AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52388

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52388.t1 MTR_2g436310 97.973 148 3 0 1 148 1 148 2.50e-101 290
MS.gene52388.t1 MTR_5g067530 43.056 144 82 0 5 148 10 153 4.70e-36 125
MS.gene52388.t1 MTR_6g007633 46.528 144 73 3 8 148 11 153 2.92e-35 122
MS.gene52388.t1 MTR_6g007637 43.056 144 78 3 8 148 12 154 1.67e-32 115
MS.gene52388.t1 MTR_6g007623 44.444 144 76 3 8 148 8 150 9.73e-32 113
MS.gene52388.t1 MTR_3g098910 40.000 145 86 1 5 148 9 153 2.40e-31 114
MS.gene52388.t1 MTR_8g099730 46.154 143 75 1 8 148 21 163 3.38e-31 112
MS.gene52388.t1 MTR_8g096320 42.759 145 82 1 5 148 9 153 1.21e-30 111
MS.gene52388.t1 MTR_3g080990 43.357 143 79 1 8 148 11 153 2.53e-30 110
MS.gene52388.t1 MTR_3g098930 42.069 145 82 2 5 148 10 153 2.54e-30 108
MS.gene52388.t1 MTR_1g029380 41.379 145 82 2 6 148 6 149 1.89e-29 107
MS.gene52388.t1 MTR_7g007490 37.143 140 88 0 9 148 14 153 1.87e-28 105
MS.gene52388.t1 MTR_3g089125 41.958 143 78 3 9 148 9 149 3.29e-28 104
MS.gene52388.t1 MTR_7g405730 41.781 146 85 0 5 150 9 154 5.88e-28 104
MS.gene52388.t1 MTR_8g096310 37.500 144 89 1 6 148 10 153 1.02e-27 103
MS.gene52388.t1 MTR_5g092600 36.429 140 88 1 9 148 14 152 1.30e-27 103
MS.gene52388.t1 MTR_2g007890 35.211 142 91 1 9 150 16 156 1.07e-26 101
MS.gene52388.t1 MTR_1g028460 40.690 145 82 1 8 148 9 153 2.57e-26 100
MS.gene52388.t1 MTR_3g090950 37.931 145 86 1 8 148 9 153 1.13e-25 98.2
MS.gene52388.t1 MTR_3g090940 40.411 146 81 3 8 148 9 153 5.11e-25 96.7
MS.gene52388.t1 MTR_7g405710 38.194 144 89 0 5 148 9 152 2.52e-24 95.1
MS.gene52388.t1 MTR_8g042490 40.411 146 76 4 9 148 18 158 2.60e-23 91.7
MS.gene52388.t1 MTR_2g073190 40.714 140 78 3 9 145 18 155 5.28e-21 88.6
MS.gene52388.t1 MTR_4g106990 39.370 127 73 3 25 148 35 160 4.14e-18 78.2
MS.gene52388.t1 MTR_6g007610 34.810 158 78 5 8 148 11 160 2.11e-17 76.3
MS.gene52388.t1 MTR_8g099730 39.796 98 57 1 53 148 2 99 1.01e-12 62.8
MS.gene52388.t1 MTR_8g096320 39.175 97 58 1 53 148 2 98 3.14e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52388.t1 AT4G15920 59.060 149 60 1 1 148 1 149 1.20e-60 187
MS.gene52388.t1 AT3G16690 54.000 150 68 1 1 149 1 150 2.51e-55 172
MS.gene52388.t1 AT3G16690 55.102 147 65 1 1 146 1 147 6.69e-54 170
MS.gene52388.t1 AT3G16690 55.102 147 65 1 1 146 36 182 1.34e-53 170
MS.gene52388.t1 AT5G50800 42.759 145 82 1 5 148 9 153 2.06e-35 124
MS.gene52388.t1 AT5G40260 40.972 144 81 3 5 144 8 151 4.02e-33 116
MS.gene52388.t1 AT5G40260 40.972 144 81 3 5 144 8 151 1.04e-32 116
