AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1412050

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1412050 MtrunA17_Chr1g0190231 97.802 182 4 0 1 182 1 182 1.88e-133 370
Msa1412050 MtrunA17_Chr5g0431211 79.433 141 28 1 31 170 28 168 2.91e-83 245
Msa1412050 MtrunA17_Chr7g0274631 64.865 185 47 6 1 182 1 170 3.33e-79 233
Msa1412050 MtrunA17_Chr1g0167411 83.200 125 21 0 40 164 65 189 4.12e-79 234
Msa1412050 MtrunA17_Chr4g0051251 73.333 135 36 0 35 169 41 175 3.59e-76 228
Msa1412050 MtrunA17_Chr1g0187671 79.710 138 28 0 32 169 45 182 8.04e-74 220
Msa1412050 MtrunA17_Chr7g0261381 81.203 133 25 0 37 169 61 193 1.19e-71 215
Msa1412050 MtrunA17_Chr3g0105921 63.736 182 63 2 1 179 1 182 1.35e-70 213
Msa1412050 MtrunA17_Chr1g0183761 81.538 130 24 0 40 169 45 174 2.86e-70 212
Msa1412050 MtrunA17_Chr2g0325831 68.056 144 46 0 20 163 3 146 4.41e-70 209
Msa1412050 MtrunA17_Chr2g0283861 63.462 156 45 2 20 163 3 158 1.42e-69 209
Msa1412050 MtrunA17_Chr4g0041141 69.630 135 41 0 29 163 18 152 2.13e-69 208
Msa1412050 MtrunA17_Chr2g0315791 76.000 125 30 0 39 163 32 156 2.83e-69 208
Msa1412050 MtrunA17_Chr8g0379061 68.800 125 39 0 39 163 84 208 2.87e-52 167
Msa1412050 MtrunA17_Chr1g0211641 82.222 45 8 0 33 77 64 108 1.81e-23 89.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1412050 AT3G04510.1 75.000 176 37 2 1 176 1 169 2.30e-78 232
Msa1412050 AT1G07090.1 64.881 168 56 2 13 177 1 168 3.26e-78 232
Msa1412050 AT5G28490.1 73.964 169 29 2 1 169 1 154 3.75e-78 231
Msa1412050 AT5G58500.1 71.528 144 39 2 39 180 18 161 8.30e-75 223
Msa1412050 AT2G31160.1 71.098 173 42 3 7 172 16 187 4.82e-73 219
Msa1412050 AT3G23290.2 85.714 126 18 0 39 164 47 172 1.61e-71 214
Msa1412050 AT2G42610.1 71.852 135 36 1 31 163 14 148 1.29e-67 204
Msa1412050 AT2G42610.2 71.852 135 36 1 31 163 14 148 1.29e-67 204
Msa1412050 AT1G78815.1 68.800 125 39 0 39 163 39 163 2.71e-65 199
Msa1412050 AT4G18610.1 56.522 161 69 1 4 163 1 161 9.26e-63 192
Msa1412050 AT1G16910.1 63.910 133 48 0 36 168 19 151 4.06e-61 187

Find 58 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCTGTTAGGATTTATTTA+AGG 0.161002 tig0023869:-12945 Msa1412050:CDS
TGTTCCAGTCTCTTCTCTTT+TGG 0.228365 tig0023869:+13241 None:intergenic
GGACAAGGAGCTGGTGGATT+AGG 0.248534 tig0023869:+13075 None:intergenic
