AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0237040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0237040 MtrunA17_Chr2g0286251 100.000 102 0 0 1 102 1 102 3.18e-72 209
Msa0237040 MtrunA17_Chr4g0066791 78.641 103 21 1 1 102 1 103 4.07e-56 169
Msa0237040 MtrunA17_Chr4g0066801 78.641 103 21 1 1 102 1 103 4.07e-56 169
Msa0237040 MtrunA17_Chr4g0066811 78.641 103 21 1 1 102 1 103 4.07e-56 169
Msa0237040 MtrunA17_Chr2g0286271 63.725 102 37 0 1 102 1 102 7.96e-45 140
Msa0237040 MtrunA17_Chr1g0195951 53.922 102 47 0 1 102 1 102 6.51e-40 128
Msa0237040 MtrunA17_Chr7g0268751 52.941 102 48 0 1 102 1 102 6.66e-40 127
Msa0237040 MtrunA17_Chr1g0195971 58.416 101 42 0 1 101 1 101 3.52e-39 126
Msa0237040 MtrunA17_Chr1g0195981 58.947 95 39 0 1 95 1 95 4.78e-39 125
Msa0237040 MtrunA17_Chr1g0195991 56.842 95 41 0 1 95 1 95 6.08e-39 125
Msa0237040 MtrunA17_Chr7g0224091 57.282 103 43 1 1 102 22 124 1.21e-38 125
Msa0237040 MtrunA17_Chr7g0268711 55.789 95 42 0 1 95 1 95 2.12e-37 121
Msa0237040 MtrunA17_Chr7g0222551 53.398 103 47 1 1 102 30 132 7.15e-37 121
Msa0237040 MtrunA17_Chr7g0268731 55.882 102 44 1 1 101 1 102 2.06e-36 119
Msa0237040 MtrunA17_Chr7g0222541 52.427 103 48 1 1 102 30 132 5.77e-36 119
Msa0237040 MtrunA17_Chr7g0268721 54.902 102 45 1 1 101 1 102 1.37e-35 117
Msa0237040 MtrunA17_Chr7g0222491 51.456 103 49 1 1 102 30 132 2.75e-35 117
Msa0237040 MtrunA17_Chr1g0195931 50.000 102 51 0 1 102 1 102 4.17e-31 105
Msa0237040 MtrunA17_Chr7g0268761 44.554 101 56 0 1 101 1 101 6.59e-29 100
Msa0237040 MtrunA17_Chr2g0303741 46.667 105 52 1 2 102 40 144 2.58e-25 92.4
Msa0237040 MtrunA17_Chr2g0282951 41.346 104 51 3 4 102 29 127 3.29e-23 86.7
Msa0237040 MtrunA17_Chr2g0325001 37.864 103 57 2 4 102 41 140 9.87e-23 85.5
Msa0237040 MtrunA17_Chr1g0151231 44.118 102 55 1 3 102 48 149 1.84e-21 82.8
Msa0237040 MtrunA17_Chr4g0040601 39.000 100 56 2 6 102 58 155 2.55e-21 82.4
Msa0237040 MtrunA17_Chr7g0228311 40.000 100 60 0 1 100 3 102 1.11e-20 79.3
Msa0237040 MtrunA17_Chr3g0117411 38.000 100 62 0 1 100 18 117 2.33e-19 76.6
Msa0237040 MtrunA17_Chr3g0117391 37.000 100 63 0 1 100 21 120 1.93e-18 74.3
Msa0237040 MtrunA17_Chr3g0135811 39.604 101 53 3 3 101 23 117 1.03e-17 72.4
Msa0237040 MtrunA17_Chr5g0434201 40.777 103 59 1 2 102 21 123 1.93e-16 68.9
Msa0237040 MtrunA17_Chr1g0182971 36.364 99 62 1 2 99 84 182 3.79e-15 67.4
Msa0237040 MtrunA17_Chr8g0376641 38.835 103 61 1 2 102 21 123 6.30e-14 62.8
Msa0237040 MtrunA17_Chr2g0299021 33.333 84 56 0 2 85 84 167 2.18e-11 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0237040 AT5G18600.1 76.471 102 24 0 1 102 1 102 2.92e-55 167
Msa0237040 AT4G15690.1 72.549 102 28 0 1 102 1 102 6.58e-55 166
Msa0237040 AT4G15680.1 69.608 102 31 0 1 102 1 102 4.95e-54 164
Msa0237040 AT4G15670.1 69.608 102 31 0 1 102 1 102 1.42e-53 162
Msa0237040 AT4G15700.1 70.588 102 30 0 1 102 1 102 2.43e-53 162
Msa0237040 AT4G15660.1 68.627 102 32 0 1 102 1 102 4.81e-52 159
Msa0237040 AT1G03020.1 60.784 102 40 0 1 102 1 102 9.74e-44 138
Msa0237040 AT3G62930.1 59.804 102 41 0 1 102 1 102 1.13e-42 135
Msa0237040 AT3G21460.1 59.804 102 41 0 1 102 1 102 2.24e-41 132
Msa0237040 AT2G47870.1 57.282 103 43 1 1 102 1 103 4.03e-40 129
Msa0237040 AT1G06830.1 55.789 95 42 0 1 95 1 95 8.86e-39 125
Msa0237040 AT2G47880.1 54.000 100 46 0 1 100 1 100 2.30e-38 124
Msa0237040 AT3G62950.1 53.398 103 47 1 1 102 1 103 2.83e-38 124
Msa0237040 AT2G30540.1 55.789 95 42 0 1 95 1 95 5.47e-38 123
Msa0237040 AT3G62960.1 52.632 95 45 0 1 95 1 95 1.16e-35 117
Msa0237040 AT5G14070.1 49.091 110 48 2 1 102 31 140 9.35e-33 111
Msa0237040 AT3G02000.1 52.830 106 44 1 3 102 31 136 2.21e-31 107
Msa0237040 AT4G33040.1 42.478 113 43 3 3 102 41 144 3.39e-21 82.0
Msa0237040 AT1G28480.1 35.238 105 64 1 2 102 33 137 1.07e-20 80.9
Msa0237040 AT5G63030.1 39.796 98 59 0 3 100 21 118 1.02e-19 77.8
Msa0237040 AT5G11930.1 44.000 100 46 3 3 101 57 147 1.88e-19 77.8
Msa0237040 AT5G40370.1 37.000 100 63 0 1 100 3 102 9.20e-19 75.1
Msa0237040 AT1G03850.2 37.634 93 54 1 10 102 62 150 2.34e-16 70.1
Msa0237040 AT4G28730.1 37.113 97 60 1 2 97 71 167 1.82e-14 65.5
Msa0237040 AT5G40370.2 38.372 86 53 0 15 100 42 127 1.46e-13 62.4
Msa0237040 AT2G20270.1 35.052 97 62 1 2 97 76 172 2.42e-13 62.8
Msa0237040 AT5G20500.1 34.737 95 62 0 4 98 35 129 2.07e-12 59.3