MS.gene52388.t1 AT4G25010 41.135 141 82 1 9 148 13 153 1.07e-32 117
MS.gene52388.t1 AT3G48740 38.194 144 89 0 5 148 11 154 2.62e-32 116
MS.gene52388.t1 AT1G21460 43.056 144 75 3 9 148 9 149 7.45e-32 112
MS.gene52388.t1 AT4G10850 41.781 146 78 3 8 148 13 156 1.35e-31 114
MS.gene52388.t1 AT1G21460 43.056 144 75 3 9 148 9 149 1.93e-31 113
MS.gene52388.t1 AT5G23660 36.806 144 91 0 5 148 11 154 4.68e-30 110
MS.gene52388.t1 AT5G13170 37.241 145 90 1 5 148 11 155 1.24e-29 109
MS.gene52388.t1 AT5G62850 37.013 154 90 4 1 148 1 153 1.35e-29 107
MS.gene52388.t1 AT2G39060 38.889 144 88 0 5 148 9 152 6.10e-29 107
MS.gene52388.t1 AT5G62850 37.013 154 90 4 1 148 1 153 8.47e-29 106
MS.gene52388.t1 AT5G53190 38.926 149 79 4 8 148 9 153 2.60e-26 100
MS.gene52388.t1 AT5G50790 35.000 140 91 0 9 148 13 152 3.15e-26 100
MS.gene52388.t1 AT1G66770 37.671 146 84 4 8 148 13 156 5.40e-25 96.7
MS.gene52388.t1 AT3G28007 38.462 143 84 3 9 148 12 153 2.79e-20 84.0
MS.gene52388.t1 AT3G14770 34.507 142 90 2 9 148 18 158 7.39e-18 77.4

Find 29 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAATTCTTGCTGGGATTT+TGG 0.124715 2.3:-54892003 MS.gene52388:CDS
TATAATGCAGACCAACATTT+TGG 0.198727 2.3:-54892729 MS.gene52388:intron
TACCTTGTGGCCACTGTTAA+TGG 0.201020 2.3:-54892598 MS.gene52388:CDS
AGTTTCTTTGTTGGAGTTAT+AGG 0.210484 2.3:-54893025 MS.gene52388:intron
TCTTCATTGTGGACTTACTA+TGG 0.279770 2.3:-54892640 MS.gene52388:CDS
GTGGCCACTGTTAATGGCTT+TGG 0.323328 2.3:-54892592 MS.gene52388:CDS
GCTTTGAACATTCTTATGTA+TGG 0.363700 2.3:-54891891 MS.gene52388:CDS
GTGAAGACTGCAATTCTTGC+TGG 0.366290 2.3:-54892011 MS.gene52388:CDS
TAGTGGTGCTGTTGGTATCA+TGG 0.401798 2.3:-54891919 MS.gene52388:CDS
GCAGATCCAAGTTTCTTTGT+TGG 0.416684 2.3:-54893034 MS.gene52388:CDS
TGGCTCACCTCTTGCTGTCA+TGG 0.454725 2.3:-54891871 MS.gene52388:intron
TTAAGCAATGTGCATATGTA+AGG 0.458717 2.3:+54892664 None:intergenic
TACTACTCAATTAGCATTGG+AGG 0.468548 2.3:-54891952 MS.gene52388:CDS
TACTATGGAACTATAAAAGC+TGG 0.493273 2.3:-54892625 MS.gene52388:CDS
TTTATTATTCTCCAAAATGT+TGG 0.503864 2.3:+54892718 None:intergenic
TGAAGACTGCAATTCTTGCT+GGG 0.514788 2.3:-54892010 MS.gene52388:CDS
ATAACTCCAACAAAGAAACT+TGG 0.519013 2.3:+54893028 None:intergenic
GATTACTACTCAATTAGCAT+TGG 0.521186 2.3:-54891955 MS.gene52388:CDS
AGTGGTGCTGTTGGTATCAT+GGG 0.532404 2.3:-54891918 MS.gene52388:CDS
AAACTTACCATGACAGCAAG+AGG 0.581451 2.3:+54891864 None:intergenic
GAAGCTCGTAGTGGTGCTGT+TGG 0.583483 2.3:-54891927 MS.gene52388:CDS
ACTACTCAATTAGCATTGGA+GGG 0.594157 2.3:-54891951 MS.gene52388:CDS
AGCCATTAACAGTGGCCACA+AGG 0.600324 2.3:+54892596 None:intergenic