CGCTCTCATCGGTCGTCTTC+GGG 0.260569 tig0023869:-13019 Msa1412050:CDS
AACCATCCTTGTCCTTTCTT+TGG 0.263470 tig0023869:-13102 Msa1412050:CDS
ATCTTCATCCTCCATGGATT+TGG 0.293649 tig0023869:-13382 None:intergenic
ACGCTCTCATCGGTCGTCTT+CGG 0.308665 tig0023869:-13020 Msa1412050:CDS
CTCAACTATCTTGACCAGTT+TGG 0.334013 tig0023869:-13141 Msa1412050:CDS
TTCTGTTAGGATTTATTTAA+GGG 0.334103 tig0023869:-12944 Msa1412050:CDS
CGTCCTGAGACTAACCCTTT+TGG 0.356884 tig0023869:-12973 Msa1412050:CDS
GACAAGGAGCTGGTGGATTA+GGG 0.371455 tig0023869:+13076 None:intergenic
GTTGTAGATACCTTAGGTTT+AGG 0.383180 tig0023869:+12862 None:intergenic
TCCATGGATTTGGTTTCATC+AGG 0.387953 tig0023869:-13372 Msa1412050:CDS
TGATGTTGAACTTCCACTTC+CGG 0.415099 tig0023869:+13290 None:intergenic
GTCATTGAAGATCCACTTGT+TGG 0.419117 tig0023869:+13324 None:intergenic
TCCACTTCCGGTGCTATTGT+TGG 0.438537 tig0023869:+13302 None:intergenic
AGAGTGGTGGACGGTGGTTT+CGG 0.448012 tig0023869:+13202 None:intergenic
ACAAGGATGGTTGTGAACTT+TGG 0.448409 tig0023869:+13113 None:intergenic
GTGTTAGCTATGAAAAGAAA+AGG 0.462297 tig0023869:-12891 Msa1412050:CDS
GCAGTGGTTGTAGATACCTT+AGG 0.484827 tig0023869:+12856 None:intergenic
GGACATGGGAACCGCTACAT+AGG 0.494340 tig0023869:+13172 None:intergenic
ACCAACAATAGCACCGGAAG+TGG 0.495122 tig0023869:-13303 Msa1412050:CDS
CTAACAGAACGAGAACCAAA+AGG 0.506615 tig0023869:+12958 None:intergenic
CATGTCCTCTTCGTCAAGCG+TGG 0.509192 tig0023869:-13053 Msa1412050:CDS
ATGTCCTCTTCGTCAAGCGT+GGG 0.521066 tig0023869:-13052 Msa1412050:CDS
CACGCTTGACGAAGAGGACA+TGG 0.538595 tig0023869:+13054 None:intergenic
GAACCAAAAGGGTTAGTCTC+AGG 0.546578 tig0023869:+12970 None:intergenic
AAGGAAGAGGCCTAAACCTA+AGG 0.549128 tig0023869:-12872 Msa1412050:CDS
TTGTTGGACTCTCTACACTC+TGG 0.549585 tig0023869:+13340 None:intergenic
AAAACCAAAAGAGAAGAGAC+TGG 0.553636 tig0023869:-13245 Msa1412050:CDS
GGATTAGGGATGCCAAAGAA+AGG 0.556995 tig0023869:+13090 None:intergenic
AGAGGACATGGACAAGGAGC+TGG 0.558895 tig0023869:+13066 None:intergenic
TCCTGATGAAACCAAATCCA+TGG 0.559307 tig0023869:+13371 None:intergenic
TAACAGAACGAGAACCAAAA+GGG 0.559474 tig0023869:+12959 None:intergenic
AAGGTATCTACAACCACTGC+TGG 0.564271 tig0023869:-12853 Msa1412050:CDS
GACATGGGAACCGCTACATA+GGG 0.570761 tig0023869:+13173 None:intergenic
CTACCCCACGCTTGACGAAG+AGG 0.572444 tig0023869:+13048 None:intergenic
GGTAGTCTCGACGCTCTCAT+CGG 0.573996 tig0023869:-13030 Msa1412050:CDS