Find 26 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGAAGAGCAGGAGCTATT+TGG 0.243476 2_2:-10108607 Msa0237040:CDS
TCATCAAGTTCATGAACTTC+TGG 0.278380 2_2:+10108776 None:intergenic
TTGGAATCAAAGACCTATTA+AGG 0.291286 2_2:+10108633 None:intergenic
TTATGAGCCTTCACCTTAAT+AGG 0.313253 2_2:-10108646 Msa0237040:CDS
TAGAAGAGCAGGAGCTATTT+GGG 0.338414 2_2:-10108606 Msa0237040:CDS
TCTGTGCCTGCTGTGTTCAT+TGG 0.345825 2_2:-10108698 Msa0237040:CDS
AAAACCCTCTTCAGTGACTT+TGG 0.383168 2_2:-10108806 Msa0237040:CDS
TTCATTGGTGGTGAGCTTGT+TGG 0.448261 2_2:-10108683 Msa0237040:CDS
GTGCCTGCTGTGTTCATTGG+TGG 0.469372 2_2:-10108695 Msa0237040:CDS
ATTCCAATGCTTAGAAGAGC+AGG 0.473528 2_2:-10108617 Msa0237040:CDS
GCTCCTGCTCTTCTAAGCAT+TGG 0.494845 2_2:+10108614 None:intergenic
ATTGGTGGTGAGCTTGTTGG+TGG 0.505118 2_2:-10108680 Msa0237040:CDS
CACTCCAAAGTCACTGAAGA+GGG 0.526613 2_2:+10108802 None:intergenic
ATGAACACAGCAGGCACAGA+AGG 0.552108 2_2:+10108701 None:intergenic
TCACCACCAATGAACACAGC+AGG 0.561831 2_2:+10108692 None:intergenic
TCAAAGACCTATTAAGGTGA+AGG 0.569141 2_2:+10108639 None:intergenic
CAACCTTACATTAATGGAGA+GGG 0.591764 2_2:-10108900 None:intergenic
AATGGAGAGGGTGACACAGT+TGG 0.593802 2_2:-10108888 Msa0237040:CDS
AACTTGATGAAATGAGTGGA+GGG 0.608563 2_2:-10108763 Msa0237040:CDS
TCAACCTTACATTAATGGAG+AGG 0.626935 2_2:-10108901 None:intergenic
TCACTCCAAAGTCACTGAAG+AGG 0.628179 2_2:+10108801 None:intergenic
TGAACACAGCAGGCACAGAA+GGG 0.649613 2_2:+10108702 None:intergenic
CATGAACTTGATGAAATGAG+TGG 0.667717 2_2:-10108767 Msa0237040:CDS
GAACTTGATGAAATGAGTGG+AGG 0.668923 2_2:-10108764 Msa0237040:CDS
GTTGGCATCAGAGAGGTCAG+TGG 0.695839 2_2:-10108870 Msa0237040:CDS
TGACACAGTTGGCATCAGAG+AGG 0.724593 2_2:-10108877 Msa0237040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACATTGAACAAGCACTTTTA+AGG - chr2_2:10108752-10108771 Msa0237040:CDS 30.0%
TTGGAATCAAAGACCTATTA+AGG + chr2_2:10108858-10108877 None:intergenic 30.0%
TCATCAAGTTCATGAACTTC+TGG + chr2_2:10108715-10108734 None:intergenic 35.0%
CATGAACTTGATGAAATGAG+TGG - chr2_2:10108721-10108740 Msa0237040:CDS 35.0%
AACTTGATGAAATGAGTGGA+GGG - chr2_2:10108725-10108744 Msa0237040:CDS 35.0%
TTATGAGCCTTCACCTTAAT+AGG - chr2_2:10108842-10108861 Msa0237040:CDS 35.0%
TCAAAGACCTATTAAGGTGA+AGG + chr2_2:10108852-10108871 None:intergenic 35.0%
