AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1353470


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1353470 MtrunA17_Chr2g0302641 97.546 163 4 0 2 164 102 264 1.82e-116 330
Msa1353470 MtrunA17_Chr7g0271631 46.479 142 75 1 6 146 2 143 4.45e-38 128
Msa1353470 MtrunA17_Chr1g0192921 43.421 152 85 1 7 157 34 185 1.57e-36 125
Msa1353470 MtrunA17_Chr7g0265421 43.382 136 76 1 6 140 2 137 1.61e-36 123
Msa1353470 MtrunA17_Chr2g0285991 38.129 139 86 0 15 153 16 154 3.70e-32 112
Msa1353470 MtrunA17_Chr2g0325571 40.909 132 78 0 11 142 3 134 7.41e-28 100
Msa1353470 MtrunA17_Chr2g0325561 38.462 130 80 0 11 140 3 132 5.80e-27 98.6
Msa1353470 MtrunA17_Chr4g0068821 36.986 146 85 4 7 147 3 146 4.69e-24 91.7
Msa1353470 MtrunA17_Chr2g0283761 40.984 122 68 3 24 142 3 123 2.87e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1353470 AT4G24130.1 68.667 150 46 1 1 149 1 150 5.60e-72 214
Msa1353470 AT1G09310.1 46.207 145 76 2 7 150 3 146 1.34e-34 119
Msa1353470 AT1G56580.1 44.595 148 79 3 7 151 3 150 3.24e-34 118
Msa1353470 AT5G46230.1 37.121 132 83 0 9 140 8 139 1.66e-31 110
Msa1353470 AT1G30020.1 33.846 130 82 1 7 136 6 131 1.06e-25 96.3
Msa1353470 AT5G49600.1 34.694 147 85 4 7 143 1 146 1.42e-20 83.6