AGTTGAGAAACTCAAGGACA+TGG 0.576269 tig0023869:+13157 None:intergenic
GCTATGAAAAGAAAAGGAAG+AGG 0.585681 tig0023869:-12885 Msa1412050:CDS
GGAACCGCTACATAGGGCTA+AGG 0.607722 tig0023869:+13179 None:intergenic
AGTGTAGAGAGTCCAACAAG+TGG 0.618422 tig0023869:-13336 Msa1412050:CDS
CTACATAGGGCTAAGGAGAG+TGG 0.621558 tig0023869:+13186 None:intergenic
TCAATGACCAACAATAGCAC+CGG 0.625940 tig0023869:-13309 Msa1412050:CDS
GTCTTAACTAGCACCAGCAG+TGG 0.629792 tig0023869:+12840 None:intergenic
GGGCTAAGGAGAGTGGTGGA+CGG 0.632875 tig0023869:+13193 None:intergenic
CTAAGGAGAGTGGTGGACGG+TGG 0.639457 tig0023869:+13196 None:intergenic
CAAGATAGTTGAGAAACTCA+AGG 0.640517 tig0023869:+13151 None:intergenic
GGACATGGACAAGGAGCTGG+TGG 0.641101 tig0023869:+13069 None:intergenic
TGTCCTCTTCGTCAAGCGTG+GGG 0.649722 tig0023869:-13051 Msa1412050:CDS
TGCCAAAGAAAGGACAAGGA+TGG 0.651402 tig0023869:+13100 None:intergenic
TGACGAAGAGGACATGGACA+AGG 0.652351 tig0023869:+13060 None:intergenic
CATAGGGCTAAGGAGAGTGG+TGG 0.653546 tig0023869:+13189 None:intergenic
CTCTCCTTAGCCCTATGTAG+CGG 0.658117 tig0023869:-13183 Msa1412050:CDS
GTTGAGAAACTCAAGGACAT+GGG 0.658451 tig0023869:+13158 None:intergenic
CGGGCTGCTTACGAAGAGAA+CGG 0.659740 tig0023869:-13000 Msa1412050:CDS
GGGATGCCAAAGAAAGGACA+AGG 0.667842 tig0023869:+13096 None:intergenic
GCTGCTTACGAAGAGAACGG+TGG 0.749462 tig0023869:-12997 Msa1412050:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTGTTAGGATTTATTTAA+GGG - tig0023869:13268-13287 Msa1412050:CDS 20.0%
!!! TTCTCTTTTGGTTTTCATAA+CGG + tig0023869:12962-12981 None:intergenic 25.0%
! GTTCTGTTAGGATTTATTTA+AGG - tig0023869:13267-13286 Msa1412050:CDS 25.0%
!! GATTTTCAAGCAAAATCTAG+AGG - tig0023869:13299-13318 Msa1412050:CDS 30.0%
GTGTTAGCTATGAAAAGAAA+AGG - tig0023869:13321-13340 Msa1412050:CDS 30.0%
! TTTTCATAACGGCTTGAAGT+TGG + tig0023869:12951-12970 None:intergenic 35.0%
AAAACCAAAAGAGAAGAGAC+TGG - tig0023869:12967-12986 Msa1412050:CDS 35.0%
CAAGATAGTTGAGAAACTCA+AGG + tig0023869:13064-13083 None:intergenic 35.0%
!!! GAACTTTGGTTTTTCCAAAC+TGG + tig0023869:13088-13107 None:intergenic 35.0%
TAACAGAACGAGAACCAAAA+GGG + tig0023869:13256-13275 None:intergenic 35.0%
GCTATGAAAAGAAAAGGAAG+AGG - tig0023869:13327-13346 Msa1412050:CDS 35.0%
GTTGTAGATACCTTAGGTTT+AGG + tig0023869:13353-13372 None:intergenic 35.0%
