AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004537

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004537.t1 MTR_2g436310 97.973 148 3 0 1 148 1 148 2.50e-101 290
MS.gene004537.t1 MTR_5g067530 43.056 144 82 0 5 148 10 153 4.70e-36 125
MS.gene004537.t1 MTR_6g007633 46.528 144 73 3 8 148 11 153 2.92e-35 122
MS.gene004537.t1 MTR_6g007637 43.056 144 78 3 8 148 12 154 1.67e-32 115
MS.gene004537.t1 MTR_6g007623 44.444 144 76 3 8 148 8 150 9.73e-32 113
MS.gene004537.t1 MTR_3g098910 40.000 145 86 1 5 148 9 153 2.40e-31 114
MS.gene004537.t1 MTR_8g099730 46.154 143 75 1 8 148 21 163 3.38e-31 112
MS.gene004537.t1 MTR_8g096320 42.759 145 82 1 5 148 9 153 1.21e-30 111
MS.gene004537.t1 MTR_3g080990 43.357 143 79 1 8 148 11 153 2.53e-30 110
MS.gene004537.t1 MTR_3g098930 42.069 145 82 2 5 148 10 153 2.54e-30 108
MS.gene004537.t1 MTR_1g029380 41.379 145 82 2 6 148 6 149 1.89e-29 107
MS.gene004537.t1 MTR_7g007490 37.143 140 88 0 9 148 14 153 1.87e-28 105
MS.gene004537.t1 MTR_3g089125 41.958 143 78 3 9 148 9 149 3.29e-28 104
MS.gene004537.t1 MTR_7g405730 41.781 146 85 0 5 150 9 154 5.88e-28 104
MS.gene004537.t1 MTR_8g096310 37.500 144 89 1 6 148 10 153 1.02e-27 103
MS.gene004537.t1 MTR_5g092600 36.429 140 88 1 9 148 14 152 1.30e-27 103
MS.gene004537.t1 MTR_2g007890 35.211 142 91 1 9 150 16 156 1.07e-26 101
MS.gene004537.t1 MTR_1g028460 40.690 145 82 1 8 148 9 153 2.57e-26 100
MS.gene004537.t1 MTR_3g090950 37.931 145 86 1 8 148 9 153 1.13e-25 98.2
MS.gene004537.t1 MTR_3g090940 40.411 146 81 3 8 148 9 153 5.11e-25 96.7
MS.gene004537.t1 MTR_7g405710 38.194 144 89 0 5 148 9 152 2.52e-24 95.1
MS.gene004537.t1 MTR_8g042490 40.411 146 76 4 9 148 18 158 2.60e-23 91.7
MS.gene004537.t1 MTR_2g073190 40.714 140 78 3 9 145 18 155 5.28e-21 88.6
MS.gene004537.t1 MTR_4g106990 39.370 127 73 3 25 148 35 160 4.14e-18 78.2
MS.gene004537.t1 MTR_6g007610 34.810 158 78 5 8 148 11 160 2.11e-17 76.3
MS.gene004537.t1 MTR_8g099730 39.796 98 57 1 53 148 2 99 1.01e-12 62.8
MS.gene004537.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.gene004537.t1 AT4G15920 59.060 149 60 1 1 148 1 149 1.20e-60 187
MS.gene004537.t1 AT3G16690 54.000 150 68 1 1 149 1 150 2.51e-55 172
MS.gene004537.t1 AT3G16690 55.102 147 65 1 1 146 1 147 6.69e-54 170
MS.gene004537.t1 AT3G16690 55.102 147 65 1 1 146 36 182 1.34e-53 170
MS.gene004537.t1 AT5G50800 42.759 145 82 1 5 148 9 153 2.06e-35 124
MS.gene004537.t1 AT5G40260 40.972 144 81 3 5 144 8 151 4.02e-33 116
MS.gene004537.t1 AT5G40260 40.972 144 81 3 5 144 8 151 1.04e-32 116
