AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0277280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0277280 MtrunA17_Chr2g0290521 95.370 108 5 0 1 108 20 127 2.23e-69 203
Msa0277280 MtrunA17_Chr4g0060391 54.630 108 45 2 1 107 18 122 1.00e-29 103
Msa0277280 MtrunA17_Chr4g0056371 63.095 84 30 1 26 108 49 132 1.44e-29 103
Msa0277280 MtrunA17_Chr4g0056391 67.949 78 24 1 24 100 57 134 5.63e-29 102
Msa0277280 MtrunA17_Chr1g0149481 57.303 89 37 1 21 108 76 164 1.96e-27 98.6
Msa0277280 MtrunA17_Chr1g0149491 60.241 83 32 1 27 108 69 151 3.43e-27 97.4
Msa0277280 MtrunA17_Chr4g0056411 61.176 85 31 2 25 107 84 168 6.52e-27 97.4
Msa0277280 MtrunA17_Chr1g0149471 60.241 83 32 1 27 108 128 210 1.32e-26 97.8
Msa0277280 MtrunA17_Chr3g0137521 61.176 85 31 2 25 107 45 129 3.64e-26 94.4
Msa0277280 MtrunA17_Chr4g0056401 55.294 85 36 2 26 108 50 134 3.62e-25 92.0
Msa0277280 MtrunA17_Chr3g0137531 55.814 86 36 2 24 107 43 128 1.37e-18 75.1
Msa0277280 MtrunA17_Chr4g0056381 52.381 84 37 3 26 107 104 186 1.89e-17 73.6
Msa0277280 MtrunA17_Chr5g0399081 41.860 86 47 3 24 107 92 176 2.09e-17 73.2
Msa0277280 MtrunA17_Chr5g0399091 41.860 86 47 3 24 107 85 169 5.17e-17 72.0
Msa0277280 MtrunA17_Chr2g0290571 50.633 79 36 2 30 107 122 198 1.00e-16 72.0
Msa0277280 MtrunA17_Chr2g0290561 51.899 79 35 3 30 107 118 194 3.74e-16 70.5
Msa0277280 MtrunA17_Chr2g0290531 44.872 78 37 3 34 108 186 260 3.36e-13 63.5
Msa0277280 MtrunA17_Chr3g0120411 41.860 86 47 3 24 107 251 335 1.26e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0277280 AT5G46900.1 70.455 88 22 3 21 107 42 126 3.67e-31 107
Msa0277280 AT2G45180.1 63.953 86 30 1 24 108 49 134 3.72e-31 107
Msa0277280 AT4G12480.1 65.517 87 28 2 24 108 82 168 1.21e-30 107
Msa0277280 AT4G12520.1 65.882 85 27 2 25 107 44 128 1.75e-30 105
Msa0277280 AT4G12510.1 65.882 85 27 2 25 107 44 128 1.75e-30 105
Msa0277280 AT4G12550.1 58.242 91 36 2 19 107 20 110 1.85e-30 105
Msa0277280 AT4G12490.1 63.441 93 32 2 17 107 89 181 2.70e-30 106
Msa0277280 AT4G12500.1 66.279 86 27 2 24 107 91 176 9.92e-30 105
Msa0277280 AT4G12470.1 63.636 88 30 2 22 107 73 160 9.92e-30 104
Msa0277280 AT1G62510.1 67.470 83 25 2 27 107 67 149 1.04e-29 104
Msa0277280 AT5G46890.1 68.182 88 24 3 21 107 42 126 1.77e-29 103
Msa0277280 AT4G12545.1 62.500 88 28 3 22 107 23 107 8.05e-29 100