GTCATTGAAGATCCACTTGT+TGG + tig0023869:12891-12910 None:intergenic 40.0%
TCAATGACCAACAATAGCAC+CGG - tig0023869:12903-12922 Msa1412050:CDS 40.0%
TGATGTTGAACTTCCACTTC+CGG + tig0023869:12925-12944 None:intergenic 40.0%
! TGTTCCAGTCTCTTCTCTTT+TGG + tig0023869:12974-12993 None:intergenic 40.0%
GTTGAGAAACTCAAGGACAT+GGG + tig0023869:13057-13076 None:intergenic 40.0%
AGTTGAGAAACTCAAGGACA+TGG + tig0023869:13058-13077 None:intergenic 40.0%
CTCAACTATCTTGACCAGTT+TGG - tig0023869:13071-13090 Msa1412050:CDS 40.0%
ACAAGGATGGTTGTGAACTT+TGG + tig0023869:13102-13121 None:intergenic 40.0%
AACCATCCTTGTCCTTTCTT+TGG - tig0023869:13110-13129 Msa1412050:CDS 40.0%
CTAACAGAACGAGAACCAAA+AGG + tig0023869:13257-13276 None:intergenic 40.0%
!!! CTTTTGGTTCTCGTTCTGTT+AGG - tig0023869:13255-13274 Msa1412050:CDS 40.0%
TTGTTGGACTCTCTACACTC+TGG + tig0023869:12875-12894 None:intergenic 45.0%
AGTGTAGAGAGTCCAACAAG+TGG - tig0023869:12876-12895 Msa1412050:CDS 45.0%
TGCCAAAGAAAGGACAAGGA+TGG + tig0023869:13115-13134 None:intergenic 45.0%
GGATTAGGGATGCCAAAGAA+AGG + tig0023869:13125-13144 None:intergenic 45.0%
!! GAACCAAAAGGGTTAGTCTC+AGG + tig0023869:13245-13264 None:intergenic 45.0%
AAGGAAGAGGCCTAAACCTA+AGG - tig0023869:13340-13359 Msa1412050:CDS 45.0%
GCAGTGGTTGTAGATACCTT+AGG + tig0023869:13359-13378 None:intergenic 45.0%
! AAGGTATCTACAACCACTGC+TGG - tig0023869:13359-13378 Msa1412050:CDS 45.0%
! ACCAACAATAGCACCGGAAG+TGG - tig0023869:12909-12928 Msa1412050:CDS 50.0%
!! TCCACTTCCGGTGCTATTGT+TGG + tig0023869:12913-12932 None:intergenic 50.0%
CTACATAGGGCTAAGGAGAG+TGG + tig0023869:13029-13048 None:intergenic 50.0%
CTCTCCTTAGCCCTATGTAG+CGG - tig0023869:13029-13048 Msa1412050:CDS 50.0%
GACATGGGAACCGCTACATA+GGG + tig0023869:13042-13061 None:intergenic 50.0%
GGGATGCCAAAGAAAGGACA+AGG + tig0023869:13119-13138 None:intergenic 50.0%
!! GACAAGGAGCTGGTGGATTA+GGG + tig0023869:13139-13158 None:intergenic 50.0%
TGACGAAGAGGACATGGACA+AGG + tig0023869:13155-13174 None:intergenic 50.0%
ATGTCCTCTTCGTCAAGCGT+GGG - tig0023869:13160-13179 Msa1412050:CDS 50.0%
! CGTCCTGAGACTAACCCTTT+TGG - tig0023869:13239-13258 Msa1412050:CDS 50.0%
!! AGAGTGGTGGACGGTGGTTT+CGG + tig0023869:13013-13032 None:intergenic 55.0%
CATAGGGCTAAGGAGAGTGG+TGG + tig0023869:13026-13045 None:intergenic 55.0%
GGAACCGCTACATAGGGCTA+AGG + tig0023869:13036-13055 None:intergenic 55.0%
