AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene43521

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43521.t1 MTR_5g015090 96.178 157 6 0 1 157 1 157 1.21e-109 308
MS.gene43521.t1 MTR_4g097440 56.322 174 59 6 1 157 1 174 1.73e-55 172
MS.gene43521.t1 MTR_3g103360 38.346 133 70 2 7 136 8 131 2.54e-17 73.9
MS.gene43521.t1 MTR_1g017570 65.152 66 23 0 60 125 59 124 2.19e-16 71.6
MS.gene43521.t1 MTR_7g029400 42.708 96 48 1 58 153 81 169 7.48e-16 71.2
MS.gene43521.t1 MTR_4g070860 45.679 81 44 0 58 138 27 107 2.14e-15 69.3
MS.gene43521.t1 MTR_8g015250 41.667 96 49 1 58 153 71 159 8.28e-15 68.6
MS.gene43521.t1 MTR_8g086020 32.414 145 71 5 29 152 8 146 6.57e-14 65.5
MS.gene43521.t1 MTR_3g117120 39.583 96 50 1 58 145 27 122 3.28e-13 63.5
MS.gene43521.t1 MTR_1g022495 39.048 105 60 1 36 136 1 105 7.54e-13 62.8
MS.gene43521.t1 MTR_1g087040 37.778 90 41 2 36 125 8 82 2.39e-12 61.2
MS.gene43521.t1 MTR_6g016375 46.835 79 42 0 58 136 87 165 1.17e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43521.t1 AT3G49760 41.007 139 81 1 5 142 15 153 3.04e-31 110
MS.gene43521.t1 AT4G37730 41.304 138 73 2 7 136 135 272 5.08e-20 84.7
MS.gene43521.t1 AT2G22850 49.412 85 43 0 59 143 127 211 1.54e-19 82.0
MS.gene43521.t1 AT2G22850 49.412 85 43 0 59 143 127 211 1.54e-19 82.0
MS.gene43521.t1 AT3G30530 38.926 149 85 3 1 146 18 163 1.85e-16 72.8
MS.gene43521.t1 AT1G75390 38.333 120 73 1 31 149 10 129 1.07e-15 70.5
MS.gene43521.t1 AT1G75390 42.708 96 54 1 31 125 10 105 1.16e-14 66.6
MS.gene43521.t1 AT2G18160 39.362 94 50 1 52 138 15 108 6.07e-14 65.9
MS.gene43521.t1 AT4G34590 42.353 85 49 0 58 142 24 108 3.52e-13 63.5
MS.gene43521.t1 AT4G36730 35.398 113 54 2 48 141 192 304 5.21e-13 65.5
MS.gene43521.t1 AT4G36730 35.398 113 54 2 48 141 194 306 5.37e-13 65.5
MS.gene43521.t1 AT5G38800 42.727 110 53 3 38 146 56 156 7.25e-13 63.2
MS.gene43521.t1 AT1G13600 50.633 79 39 0 58 136 83 161 7.66e-13 63.5
MS.gene43521.t1 AT2G04038 44.792 96 48 1 36 131 54 144 1.92e-12 62.0
MS.gene43521.t1 AT5G15830 46.835 79 42 0 58 136 71 149 7.73e-12 60.8

Find 47 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGACATCTTGAGAATTTA+AGG 0.114350 5.3:-8201652 MS.gene43521:CDS
GTCAAACATAAGTCAAAATA+TGG 0.276559 5.3:-8201495 MS.gene43521:CDS
ATATCATTCTCCTCCGCTTT+CGG 0.304688 5.3:+8201714 None:intergenic
GGATGGCTCGAACCGGAATA+TGG 0.309967 5.3:-8201741 MS.gene43521:CDS
GTGATCTTCTTGCTGATTCC+CGG 0.333227 5.3:+8201687 None:intergenic
TTCATTTGGTTCGCCTGAAC+CGG 0.351868 5.3:+8201775 None:intergenic
GCAACCCGTTGTTCAATTCC+CGG 0.358900 5.3:+8201600 None:intergenic
