AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0345410


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0345410 MtrunA17_Chr3g0085291 96.257 187 7 0 1 187 1 187 2.61e-134 373
Msa0345410 MtrunA17_Chr3g0085311 91.534 189 14 1 1 187 1 189 8.86e-127 354
Msa0345410 MtrunA17_Chr3g0085301 65.079 189 64 2 1 187 6 194 1.38e-87 255
Msa0345410 MtrunA17_Chr3g0085321 63.492 189 67 1 1 187 1 189 1.02e-85 250
Msa0345410 MtrunA17_Chr4g0040551 61.878 181 62 2 8 186 9 184 2.65e-78 231
Msa0345410 MtrunA17_Chr3g0090231 60.541 185 66 2 4 186 5 184 3.35e-77 229
Msa0345410 MtrunA17_Chr1g0177051 46.739 184 89 4 10 186 4 185 1.61e-51 163
Msa0345410 MtrunA17_Chr4g0005081 52.027 148 67 1 43 186 49 196 8.18e-48 154
Msa0345410 MtrunA17_Chr4g0005071 50.000 148 70 1 43 186 48 195 3.03e-46 150
Msa0345410 MtrunA17_Chr4g0005031 46.497 157 78 2 34 186 66 220 2.31e-43 144
Msa0345410 MtrunA17_Chr7g0259091 50.336 149 69 2 43 186 45 193 6.57e-43 142
Msa0345410 MtrunA17_Chr4g0005041 47.682 151 75 2 40 186 47 197 6.98e-43 142
Msa0345410 MtrunA17_Chr1g0175911 44.022 184 96 4 8 186 10 191 3.12e-42 140
Msa0345410 MtrunA17_Chr7g0243501 43.011 186 98 3 7 186 8 191 3.19e-42 140
Msa0345410 MtrunA17_Chr7g0259071 47.651 149 73 2 43 186 42 190 2.49e-41 137
Msa0345410 MtrunA17_Chr4g0037481 42.208 154 82 2 38 186 40 191 3.37e-40 135
Msa0345410 MtrunA17_Chr7g0259101 50.336 149 69 2 43 186 45 193 4.81e-40 140
Msa0345410 MtrunA17_Chr7g0259101 47.651 149 73 2 43 186 244 392 2.00e-38 135
Msa0345410 MtrunA17_Chr4g0005111 40.816 147 84 1 43 186 43 189 1.01e-38 131
Msa0345410 MtrunA17_Chr4g0005011 45.161 155 77 3 34 184 44 194 1.08e-38 131
Msa0345410 MtrunA17_Chr5g0446751 38.220 191 97 5 7 186 8 188 1.78e-34 120
Msa0345410 MtrunA17_Chr3g0136631 42.384 151 80 2 43 186 38 188 1.08e-33 118
Msa0345410 MtrunA17_Chr3g0136641 42.384 151 79 3 43 186 38 187 3.03e-33 117
Msa0345410 MtrunA17_Chr4g0005131 41.781 146 80 1 46 186 45 190 3.09e-33 117
Msa0345410 MtrunA17_Chr7g0259121 44.156 154 75 5 43 186 40 192 2.89e-31 112
Msa0345410 MtrunA17_Chr4g0024961 30.519 154 103 1 38 187 25 178 7.65e-20 82.4
Msa0345410 MtrunA17_Chr4g0068391 32.738 168 93 3 3 166 8 159 1.08e-19 82.0
Msa0345410 MtrunA17_Chr4g0024951 30.769 182 110 3 10 187 9 178 1.22e-19 81.6
Msa0345410 MtrunA17_Chr4g0005091 32.903 155 86 2 36 186 34 174 3.12e-19 80.5
Msa0345410 MtrunA17_Chr4g0068381 32.414 145 94 1 46 186 35 179 3.99e-19 80.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0345410 AT1G65870.1 47.826 161 80 1 30 186 29 189 1.68e-46 151
Msa0345410 AT5G42500.1 45.399 163 83 2 28 186 25 185 2.28e-45 148
Msa0345410 AT2G21100.1 42.763 152 83 1 39 186 36 187 4.15e-42 140
Msa0345410 AT2G21100.2 42.763 152 83 1 39 186 36 187 4.15e-42 140
Msa0345410 AT1G22900.1 45.161 155 79 2 36 186 41 193 1.26e-41 139
Msa0345410 AT5G42510.1 45.806 155 78 3 36 186 30 182 3.43e-41 137
Msa0345410 AT1G55210.1 44.595 148 81 1 40 186 39 186 1.73e-38 130
Msa0345410 AT1G55210.2 44.595 148 81 1 40 186 39 186 1.73e-38 130
Msa0345410 AT3G13650.1 44.138 145 80 1 43 186 41 185 3.03e-38 130
Msa0345410 AT1G58170.1 37.895 190 108 3 1 186 1 184 1.06e-37 129
Msa0345410 AT5G49040.1 43.624 149 78 3 43 186 43 190 8.94e-37 126
Msa0345410 AT5G49030.3 47.656 128 63 1 43 166 43 170 1.47e-33 126
Msa0345410 AT3G13662.1 46.400 125 66 1 43 166 40 164 1.00e-32 115
Msa0345410 AT3G58090.1 52.336 107 51 0 80 186 165 271 7.72e-32 116
Msa0345410 AT4G38700.1 42.857 154 78 3 43 186 36 189 1.42e-31 113
Msa0345410 AT2G21110.1 33.871 186 104 4 9 186 11 185 2.86e-29 107
Msa0345410 AT3G13660.1 38.710 124 76 0 63 186 1 124 1.34e-25 95.9
Msa0345410 AT4G11210.1 29.032 186 123 5 1 184 1 179 1.23e-16 74.3
Msa0345410 AT4G23690.1 33.071 127 78 3 43 163 38 163 1.21e-11 60.8

