AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1218960


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1218960 MtrunA17_Chr4g0068711 93.220 177 8 1 1 177 1 173 8.84e-118 330
Msa1218960 MtrunA17_Chr4g0068731 70.286 175 45 3 1 172 1 171 7.23e-80 234
Msa1218960 MtrunA17_Chr4g0068791 54.749 179 75 4 1 177 1 175 9.65e-62 189
Msa1218960 MtrunA17_Chr4g0068751 51.648 182 83 1 1 177 1 182 5.06e-59 182
Msa1218960 MtrunA17_Chr4g0001591 50.926 108 51 2 72 177 1 108 2.17e-26 97.1
Msa1218960 MtrunA17_Chr2g0294121 36.842 171 96 4 19 177 6 176 6.19e-23 90.1
Msa1218960 MtrunA17_Chr4g0068701 36.076 158 96 3 25 177 20 177 8.34e-21 84.3
Msa1218960 MtrunA17_Chr4g0068651 28.415 183 121 5 1 177 1 179 8.85e-20 82.0
Msa1218960 MtrunA17_Chr4g0068681 31.973 147 96 2 35 177 39 185 2.08e-15 72.8
Msa1218960 MtrunA17_Chr4g0068681 31.724 145 96 2 35 177 230 373 1.68e-14 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1218960 AT1G47960.2 47.260 146 77 0 32 177 21 166 1.75e-46 150
Msa1218960 AT1G47960.1 46.479 142 76 0 32 173 21 162 2.12e-43 143
Msa1218960 AT3G17152.1 30.286 175 120 1 4 176 1 175 5.27e-17 74.7
Msa1218960 AT3G17150.1 31.944 144 94 2 37 177 39 181 5.86e-15 69.7
Msa1218960 AT5G64620.1 38.776 98 56 3 15 108 8 105 9.55e-11 58.2

