AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1398860


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1398860 MtrunA17_Chr7g0271631 96.532 173 2 3 1 172 1 170 1.13e-114 322
Msa1398860 MtrunA17_Chr7g0265421 85.065 154 21 1 1 154 1 152 3.14e-92 265
Msa1398860 MtrunA17_Chr1g0192921 71.233 146 42 0 1 146 32 177 4.31e-73 218
Msa1398860 MtrunA17_Chr2g0285991 49.254 134 68 0 10 143 14 147 6.95e-49 155
Msa1398860 MtrunA17_Chr4g0068821 50.714 140 65 2 1 138 1 138 5.31e-39 130
Msa1398860 MtrunA17_Chr2g0302641 44.375 160 88 1 2 161 106 264 6.91e-39 133
Msa1398860 MtrunA17_Chr2g0325561 45.528 123 67 0 17 139 12 134 8.09e-34 116
Msa1398860 MtrunA17_Chr2g0325571 53.636 110 51 0 28 137 23 132 9.31e-33 114
Msa1398860 MtrunA17_Chr2g0283761 47.368 95 50 0 43 137 27 121 9.06e-18 75.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1398860 AT1G09310.1 62.222 180 55 2 1 168 1 179 1.01e-69 209
Msa1398860 AT1G56580.1 63.953 172 51 4 1 167 1 166 1.12e-68 206
Msa1398860 AT5G46230.1 47.692 130 68 0 12 141 14 143 4.01e-46 148
Msa1398860 AT4G24130.1 45.185 135 74 0 9 143 13 147 4.14e-39 130
Msa1398860 AT1G30020.1 43.571 140 77 1 13 150 15 154 8.61e-37 125
Msa1398860 AT5G49600.1 46.207 145 68 4 3 138 1 144 6.31e-35 120