Find 37 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCTACTGCTAAGAGTGTT+TGG 0.319714 3_1:+4652133 Msa0345410:CDS
TTGGCGGCACCGGCGTGTTT+AGG 0.334517 3_1:+4652097 Msa0345410:CDS
TCAGTGCTTTGTTGATTTGT+TGG 0.368171 3_1:-4651757 None:intergenic
CTGCCTATTGTTGGCGGCAC+CGG 0.371881 3_1:+4652087 Msa0345410:CDS
CCATCAAATACAGTTGGGTT+TGG 0.383222 3_1:+4651856 Msa0345410:CDS
CCGGCGTGTTTAGGTTTGCT+AGG 0.384387 3_1:+4652106 Msa0345410:CDS
AGCTCAAGGGATGTTTGGTT+TGG 0.396536 3_1:+4651945 Msa0345410:CDS
ACGCCGGTGCCGCCAACAAT+AGG 0.397084 3_1:-4652090 None:intergenic
CCAAACCCAACTGTATTTGA+TGG 0.400788 3_1:-4651856 None:intergenic
TCTCTAACCGTGTCTTGAAC+AGG 0.414606 3_1:-4652063 None:intergenic
TGCTACTGCTAAGAGTGTTT+GGG 0.423437 3_1:+4652134 Msa0345410:CDS
GCTCTTGTCCTTCAGTTAAG+AGG 0.424118 3_1:-4651900 None:intergenic
GGTAGAGCTCAAGGGATGTT+TGG 0.428431 3_1:+4651940 Msa0345410:CDS
CGGCGTGTTTAGGTTTGCTA+GGG 0.449156 3_1:+4652107 Msa0345410:CDS
ATTTGTTGGTAACATGATGT+TGG 0.455637 3_1:-4651743 None:intergenic
TCAATAATTTGTACAACCGT+TGG 0.456883 3_1:-4651832 None:intergenic
TAACATGATGTTGGATTGTT+CGG 0.468734 3_1:-4651734 None:intergenic
GGTAGTACTCTTAGTATGCT+TGG 0.469670 3_1:+4652033 Msa0345410:CDS
GTTAGAGAACTGCCTATTGT+TGG 0.476698 3_1:+4652078 Msa0345410:CDS
ATTAATCTTGCTTTCACCGA+TGG 0.478192 3_1:+4652000 Msa0345410:CDS
ATTGATCCATCAAATACAGT+TGG 0.481548 3_1:+4651850 Msa0345410:CDS
TTGATCCATCAAATACAGTT+GGG 0.483436 3_1:+4651851 Msa0345410:CDS
AAACCTGTCGGTAGAGCTCA+AGG 0.523725 3_1:+4651931 Msa0345410:CDS
GTTTGGAGCAAGTTACATGA+TGG 0.529133 3_1:+4651873 Msa0345410:CDS
AGAGAACTGCCTATTGTTGG+CGG 0.541168 3_1:+4652081 Msa0345410:CDS
ATCCCTTGAGCTCTACCGAC+AGG 0.544812 3_1:-4651934 None:intergenic
GTACTCTTAGTATGCTTGGA+AGG 0.545035 3_1:+4652037 Msa0345410:CDS
TTGTTCGGAGAACACTCCAT+TGG 0.582295 3_1:-4651719 None:intergenic
ATGGACAACCTCTTAACTGA+AGG 0.591801 3_1:+4651892 Msa0345410:CDS
TTGGCATCTTTGCATGATCG+TGG 0.594187 3_1:+4651964 Msa0345410:CDS
ATCTTTGCATGATCGTGGAA+TGG 0.599273 3_1:+4651969 Msa0345410:CDS
GAGCTAACATCAAAACCTGT+CGG 0.634037 3_1:+4651919 Msa0345410:CDS
GGCGTGTTTAGGTTTGCTAG+GGG 0.673525 3_1:+4652108 Msa0345410:CDS
AAGGAATCCTGTTCAAGACA+CGG 0.674439 3_1:+4652056 Msa0345410:CDS
ACTACCAGCAAAATCACCAT+CGG 0.683340 3_1:-4652016 None:intergenic
AACCTGTCGGTAGAGCTCAA+GGG 0.694023 3_1:+4651932 Msa0345410:CDS
CCTAGCAAACCTAAACACGC+CGG 0.714305 3_1:-4652106 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGGTAAAAAAAGTGCAAAT+GGG - chr3_1:4651791-4651810 None:intergenic 25.0%
TAACATGATGTTGGATTGTT+CGG - chr3_1:4651737-4651756 None:intergenic 30.0%
!! ATTTGTTGGTAACATGATGT+TGG - chr3_1:4651746-4651765 None:intergenic 30.0%
! CATGGTAAAAAAAGTGCAAA+TGG - chr3_1:4651792-4651811 None:intergenic 30.0%
! TTTTACCATGACATCTTAGA+AGG + chr3_1:4651802-4651821 Msa0345410:CDS 30.0%
!!! TTTTACCTTCTAAGATGTCA+TGG - chr3_1:4651810-4651829 None:intergenic 30.0%
CTTAGAAGGTAAAAATCCAA+CGG + chr3_1:4651816-4651835 Msa0345410:CDS 30.0%
! TCAATAATTTGTACAACCGT+TGG - chr3_1:4651835-4651854 None:intergenic 30.0%