Msa0277280 AT1G12090.1 65.000 80 26 2 30 107 58 137 3.20e-26 95.1
Msa0277280 AT4G22460.1 59.551 89 32 2 19 103 39 127 4.79e-26 94.4
Msa0277280 AT1G12100.1 49.474 95 46 2 7 100 30 123 2.31e-25 92.8
Msa0277280 AT4G00165.1 53.012 83 37 2 27 107 46 128 9.14e-24 88.6
Msa0277280 AT4G00165.2 53.012 83 37 2 27 107 46 128 9.14e-24 88.6
Msa0277280 AT4G12530.1 53.012 83 38 1 26 107 33 115 2.14e-23 87.4
Msa0277280 AT2G10940.2 50.575 87 40 3 24 108 205 290 2.59e-18 77.8
Msa0277280 AT2G10940.1 50.575 87 40 3 24 108 205 290 2.59e-18 77.8
Msa0277280 AT1G62500.1 47.674 86 42 3 24 107 209 293 7.64e-16 71.2
Msa0277280 AT3G22142.1 46.067 89 35 5 26 107 1396 1478 3.33e-15 70.5
Msa0277280 AT4G15160.2 46.512 86 41 4 26 107 98 182 8.40e-14 64.3
Msa0277280 AT4G15160.1 46.512 86 41 4 26 107 180 264 2.21e-13 64.3
Msa0277280 AT3G22120.2 47.059 85 41 4 26 107 266 349 6.41e-13 63.5
Msa0277280 AT3G22120.1 47.059 85 41 4 26 107 249 332 9.64e-13 63.2

Find 37 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGATTGGAACTGGGATTTC+AGG 0.160812 2_3:-9778733 None:intergenic
GACCAAGGACATTAGCTTTA+AGG 0.172237 2_3:-9778936 None:intergenic
CCTAACTTAAGTGCATTTAT+AGG 0.239997 2_3:-9778793 None:intergenic
AACTTGGTCAAAGTTAAATT+AGG 0.277653 2_3:+9778835 Msa0277280:CDS
TTTGGAGAAGGGTCATATAT+TGG 0.304460 2_3:-9778760 None:intergenic
CCTTGTTGCTCACTCATTCA+AGG 0.350456 2_3:+9778874 Msa0277280:CDS
ATTGGGTCTGGGATTGGAAC+TGG 0.356899 2_3:-9778742 None:intergenic
TTGGAGAAGGGTCATATATT+GGG 0.368675 2_3:-9778759 None:intergenic
ACTTGGTCAAAGTTAAATTA+GGG 0.373507 2_3:+9778836 Msa0277280:CDS
AGAATGACACTCAAGGAAAT+AGG 0.388403 2_3:-9778973 None:intergenic
ACCAAGGACATTAGCTTTAA+GGG 0.388445 2_3:-9778935 None:intergenic
GAAGGGTCATATATTGGGTC+TGG 0.389255 2_3:-9778754 None:intergenic
TTTATAGGACATGTACCCTT+TGG 0.402117 2_3:-9778778 None:intergenic
CCTATAAATGCACTTAAGTT+AGG 0.406380 2_3:+9778793 Msa0277280:CDS
TCATATATTGGGTCTGGGAT+TGG 0.411255 2_3:-9778748 None:intergenic
GGATTGGAACTGGGATTTCA+GGG 0.445515 2_3:-9778732 None:intergenic
GCCCTTAAAGCTAATGTCCT+TGG 0.495398 2_3:+9778934 Msa0277280:CDS
TTGGGTCTGGGATTGGAACT+GGG 0.520356 2_3:-9778741 None:intergenic
GAGCAACAAGGGAGTGTTGG+TGG 0.532377 2_3:-9778862 None:intergenic
ATATATGACCCTTCTCCAAA+GGG 0.532446 2_3:+9778763 Msa0277280:CDS
GGACATGTACCCTTTGGAGA+AGG 0.541046 2_3:-9778772 None:intergenic