MS.gene004537.t1 AT4G25010 41.135 141 82 1 9 148 13 153 1.07e-32 117
MS.gene004537.t1 AT3G48740 38.194 144 89 0 5 148 11 154 2.62e-32 116
MS.gene004537.t1 AT1G21460 43.056 144 75 3 9 148 9 149 7.45e-32 112
MS.gene004537.t1 AT4G10850 41.781 146 78 3 8 148 13 156 1.35e-31 114
MS.gene004537.t1 AT1G21460 43.056 144 75 3 9 148 9 149 1.93e-31 113
MS.gene004537.t1 AT5G23660 36.806 144 91 0 5 148 11 154 4.68e-30 110
MS.gene004537.t1 AT5G13170 37.241 145 90 1 5 148 11 155 1.24e-29 109
MS.gene004537.t1 AT5G62850 37.013 154 90 4 1 148 1 153 1.35e-29 107
MS.gene004537.t1 AT2G39060 38.889 144 88 0 5 148 9 152 6.10e-29 107
MS.gene004537.t1 AT5G62850 37.013 154 90 4 1 148 1 153 8.47e-29 106
MS.gene004537.t1 AT5G53190 38.926 149 79 4 8 148 9 153 2.60e-26 100
MS.gene004537.t1 AT5G50790 35.000 140 91 0 9 148 13 152 3.15e-26 100
MS.gene004537.t1 AT1G66770 37.671 146 84 4 8 148 13 156 5.40e-25 96.7
MS.gene004537.t1 AT3G28007 38.462 143 84 3 9 148 12 153 2.79e-20 84.0
MS.gene004537.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 2.1:-57014161 MS.gene004537:CDS
TATAATGCAGACCAACATTT+TGG 0.198727 2.1:-57014885 MS.gene004537:intron
TACCTTGTGGCCACTGTTAA+TGG 0.201020 2.1:-57014754 MS.gene004537:CDS
AGTTTCTTTGTTGGAGTTAT+AGG 0.210484 2.1:-57015182 MS.gene004537:intron
TCTTCATTGTGGACTTACTA+TGG 0.279770 2.1:-57014796 MS.gene004537:CDS
GTGGCCACTGTTAATGGCTT+TGG 0.323328 2.1:-57014748 MS.gene004537:CDS
GCTTTGAACATTCTTATGTA+TGG 0.363700 2.1:-57014049 MS.gene004537:CDS
GTGAAGACTGCAATTCTTGC+TGG 0.366290 2.1:-57014169 MS.gene004537:CDS
TAGTGGTGCTGTTGGTATCA+TGG 0.401798 2.1:-57014077 MS.gene004537:CDS
GCAGATCCAAGTTTCTTTGT+TGG 0.416684 2.1:-57015191 MS.gene004537:CDS
TGGCTCACCTCTTGCTGTCA+TGG 0.454725 2.1:-57014029 MS.gene004537:intron
TTAAGCAATGTGCATATGTA+AGG 0.458717 2.1:+57014820 None:intergenic
TACTACTCAATTAGCATTGG+AGG 0.468548 2.1:-57014110 MS.gene004537:CDS
TACTATGGAACTATAAAAGC+TGG 0.493273 2.1:-57014781 MS.gene004537:CDS
TTTATTATTCTCCAAAATGT+TGG 0.503864 2.1:+57014874 None:intergenic
TGAAGACTGCAATTCTTGCT+GGG 0.514788 2.1:-57014168 MS.gene004537:CDS
ATAACTCCAACAAAGAAACT+TGG 0.519013 2.1:+57015185 None:intergenic
GATTACTACTCAATTAGCAT+TGG 0.521186 2.1:-57014113 MS.gene004537:CDS
AGTGGTGCTGTTGGTATCAT+GGG 0.532404 2.1:-57014076 MS.gene004537:CDS
AAACTTACCATGACAGCAAG+AGG 0.581451 2.1:+57014022 None:intergenic
GAAGCTCGTAGTGGTGCTGT+TGG 0.583483 2.1:-57014085 MS.gene004537:CDS
ACTACTCAATTAGCATTGGA+GGG 0.594157 2.1:-57014109 MS.gene004537:CDS
AGCCATTAACAGTGGCCACA+AGG 0.600324 2.1:+57014752 None:intergenic
CATTGCTTAACTCTTCATTG+TGG 0.620597 2.1:-57014807 MS.gene004537:CDS