ATTGATCCATCAAATACAGT+TGG + chr3_1:4651850-4651869 Msa0345410:CDS 30.0%
TTGATCCATCAAATACAGTT+GGG + chr3_1:4651851-4651870 Msa0345410:CDS 30.0%
! GCTCAATTTTTCACTACCAA+TGG + chr3_1:4651703-4651722 Msa0345410:CDS 35.0%
!! TCAGTGCTTTGTTGATTTGT+TGG - chr3_1:4651760-4651779 None:intergenic 35.0%
ATTAATCTTGCTTTCACCGA+TGG + chr3_1:4652000-4652019 Msa0345410:CDS 35.0%
CCAAACCCAACTGTATTTGA+TGG - chr3_1:4651859-4651878 None:intergenic 40.0%
CCATCAAATACAGTTGGGTT+TGG + chr3_1:4651856-4651875 Msa0345410:CDS 40.0%
! GTTTGGAGCAAGTTACATGA+TGG + chr3_1:4651873-4651892 Msa0345410:CDS 40.0%
ATGGACAACCTCTTAACTGA+AGG + chr3_1:4651892-4651911 Msa0345410:CDS 40.0%
GAGCTAACATCAAAACCTGT+CGG + chr3_1:4651919-4651938 Msa0345410:CDS 40.0%
ATCTTTGCATGATCGTGGAA+TGG + chr3_1:4651969-4651988 Msa0345410:CDS 40.0%
ACTACCAGCAAAATCACCAT+CGG - chr3_1:4652019-4652038 None:intergenic 40.0%
GGTAGTACTCTTAGTATGCT+TGG + chr3_1:4652033-4652052 Msa0345410:CDS 40.0%
GTACTCTTAGTATGCTTGGA+AGG + chr3_1:4652037-4652056 Msa0345410:CDS 40.0%
AAGGAATCCTGTTCAAGACA+CGG + chr3_1:4652056-4652075 Msa0345410:CDS 40.0%
GTTAGAGAACTGCCTATTGT+TGG + chr3_1:4652078-4652097 Msa0345410:CDS 40.0%
!! ATGCTACTGCTAAGAGTGTT+TGG + chr3_1:4652133-4652152 Msa0345410:CDS 40.0%
!! TGCTACTGCTAAGAGTGTTT+GGG + chr3_1:4652134-4652153 Msa0345410:CDS 40.0%
TTGTTCGGAGAACACTCCAT+TGG - chr3_1:4651722-4651741 None:intergenic 45.0%
GCTCTTGTCCTTCAGTTAAG+AGG - chr3_1:4651903-4651922 None:intergenic 45.0%
AGCTCAAGGGATGTTTGGTT+TGG + chr3_1:4651945-4651964 Msa0345410:CDS 45.0%
TTGGCATCTTTGCATGATCG+TGG + chr3_1:4651964-4651983 Msa0345410:CDS 45.0%
! TTCACCGATGGTGATTTTGC+TGG + chr3_1:4652012-4652031 Msa0345410:CDS 45.0%
TCTCTAACCGTGTCTTGAAC+AGG - chr3_1:4652066-4652085 None:intergenic 45.0%
AGAGAACTGCCTATTGTTGG+CGG + chr3_1:4652081-4652100 Msa0345410:CDS 45.0%
AAACCTGTCGGTAGAGCTCA+AGG + chr3_1:4651931-4651950 Msa0345410:CDS 50.0%
AACCTGTCGGTAGAGCTCAA+GGG + chr3_1:4651932-4651951 Msa0345410:CDS 50.0%
GGTAGAGCTCAAGGGATGTT+TGG + chr3_1:4651940-4651959 Msa0345410:CDS 50.0%
CCTAGCAAACCTAAACACGC+CGG - chr3_1:4652109-4652128 None:intergenic 50.0%
!! CGGCGTGTTTAGGTTTGCTA+GGG + chr3_1:4652107-4652126 Msa0345410:CDS 50.0%
!! GGCGTGTTTAGGTTTGCTAG+GGG + chr3_1:4652108-4652127 Msa0345410:CDS 50.0%
ATCCCTTGAGCTCTACCGAC+AGG - chr3_1:4651937-4651956 None:intergenic 55.0%
! CCGGCGTGTTTAGGTTTGCT+AGG + chr3_1:4652106-4652125 Msa0345410:CDS 55.0%
CTGCCTATTGTTGGCGGCAC+CGG + chr3_1:4652087-4652106 Msa0345410:CDS 60.0%
!! ACGCCGGTGCCGCCAACAAT+AGG - chr3_1:4652093-4652112 None:intergenic 65.0%
!! TTGGCGGCACCGGCGTGTTT+AGG + chr3_1:4652097-4652116 Msa0345410:CDS 65.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 4651652 4652215 4651652 ID=Msa0345410;Name=Msa0345410
chr3_1 mRNA 4651652 4652215 4651652 ID=Msa0345410-mRNA-1;Parent=Msa0345410;Name=Msa0345410-mRNA-1;_AED=0.24;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|187
chr3_1 exon 4651652 4652215 4651652 ID=Msa0345410-mRNA-1:exon:1499;Parent=Msa0345410-mRNA-1
chr3_1 CDS 4651652 4652215 4651652 ID=Msa0345410-mRNA-1:cds;Parent=Msa0345410-mRNA-1
Gene Sequence

