AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene91270

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene91270.t1 MTR_2g084495 96.403 139 5 0 3 141 1 139 2.24e-99 285
MS.gene91270.t1 MTR_2g060500 70.922 141 41 0 1 141 5 145 1.04e-69 207
MS.gene91270.t1 MTR_2g060540 70.213 141 42 0 1 141 5 145 3.78e-69 205
MS.gene91270.t1 MTR_2g084525 65.468 139 48 0 3 141 1 139 3.33e-64 196
MS.gene91270.t1 MTR_2g084510 60.870 138 54 0 4 141 1 138 1.64e-58 182
MS.gene91270.t1 MTR_1g062160 50.000 142 61 4 1 141 1 133 3.31e-41 136
MS.gene91270.t1 MTR_5g030130 48.148 135 60 3 7 141 36 160 1.87e-40 134
MS.gene91270.t1 MTR_5g030130 48.148 135 60 3 7 141 36 160 1.89e-40 135
MS.gene91270.t1 MTR_5g007230 47.407 135 61 3 7 141 22 146 1.21e-38 130
MS.gene91270.t1 MTR_7g102790 48.227 141 62 5 7 145 8 139 2.88e-38 129
MS.gene91270.t1 MTR_4g078170 46.667 135 62 3 7 141 16 140 2.64e-37 127
MS.gene91270.t1 MTR_8g066820 45.926 135 63 3 7 141 34 158 1.44e-36 125
MS.gene91270.t1 MTR_2g083720 54.098 122 18 2 1 122 1 84 9.45e-33 111
MS.gene91270.t1 MTR_2g083710 79.032 62 13 0 1 62 1 62 1.14e-30 105
MS.gene91270.t1 MTR_2g055210 39.130 138 72 5 8 145 104 229 1.07e-24 97.1
MS.gene91270.t1 MTR_4g094680 38.806 134 77 4 8 141 24 152 1.78e-23 92.0
MS.gene91270.t1 MTR_4g116300 38.806 134 71 4 8 141 8 130 8.26e-21 85.1
MS.gene91270.t1 MTR_2g036170 38.806 134 65 5 8 141 39 155 6.45e-18 77.8
MS.gene91270.t1 MTR_8g105930 28.571 147 88 5 8 141 15 157 6.13e-12 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene91270.t1 AT1G43000 47.857 140 63 3 2 141 12 141 5.49e-40 134
MS.gene91270.t1 AT1G43000 47.857 140 63 3 2 141 5 134 5.64e-40 134
MS.gene91270.t1 AT4G17900 50.000 136 57 4 7 141 35 160 5.22e-38 129
MS.gene91270.t1 AT4G17900 50.000 136 57 4 7 141 21 146 5.93e-38 128
MS.gene91270.t1 AT1G32700 48.507 134 59 3 8 141 14 137 2.76e-37 127
MS.gene91270.t1 AT1G21000 45.714 140 66 4 2 141 9 138 2.84e-35 122
MS.gene91270.t1 AT1G21000 45.714 140 66 4 2 141 12 141 3.48e-35 122
MS.gene91270.t1 AT2G27930 45.070 142 72 3 3 141 1 139 4.32e-35 120
MS.gene91270.t1 AT2G27930 45.070 142 72 3 3 141 1 139 4.32e-35 120
MS.gene91270.t1 AT2G27930 45.070 142 72 3 3 141 1 139 4.47e-35 120
MS.gene91270.t1 AT2G27930 45.070 142 72 3 3 141 1 139 4.47e-35 120
MS.gene91270.t1 AT1G76590 43.704 135 66 4 7 141 19 143 3.69e-31 112
MS.gene91270.t1 AT1G32700 48.214 112 49 2 35 146 1 103 7.60e-30 107
MS.gene91270.t1 AT5G46710 43.704 135 65 4 8 141 30 154 3.50e-28 102
MS.gene91270.t1 AT5G46710 43.704 135 65 4 8 141 14 138 5.60e-28 103