Find 29 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAAGGTGTTCTTCCCTTAA+AGG 0.146605 tig0013491:-10740 Msa1353470:CDS
ACATTCAACAAGATCCTTTA+AGG 0.179628 tig0013491:+10726 None:intergenic
AGAGTAAGCAATTGTTTGTT+TGG 0.287883 tig0013491:-10555 Msa1353470:CDS
TGTGGAAGAGTTAGAGAAAC+TGG 0.316514 tig0013491:-10706 Msa1353470:CDS
TCAATACTCATTTCAACTAT+AGG 0.386964 tig0013491:+10529 None:intergenic
CTTTAAGGGAAGAACACCTT+TGG 0.399056 tig0013491:+10741 None:intergenic
GAGTAAGCAATTGTTTGTTT+GGG 0.413681 tig0013491:-10554 Msa1353470:CDS
GAAGTTGCAATTGAAGGATA+AGG 0.421440 tig0013491:-10404 Msa1353470:CDS
CATTCAACAAGATCCTTTAA+GGG 0.423103 tig0013491:+10727 None:intergenic
TTTAAGGGAAGAACACCTTT+GGG 0.434347 tig0013491:+10742 None:intergenic
ATACAACTCTTAGAAGAGCT+TGG 0.448905 tig0013491:-10769 Msa1353470:CDS
TTTAAGACTCCTATGGGGAT+TGG 0.453850 tig0013491:-10481 Msa1353470:CDS
GTATGAGAAGTTGCAATTGA+AGG 0.453990 tig0013491:-10410 Msa1353470:CDS
AATTGAAGTTACTGCTTATG+TGG 0.459578 tig0013491:-10611 Msa1353470:CDS
ATAGTTGAAATGAGTATTGA+GGG 0.460794 tig0013491:-10526 Msa1353470:CDS
AAGCTCTTCTAAGAGTTGTA+TGG 0.469293 tig0013491:+10771 None:intergenic
CCTTCAAAATAATGTTCACT+TGG 0.482969 tig0013491:+10658 None:intergenic
TATAGTTGAAATGAGTATTG+AGG 0.501110 tig0013491:-10527 Msa1353470:CDS
TTAAAGGATCTTGTTGAATG+TGG 0.521582 tig0013491:-10724 Msa1353470:CDS
CTTCTAAGAGTTGTATGGAA+TGG 0.521965 tig0013491:+10776 None:intergenic
GTTGCAATTGAAGGATAAGG+AGG 0.546376 tig0013491:-10401 Msa1353470:CDS
GCAGGTGCAGAAATAGTGTA+TGG 0.551940 tig0013491:-10817 Msa1353470:CDS
TACTTCATTTATGAGTGTTG+AGG 0.556318 tig0013491:-10443 Msa1353470:CDS
TTCAAGATGAAGAAAATGAG+TGG 0.567086 tig0013491:-10583 Msa1353470:CDS
ACAAAGACTCTTGTGAGCTA+CGG 0.601286 tig0013491:-10634 Msa1353470:CDS
GAAGAGCTTGGATTTCCCAA+AGG 0.601476 tig0013491:-10757 Msa1353470:CDS
ATGGTAACAAATGAACGTGC+AGG 0.612544 tig0013491:-10835 Msa1353470:CDS
AAAGACTTACCAATCCCCAT+AGG 0.653062 tig0013491:+10472 None:intergenic
AATGGCTAGCAACAGCACAA+TGG 0.699467 tig0013491:-10854 Msa1353470:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGTTTGGATGAAACAAA+AGG - tig0013491:10551-10570 Msa1353470:CDS 25.0%
! TCAATACTCATTTCAACTAT+AGG + tig0013491:10708-10727 None:intergenic 25.0%
!! TATAGTTGAAATGAGTATTG+AGG - tig0013491:10707-10726 Msa1353470:CDS 25.0%
!!! ATAGTTGAAATGAGTATTGA+GGG - tig0013491:10708-10727 Msa1353470:CDS 25.0%
!!! ATGTATTTTAAGACTCCTAT+GGG - tig0013491:10747-10766 Msa1353470:CDS 25.0%
CATTCAACAAGATCCTTTAA+GGG + tig0013491:10510-10529 None:intergenic 30.0%
ACATTCAACAAGATCCTTTA+AGG + tig0013491:10511-10530 None:intergenic 30.0%
TTAAAGGATCTTGTTGAATG+TGG - tig0013491:10510-10529 Msa1353470:CDS 30.0%
!!! TTAGAGAAACTGGTTTTGTT+TGG - tig0013491:10538-10557 Msa1353470:CDS 30.0%
CCTTCAAAATAATGTTCACT+TGG + tig0013491:10579-10598 None:intergenic 30.0%
!!! CCAAGTGAACATTATTTTGA+AGG - tig0013491:10576-10595 Msa1353470:CDS 30.0%
AATTGAAGTTACTGCTTATG+TGG - tig0013491:10623-10642 Msa1353470:CDS 30.0%
TTCAAGATGAAGAAAATGAG+TGG - tig0013491:10651-10670 Msa1353470:CDS 30.0%
AGAGTAAGCAATTGTTTGTT+TGG - tig0013491:10679-10698 Msa1353470:CDS 30.0%
GAGTAAGCAATTGTTTGTTT+GGG - tig0013491:10680-10699 Msa1353470:CDS 30.0%
!!! ATGAGTATTGAGGGTTTTAA+TGG - tig0013491:10717-10736 Msa1353470:CDS 30.0%
!!! GATGTATTTTAAGACTCCTA+TGG - tig0013491:10746-10765 Msa1353470:CDS 30.0%
!!! TGTATTTTAAGACTCCTATG+GGG - tig0013491:10748-10767 Msa1353470:CDS 30.0%
! TACTTCATTTATGAGTGTTG+AGG - tig0013491:10791-10810 Msa1353470:CDS 30.0%
! CTTCTAAGAGTTGTATGGAA+TGG + tig0013491:10461-10480 None:intergenic 35.0%
! AAGCTCTTCTAAGAGTTGTA+TGG + tig0013491:10466-10485 None:intergenic 35.0%
ATACAACTCTTAGAAGAGCT+TGG - tig0013491:10465-10484 Msa1353470:CDS 35.0%
TTTAAGGGAAGAACACCTTT+GGG + tig0013491:10495-10514 None:intergenic 35.0%
GTATGAGAAGTTGCAATTGA+AGG - tig0013491:10824-10843 Msa1353470:CDS 35.0%
GAAGTTGCAATTGAAGGATA+AGG - tig0013491:10830-10849 Msa1353470:CDS 35.0%
ATGGTAACAAATGAACGTGC+AGG - tig0013491:10399-10418 Msa1353470:CDS 40.0%
! CTTTAAGGGAAGAACACCTT+TGG + tig0013491:10496-10515 None:intergenic 40.0%
!! CAAAGGTGTTCTTCCCTTAA+AGG - tig0013491:10494-10513 Msa1353470:CDS 40.0%
TGTGGAAGAGTTAGAGAAAC+TGG - tig0013491:10528-10547 Msa1353470:CDS 40.0%
ACAAAGACTCTTGTGAGCTA+CGG - tig0013491:10600-10619 Msa1353470:CDS 40.0%
! TTTAAGACTCCTATGGGGAT+TGG - tig0013491:10753-10772 Msa1353470:CDS 40.0%
AAAGACTTACCAATCCCCAT+AGG + tig0013491:10765-10784 None:intergenic 40.0%
GTTGCAATTGAAGGATAAGG+AGG - tig0013491:10833-10852 Msa1353470:CDS 40.0%
GCAGGTGCAGAAATAGTGTA+TGG - tig0013491:10417-10436 Msa1353470:CDS 45.0%
GAAGAGCTTGGATTTCCCAA+AGG - tig0013491:10477-10496 Msa1353470:CDS 45.0%
Chromosome Type Strat End Strand Name
tig0013491 gene 10381 10875 10381 ID=Msa1353470;Name=Msa1353470
tig0013491 mRNA 10381 10875 10381 ID=Msa1353470-mRNA-1;Parent=Msa1353470;Name=Msa1353470-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|164
tig0013491 exon 10381 10875 10381 ID=Msa1353470-mRNA-1:exon:8683;Parent=Msa1353470-mRNA-1
tig0013491 CDS 10381 10875 10381 ID=Msa1353470-mRNA-1:cds;Parent=Msa1353470-mRNA-1
Gene Sequence

