AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0187310


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0187310 MtrunA17_Chr8g0387601 94.273 227 13 0 1 227 1 227 3.49e-150 416
Msa0187310 MtrunA17_Chr8g0348161 37.500 216 116 7 1 210 1 203 7.81e-31 113
Msa0187310 MtrunA17_Chr5g0397141 26.994 163 113 4 64 221 28 189 1.33e-14 69.7
Msa0187310 MtrunA17_Chr8g0334401 30.818 159 106 1 50 204 12 170 1.69e-14 69.3
Msa0187310 MtrunA17_Chr4g0024221 28.049 164 112 4 50 210 9 169 3.45e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0187310 AT2G46150.1 34.234 222 128 8 7 221 5 215 1.88e-32 117
Msa0187310 AT4G23610.1 26.066 211 145 7 1 204 5 211 4.71e-20 85.5
Msa0187310 AT3G54200.1 29.771 131 88 1 69 195 74 204 1.68e-11 62.4

Find 38 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTTGAAACTTCCACTTATA+AGG 0.143507 2_1:-2023039 None:intergenic
TATTGGATTCATTAATATTT+AGG 0.155942 2_1:+2023447 Msa0187310:CDS
ATACAAATTCATTCACTTTC+AGG 0.174928 2_1:+2023113 Msa0187310:CDS
TTCTATAATGGAATTGATAT+TGG 0.258144 2_1:+2023160 Msa0187310:CDS
GATATGAAATTTGGTGCTAT+AGG 0.317510 2_1:-2022815 None:intergenic
AATATGTTCAAGAGGTCAAT+TGG 0.340166 2_1:+2023358 Msa0187310:CDS
GTTGAAACTTCCACTTATAA+GGG 0.363902 2_1:-2023038 None:intergenic
GTTGTTAATGATATGAAATT+TGG 0.399182 2_1:-2022824 None:intergenic
TGTTGTTGATTATCTGCACT+TGG 0.400611 2_1:-2022860 None:intergenic
ACACGTGGTGATAATTGTAT+TGG 0.405537 2_1:+2023430 Msa0187310:CDS
AATTCATTCACTTTCAGGTA+TGG 0.412565 2_1:+2023118 Msa0187310:CDS
ACACTATTCATTCTAACTTC+AGG 0.414388 2_1:-2023013 None:intergenic
AGTACTTATACGAAGATCAA+TGG 0.434098 2_1:+2023319 Msa0187310:CDS
AGCTTGTGGACAATCAAGAT+TGG 0.439651 2_1:+2023263 Msa0187310:CDS
ATATGTTCAAGAGGTCAATT+GGG 0.448508 2_1:+2023359 Msa0187310:CDS
AATAGTGTTACCCTTATAAG+TGG 0.474862 2_1:+2023028 Msa0187310:CDS
ATTCATTCACTTTCAGGTAT+GGG 0.482613 2_1:+2023119 Msa0187310:CDS
GCATAAAGAAGTTTGTCATA+TGG 0.485001 2_1:+2022909 Msa0187310:CDS
TATAATGGAATTGATATTGG+AGG 0.495203 2_1:+2023163 Msa0187310:CDS
AGTACATACGATATCCCAAC+AGG 0.525073 2_1:+2023400 Msa0187310:CDS
AAAAGCTAAGGCGCAAAGAA+CGG 0.530162 2_1:+2023204 Msa0187310:CDS
CACGTGTGATTGAACCTGTT+GGG 0.532056 2_1:-2023414 None:intergenic
TTCATTCACTTTCAGGTATG+GGG 0.551722 2_1:+2023120 Msa0187310:CDS
GTTGTTGATTATCTGCACTT+GGG 0.554868 2_1:-2022859 None:intergenic
AATGGAATTGATATTGGAGG+AGG 0.560744 2_1:+2023166 Msa0187310:CDS
CTTATAAGTGGAAGTTTCAA+CGG 0.570737 2_1:+2023040 Msa0187310:CDS
TGGAGGAGGAATACAACCAC+CGG 0.577353 2_1:+2023180 Msa0187310:CDS
ACAACCACCGGGAAAAGCTA+AGG 0.582230 2_1:+2023192 Msa0187310:CDS
AAATATTGAATATGTTCAAG+AGG 0.596331 2_1:+2023350 Msa0187310:CDS
CCACGTGTGATTGAACCTGT+TGG 0.609505 2_1:-2023415 None:intergenic
CTAAGGCGCAAAGAACGGCA+AGG 0.613584 2_1:+2023209 Msa0187310:CDS
GGCAAGGGTAAACGTGACAT+TGG 0.620256 2_1:+2023225 Msa0187310:CDS
TAAGGCGCAAAGAACGGCAA+GGG 0.636962 2_1:+2023210 Msa0187310:CDS
AAGAAGTTTGTCATATGGTG+TGG 0.646428 2_1:+2022914 Msa0187310:CDS
TATGTTCAAGAGGTCAATTG+GGG 0.679448 2_1:+2023360 Msa0187310:CDS
GGAGGAGGAATACAACCACC+GGG 0.691763 2_1:+2023181 Msa0187310:CDS
CCAACAGGTTCAATCACACG+TGG 0.713111 2_1:+2023415 Msa0187310:CDS
AATTCCATTATAGAAAACAG+TGG 0.718426 2_1:-2023152 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTGTTAATGATATGAAATT+TGG - chr2_1:2022827-2022846 None:intergenic 20.0%