TGAGCTTAGGGCTGGTGGTT+TGG 0.381731 5.3:+8201807 None:intergenic
CTTAGGGCTGGTGGTTTGGA+AGG 0.385289 5.3:+8201811 None:intergenic
CCTCTATGCCTCTGATTTCA+CGG 0.386220 5.3:-8201882 MS.gene43521:CDS
GCTTTCGGTCCTCCATATTC+CGG 0.399400 5.3:+8201729 None:intergenic
CTCACTTCAAGCTCCGGTTC+AGG 0.426863 5.3:-8201788 MS.gene43521:CDS
CCGGAGCTTGAAGTGAGCTT+AGG 0.429061 5.3:+8201794 None:intergenic
CAACTCTCAACCGGTTCACC+TGG 0.449634 5.3:+8201627 None:intergenic
AAAACCGGGAATTGAACAAC+GGG 0.452979 5.3:-8201604 MS.gene43521:CDS
ATTTAAGGAACCAGGTGAAC+CGG 0.458904 5.3:-8201637 MS.gene43521:CDS
CGGTTGGAACGAACCATGTT+GGG 0.461184 5.3:-8201527 MS.gene43521:CDS
ACCGGTTGAGAGTTGAAAAC+CGG 0.462964 5.3:-8201619 MS.gene43521:CDS
CGGAGCTTGAAGTGAGCTTA+GGG 0.479442 5.3:+8201795 None:intergenic
CGGTCATGGATGGCTCGAAC+CGG 0.489104 5.3:-8201748 MS.gene43521:CDS
CCAACATGGTTCGTTCCAAC+CGG 0.489681 5.3:+8201528 None:intergenic
CGGTTCGAGCCATCCATGAC+CGG 0.490515 5.3:+8201749 None:intergenic
TTCAACCTTTCTCATCTGCA+TGG 0.491200 5.3:-8201469 MS.gene43521:CDS
GGAGGAGAATGATATCGAAC+CGG 0.493828 5.3:-8201706 MS.gene43521:CDS
TTAGGGCTGGTGGTTTGGAA+GGG 0.512467 5.3:+8201812 None:intergenic
GGCATAGAGGGAAGAGAGCA+TGG 0.513902 5.3:+8201895 None:intergenic
CCTAAGCTCACTTCAAGCTC+CGG 0.518730 5.3:-8201794 MS.gene43521:CDS
TGAAGTGAGCTTAGGGCTGG+TGG 0.522709 5.3:+8201802 None:intergenic
GAACCGAAAATGAGTGGCTC+CGG 0.546667 5.3:-8201547 MS.gene43521:CDS
CCGGTTGGAACGAACCATGT+TGG 0.552100 5.3:-8201528 MS.gene43521:CDS
CCGTGAAATCAGAGGCATAG+AGG 0.553569 5.3:+8201882 None:intergenic
CGAAAATGAGTGGCTCCGGT+TGG 0.563412 5.3:-8201543 MS.gene43521:CDS
CGTGAAATCAGAGGCATAGA+GGG 0.567767 5.3:+8201883 None:intergenic
CATGGCCATGCAGATGAGAA+AGG 0.571565 5.3:+8201464 None:intergenic
GCTTGAAGTGAGCTTAGGGC+TGG 0.571567 5.3:+8201799 None:intergenic
TCTTGAGAATTTAAGGAACC+AGG 0.576304 5.3:-8201645 MS.gene43521:CDS
GAGGAGAATGATATCGAACC+GGG 0.576305 5.3:-8201705 MS.gene43521:CDS
CCGGTTGAGAGTTGAAAACC+GGG 0.579962 5.3:-8201618 MS.gene43521:CDS
AGACGAAAGTTTAACGCCGT+GGG 0.587172 5.3:-8201855 MS.gene43521:CDS
TAGACGAAAGTTTAACGCCG+TGG 0.603199 5.3:-8201856 MS.gene43521:CDS
GGAATATGGAGGACCGAAAG+CGG 0.611264 5.3:-8201727 MS.gene43521:CDS
GTCTAATGCCGTGAAATCAG+AGG 0.632780 5.3:+8201874 None:intergenic
TCAGCTGTGACAATATTGCA+TGG 0.636378 5.3:+8201446 None:intergenic
GTCTACGAACCGAAAATGAG+TGG 0.656434 5.3:-8201553 MS.gene43521:CDS
GAAAACCGGGAATTGAACAA+CGG 0.656607 5.3:-8201605 MS.gene43521:CDS
ATATGGAGGACCGAAAGCGG+AGG 0.670255 5.3:-8201724 MS.gene43521:CDS
