATATCATGAAAAAATTGTAAGCAAATGTTGTTGCAACCATAATAACATATCAGTTATGTAGACCTTTGAAATTATTGTTATTTTCACAATATTTTAAGATCATGTCGGTTATAGTATACATTTTTTCAGTTTCACATTTCTCTCAACTCTCTCACGGGTTTTGTTGTGTTTTTCAACAGGTATAACTAAGAAGATTAGTGAAATCACCACACTTTGTGGAATTGATGCATGTGGTATAATCTATGATGAAAACAATGATGGAGCAACGGTTTATCCATCAAAAGAAGGAGTCCAGATGGTGTTGGACAAGTTTAGGAGCTTTCCTGAATCGGAACAAAGAAAAGGAAAGCTGGATCATGAGGGCTTTTTGAGACAATCCATAATGAAATCGAAGGAGAAGTTGAAGAAACAAAAGGACAGGTCCAAGAAGAAGAAAATGAATGATCTACTTGGTGAATTCATTCATACGGGTGAATTTGATGGAAATGTGAGCGAGAATGATCTCGAAGATCTATCATTGCTTATTGGTGATTACCGAAAAGAAGTCGATGAGAGGATCGAATCAAGTCAAACCTGA
Protein sequence

>MS.gene00393.t1

MADKNMRVDYITDDLKRKTTFNKRKHGITKKISEITTLCGIDACGIIYDENNDGATVYPSKEGVQMVLDKFRSFPESEQRKGKLDHEGFLRQSIMKSKEKLKKQKDRSKKKKMNDLLGEFIHTGEFDGNVSENDLEDLSLLIGDYRKEVDERIESSQT