CATTGCTTAACTCTTCATTG+TGG 0.620597 2.3:-54892651 MS.gene52388:CDS
TAATGGCTTTGGCATCGTGG+TGG 0.662663 2.3:-54892581 MS.gene52388:CDS
TGTTAATGGCTTTGGCATCG+TGG 0.667290 2.3:-54892584 MS.gene52388:CDS
TTGGAGGGAGAAGCTCGTAG+TGG 0.699075 2.3:-54891936 MS.gene52388:CDS
AAAAGCTGGAGAATACCTTG+TGG 0.701844 2.3:-54892611 MS.gene52388:CDS
GATGCCAAAGCCATTAACAG+TGG 0.716694 2.3:+54892588 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATATATTATTTTAAGATGTA+TGG + chr2.3:54892687-54892706 None:intergenic 10.0%
!! AAAAATGGAAATTTCATATA+TGG - chr2.3:54891933-54891952 MS.gene52388:CDS 15.0%
!!! ATATATGAAATTTCCATTTT+TGG + chr2.3:54891934-54891953 None:intergenic 15.0%
!!! TATATGAAATTTCCATTTTT+GGG + chr2.3:54891933-54891952 None:intergenic 15.0%
!! GTATATGTTTGATTAAATTC+AGG - chr2.3:54892806-54892825 MS.gene52388:intron 20.0%
!! TTTATTATTCTCCAAAATGT+TGG + chr2.3:54892124-54892143 None:intergenic 20.0%
! AAAAGGAATGAATATTAGGA+GGG + chr2.3:54891859-54891878 None:intergenic 25.0%
! AGTGAAAAGGAATGAATATT+AGG + chr2.3:54891863-54891882 None:intergenic 25.0%
!! ACTATGTTGTTTGAATTTAG+AGG - chr2.3:54892613-54892632 MS.gene52388:CDS 25.0%
!! TATTGTCTCAATTTTGCTAA+TGG - chr2.3:54892064-54892083 MS.gene52388:intron 25.0%
!!! TTTTCTTAATTTGTTGCTAC+AGG - chr2.3:54891959-54891978 MS.gene52388:CDS 25.0%
AGTTTCTTTGTTGGAGTTAT+AGG - chr2.3:54891814-54891833 MS.gene52388:intron 30.0%
ATAACTCCAACAAAGAAACT+TGG + chr2.3:54891814-54891833 None:intergenic 30.0%
CAACATAGTTCAAATATCCT+CGG + chr2.3:54892602-54892621 None:intergenic 30.0%
GAAAAGGAATGAATATTAGG+AGG + chr2.3:54891860-54891879 None:intergenic 30.0%
GATTACTACTCAATTAGCAT+TGG - chr2.3:54892884-54892903 MS.gene52388:intron 30.0%
TACTATGGAACTATAAAAGC+TGG - chr2.3:54892214-54892233 MS.gene52388:intron 30.0%
TTAAGCAATGTGCATATGTA+AGG + chr2.3:54892178-54892197 None:intergenic 30.0%
! GCTTTGAACATTCTTATGTA+TGG - chr2.3:54892948-54892967 MS.gene52388:intron 30.0%
! TATAATGCAGACCAACATTT+TGG - chr2.3:54892110-54892129 MS.gene52388:intron 30.0%
! TATATTCGTACCCTCATTTT+TGG + chr2.3:54892322-54892341 None:intergenic 30.0%
!! ATATTCGTACCCTCATTTTT+GGG + chr2.3:54892321-54892340 None:intergenic 30.0%
!! TGATTAGTGACTTGTTTATG+AGG - chr2.3:54892754-54892773 MS.gene52388:intron 30.0%
AAGATTGGTACCATCCATTA+AGG + chr2.3:54891898-54891917 None:intergenic 35.0%
CATTGCTTAACTCTTCATTG+TGG - chr2.3:54892188-54892207 MS.gene52388:intron 35.0%
GTTAGTGCAAAAGAGTGAAA+AGG + chr2.3:54891876-54891895 None:intergenic 35.0%
TATTGATCCATGCCCAAAAA+TGG - chr2.3:54891918-54891937 MS.gene52388:CDS 35.0%