MS.gene91270.t1 AT5G46710 43.704 135 65 4 8 141 30 154 9.31e-28 102
MS.gene91270.t1 AT2G12646 37.589 141 77 4 1 141 1 130 4.88e-22 88.6
MS.gene91270.t1 AT2G12646 37.589 141 77 4 1 141 1 130 4.88e-22 88.6
MS.gene91270.t1 AT2G12646 38.406 138 74 4 4 141 1 127 5.10e-22 88.6
MS.gene91270.t1 AT1G31040 37.410 139 75 5 8 146 21 147 1.81e-21 87.0
MS.gene91270.t1 AT3G60670 36.620 142 78 5 1 141 1 131 8.73e-21 85.1
MS.gene91270.t1 AT2G27930 45.238 84 41 2 61 141 61 142 8.52e-18 76.3
MS.gene91270.t1 AT2G27930 45.238 84 41 2 61 141 61 142 8.52e-18 76.3
MS.gene91270.t1 AT2G01818 32.117 137 86 4 8 141 13 145 5.65e-15 69.3

Find 17 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTAGTAGGTTGGGAATA+AGG 0.275954 2.3:-13546104 None:intergenic
TTTATGCAAGATCCACAAAA+TGG 0.291003 2.3:-13545757 None:intergenic
AATCGAAATTTACAAGCATT+TGG 0.312437 2.3:+13546019 MS.gene91270:CDS
TACAAGCATTTGGATATTCT+AGG 0.347196 2.3:+13546029 MS.gene91270:CDS
AAGAAGACGATAGGTATAAT+TGG 0.364201 2.3:+13546122 MS.gene91270:CDS
AGTTGCTAATCACATAGGTT+TGG 0.394909 2.3:-13546055 None:intergenic
ATACCTATCGTCTTCTTAGT+AGG 0.403093 2.3:-13546116 None:intergenic
GCCAGAGAGCAAAAGTAATA+AGG 0.422528 2.3:-13546194 None:intergenic
TATCGTCTTCTTAGTAGGTT+GGG 0.425885 2.3:-13546111 None:intergenic
CTATCGTCTTCTTAGTAGGT+TGG 0.480968 2.3:-13546112 None:intergenic
ATATGTCAAAGGAATCTTGT+AGG 0.494888 2.3:+13546170 MS.gene91270:CDS
TGTAAAGTTGCTAATCACAT+AGG 0.533475 2.3:-13546060 None:intergenic
AACTTCACATGATGTGAAGA+AGG 0.546693 2.3:-13545677 None:intergenic
AGGATATGATGTCCATGCCC+TGG 0.549335 2.3:+13545629 MS.gene91270:intron
CAGTTGTATTCATAAACAAG+AGG 0.585618 2.3:+13546081 MS.gene91270:CDS
CAACCTACTAAGAAGACGAT+AGG 0.603325 2.3:+13546113 MS.gene91270:CDS
ATCTTTGTAAGATATGTCAA+AGG 0.646257 2.3:+13546159 MS.gene91270:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAAGGAATTAAAAT+TGG - chr2.3:13545581-13545600 None:intergenic 10.0%
!! AAAAATTAATTAAAGAAAAG+TGG - chr2.3:13545884-13545903 None:intergenic 10.0%
!! ACAAAATAAATTAAAAAAAG+AGG - chr2.3:13546286-13546305 None:intergenic 10.0%
!! TAATTTAATGAATCTAACAA+AGG - chr2.3:13546951-13546970 None:intergenic 15.0%
!!! AATCGCTTAATTTTTTTTAT+TGG + chr2.3:13546391-13546410 MS.gene91270:intron 15.0%
!!! TGTATAATTTTTTTGACTTT+GGG + chr2.3:13545922-13545941 MS.gene91270:intron 15.0%
!!! TTGTATAATTTTTTTGACTT+TGG + chr2.3:13545921-13545940 MS.gene91270:intron 15.0%
!! AAAAAGAGGATCTATAAAAA+AGG - chr2.3:13546272-13546291 None:intergenic 20.0%
!! ATGATTTATGCCTTAAAAAA+AGG - chr2.3:13546814-13546833 None:intergenic 20.0%