TAATGGCTTTGGCATCGTGG+TGG 0.662663 2.1:-57014737 MS.gene004537:CDS
TGTTAATGGCTTTGGCATCG+TGG 0.667290 2.1:-57014740 MS.gene004537:CDS
TTGGAGGGAGAAGCTCGTAG+TGG 0.699075 2.1:-57014094 MS.gene004537:CDS
AAAAGCTGGAGAATACCTTG+TGG 0.701844 2.1:-57014767 MS.gene004537:CDS
GATGCCAAAGCCATTAACAG+TGG 0.716694 2.1:+57014744 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATATTATTTTAAGATGTA+TGG + chr2.1:57014844-57014863 None:intergenic 10.0%
!! AAAAATGGAAATTTCATATA+TGG - chr2.1:57014091-57014110 MS.gene004537:CDS 15.0%
!!! ATATATGAAATTTCCATTTT+TGG + chr2.1:57014092-57014111 None:intergenic 15.0%
!!! TATATGAAATTTCCATTTTT+GGG + chr2.1:57014091-57014110 None:intergenic 15.0%
!! GTATATGTTTGATTAAATTC+AGG - chr2.1:57014963-57014982 MS.gene004537:intron 20.0%
!! TTTATTATTCTCCAAAATGT+TGG + chr2.1:57014283-57014302 None:intergenic 20.0%
! AAAAGGAATGAATATTTGGA+GGG + chr2.1:57014017-57014036 None:intergenic 25.0%
! AGTGAAAAGGAATGAATATT+TGG + chr2.1:57014021-57014040 None:intergenic 25.0%
!! ACTATGTTGTTTGAATTTAG+AGG - chr2.1:57014770-57014789 MS.gene004537:CDS 25.0%
!! TATTGTCTCAATTTTGCTAA+TGG - chr2.1:57014223-57014242 MS.gene004537:intron 25.0%
!!! TGATTAGTGACTTTTTTATG+AGG - chr2.1:57014911-57014930 MS.gene004537:intron 25.0%
!!! TTTTCTTAATTTGTTGCTAC+AGG - chr2.1:57014118-57014137 MS.gene004537:CDS 25.0%
AGTTTCTTTGTTGGAGTTAT+AGG - chr2.1:57013972-57013991 MS.gene004537:intron 30.0%
ATAACTCCAACAAAGAAACT+TGG + chr2.1:57013972-57013991 None:intergenic 30.0%
CAACATAGTTCAAATATCCT+CGG + chr2.1:57014759-57014778 None:intergenic 30.0%
GAAAAGGAATGAATATTTGG+AGG + chr2.1:57014018-57014037 None:intergenic 30.0%
GATTACTACTCAATTAGCAT+TGG - chr2.1:57015041-57015060 MS.gene004537:intron 30.0%
TACTATGGAACTATAAAAGC+TGG - chr2.1:57014373-57014392 MS.gene004537:intron 30.0%
TTAAGCAATGTGCATATGTA+AGG + chr2.1:57014337-57014356 None:intergenic 30.0%
! GCTTTGAACATTCTTATGTA+TGG - chr2.1:57015105-57015124 MS.gene004537:intron 30.0%
! TATAATGCAGACCAACATTT+TGG - chr2.1:57014269-57014288 MS.gene004537:intron 30.0%
! TATATTCGTACCCTCATTTT+TGG + chr2.1:57014481-57014500 None:intergenic 30.0%
!! ATATTCGTACCCTCATTTTT+GGG + chr2.1:57014480-57014499 None:intergenic 30.0%
AAGATTGGTACCATCCATTA+AGG + chr2.1:57014056-57014075 None:intergenic 35.0%
CATTGCTTAACTCTTCATTG+TGG - chr2.1:57014347-57014366 MS.gene004537:intron 35.0%
GTTAGTGCAAAAGAGTGAAA+AGG + chr2.1:57014034-57014053 None:intergenic 35.0%
TATTGATCCATGCCCAAAAA+TGG - chr2.1:57014076-57014095 MS.gene004537:CDS 35.0%
TCTTCATTGTGGACTTACTA+TGG - chr2.1:57014358-57014377 MS.gene004537:intron 35.0%