TCTTCATTGTGGACTTACTA+TGG - chr2.3:54892199-54892218 MS.gene52388:intron 35.0%
TTTGCACTAACCTTAATGGA+TGG - chr2.3:54891885-54891904 MS.gene52388:CDS 35.0%
! ACTACTCAATTAGCATTGGA+GGG - chr2.3:54892888-54892907 MS.gene52388:intron 35.0%
! CTCTTTTGCACTAACCTTAA+TGG - chr2.3:54891881-54891900 MS.gene52388:CDS 35.0%
! TACTACTCAATTAGCATTGG+AGG - chr2.3:54892887-54892906 MS.gene52388:intron 35.0%
! TGACATTTTACAATGTTCCG+AGG - chr2.3:54892582-54892601 MS.gene52388:CDS 35.0%
!! GAAATTTCCATTTTTGGGCA+TGG + chr2.3:54891928-54891947 None:intergenic 35.0%
!! TATTCGTACCCTCATTTTTG+GGG + chr2.3:54892320-54892339 None:intergenic 35.0%
AAAAGCTGGAGAATACCTTG+TGG - chr2.3:54892228-54892247 MS.gene52388:intron 40.0%
AAACTTACCATGACAGCAAG+AGG + chr2.3:54892978-54892997 None:intergenic 40.0%
AGAGTGTAAAGAGCTTACAC+AGG + chr2.3:54892016-54892035 None:intergenic 40.0%
ATATGCACCCCCAAAAATGA+GGG - chr2.3:54892309-54892328 MS.gene52388:intron 40.0%
GCAGATCCAAGTTTCTTTGT+TGG - chr2.3:54891805-54891824 MS.gene52388:intron 40.0%
GGGCATGGATCAATAAAGAT+TGG + chr2.3:54891913-54891932 None:intergenic 40.0%
TATATGCACCCCCAAAAATG+AGG - chr2.3:54892308-54892327 MS.gene52388:intron 40.0%
TGAAGACTGCAATTCTTGCT+GGG - chr2.3:54892829-54892848 MS.gene52388:intron 40.0%
TTGCTGTCATGGTAAGTTTC+TGG - chr2.3:54892979-54892998 MS.gene52388:intron 40.0%
! TGCAATTCTTGCTGGGATTT+TGG - chr2.3:54892836-54892855 MS.gene52388:intron 40.0%
!! ATTCGTACCCTCATTTTTGG+GGG + chr2.3:54892319-54892338 None:intergenic 40.0%
GATGCCAAAGCCATTAACAG+TGG + chr2.3:54892254-54892273 None:intergenic 45.0%
GTGAAGACTGCAATTCTTGC+TGG - chr2.3:54892828-54892847 MS.gene52388:intron 45.0%
TACCTTGTGGCCACTGTTAA+TGG - chr2.3:54892241-54892260 MS.gene52388:intron 45.0%
! GATTTTGGACGTGGTGATCT+TGG - chr2.3:54892851-54892870 MS.gene52388:CDS 45.0%
!! AGTGGTGCTGTTGGTATCAT+GGG - chr2.3:54892921-54892940 MS.gene52388:intron 45.0%
!! TAGTGGTGCTGTTGGTATCA+TGG - chr2.3:54892920-54892939 MS.gene52388:intron 45.0%
!! TGTTAATGGCTTTGGCATCG+TGG - chr2.3:54892255-54892274 MS.gene52388:intron 45.0%
AGCCATTAACAGTGGCCACA+AGG + chr2.3:54892246-54892265 None:intergenic 50.0%
GTGGCCACTGTTAATGGCTT+TGG - chr2.3:54892247-54892266 MS.gene52388:intron 50.0%
! TCTTGCTGGGATTTTGGACG+TGG - chr2.3:54892842-54892861 MS.gene52388:intron 50.0%
!! TAATGGCTTTGGCATCGTGG+TGG - chr2.3:54892258-54892277 MS.gene52388:intron 50.0%
TTGGAGGGAGAAGCTCGTAG+TGG - chr2.3:54892903-54892922 MS.gene52388:intron 55.0%
! TGGCTCACCTCTTGCTGTCA+TGG - chr2.3:54892968-54892987 MS.gene52388:intron 55.0%