Find 31 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATTTCTTTGAGAAGCTCTT+TGG 0.291146 tig0022300:+21875 None:intergenic
TTCAATGGTAAAAGACCATT+TGG 0.295506 tig0022300:+21846 None:intergenic
GTCACTGCTTACGTTGAAAA+TGG 0.305607 tig0022300:-21708 Msa1398860:CDS
ATCACATTCAAAACACCTTC+TGG 0.305889 tig0022300:-21591 Msa1398860:CDS
AACCCAAATCAAAAGCTCTT+TGG 0.308533 tig0022300:+21656 None:intergenic
TCAATTTCAAAAGCAGAAAC+AGG 0.316797 tig0022300:+21552 None:intergenic
TCCATGGTAAACCTCGGATT+TGG 0.319079 tig0022300:+21920 None:intergenic
GTTGGTTACAACAGAGAAAC+AGG 0.372734 tig0022300:-21810 Msa1398860:CDS
ACACACAAATTCGAAAAGAT+TGG 0.384478 tig0022300:-21756 Msa1398860:CDS
ATCAAGTGGTGCTACTGTTA+AGG 0.417389 tig0022300:-21514 Msa1398860:CDS
ACTGTTGCTGCTACTGCTGC+TGG 0.440092 tig0022300:-21468 Msa1398860:CDS
ACTTCGGTAGCATAGGAAAC+AGG 0.457776 tig0022300:+21729 None:intergenic
TATATTGATGATCCACCAAC+TGG 0.471274 tig0022300:-21618 Msa1398860:CDS
CACACAAATTCGAAAAGATT+GGG 0.476488 tig0022300:-21755 Msa1398860:CDS
TTGAAAGACATCACTGAAGT+TGG 0.485594 tig0022300:-21828 Msa1398860:CDS
AAAGAAATCTCTCTCCCAAA+TGG 0.487795 tig0022300:-21861 Msa1398860:CDS
TCAATGGTAAAAGACCATTT+GGG 0.506164 tig0022300:+21847 None:intergenic
CCATGGAGACGAAATGTGTC+AGG 0.515719 tig0022300:-21904 Msa1398860:CDS
ACTTCAGTGATGTCTTTCAA+TGG 0.520310 tig0022300:+21831 None:intergenic
TACTGCTGCTGGTGTTAAAG+AGG 0.555141 tig0022300:-21457 Msa1398860:CDS
CCTGACACATTTCGTCTCCA+TGG 0.557991 tig0022300:+21904 None:intergenic
GAAGAGAAAGAGAAATCAAG+TGG 0.560001 tig0022300:-21528 Msa1398860:CDS
TGTTAAGGAAGCTGCTAACA+AGG 0.566122 tig0022300:-21499 Msa1398860:CDS
TTCGTCTCCATGGTAAACCT+CGG 0.581474 tig0022300:+21914 None:intergenic
TTCAACGTAAGCAGTGACTT+CGG 0.602234 tig0022300:+21713 None:intergenic
CAATTTCAAAAGCAGAAACA+GGG 0.604117 tig0022300:+21553 None:intergenic
AGCAGTGACTTCGGTAGCAT+AGG 0.607903 tig0022300:+21722 None:intergenic
TCCAAATCCGAGGTTTACCA+TGG 0.611352 tig0022300:-21921 Msa1398860:CDS
CAACCCCAAAACGATGTCGT+TGG 0.618459 tig0022300:-21961 None:intergenic
GGTAAGATCAAGAAACTGAA+CGG 0.640251 tig0022300:-21687 Msa1398860:CDS
AGAAATCAAATCCAAATCCG+AGG 0.652928 tig0022300:-21931 Msa1398860:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCAATGGTAAAAGACCATTT+GGG + tig0022300:21556-21575 None:intergenic 30.0%
TTCAATGGTAAAAGACCATT+TGG + tig0022300:21557-21576 None:intergenic 30.0%
ACACACAAATTCGAAAAGAT+TGG - tig0022300:21644-21663 Msa1398860:CDS 30.0%
CACACAAATTCGAAAAGATT+GGG - tig0022300:21645-21664 Msa1398860:CDS 30.0%
!! AAACCAAAGAGCTTTTGATT+TGG - tig0022300:21741-21760 Msa1398860:CDS 30.0%
!!! AACCAAAGAGCTTTTGATTT+GGG - tig0022300:21742-21761 Msa1398860:CDS 30.0%
! TTGAATGTGATTTTACCAGT+TGG + tig0022300:21800-21819 None:intergenic 30.0%
! AAACTTCTAAAAAGTCCAGA+AGG + tig0022300:21827-21846 None:intergenic 30.0%
CAATTTCAAAAGCAGAAACA+GGG + tig0022300:21850-21869 None:intergenic 30.0%
TCAATTTCAAAAGCAGAAAC+AGG + tig0022300:21851-21870 None:intergenic 30.0%
AGAAATCAAATCCAAATCCG+AGG - tig0022300:21469-21488 Msa1398860:CDS 35.0%
! GATTTCTTTGAGAAGCTCTT+TGG + tig0022300:21528-21547 None:intergenic 35.0%
AAAGAAATCTCTCTCCCAAA+TGG - tig0022300:21539-21558 Msa1398860:CDS 35.0%
ACTTCAGTGATGTCTTTCAA+TGG + tig0022300:21572-21591 None:intergenic 35.0%
TTGAAAGACATCACTGAAGT+TGG - tig0022300:21572-21591 Msa1398860:CDS 35.0%
!!! ACAGAGAAACAGGTTTTGTT+TGG - tig0022300:21600-21619 Msa1398860:CDS 35.0%
GGTAAGATCAAGAAACTGAA+CGG - tig0022300:21713-21732 Msa1398860:CDS 35.0%
AACCCAAATCAAAAGCTCTT+TGG + tig0022300:21747-21766 None:intergenic 35.0%
! TATATTGATGATCCACCAAC+TGG - tig0022300:21782-21801 Msa1398860:CDS 35.0%
! AATGTGATTTTACCAGTTGG+TGG + tig0022300:21797-21816 None:intergenic 35.0%
ATCACATTCAAAACACCTTC+TGG - tig0022300:21809-21828 Msa1398860:CDS 35.0%
GAAGAGAAAGAGAAATCAAG+TGG - tig0022300:21872-21891 Msa1398860:CDS 35.0%
GTTGGTTACAACAGAGAAAC+AGG - tig0022300:21590-21609 Msa1398860:CDS 40.0%
TTCAACGTAAGCAGTGACTT+CGG + tig0022300:21690-21709 None:intergenic 40.0%
GTCACTGCTTACGTTGAAAA+TGG - tig0022300:21692-21711 Msa1398860:CDS 40.0%
!! ATCAAGTGGTGCTACTGTTA+AGG - tig0022300:21886-21905 Msa1398860:CDS 40.0%
TGTTAAGGAAGCTGCTAACA+AGG - tig0022300:21901-21920 Msa1398860:CDS 40.0%
TCCAAATCCGAGGTTTACCA+TGG - tig0022300:21479-21498 Msa1398860:CDS 45.0%
TCCATGGTAAACCTCGGATT+TGG + tig0022300:21483-21502 None:intergenic 45.0%
TTCGTCTCCATGGTAAACCT+CGG + tig0022300:21489-21508 None:intergenic 45.0%
ACTTCGGTAGCATAGGAAAC+AGG + tig0022300:21674-21693 None:intergenic 45.0%
! TACTGCTGCTGGTGTTAAAG+AGG - tig0022300:21943-21962 Msa1398860:CDS 45.0%
CCTGACACATTTCGTCTCCA+TGG + tig0022300:21499-21518 None:intergenic 50.0%
CCATGGAGACGAAATGTGTC+AGG - tig0022300:21496-21515 Msa1398860:CDS 50.0%
AGCAGTGACTTCGGTAGCAT+AGG + tig0022300:21681-21700 None:intergenic 50.0%
ACTGTTGCTGCTACTGCTGC+TGG - tig0022300:21932-21951 Msa1398860:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0022300 gene 21452 21970 21452 ID=Msa1398860;Name=Msa1398860
tig0022300 mRNA 21452 21970 21452 ID=Msa1398860-mRNA-1;Parent=Msa1398860;Name=Msa1398860-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|172
tig0022300 exon 21452 21970 21452 ID=Msa1398860-mRNA-1:exon:16857;Parent=Msa1398860-mRNA-1
tig0022300 CDS 21452 21970 21452 ID=Msa1398860-mRNA-1:cds;Parent=Msa1398860-mRNA-1
Gene Sequence