Find 23 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAATGCAATTTGCATAATT+TGG 0.146977 8_1:+81653099 None:intergenic
GCACCATCTTCTGCAAATTT+AGG 0.160091 8_1:+81652850 None:intergenic
ATCAAATTAGCATTGGATTT+TGG 0.186303 8_1:+81653144 None:intergenic
TTGAGAGCTGCAACAGATTT+TGG 0.208499 8_1:+81652883 None:intergenic
ACATCTGCATCAGAGCTTCT+TGG 0.293970 8_1:+81653060 None:intergenic
CAAAATCAATCAGTTGATTA+AGG 0.305258 8_1:-81652977 Msa1218960:CDS
TGGTAGATACAAAGCAATTT+TGG 0.313317 8_1:-81652917 Msa1218960:CDS
AATGCTAATGCTAATGCTAA+TGG 0.350974 8_1:+81653216 None:intergenic
GTTTAAGGCAGTGTTTGCTT+TGG 0.395895 8_1:+81652999 None:intergenic
AGCTCTGATGCAGATGTAAC+AGG 0.425806 8_1:-81653054 Msa1218960:CDS
ACTTGTGAGAATGGCTTCAA+TGG 0.435357 8_1:-81652802 Msa1218960:CDS
AGCTTCTTGGATCAGATTTG+AGG 0.439581 8_1:+81653073 None:intergenic
GAAGCCACTACTTGTGAGAA+TGG 0.448649 8_1:-81652811 Msa1218960:CDS
TTGCTGTATCAAATTAGCAT+TGG 0.473617 8_1:+81653137 None:intergenic
TAAGGAGAGCCATGATCAAA+AGG 0.474578 8_1:-81652959 Msa1218960:CDS
CTTGTGAGAATGGCTTCAAT+GGG 0.531153 8_1:-81652801 Msa1218960:CDS
GATCCTAAATTTGCAGAAGA+TGG 0.542535 8_1:-81652853 Msa1218960:CDS
GAAGCTTTGAATTCATGTGC+TGG 0.550109 8_1:-81652937 Msa1218960:CDS
AACAGGTCTAGCACTAATCA+TGG 0.552410 8_1:-81653037 Msa1218960:CDS
GAAGCCATTCTCACAAGTAG+TGG 0.571548 8_1:+81652807 None:intergenic
TCTGTTGCAGCTCTCAAGCA+AGG 0.585277 8_1:-81652877 Msa1218960:CDS
GCAATATTCTCATCAGAGAG+TGG 0.649907 8_1:+81652772 None:intergenic
AGGTCTAGCACTAATCATGG+TGG 0.723735 8_1:-81653034 Msa1218960:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCAAATTAGCATTGGATTT+TGG + chr8_1:81652810-81652829 None:intergenic 25.0%
! TGAATGCAATTTGCATAATT+TGG + chr8_1:81652855-81652874 None:intergenic 25.0%
!!! CAACTGATTGATTTTGTTTA+AGG + chr8_1:81652970-81652989 None:intergenic 25.0%
! CAAAATCAATCAGTTGATTA+AGG - chr8_1:81652974-81652993 Msa1218960:CDS 25.0%
AATGCTAATGCTAATGCTAA+TGG + chr8_1:81652738-81652757 None:intergenic 30.0%
!! AATTAGCATTGGATTTTGGA+TGG + chr8_1:81652806-81652825 None:intergenic 30.0%
TTGCTGTATCAAATTAGCAT+TGG + chr8_1:81652817-81652836 None:intergenic 30.0%
! TGGTAGATACAAAGCAATTT+TGG - chr8_1:81653034-81653053 Msa1218960:CDS 30.0%
! TCAAAGCTTCCTTTTGATCA+TGG + chr8_1:81653004-81653023 None:intergenic 35.0%
GATCCTAAATTTGCAGAAGA+TGG - chr8_1:81653098-81653117 Msa1218960:CDS 35.0%
AGCTTCTTGGATCAGATTTG+AGG + chr8_1:81652881-81652900 None:intergenic 40.0%
AACAGGTCTAGCACTAATCA+TGG - chr8_1:81652914-81652933 Msa1218960:CDS 40.0%
! GTTTAAGGCAGTGTTTGCTT+TGG + chr8_1:81652955-81652974 None:intergenic 40.0%
TAAGGAGAGCCATGATCAAA+AGG - chr8_1:81652992-81653011 Msa1218960:CDS 40.0%
!! GAAGCTTTGAATTCATGTGC+TGG - chr8_1:81653014-81653033 Msa1218960:CDS 40.0%
! TTGAGAGCTGCAACAGATTT+TGG + chr8_1:81653071-81653090 None:intergenic 40.0%
GCACCATCTTCTGCAAATTT+AGG + chr8_1:81653104-81653123 None:intergenic 40.0%
ACTTGTGAGAATGGCTTCAA+TGG - chr8_1:81653149-81653168 Msa1218960:CDS 40.0%
CTTGTGAGAATGGCTTCAAT+GGG - chr8_1:81653150-81653169 Msa1218960:CDS 40.0%
GCAATATTCTCATCAGAGAG+TGG + chr8_1:81653182-81653201 None:intergenic 40.0%
ACATCTGCATCAGAGCTTCT+TGG + chr8_1:81652894-81652913 None:intergenic 45.0%
! AGCTCTGATGCAGATGTAAC+AGG - chr8_1:81652897-81652916 Msa1218960:CDS 45.0%
AGGTCTAGCACTAATCATGG+TGG - chr8_1:81652917-81652936 Msa1218960:CDS 45.0%
GAAGCCACTACTTGTGAGAA+TGG - chr8_1:81653140-81653159 Msa1218960:CDS 45.0%
GAAGCCATTCTCACAAGTAG+TGG + chr8_1:81653147-81653166 None:intergenic 45.0%
TCTGTTGCAGCTCTCAAGCA+AGG - chr8_1:81653074-81653093 Msa1218960:CDS 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 81652720 81653253 81652720 ID=Msa1218960;Name=Msa1218960
chr8_1 mRNA 81652720 81653253 81652720 ID=Msa1218960-mRNA-1;Parent=Msa1218960;Name=Msa1218960-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|177
chr8_1 exon 81652720 81653253 81652720 ID=Msa1218960-mRNA-1:exon:28945;Parent=Msa1218960-mRNA-1
chr8_1 CDS 81652720 81653253 81652720 ID=Msa1218960-mRNA-1:cds;Parent=Msa1218960-mRNA-1
Gene Sequence

>Msa1218960

ATGACAAAGATGAATCCATTAGCATTAGCATTAGCATTAGCTATCATCTTGTGCACTATTGTTTCAAGTCACTGCATAATTATCCATCCAAAATCCAATGCTAATTTGATACAGCAAACTTGCAAACAAACTCCAAATTATGCAAATTGCATTCAATACCTCAAATCTGATCCAAGAAGCTCTGATGCAGATGTAACAGGTCTAGCACTAATCATGGTGGACATAATCAAATCCAAAGCAAACACTGCCTTAAACAAAATCAATCAGTTGATTAAGGAGAGCCATGATCAAAAGGAAGCTTTGAATTCATGTGCTGGTAGATACAAAGCAATTTTGGTAGCTGATGTGCCAAAATCTGTTGCAGCTCTCAAGCAAGGTGATCCTAAATTTGCAGAAGATGGTGCAAATGATGTTGCAATTGAAGCCACTACTTGTGAGAATGGCTTCAATGGGAAATCACCACTCTCTGATGAGAATATTGCTATGCATGATGTAGCAGTCATAGCAGCAGCTATTGTTAAACAATTGCTCTAG

Protein sequence

>Msa1218960

MTKMNPLALALALAIILCTIVSSHCIIIHPKSNANLIQQTCKQTPNYANCIQYLKSDPRSSDADVTGLALIMVDIIKSKANTALNKINQLIKESHDQKEALNSCAGRYKAILVADVPKSVAALKQGDPKFAEDGANDVAIEATTCENGFNGKSPLSDENIAMHDVAVIAAAIVKQLL*