TTTGCACTAACCTTAATGGA+TGG - chr2.1:57014043-57014062 MS.gene004537:CDS 35.0%
! ACTACTCAATTAGCATTGGA+GGG - chr2.1:57015045-57015064 MS.gene004537:intron 35.0%
! CTCTTTTGCACTAACCTTAA+TGG - chr2.1:57014039-57014058 MS.gene004537:CDS 35.0%
! TACTACTCAATTAGCATTGG+AGG - chr2.1:57015044-57015063 MS.gene004537:intron 35.0%
! TGACATTTTACAATGTTCCG+AGG - chr2.1:57014739-57014758 MS.gene004537:CDS 35.0%
!! GAAATTTCCATTTTTGGGCA+TGG + chr2.1:57014086-57014105 None:intergenic 35.0%
!! TATTCGTACCCTCATTTTTG+GGG + chr2.1:57014479-57014498 None:intergenic 35.0%
AAAAGCTGGAGAATACCTTG+TGG - chr2.1:57014387-57014406 MS.gene004537:intron 40.0%
AAACTTACCATGACAGCAAG+AGG + chr2.1:57015135-57015154 None:intergenic 40.0%
AGAGTGTAAAGAGCTTACAC+AGG + chr2.1:57014175-57014194 None:intergenic 40.0%
ATATGCACCCCCAAAAATGA+GGG - chr2.1:57014468-57014487 MS.gene004537:intron 40.0%
GCAGATCCAAGTTTCTTTGT+TGG - chr2.1:57013963-57013982 MS.gene004537:intron 40.0%
GGGCATGGATCAATAAAGAT+TGG + chr2.1:57014071-57014090 None:intergenic 40.0%
TATATGCACCCCCAAAAATG+AGG - chr2.1:57014467-57014486 MS.gene004537:intron 40.0%
TGAAGACTGCAATTCTTGCT+GGG - chr2.1:57014986-57015005 MS.gene004537:intron 40.0%
TTGCTGTCATGGTAAGTTTC+TGG - chr2.1:57015136-57015155 MS.gene004537:intron 40.0%
! TGCAATTCTTGCTGGGATTT+TGG - chr2.1:57014993-57015012 MS.gene004537:intron 40.0%
!! ATTCGTACCCTCATTTTTGG+GGG + chr2.1:57014478-57014497 None:intergenic 40.0%
GATGCCAAAGCCATTAACAG+TGG + chr2.1:57014413-57014432 None:intergenic 45.0%
GTGAAGACTGCAATTCTTGC+TGG - chr2.1:57014985-57015004 MS.gene004537:intron 45.0%
TACCTTGTGGCCACTGTTAA+TGG - chr2.1:57014400-57014419 MS.gene004537:intron 45.0%
! GATTTTGGACGTGGTGATCT+TGG - chr2.1:57015008-57015027 MS.gene004537:CDS 45.0%
!! AGTGGTGCTGTTGGTATCAT+GGG - chr2.1:57015078-57015097 MS.gene004537:intron 45.0%
!! TAGTGGTGCTGTTGGTATCA+TGG - chr2.1:57015077-57015096 MS.gene004537:intron 45.0%
!! TGTTAATGGCTTTGGCATCG+TGG - chr2.1:57014414-57014433 MS.gene004537:intron 45.0%
AGCCATTAACAGTGGCCACA+AGG + chr2.1:57014405-57014424 None:intergenic 50.0%
GTGGCCACTGTTAATGGCTT+TGG - chr2.1:57014406-57014425 MS.gene004537:intron 50.0%
! TCTTGCTGGGATTTTGGACG+TGG - chr2.1:57014999-57015018 MS.gene004537:intron 50.0%
!! TAATGGCTTTGGCATCGTGG+TGG - chr2.1:57014417-57014436 MS.gene004537:intron 50.0%
TTGGAGGGAGAAGCTCGTAG+TGG - chr2.1:57015060-57015079 MS.gene004537:intron 55.0%
! TGGCTCACCTCTTGCTGTCA+TGG - chr2.1:57015125-57015144 MS.gene004537:intron 55.0%