AAAACCCTCTTCAGTGACTT+TGG - chr2_2:10108682-10108701 Msa0237040:CDS 40.0%
GAACTTGATGAAATGAGTGG+AGG - chr2_2:10108724-10108743 Msa0237040:CDS 40.0%
!!! GAACAAGCACTTTTAAGGCT+AGG - chr2_2:10108757-10108776 Msa0237040:CDS 40.0%
ATTCCAATGCTTAGAAGAGC+AGG - chr2_2:10108871-10108890 Msa0237040:CDS 40.0%
TTAGAAGAGCAGGAGCTATT+TGG - chr2_2:10108881-10108900 Msa0237040:CDS 40.0%
TAGAAGAGCAGGAGCTATTT+GGG - chr2_2:10108882-10108901 Msa0237040:CDS 40.0%
CACTCCAAAGTCACTGAAGA+GGG + chr2_2:10108689-10108708 None:intergenic 45.0%
TCACTCCAAAGTCACTGAAG+AGG + chr2_2:10108690-10108709 None:intergenic 45.0%
!! TTCATTGGTGGTGAGCTTGT+TGG - chr2_2:10108805-10108824 Msa0237040:CDS 45.0%
TGACACAGTTGGCATCAGAG+AGG - chr2_2:10108611-10108630 Msa0237040:CDS 50.0%
TGAACACAGCAGGCACAGAA+GGG + chr2_2:10108789-10108808 None:intergenic 50.0%
ATGAACACAGCAGGCACAGA+AGG + chr2_2:10108790-10108809 None:intergenic 50.0%
TCTGTGCCTGCTGTGTTCAT+TGG - chr2_2:10108790-10108809 Msa0237040:CDS 50.0%
TCACCACCAATGAACACAGC+AGG + chr2_2:10108799-10108818 None:intergenic 50.0%
!! ATTGGTGGTGAGCTTGTTGG+TGG - chr2_2:10108808-10108827 Msa0237040:CDS 50.0%
GCTCCTGCTCTTCTAAGCAT+TGG + chr2_2:10108877-10108896 None:intergenic 50.0%
GTTGGCATCAGAGAGGTCAG+TGG - chr2_2:10108618-10108637 Msa0237040:CDS 55.0%
GTGCCTGCTGTGTTCATTGG+TGG - chr2_2:10108793-10108812 Msa0237040:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 10108601 10108909 10108601 ID=Msa0237040;Name=Msa0237040
chr2_2 mRNA 10108601 10108909 10108601 ID=Msa0237040-mRNA-1;Parent=Msa0237040;Name=Msa0237040-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|-1|0|1|-1|1|1|0|102
chr2_2 exon 10108601 10108909 10108601 ID=Msa0237040-mRNA-1:exon:4355;Parent=Msa0237040-mRNA-1
chr2_2 CDS 10108601 10108909 10108601 ID=Msa0237040-mRNA-1:cds;Parent=Msa0237040-mRNA-1
Gene Sequence

>Msa0237040

ATGGAGAGGGTGACACAGTTGGCATCAGAGAGGTCAGTGGTGATATTCAGCAAGAGTAGTTGTTGCATGTGTCACACAATCAAAACCCTCTTCAGTGACTTTGGAGTGAATCCAGAAGTTCATGAACTTGATGAAATGAGTGGAGGGAGAGACATTGAACAAGCACTTTTAAGGCTAGGATGTAACCCTTCTGTGCCTGCTGTGTTCATTGGTGGTGAGCTTGTTGGTGGAGCTAATGAAGTTATGAGCCTTCACCTTAATAGGTCTTTGATTCCAATGCTTAGAAGAGCAGGAGCTATTTGGGTTTGA

Protein sequence

>Msa0237040

MERVTQLASERSVVIFSKSSCCMCHTIKTLFSDFGVNPEVHELDEMSGGRDIEQALLRLGCNPSVPAVFIGGELVGGANEVMSLHLNRSLIPMLRRAGAIWV*