!! GAAGCTCGTAGTGGTGCTGT+TGG - chr2.3:54892912-54892931 MS.gene52388:intron 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 54891802 54893059 54891802 ID=MS.gene52388
chr2.3 mRNA 54891802 54893059 54891802 ID=MS.gene52388.t1;Parent=MS.gene52388
chr2.3 exon 54893026 54893059 54893026 ID=MS.gene52388.t1.exon1;Parent=MS.gene52388.t1
chr2.3 CDS 54893026 54893059 54893026 ID=cds.MS.gene52388.t1;Parent=MS.gene52388.t1
chr2.3 exon 54892844 54892880 54892844 ID=MS.gene52388.t1.exon2;Parent=MS.gene52388.t1
chr2.3 CDS 54892844 54892880 54892844 ID=cds.MS.gene52388.t1;Parent=MS.gene52388.t1
chr2.3 exon 54892531 54892741 54892531 ID=MS.gene52388.t1.exon3;Parent=MS.gene52388.t1
chr2.3 CDS 54892531 54892741 54892531 ID=cds.MS.gene52388.t1;Parent=MS.gene52388.t1
chr2.3 exon 54891872 54892033 54891872 ID=MS.gene52388.t1.exon4;Parent=MS.gene52388.t1
chr2.3 CDS 54891872 54892033 54891872 ID=cds.MS.gene52388.t1;Parent=MS.gene52388.t1
chr2.3 exon 54891802 54891810 54891802 ID=MS.gene52388.t1.exon5;Parent=MS.gene52388.t1
chr2.3 CDS 54891802 54891810 54891802 ID=cds.MS.gene52388.t1;Parent=MS.gene52388.t1
Gene Sequence

>MS.gene52388

ATGGCAGATCCAAGTTTCTTTGTTGGAGTTATAGGTAACACATGCATATGAATACCCTCCTAATATTCATTCCTTTTCACTCTTTTGCACTAACCTTAATGGATGGTACCAATCTTTATTGATCCATGCCCAAAAATGGAAATTTCATATATGGTTTTTTTCTTAATTTGTTGCTACAGGTAACATCATCTCAATTCTCATGTTTCTTTCTCCTGTGTAAGCTCTTTACACTCTACACAACTTTAATTAATTATTTGTAAATTATTGTCTCAATTTTGCTAATGGATAATATTTGTCTTCTTAAATTATATAATGCAGACCAACATTTTGGAGAATAATAAAGCAGAAATCTACAGAAGAATTCTCTAGTTTTCCTTACATATGCACATTGCTTAACTCTTCATTGTGGACTTACTATGGAACTATAAAAGCTGGAGAATACCTTGTGGCCACTGTTAATGGCTTTGGCATCGTGGTGGAGACAATCTACATTCTTCTATTTCTCATATATGCACCCCCAAAAATGAGGGTACGAATATACTTTTACAAAATCAAATTAATTTATTAACATAAAAAATTAAATTAATTTATAATTTTGAAGTCTATGATACTTACAGATGAAATTAGAAACAAATTTCATTTTTTTTTTGTCTTTAATTTTTTGTTGTTACTTCAATTTTTCTCTCACTCTTATAATTTTATACAAAAATGAAAAAATGAGAAATTATTTTTTTAGTAAAAAAATGAAAAATTATTATTAGTTACAGTGATATATATTGTTGACATTTTACAATGTTCCGAGGATATTTGAACTATGTTGTTTGAATTTAGAGGTTCAAAGTTCAAACTCTTATTACTGATCTGACACTCGTGTATTCACTACCATACATCTTAAAATAATATATATTTTTTTGACAATAAAAAAAAAAATTTATTATATTTTTCTCTAATTTGATTAGTGACTTGTTTATGAGGCTCATTTGATTAATAGTAATTAAACATATGTATATGTTTGATTAAATTCAGGTGAAGACTGCAATTCTTGCTGGGATTTTGGACGTGGTGATCTTGGCAGCAGCAGTGATTACTACTCAATTAGCATTGGAGGGAGAAGCTCGTAGTGGTGCTGTTGGTATCATGGGTGCAGCTTTGAACATTCTTATGTATGGCTCACCTCTTGCTGTCATGGTAAGTTTCTGGAGCTTTCTATAATTATTTAAGTTTGTCTTATCTCTTTATGATCATCTAGATTCATTAA
Protein sequence

>MS.gene52388.t1

MADPSFFVGVIGNIISILMFLSPVPTFWRIIKQKSTEEFSSFPYICTLLNSSLWTYYGTIKAGEYLVATVNGFGIVVETIYILLFLIYAPPKMRVKTAILAGILDVVILAAAVITTQLALEGEARSGAVGIMGAALNILMYGSPLAVMIH