>Msa1398860

ATGTCGTTGGTAACAGAAGAAATCAAATCCAAATCCGAGGTTTACCATGGAGACGAAATGTGTCAGGTGAAATCCAAAGAGCTTCTCAAAGAAATCTCTCTCCCAAATGGTCTTTTACCATTGAAAGACATCACTGAAGTTGGTTACAACAGAGAAACAGGTTTTGTTTGGCTGAAACAGAAGAAAAGCATAACACACAAATTCGAAAAGATTGGGAAACCTGTTTCCTATGCTACCGAAGTCACTGCTTACGTTGAAAATGGTAAGATCAAGAAACTGAACGGTGTTAAAACCAAAGAGCTTTTGATTTGGGTTACTTTGTGTGATATTTATATTGATGATCCACCAACTGGTAAAATCACATTCAAAACACCTTCTGGACTTTTTAGAAGTTTCCCTGTTTCTGCTTTTGAAATTGAAGAAGAGAAAGAGAAATCAAGTGGTGCTACTGTTAAGGAAGCTGCTAACAAGGTCAATGAAACTGTTGCTGCTACTGCTGCTGGTGTTAAAGAGGTCTAA

Protein sequence

>Msa1398860

MSLVTEEIKSKSEVYHGDEMCQVKSKELLKEISLPNGLLPLKDITEVGYNRETGFVWLKQKKSITHKFEKIGKPVSYATEVTAYVENGKIKKLNGVKTKELLIWVTLCDIYIDDPPTGKITFKTPSGLFRSFPVSAFEIEEEKEKSSGATVKEAANKVNETVAATAAGVKEV*