!! GATTGTAGTAAGAAAAAAAA+AGG - chr2.3:13545593-13545612 None:intergenic 20.0%
!! TGATTTATGCCTTAAAAAAA+GGG - chr2.3:13546813-13546832 None:intergenic 20.0%
!! TTATCATGAGAACATAAATA+CGG - chr2.3:13546897-13546916 None:intergenic 20.0%
!!! TTTTTATTGGTGTAAAGAAT+GGG + chr2.3:13546404-13546423 MS.gene91270:intron 20.0%
!!! TTTTTTATTGGTGTAAAGAA+TGG + chr2.3:13546403-13546422 MS.gene91270:intron 20.0%
! AAAACGAAAAGTAAATGAAG+CGG + chr2.3:13546656-13546675 MS.gene91270:intron 25.0%
! AATCGAAATTTACAAGCATT+TGG + chr2.3:13546019-13546038 MS.gene91270:CDS 25.0%
! ATAAAAAAGGAGACATGATA+AGG - chr2.3:13546259-13546278 None:intergenic 25.0%
! ATCTTTGTAAGATATGTCAA+AGG + chr2.3:13546159-13546178 MS.gene91270:CDS 25.0%
! TATACTTGCAATTACAAATC+AGG + chr2.3:13545962-13545981 MS.gene91270:intron 25.0%
!!! GATTTTTTGGCTTTTTGTTT+TGG - chr2.3:13546621-13546640 None:intergenic 25.0%
AAACAATGAAGAAAACGAAG+AGG + chr2.3:13546683-13546702 MS.gene91270:intron 30.0%
AAACGAAAAGTAAATGAAGC+GGG + chr2.3:13546657-13546676 MS.gene91270:intron 30.0%
AAAGCCAAATTCAAGAAGAA+AGG + chr2.3:13546770-13546789 MS.gene91270:intron 30.0%
AAGAAGACGATAGGTATAAT+TGG + chr2.3:13546122-13546141 MS.gene91270:CDS 30.0%
AAGCCAAATTCAAGAAGAAA+GGG + chr2.3:13546771-13546790 MS.gene91270:intron 30.0%
AATTGGCATTGTAATTGAAG+TGG - chr2.3:13545564-13545583 None:intergenic 30.0%
AGAAGAAATGGAAAGATTGT+TGG + chr2.3:13546578-13546597 MS.gene91270:intron 30.0%
ATATGTCAAAGGAATCTTGT+AGG + chr2.3:13546170-13546189 MS.gene91270:CDS 30.0%
ATTCCCTTTCTTCTTGAATT+TGG - chr2.3:13546777-13546796 None:intergenic 30.0%
ATTGGCATTGTAATTGAAGT+GGG - chr2.3:13545563-13545582 None:intergenic 30.0%
CAAGTTTGAATGCATAAAGA+AGG + chr2.3:13546524-13546543 MS.gene91270:intron 30.0%
CAGTTGTATTCATAAACAAG+AGG + chr2.3:13546081-13546100 MS.gene91270:CDS 30.0%
TACAAGCATTTGGATATTCT+AGG + chr2.3:13546029-13546048 MS.gene91270:CDS 30.0%
TGTAAAGTTGCTAATCACAT+AGG - chr2.3:13546063-13546082 None:intergenic 30.0%
TTGAATGCATAAAGAAGGAT+GGG + chr2.3:13546529-13546548 MS.gene91270:intron 30.0%
TTTATGCAAGATCCACAAAA+TGG - chr2.3:13545760-13545779 None:intergenic 30.0%
TTTGAATGCATAAAGAAGGA+TGG + chr2.3:13546528-13546547 MS.gene91270:intron 30.0%
! ATTTTGTTCACGCGATTTTT+TGG - chr2.3:13546634-13546653 None:intergenic 30.0%
! CAAAAATTTGCTTGCAATCA+CGG + chr2.3:13545654-13545673 MS.gene91270:CDS 30.0%
!!! AATCGTTGTTTTTGTCACTT+AGG + chr2.3:13545609-13545628 MS.gene91270:intron 30.0%
!!! CTTGAATTTGGCTTTTTGAT+AGG - chr2.3:13546765-13546784 None:intergenic 30.0%
AACTTCACATGATGTGAAGA+AGG - chr2.3:13545680-13545699 None:intergenic 35.0%