!!! TTCTATAATGGAATTGATAT+TGG + chr2_1:2023160-2023179 Msa0187310:CDS 20.0%
!! AAATATTGAATATGTTCAAG+AGG + chr2_1:2023350-2023369 Msa0187310:CDS 20.0%
! ATACAAATTCATTCACTTTC+AGG + chr2_1:2023113-2023132 Msa0187310:CDS 25.0%
! AATTCCATTATAGAAAACAG+TGG - chr2_1:2023155-2023174 None:intergenic 25.0%
!! TATAATGGAATTGATATTGG+AGG + chr2_1:2023163-2023182 Msa0187310:CDS 25.0%
!! GATATGAAATTTGGTGCTAT+AGG - chr2_1:2022818-2022837 None:intergenic 30.0%
GCATAAAGAAGTTTGTCATA+TGG + chr2_1:2022909-2022928 Msa0187310:CDS 30.0%
ACACTATTCATTCTAACTTC+AGG - chr2_1:2023016-2023035 None:intergenic 30.0%
AATAGTGTTACCCTTATAAG+TGG + chr2_1:2023028-2023047 Msa0187310:CDS 30.0%
GTTGAAACTTCCACTTATAA+GGG - chr2_1:2023041-2023060 None:intergenic 30.0%
CTTATAAGTGGAAGTTTCAA+CGG + chr2_1:2023040-2023059 Msa0187310:CDS 30.0%
! AATTCATTCACTTTCAGGTA+TGG + chr2_1:2023118-2023137 Msa0187310:CDS 30.0%
! ATTCATTCACTTTCAGGTAT+GGG + chr2_1:2023119-2023138 Msa0187310:CDS 30.0%
! AACACCACTGTTTTCTATAA+TGG + chr2_1:2023148-2023167 Msa0187310:CDS 30.0%
AGTACTTATACGAAGATCAA+TGG + chr2_1:2023319-2023338 Msa0187310:CDS 30.0%
AATATGTTCAAGAGGTCAAT+TGG + chr2_1:2023358-2023377 Msa0187310:CDS 30.0%
ATATGTTCAAGAGGTCAATT+GGG + chr2_1:2023359-2023378 Msa0187310:CDS 30.0%
! GTTGTTGATTATCTGCACTT+GGG - chr2_1:2022862-2022881 None:intergenic 35.0%
! TGTTGTTGATTATCTGCACT+TGG - chr2_1:2022863-2022882 None:intergenic 35.0%
AAGAAGTTTGTCATATGGTG+TGG + chr2_1:2022914-2022933 Msa0187310:CDS 35.0%
CGTTGAAACTTCCACTTATA+AGG - chr2_1:2023042-2023061 None:intergenic 35.0%
! TTCATTCACTTTCAGGTATG+GGG + chr2_1:2023120-2023139 Msa0187310:CDS 35.0%
AATGGAATTGATATTGGAGG+AGG + chr2_1:2023166-2023185 Msa0187310:CDS 35.0%
GATTAATGCGAAAAAGCTTG+TGG + chr2_1:2023249-2023268 Msa0187310:CDS 35.0%
TATGTTCAAGAGGTCAATTG+GGG + chr2_1:2023360-2023379 Msa0187310:CDS 35.0%
ACACGTGGTGATAATTGTAT+TGG + chr2_1:2023430-2023449 Msa0187310:CDS 35.0%
AAAAGCTAAGGCGCAAAGAA+CGG + chr2_1:2023204-2023223 Msa0187310:CDS 40.0%
AGCTTGTGGACAATCAAGAT+TGG + chr2_1:2023263-2023282 Msa0187310:CDS 40.0%
AGTACATACGATATCCCAAC+AGG + chr2_1:2023400-2023419 Msa0187310:CDS 40.0%
CACGTGTGATTGAACCTGTT+GGG - chr2_1:2023417-2023436 None:intergenic 45.0%
TGGAGGAGGAATACAACCAC+CGG + chr2_1:2023180-2023199 Msa0187310:CDS 50.0%
ACAACCACCGGGAAAAGCTA+AGG + chr2_1:2023192-2023211 Msa0187310:CDS 50.0%
!! CTTTGCGCCTTAGCTTTTCC+CGG - chr2_1:2023202-2023221 None:intergenic 50.0%
TAAGGCGCAAAGAACGGCAA+GGG + chr2_1:2023210-2023229 Msa0187310:CDS 50.0%
GGCAAGGGTAAACGTGACAT+TGG + chr2_1:2023225-2023244 Msa0187310:CDS 50.0%
CCACGTGTGATTGAACCTGT+TGG - chr2_1:2023418-2023437 None:intergenic 50.0%
CCAACAGGTTCAATCACACG+TGG + chr2_1:2023415-2023434 Msa0187310:CDS 50.0%
GGAGGAGGAATACAACCACC+GGG + chr2_1:2023181-2023200 Msa0187310:CDS 55.0%
CTAAGGCGCAAAGAACGGCA+AGG + chr2_1:2023209-2023228 Msa0187310:CDS 55.0%
!! TGCGCCTTAGCTTTTCCCGG+TGG - chr2_1:2023199-2023218 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 2022785 2023468 2022785 ID=Msa0187310;Name=Msa0187310
chr2_1 mRNA 2022785 2023468 2022785 ID=Msa0187310-mRNA-1;Parent=Msa0187310;Name=Msa0187310-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|227
chr2_1 exon 2022785 2023468 2022785 ID=Msa0187310-mRNA-1:exon:922;Parent=Msa0187310-mRNA-1
chr2_1 CDS 2022785 2023468 2022785 ID=Msa0187310-mRNA-1:cds;Parent=Msa0187310-mRNA-1
Gene Sequence