AATATATGACCCTTCTCCAA+AGG 0.548759 2_3:+9778762 Msa0277280:CDS
AAGGGTCATATATTGGGTCT+GGG 0.551516 2_3:-9778753 None:intergenic
AGCAACAAGGGAGTGTTGGT+GGG 0.555115 2_3:-9778861 None:intergenic
AGGAAATAGGAACATCAAGA+TGG 0.560269 2_3:-9778960 None:intergenic
GACATGTACCCTTTGGAGAA+GGG 0.569046 2_3:-9778771 None:intergenic
AATTGTGGAAGGAACAACTC+TGG 0.577791 2_3:+9779000 Msa0277280:CDS
TAGCTTTAAGGGCAGTGCAA+AGG 0.582397 2_3:-9778924 None:intergenic
AGTGTCATTCTCAACAATTG+TGG 0.590474 2_3:+9778985 Msa0277280:CDS
CTTGAATGAGTGAGCAACAA+GGG 0.595201 2_3:-9778873 None:intergenic
GCAACAAGGGAGTGTTGGTG+GGG 0.610643 2_3:-9778860 None:intergenic
CCTTGAATGAGTGAGCAACA+AGG 0.614845 2_3:-9778874 None:intergenic
AGTGAGCAACAAGGGAGTGT+TGG 0.617453 2_3:-9778865 None:intergenic
ATTGTTGAGAATGACACTCA+AGG 0.634515 2_3:-9778980 None:intergenic
TCATTCTCAACAATTGTGGA+AGG 0.636203 2_3:+9778989 Msa0277280:CDS
GTGTGCAAAAGTGTTGAACT+TGG 0.636381 2_3:+9778819 Msa0277280:CDS
GAACATCAAGATGGAGACCA+AGG 0.649528 2_3:-9778951 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AACTTGGTCAAAGTTAAATT+AGG + chr2_3:9778835-9778854 Msa0277280:CDS 25.0%
! ACTTGGTCAAAGTTAAATTA+GGG + chr2_3:9778836-9778855 Msa0277280:CDS 25.0%
CCTAACTTAAGTGCATTTAT+AGG - chr2_3:9778796-9778815 None:intergenic 30.0%
CCTATAAATGCACTTAAGTT+AGG + chr2_3:9778793-9778812 Msa0277280:CDS 30.0%
TTGGAGAAGGGTCATATATT+GGG - chr2_3:9778762-9778781 None:intergenic 35.0%
TTTGGAGAAGGGTCATATAT+TGG - chr2_3:9778763-9778782 None:intergenic 35.0%
AATATATGACCCTTCTCCAA+AGG + chr2_3:9778762-9778781 Msa0277280:CDS 35.0%
ATATATGACCCTTCTCCAAA+GGG + chr2_3:9778763-9778782 Msa0277280:CDS 35.0%
TTTATAGGACATGTACCCTT+TGG - chr2_3:9778781-9778800 None:intergenic 35.0%
!! ACCAAGGACATTAGCTTTAA+GGG - chr2_3:9778938-9778957 None:intergenic 35.0%
AGGAAATAGGAACATCAAGA+TGG - chr2_3:9778963-9778982 None:intergenic 35.0%
AGAATGACACTCAAGGAAAT+AGG - chr2_3:9778976-9778995 None:intergenic 35.0%
ATTGTTGAGAATGACACTCA+AGG - chr2_3:9778983-9779002 None:intergenic 35.0%
! AGTGTCATTCTCAACAATTG+TGG + chr2_3:9778985-9779004 Msa0277280:CDS 35.0%
TCATTCTCAACAATTGTGGA+AGG + chr2_3:9778989-9779008 Msa0277280:CDS 35.0%
! TCATATATTGGGTCTGGGAT+TGG - chr2_3:9778751-9778770 None:intergenic 40.0%
AAGGGTCATATATTGGGTCT+GGG - chr2_3:9778756-9778775 None:intergenic 40.0%
!! GTGTGCAAAAGTGTTGAACT+TGG + chr2_3:9778819-9778838 Msa0277280:CDS 40.0%