ACGAAGAGGATGAAGAAAAA+AGG + chr2.3:13546697-13546716 MS.gene91270:intron 35.0%
AGAAATGGAAAGATTGTTGG+AGG + chr2.3:13546581-13546600 MS.gene91270:intron 35.0%
AGTTGCTAATCACATAGGTT+TGG - chr2.3:13546058-13546077 None:intergenic 35.0%
ATACCTATCGTCTTCTTAGT+AGG - chr2.3:13546119-13546138 None:intergenic 35.0%
ATTGTTGGAGGAATCAATCA+AGG + chr2.3:13546593-13546612 MS.gene91270:intron 35.0%
CCAAGTGAGTGTTCTTTAAA+GGG + chr2.3:13545807-13545826 MS.gene91270:intron 35.0%
CGAAGAGGATGAAGAAAAAA+GGG + chr2.3:13546698-13546717 MS.gene91270:intron 35.0%
TATCGTCTTCTTAGTAGGTT+GGG - chr2.3:13546114-13546133 None:intergenic 35.0%
TCCAAGTGAGTGTTCTTTAA+AGG + chr2.3:13545806-13545825 MS.gene91270:intron 35.0%
TGAATGCATAAAGAAGGATG+GGG + chr2.3:13546530-13546549 MS.gene91270:intron 35.0%
TTGCAATTACAAATCAGGTG+AGG + chr2.3:13545967-13545986 MS.gene91270:intron 35.0%
! TGCAATGACAATCCATTTTG+TGG + chr2.3:13545745-13545764 MS.gene91270:CDS 35.0%
! TTCTTAGTAGGTTGGGAATA+AGG - chr2.3:13546107-13546126 None:intergenic 35.0%
!! ACCTTATTACTTTTGCTCTC+TGG + chr2.3:13546193-13546212 MS.gene91270:CDS 35.0%
AAGAAAGGGAATACCTCGTA+GGG + chr2.3:13546785-13546804 MS.gene91270:intron 40.0%
AGAGGATGAAGAAAAAAGGG+AGG + chr2.3:13546701-13546720 MS.gene91270:intron 40.0%
CAACCTACTAAGAAGACGAT+AGG + chr2.3:13546113-13546132 MS.gene91270:CDS 40.0%
CTATCGTCTTCTTAGTAGGT+TGG - chr2.3:13546115-13546134 None:intergenic 40.0%
GAATGCATAAAGAAGGATGG+GGG + chr2.3:13546531-13546550 MS.gene91270:intron 40.0%
GCCAGAGAGCAAAAGTAATA+AGG - chr2.3:13546197-13546216 None:intergenic 40.0%
TGCAAAGGAGACAGAAGAAA+TGG + chr2.3:13546566-13546585 MS.gene91270:intron 40.0%
! CCCTTTAAAGAACACTCACT+TGG - chr2.3:13545810-13545829 None:intergenic 40.0%
!! GCAAGCAAATTTTTGAGCCA+GGG - chr2.3:13545649-13545668 None:intergenic 40.0%
!! TGCAAGCAAATTTTTGAGCC+AGG - chr2.3:13545650-13545669 None:intergenic 40.0%
CTTCTGTCTCCTTTGCACTT+AGG - chr2.3:13546563-13546582 None:intergenic 45.0%
GAAGAAAGGGAATACCTCGT+AGG + chr2.3:13546784-13546803 MS.gene91270:intron 45.0%
!! CAAATTTTTGAGCCAGGGCA+TGG - chr2.3:13545644-13545663 None:intergenic 45.0%
!! GGGCTTTTTCCTAAGTGCAA+AGG + chr2.3:13546551-13546570 MS.gene91270:intron 45.0%
!! TAAAAAAAGGGTGCCCTACG+AGG - chr2.3:13546801-13546820 None:intergenic 45.0%
!!! CGTAGGGCACCCTTTTTTTA+AGG + chr2.3:13546801-13546820 MS.gene91270:intron 45.0%
!!! TTATGTTTATTAATTTTTAT+TGG + chr2.3:13546362-13546381 MS.gene91270:intron 5.0%
AGGATATGATGTCCATGCCC+TGG + chr2.3:13545629-13545648 MS.gene91270:intron 50.0%
! CTTTTGCTCTCTGGCATGCA+AGG + chr2.3:13546202-13546221 MS.gene91270:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 13545547 13547034 13545547 ID=MS.gene91270