>Msa1353470

ATGGCTAGCAACAGCACAATGGTAACAAATGAACGTGCAGGTGCAGAAATAGTGTATGGTTCTGAAGAATGTTTCAACCATTCCATACAACTCTTAGAAGAGCTTGGATTTCCCAAAGGTGTTCTTCCCTTAAAGGATCTTGTTGAATGTGGAAGAGTTAGAGAAACTGGTTTTGTTTGGATGAAACAAAAGGCACCAAGTGAACATTATTTTGAAGGTACAAAGACTCTTGTGAGCTACGGAATTGAAGTTACTGCTTATGTGGAGAAATTCAAGATGAAGAAAATGAGTGGAATTAAGAGTAAGCAATTGTTTGTTTGGGTGCCTATAGTTGAAATGAGTATTGAGGGTTTTAATGGAAAGAAGATGTATTTTAAGACTCCTATGGGGATTGGTAAGTCTTTTCATGTTACTTCATTTATGAGTGTTGAGGAAAAAGAAAAGTATGAGAAGTTGCAATTGAAGGATAAGGAGGTTGAGATCAAAGAAAATTAA

Protein sequence

>Msa1353470

MASNSTMVTNERAGAEIVYGSEECFNHSIQLLEELGFPKGVLPLKDLVECGRVRETGFVWMKQKAPSEHYFEGTKTLVSYGIEVTAYVEKFKMKKMSGIKSKQLFVWVPIVEMSIEGFNGKKMYFKTPMGIGKSFHVTSFMSVEEKEKYEKLQLKDKEVEIKEN*