CTTGAATGAGTGAGCAACAA+GGG - chr2_3:9778876-9778895 None:intergenic 40.0%
!! GACCAAGGACATTAGCTTTA+AGG - chr2_3:9778939-9778958 None:intergenic 40.0%
AATTGTGGAAGGAACAACTC+TGG + chr2_3:9779000-9779019 Msa0277280:CDS 40.0%
GGATTGGAACTGGGATTTCA+GGG - chr2_3:9778735-9778754 None:intergenic 45.0%
GAAGGGTCATATATTGGGTC+TGG - chr2_3:9778757-9778776 None:intergenic 45.0%
! GACATGTACCCTTTGGAGAA+GGG - chr2_3:9778774-9778793 None:intergenic 45.0%
CCTTGAATGAGTGAGCAACA+AGG - chr2_3:9778877-9778896 None:intergenic 45.0%
CCTTGTTGCTCACTCATTCA+AGG + chr2_3:9778874-9778893 Msa0277280:CDS 45.0%
!! TAGCTTTAAGGGCAGTGCAA+AGG - chr2_3:9778927-9778946 None:intergenic 45.0%
GCCCTTAAAGCTAATGTCCT+TGG + chr2_3:9778934-9778953 Msa0277280:CDS 45.0%
GAACATCAAGATGGAGACCA+AGG - chr2_3:9778954-9778973 None:intergenic 45.0%
GGGATTGGAACTGGGATTTC+AGG - chr2_3:9778736-9778755 None:intergenic 50.0%
! TTGGGTCTGGGATTGGAACT+GGG - chr2_3:9778744-9778763 None:intergenic 50.0%
! ATTGGGTCTGGGATTGGAAC+TGG - chr2_3:9778745-9778764 None:intergenic 50.0%
! GGACATGTACCCTTTGGAGA+AGG - chr2_3:9778775-9778794 None:intergenic 50.0%
!! AGCAACAAGGGAGTGTTGGT+GGG - chr2_3:9778864-9778883 None:intergenic 50.0%
! AGTGAGCAACAAGGGAGTGT+TGG - chr2_3:9778868-9778887 None:intergenic 50.0%
!! GCAACAAGGGAGTGTTGGTG+GGG - chr2_3:9778863-9778882 None:intergenic 55.0%
!! GAGCAACAAGGGAGTGTTGG+TGG - chr2_3:9778865-9778884 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 9778712 9779038 9778712 ID=Msa0277280;Name=Msa0277280
chr2_3 mRNA 9778712 9779038 9778712 ID=Msa0277280-mRNA-1;Parent=Msa0277280;Name=Msa0277280-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|108
chr2_3 exon 9778712 9779038 9778712 ID=Msa0277280-mRNA-1:exon:4371;Parent=Msa0277280-mRNA-1
chr2_3 CDS 9778712 9779038 9778712 ID=Msa0277280-mRNA-1:cds;Parent=Msa0277280-mRNA-1
Gene Sequence

>Msa0277280

ATGGTGAATTGCAACTATGTCCCTGAAATCCCAGTTCCAATCCCAGACCCAATATATGACCCTTCTCCAAAGGGTACATGTCCTATAAATGCACTTAAGTTAGGTGTGTGTGCAAAAGTGTTGAACTTGGTCAAAGTTAAATTAGGGTCCCCACCAACACTCCCTTGTTGCTCACTCATTCAAGGTCTTGCTGATCTTGAAGCTGCTGCTTGCCTTTGCACTGCCCTTAAAGCTAATGTCCTTGGTCTCCATCTTGATGTTCCTATTTCCTTGAGTGTCATTCTCAACAATTGTGGAAGGAACAACTCTGGTTTCAAGTGCACTTAG

Protein sequence

>Msa0277280

MVNCNYVPEIPVPIPDPIYDPSPKGTCPINALKLGVCAKVLNLVKVKLGSPPTLPCCSLIQGLADLEAAACLCTALKANVLGLHLDVPISLSVILNNCGRNNSGFKCT*