AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1368360


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1368360 MtrunA17_Chr3g0144941 94.872 156 7 1 1 156 1 155 1.17e-89 258
Msa1368360 MtrunA17_Chr4g0035414 71.242 153 42 1 1 151 1 153 2.73e-63 191
Msa1368360 MtrunA17_Chr1g0155551 60.976 164 48 4 1 153 1 159 4.51e-57 175
Msa1368360 MtrunA17_Chr8g0378901 53.086 162 68 5 1 156 1 160 8.23e-46 147
Msa1368360 MtrunA17_Chr3g0141881 57.292 96 38 1 12 107 48 140 4.56e-30 107
Msa1368360 MtrunA17_Chr1g0194681 39.073 151 88 2 1 151 1 147 5.99e-26 96.3
Msa1368360 MtrunA17_Chr6g0456061 44.118 102 47 2 26 124 86 180 3.10e-18 77.4
Msa1368360 MtrunA17_Chr8g0341311 50.685 73 36 0 26 98 70 142 2.58e-17 74.7
Msa1368360 MtrunA17_Chr7g0225661 44.444 99 51 2 1 98 57 152 2.98e-17 74.7
Msa1368360 MtrunA17_Chr7g0220571 54.795 73 33 0 26 98 83 155 4.95e-17 74.3
Msa1368360 MtrunA17_Chr4g0054291 39.091 110 60 1 7 109 45 154 9.89e-16 70.5
Msa1368360 MtrunA17_Chr5g0400901 41.053 95 48 1 27 121 58 144 2.83e-14 66.2
Msa1368360 MtrunA17_Chr3g0139301 34.259 108 67 1 6 109 98 205 1.21e-12 63.9
Msa1368360 MtrunA17_Chr7g0269951 53.012 83 39 0 27 109 19 101 4.49e-12 60.1
Msa1368360 MtrunA17_Chr8g0369161 36.735 98 58 2 24 118 300 396 3.08e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1368360 AT1G75390.1 51.829 164 55 5 2 149 9 164 1.01e-47 152
Msa1368360 AT4G34590.1 57.143 133 49 2 26 150 23 155 5.90e-44 142
Msa1368360 AT2G18160.1 47.020 151 58 5 22 153 23 170 1.30e-36 124
Msa1368360 AT1G75390.2 60.825 97 34 2 2 94 9 105 1.05e-32 112
Msa1368360 AT3G62420.1 44.604 139 74 2 13 151 8 143 4.75e-30 107
Msa1368360 AT2G04038.1 48.837 86 41 1 16 98 57 142 5.12e-18 76.6
Msa1368360 AT5G15830.1 34.459 148 79 3 9 156 55 184 1.92e-17 75.5
Msa1368360 AT1G13600.1 45.361 97 48 2 16 107 70 166 1.03e-16 73.9
Msa1368360 AT3G30530.1 52.055 73 35 0 26 98 77 149 2.68e-16 72.4
Msa1368360 AT5G38800.1 47.500 80 42 0 19 98 61 140 1.60e-15 70.1
Msa1368360 AT5G49450.1 36.190 105 64 1 27 128 13 117 1.63e-12 61.6
Msa1368360 AT4G37730.1 45.000 80 37 1 26 98 193 272 5.58e-12 62.4
Msa1368360 AT2G22850.1 37.079 89 56 0 23 111 122 210 2.67e-11 59.7
Msa1368360 AT2G22850.2 37.079 89 56 0 23 111 122 210 2.67e-11 59.7
Msa1368360 AT3G49760.1 55.814 43 19 0 28 70 70 112 4.68e-11 58.2
Msa1368360 AT1G68880.1 38.554 83 51 0 12 94 29 111 4.71e-11 57.8