>Msa0187310

ATGGCTCATACACACAGAGAGCAATTCAAACCTATAGCACCAAATTTCATATCATTAACAACTCACTTTAGCAGCCCAAGTGCAGATAATCAACAACAACACTTATCTGAACGCAAAACAAAACGCATAAAGAAGTTTGTCATATGGTGTGGATGCATCACTGCAATTCTTTTGTTACTTATTGTCATAGTCATAATTCTAGCTTTTACTGTCTACAATGTAAAAGAACCTGAAGTTAGAATGAATAGTGTTACCCTTATAAGTGGAAGTTTCAACGGTAGCAACGCTTCGAATAACGTTACAATTCTTGCTGATATGTCTGTGAAGAATACAAATTCATTCACTTTCAGGTATGGGGCAGCAAACACCACTGTTTTCTATAATGGAATTGATATTGGAGGAGGAATACAACCACCGGGAAAAGCTAAGGCGCAAAGAACGGCAAGGGTAAACGTGACATTGGTGATTAATGCGAAAAAGCTTGTGGACAATCAAGATTGGATTATTGATGTTAGAGATCAAGCTTTGAATTTCAGTACTTATACGAAGATCAATGGAAAAGTGAAAATATTGAATATGTTCAAGAGGTCAATTGGGGTTGAGTTGAATTGTACTAGTACATACGATATCCCAACAGGTTCAATCACACGTGGTGATAATTGTATTGGATTCATTAATATTTAG

Protein sequence

>Msa0187310

MAHTHREQFKPIAPNFISLTTHFSSPSADNQQQHLSERKTKRIKKFVIWCGCITAILLLLIVIVIILAFTVYNVKEPEVRMNSVTLISGSFNGSNASNNVTILADMSVKNTNSFTFRYGAANTTVFYNGIDIGGGIQPPGKAKAQRTARVNVTLVINAKKLVDNQDWIIDVRDQALNFSTYTKINGKVKILNMFKRSIGVELNCTSTYDIPTGSITRGDNCIGFINI*