>Msa0345410

ATGGCTACATCTCTTAGATTCTTCTTTCTCTTCACTGTCACTTTCATATTTGCTCAATTTTTCACTACCAATGGAGTGTTCTCCGAACAATCCAACATCATGTTACCAACAAATCAACAAAGCACTGAAAAATTAACCCATTTGCACTTTTTTTACCATGACATCTTAGAAGGTAAAAATCCAACGGTTGTACAAATTATTGATCCATCAAATACAGTTGGGTTTGGAGCAAGTTACATGATGGACAACCTCTTAACTGAAGGACAAGAGCTAACATCAAAACCTGTCGGTAGAGCTCAAGGGATGTTTGGTTTGGCATCTTTGCATGATCGTGGAATGGTTATGTTAATTAATCTTGCTTTCACCGATGGTGATTTTGCTGGTAGTACTCTTAGTATGCTTGGAAGGAATCCTGTTCAAGACACGGTTAGAGAACTGCCTATTGTTGGCGGCACCGGCGTGTTTAGGTTTGCTAGGGGATATGCTACTGCTAAGAGTGTTTGGGAGATTTCAACATCTGAGCATTTTGTTGTTGAGTATGATGTCACTGTTTCTCATCCATAG

Protein sequence

>Msa0345410

MATSLRFFFLFTVTFIFAQFFTTNGVFSEQSNIMLPTNQQSTEKLTHLHFFYHDILEGKNPTVVQIIDPSNTVGFGASYMMDNLLTEGQELTSKPVGRAQGMFGLASLHDRGMVMLINLAFTDGDFAGSTLSMLGRNPVQDTVRELPIVGGTGVFRFARGYATAKSVWEISTSEHFVVEYDVTVSHP*