Find 20 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCCTCTGAACCTGAATT+TGG 0.134136 tig0018646:+43802 None:intergenic
CTTCAATAACCCTTTGAATA+TGG 0.156253 tig0018646:-43452 Msa1368360:CDS
CCTCACAACTCAACGATTCT+TGG 0.288929 tig0018646:-43620 Msa1368360:CDS
TGTTCAACACTTCCAAATTC+AGG 0.300497 tig0018646:-43814 Msa1368360:CDS
CTTGGATGATCTTGCTGTTC+AGG 0.305122 tig0018646:-43689 Msa1368360:CDS
TCTTCAAGTGGAACATCTTC+AGG 0.306987 tig0018646:-43838 Msa1368360:CDS
TTCAATAACCCTTTGAATAT+GGG 0.313680 tig0018646:-43451 Msa1368360:CDS
TTATTTGAACCAACCAATCA+TGG 0.433242 tig0018646:-43428 Msa1368360:CDS
TTCAAATAACCCATATTCAA+AGG 0.450188 tig0018646:+43442 None:intergenic
GAGATCTTCTTGCTGATTCG+CGG 0.468319 tig0018646:+43731 None:intergenic
ATATCTGCAGAAGCCATGAT+TGG 0.469872 tig0018646:+43415 None:intergenic
GGAAGATTTGATGCTTCTGA+TGG 0.470481 tig0018646:-43785 Msa1368360:CDS
TCAAATAACCCATATTCAAA+GGG 0.472163 tig0018646:+43443 None:intergenic
CTGTTCAGGTGAGTCAACTA+AGG 0.511341 tig0018646:-43675 Msa1368360:CDS
CTGCAGAAGCCATGATTGGT+TGG 0.535667 tig0018646:+43419 None:intergenic
AACTTCATGAATGTTGCAAA+TGG 0.546215 tig0018646:-43517 Msa1368360:CDS
TCTCACATGGCTTCTTCAAG+TGG 0.568523 tig0018646:-43850 None:intergenic
ACTTCCAAATTCAGGTTCAG+AGG 0.572504 tig0018646:-43806 Msa1368360:CDS
CAGCAAGAAGATCTCGAATG+AGG 0.587735 tig0018646:-43723 Msa1368360:CDS
CCAAGAATCGTTGAGTTGTG+AGG 0.599678 tig0018646:+43620 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTATTATTATTATCAAC+AGG + tig0018646:43759-43778 None:intergenic 10.0%
! TTCAATAACCCTTTGAATAT+GGG - tig0018646:43789-43808 Msa1368360:CDS 25.0%
! TCAAATAACCCATATTCAAA+GGG + tig0018646:43800-43819 None:intergenic 25.0%
! TTCAAATAACCCATATTCAA+AGG + tig0018646:43801-43820 None:intergenic 25.0%
AATGAGGAAACAAAAACACT+TGG - tig0018646:43533-43552 Msa1368360:CDS 30.0%
AACTTCATGAATGTTGCAAA+TGG - tig0018646:43723-43742 Msa1368360:CDS 30.0%
CTTCAATAACCCTTTGAATA+TGG - tig0018646:43788-43807 Msa1368360:CDS 30.0%
TTATTTGAACCAACCAATCA+TGG - tig0018646:43812-43831 Msa1368360:CDS 30.0%
TGTTCAACACTTCCAAATTC+AGG - tig0018646:43426-43445 Msa1368360:CDS 35.0%
TCTTCAAGTGGAACATCTTC+AGG - tig0018646:43402-43421 Msa1368360:CDS 40.0%
! ACTTCCAAATTCAGGTTCAG+AGG - tig0018646:43434-43453 Msa1368360:CDS 40.0%
TCTTCCTCTGAACCTGAATT+TGG + tig0018646:43441-43460 None:intergenic 40.0%
GGAAGATTTGATGCTTCTGA+TGG - tig0018646:43455-43474 Msa1368360:CDS 40.0%
ATATCTGCAGAAGCCATGAT+TGG + tig0018646:43828-43847 None:intergenic 40.0%
!! GAGATCTTCTTGCTGATTCG+CGG + tig0018646:43512-43531 None:intergenic 45.0%
CAGCAAGAAGATCTCGAATG+AGG - tig0018646:43517-43536 Msa1368360:CDS 45.0%
!! CTTGGATGATCTTGCTGTTC+AGG - tig0018646:43551-43570 Msa1368360:CDS 45.0%
CTGTTCAGGTGAGTCAACTA+AGG - tig0018646:43565-43584 Msa1368360:CDS 45.0%
! CCAAGAATCGTTGAGTTGTG+AGG + tig0018646:43623-43642 None:intergenic 45.0%
CCTCACAACTCAACGATTCT+TGG - tig0018646:43620-43639 Msa1368360:CDS 45.0%
CTGCAGAAGCCATGATTGGT+TGG + tig0018646:43824-43843 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0018646 gene 43396 43866 43396 ID=Msa1368360;Name=Msa1368360
tig0018646 mRNA 43396 43866 43396 ID=Msa1368360-mRNA-1;Parent=Msa1368360;Name=Msa1368360-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|156
tig0018646 exon 43396 43866 43396 ID=Msa1368360-mRNA-1:exon:421;Parent=Msa1368360-mRNA-1
tig0018646 CDS 43396 43866 43396 ID=Msa1368360-mRNA-1:cds;Parent=Msa1368360-mRNA-1
Gene Sequence

>Msa1368360

ATGGCTTCTTCAAGTGGAACATCTTCAGGCTGTTCAACACTTCCAAATTCAGGTTCAGAGGAAGATTTGATGCTTCTGATGGATCAAAGAAAAAGAAAGAGAATGATATCAAACCGCGAATCAGCAAGAAGATCTCGAATGAGGAAACAAAAACACTTGGATGATCTTGCTGTTCAGGTGAGTCAACTAAGGAATGAGAATCAACAGATTCTAACTTCAGTGAACCTCACAACTCAACGATTCTTGGCTGTTGAATCTGAAAACTCTGTGCTTAGAGCTCAACTGAATGAACTCAACAGCAGATTTGAGTCTTTGAATGAGATCATCAACTTCATGAATGTTGCAAATGGTGTTTTTGAACCTGTTGATAATAATAATAATAATGACAATTACTTCAATAACCCTTTGAATATGGGTTATTTGAACCAACCAATCATGGCTTCTGCAGATATGAACATGATACATTATTGA

Protein sequence

>Msa1368360

MASSSGTSSGCSTLPNSGSEEDLMLLMDQRKRKRMISNRESARRSRMRKQKHLDDLAVQVSQLRNENQQILTSVNLTTQRFLAVESENSVLRAQLNELNSRFESLNEIINFMNVANGVFEPVDNNNNNDNYFNNPLNMGYLNQPIMASADMNMIHY*