GGACATGGGAACCGCTACAT+AGG + tig0023869:13043-13062 None:intergenic 55.0%
!! GGACAAGGAGCTGGTGGATT+AGG + tig0023869:13140-13159 None:intergenic 55.0%
AGAGGACATGGACAAGGAGC+TGG + tig0023869:13149-13168 None:intergenic 55.0%
CACGCTTGACGAAGAGGACA+TGG + tig0023869:13161-13180 None:intergenic 55.0%
CATGTCCTCTTCGTCAAGCG+TGG - tig0023869:13159-13178 Msa1412050:CDS 55.0%
TGTCCTCTTCGTCAAGCGTG+GGG - tig0023869:13161-13180 Msa1412050:CDS 55.0%
GGTAGTCTCGACGCTCTCAT+CGG - tig0023869:13182-13201 Msa1412050:CDS 55.0%
ACGCTCTCATCGGTCGTCTT+CGG - tig0023869:13192-13211 Msa1412050:CDS 55.0%
CGGGCTGCTTACGAAGAGAA+CGG - tig0023869:13212-13231 Msa1412050:CDS 55.0%
GCTGCTTACGAAGAGAACGG+TGG - tig0023869:13215-13234 Msa1412050:CDS 55.0%
!! CTAAGGAGAGTGGTGGACGG+TGG + tig0023869:13019-13038 None:intergenic 60.0%
! GGGCTAAGGAGAGTGGTGGA+CGG + tig0023869:13022-13041 None:intergenic 60.0%
GGACATGGACAAGGAGCTGG+TGG + tig0023869:13146-13165 None:intergenic 60.0%
CTACCCCACGCTTGACGAAG+AGG + tig0023869:13167-13186 None:intergenic 60.0%
CGCTCTCATCGGTCGTCTTC+GGG - tig0023869:13193-13212 Msa1412050:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0023869 gene 12843 13391 12843 ID=Msa1412050;Name=Msa1412050
tig0023869 mRNA 12843 13391 12843 ID=Msa1412050-mRNA-1;Parent=Msa1412050;Name=Msa1412050-mRNA-1;_AED=0.34;_eAED=0.34;_QI=0|-1|0|1|-1|1|1|0|182
tig0023869 exon 12843 13391 12843 ID=Msa1412050-mRNA-1:exon:20450;Parent=Msa1412050-mRNA-1
tig0023869 CDS 12843 13391 12843 ID=Msa1412050-mRNA-1:cds;Parent=Msa1412050-mRNA-1
Gene Sequence

>Msa1412050

ATGGATTTGGTTTCATCAGGATCAACAAACCAGAGTGTAGAGAGTCCAACAAGTGGATCTTCAATGACCAACAATAGCACCGGAAGTGGAAGTTCAACATCAACTCCAACTTCAAGCCGTTATGAAAACCAAAAGAGAAGAGACTGGAACACATTCTGTCAGTATCTCCGAAACCACCGTCCACCACTCTCCTTAGCCCTATGTAGCGGTTCCCATGTCCTTGAGTTTCTCAACTATCTTGACCAGTTTGGAAAAACCAAAGTTCACAACCATCCTTGTCCTTTCTTTGGCATCCCTAATCCACCAGCTCCTTGTCCATGTCCTCTTCGTCAAGCGTGGGGTAGTCTCGACGCTCTCATCGGTCGTCTTCGGGCTGCTTACGAAGAGAACGGTGGTCGTCCTGAGACTAACCCTTTTGGTTCTCGTTCTGTTAGGATTTATTTAAGGGATGTTCGTGATTTTCAAGCAAAATCTAGAGGTGTTAGCTATGAAAAGAAAAGGAAGAGGCCTAAACCTAAGGTATCTACAACCACTGCTGGTGCTAGTTAA
Protein sequence

>Msa1412050

MDLVSSGSTNQSVESPTSGSSMTNNSTGSGSSTSTPTSSRYENQKRRDWNTFCQYLRNHRPPLSLALCSGSHVLEFLNYLDQFGKTKVHNHPCPFFGIPNPPAPCPCPLRQAWGSLDALIGRLRAAYEENGGRPETNPFGSRSVRIYLRDVRDFQAKSRGVSYEKKRKRPKPKVSTTTAGAS*