!! GAAGCTCGTAGTGGTGCTGT+TGG - chr2.1:57015069-57015088 MS.gene004537:intron 55.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 57013960 57015216 57013960 ID=MS.gene004537
chr2.1 mRNA 57013960 57015216 57013960 ID=MS.gene004537.t1;Parent=MS.gene004537
chr2.1 exon 57015183 57015216 57015183 ID=MS.gene004537.t1.exon1;Parent=MS.gene004537.t1
chr2.1 CDS 57015183 57015216 57015183 ID=cds.MS.gene004537.t1;Parent=MS.gene004537.t1
chr2.1 exon 57015000 57015036 57015000 ID=MS.gene004537.t1.exon2;Parent=MS.gene004537.t1
chr2.1 CDS 57015000 57015036 57015000 ID=cds.MS.gene004537.t1;Parent=MS.gene004537.t1
chr2.1 exon 57014687 57014897 57014687 ID=MS.gene004537.t1.exon3;Parent=MS.gene004537.t1
chr2.1 CDS 57014687 57014897 57014687 ID=cds.MS.gene004537.t1;Parent=MS.gene004537.t1
chr2.1 exon 57014030 57014191 57014030 ID=MS.gene004537.t1.exon4;Parent=MS.gene004537.t1
chr2.1 CDS 57014030 57014191 57014030 ID=cds.MS.gene004537.t1;Parent=MS.gene004537.t1
chr2.1 exon 57013960 57013968 57013960 ID=MS.gene004537.t1.exon5;Parent=MS.gene004537.t1
chr2.1 CDS 57013960 57013968 57013960 ID=cds.MS.gene004537.t1;Parent=MS.gene004537.t1
Gene Sequence

>MS.gene004537

ATGGCAGATCCAAGTTTCTTTGTTGGAGTTATAGGTAACACATGCATATGAATACCCTCCAAATATTCATTCCTTTTCACTCTTTTGCACTAACCTTAATGGATGGTACCAATCTTTATTGATCCATGCCCAAAAATGGAAATTTCATATATGGCTTTTTTTCTTAATTTGTTGCTACAGGTAACATCATCTCAATTCTCATGTTTCTTTCTCCTGTGTAAGCTCTTTACACTCTACACAACTTTAATTAATTATTTGTAAATTATTGTCTCAATTTTGCTAATGGATAATATTTGTCTTCTTAAATTATATAATGCAGACCAACATTTTGGAGAATAATAAAGCAGAAATCTACAGAAGAATTCTCTAGTTTTCCTTACATATGCACATTGCTTAACTCTTCATTGTGGACTTACTATGGAACTATAAAAGCTGGAGAATACCTTGTGGCCACTGTTAATGGCTTTGGCATCGTGGTGGAGACAATCTACATTCTTCTATTTCTCATATATGCACCCCCAAAAATGAGGGTACGAATATACTTTTACAAAATCAAATTAATTTATTAACATAAAAAATTAAATTAATTTATAATTTTGAAGTCTATGATACTTACAGATGAAATTAGAAACAAATTTCATTTTTTTTGTCTTTAACTTTTTGTTGTTACTTCAATTTTTCTCTCACTCTTATAATTTTATACAAAAATGAAAAAATGAGAAATTATTTTTTTAGTAAAAAAATGAAAAATTATTATTAGTTACAGTGATATATATTGTTGACATTTTACAATGTTCCGAGGATATTTGAACTATGTTGTTTGAATTTAGAGGTTCAAAGTTCAAACTCTTATCACTGATCTGACACTCGTGTATTCACTACCATACATCTTAAAATAATATTTTTTTTTTGACAATAAAAAAAAATAAATTATTATATTTTTCTCTAATTTGATTAGTGACTTTTTTATGAGGCTCATTTGATTAATAGTAATTAAACATATGTATATGTTTGATTAAATTCAGGTGAAGACTGCAATTCTTGCTGGGATTTTGGACGTGGTGATCTTGGCAGCAGCAGTGATTACTACTCAATTAGCATTGGAGGGAGAAGCTCGTAGTGGTGCTGTTGGTATCATGGGTGCAGCTTTGAACATTCTTATGTATGGCTCACCTCTTGCTGTCATGGTAAGTTTCTGGAGCTTTCTATAATTATTTAAGTTTGTCTTATCTCTTTATGATCATCTAGATTCATTAA
Protein sequence

>MS.gene004537.t1

MADPSFFVGVIGNIISILMFLSPVPTFWRIIKQKSTEEFSSFPYICTLLNSSLWTYYGTIKAGEYLVATVNGFGIVVETIYILLFLIYAPPKMRVKTAILAGILDVVILAAAVITTQLALEGEARSGAVGIMGAALNILMYGSPLAVMIH