chr2.3 mRNA 13545547 13547034 13545547 ID=MS.gene91270.t1;Parent=MS.gene91270
chr2.3 exon 13545547 13545549 13545547 ID=MS.gene91270.t1.exon1;Parent=MS.gene91270.t1
chr2.3 CDS 13545547 13545549 13545547 ID=cds.MS.gene91270.t1;Parent=MS.gene91270.t1
chr2.3 exon 13545631 13545810 13545631 ID=MS.gene91270.t1.exon2;Parent=MS.gene91270.t1
chr2.3 CDS 13545631 13545810 13545631 ID=cds.MS.gene91270.t1;Parent=MS.gene91270.t1
chr2.3 exon 13545984 13546223 13545984 ID=MS.gene91270.t1.exon3;Parent=MS.gene91270.t1
chr2.3 CDS 13545984 13546223 13545984 ID=cds.MS.gene91270.t1;Parent=MS.gene91270.t1
chr2.3 exon 13547017 13547034 13547017 ID=MS.gene91270.t1.exon4;Parent=MS.gene91270.t1
chr2.3 CDS 13547017 13547034 13547017 ID=cds.MS.gene91270.t1;Parent=MS.gene91270.t1
Gene Sequence

>MS.gene91270

ATGGTAAAGCATACCCACTTCAATTACAATGCCAATTTTAATTCCTTTTTTTTTCTTACTACAATCGTTGTTTTTGTCACTTAGGATATGATGTCCATGCCCTGGCTCAAAAATTTGCTTGCAATCACGGCCTTCTTCACATCATGTGAAGTTCATCTGAATGAGTCAAAAAATGAACGCAACATGTTCTGTCTCGAATGCAATGACAATCCATTTTGTGGATCTTGCATAAAATCTCATCACAAAGATCATCGAGTAATCCAAGTGAGTGTTCTTTAAAGGGATAGCTAGATCTATATAATATCTCGATAATCTATGTATCTTTATGTGATATCCACTTTTCTTTAATTAATTTTTGTTACATTCAAATAGTTTTGTATAATTTTTTTGACTTTGGGATCTAAATTTGAACTTGTATACTTGCAATTACAAATCAGGTGAGGAGATCATCTTATACAAACGTCATTAAGACAATCGAAATTTACAAGCATTTGGATATTCTAGGAATCCAAACCTATGTGATTAGCAACTTTACAGTTGTATTCATAAACAAGAGGCCTTATTCCCAACCTACTAAGAAGACGATAGGTATAATTGGTTGCAGTAGCGACTATCTTTGTAAGATATGTCAAAGGAATCTTGTAGGACCTTATTACTTTTGCTCTCTGGCATGCAAGGTAAATTGTTTTCTCGATCTCATTTTCTTTTTCCTTATCATGTCTCCTTTTTTATAGATCCTCTTTTTTTAATTTATTTTGTAAATAAATTTCAAAAATTGTGTTCAAATATTTAATTGAGAATGTAATTTATGTAATTTATGTTTATTAATTTTTATTGGTATTTCAATCGCTTAATTTTTTTTATTGGTGTAAAGAATGGGAATACTTTTTTTCGTTGATTATAATTGTTGTACTTTTATTTTTTTTTTTCTTTTTTAAATATAGTTAATTAATGTTGCGTATTGTGTGTGTATGATACAAGTTTGAATGCATAAAGAAGGATGGGGGCTTTTTCCTAAGTGCAAAGGAGACAGAAGAAATGGAAAGATTGTTGGAGGAATCAATCAAGGCACCAAAACAAAAAGCCAAAAAATCGCGTGAACAAAATCTAAAACGAAAAGTAAATGAAGCGGGAATAAACAATGAAGAAAACGAAGAGGATGAAGAAAAAAGGGAGGAAGAAGAAAATGAACAAGAAGAAAGAGAAAACATGCTTCCTATCAAAAAGCCAAATTCAAGAAGAAAGGGAATACCTCGTAGGGCACCCTTTTTTTAAGGCATAAATCATGTAATATAGAGATTTAAATAATACAATATCATCTATCTTGAGATAGATTTCTAGCTAGATCCGTATTTATGTTCTCATGATAATAAATTACTTTTGAAACATTTGATTTCGTCTCCTTTGTTAGATTCATTAAATTAATATTTGAAACATGCTAAGTTGTCTATTACGTAATGCTACATGTAGCGAAAGAAGTTGTCGTGA
Protein sequence

>MS.gene91270.t1

MDMMSMPWLKNLLAITAFFTSCEVHLNESKNERNMFCLECNDNPFCGSCIKSHHKDHRVIQVRRSSYTNVIKTIEIYKHLDILGIQTYVISNFTVVFINKRPYSQPTKKTIGIIGCSSDYLCKICQRNLVGPYYFCSLACKRKKLS