TGGCTCGAACCGGAATATGG+AGG 0.676236 5.3:-8201738 MS.gene43521:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGACATCTTGAGAATTTA+AGG - chr5.3:8201683-8201702 MS.gene43521:CDS 25.0%
! GTCAAACATAAGTCAAAATA+TGG - chr5.3:8201840-8201859 MS.gene43521:CDS 25.0%
AGAATGTTAGAAAAATCCCA+CGG + chr5.3:8201499-8201518 None:intergenic 30.0%
TCTTGAGAATTTAAGGAACC+AGG - chr5.3:8201690-8201709 MS.gene43521:CDS 35.0%
AAAACCGGGAATTGAACAAC+GGG - chr5.3:8201731-8201750 MS.gene43521:CDS 40.0%
AATGAAAAACCGGTCATGGA+TGG - chr5.3:8201577-8201596 MS.gene43521:CDS 40.0%
ACCAAATGAAAAACCGGTCA+TGG - chr5.3:8201573-8201592 MS.gene43521:CDS 40.0%
AGGCGAACCAAATGAAAAAC+CGG - chr5.3:8201567-8201586 MS.gene43521:CDS 40.0%
ATATCATTCTCCTCCGCTTT+CGG + chr5.3:8201624-8201643 None:intergenic 40.0%
ATTTAAGGAACCAGGTGAAC+CGG - chr5.3:8201698-8201717 MS.gene43521:CDS 40.0%
GAAAACCGGGAATTGAACAA+CGG - chr5.3:8201730-8201749 MS.gene43521:CDS 40.0%
TCAGCTGTGACAATATTGCA+TGG + chr5.3:8201892-8201911 None:intergenic 40.0%
TTCAACCTTTCTCATCTGCA+TGG - chr5.3:8201866-8201885 MS.gene43521:CDS 40.0%
! TGACAACTTTTGACCCAACA+TGG + chr5.3:8201824-8201843 None:intergenic 40.0%
!! TCCATGACCGGTTTTTCATT+TGG + chr5.3:8201577-8201596 None:intergenic 40.0%
ACCGGTTGAGAGTTGAAAAC+CGG - chr5.3:8201716-8201735 MS.gene43521:CDS 45.0%
AGACGAAAGTTTAACGCCGT+GGG - chr5.3:8201480-8201499 MS.gene43521:CDS 45.0%
CCTCTATGCCTCTGATTTCA+CGG - chr5.3:8201453-8201472 MS.gene43521:CDS 45.0%
GAGGAGAATGATATCGAACC+GGG - chr5.3:8201630-8201649 MS.gene43521:CDS 45.0%
GGAGGAGAATGATATCGAAC+CGG - chr5.3:8201629-8201648 MS.gene43521:CDS 45.0%
GTCTAATGCCGTGAAATCAG+AGG + chr5.3:8201464-8201483 None:intergenic 45.0%
GTCTACGAACCGAAAATGAG+TGG - chr5.3:8201782-8201801 MS.gene43521:CDS 45.0%
TAGACGAAAGTTTAACGCCG+TGG - chr5.3:8201479-8201498 MS.gene43521:CDS 45.0%
! CGTGAAATCAGAGGCATAGA+GGG + chr5.3:8201455-8201474 None:intergenic 45.0%
! TTCATTTGGTTCGCCTGAAC+CGG + chr5.3:8201563-8201582 None:intergenic 45.0%
!! GTGATCTTCTTGCTGATTCC+CGG + chr5.3:8201651-8201670 None:intergenic 45.0%
CATGGCCATGCAGATGAGAA+AGG + chr5.3:8201874-8201893 None:intergenic 50.0%
CCAACATGGTTCGTTCCAAC+CGG + chr5.3:8201810-8201829 None:intergenic 50.0%
CCGGTTGAGAGTTGAAAACC+GGG - chr5.3:8201717-8201736 MS.gene43521:CDS 50.0%
CCTAAGCTCACTTCAAGCTC+CGG - chr5.3:8201541-8201560 MS.gene43521:CDS 50.0%
CGGAGCTTGAAGTGAGCTTA+GGG + chr5.3:8201543-8201562 None:intergenic 50.0%
CGGTTGGAACGAACCATGTT+GGG - chr5.3:8201808-8201827 MS.gene43521:CDS 50.0%
GAACCGAAAATGAGTGGCTC+CGG - chr5.3:8201788-8201807 MS.gene43521:CDS 50.0%
GCAACCCGTTGTTCAATTCC+CGG + chr5.3:8201738-8201757 None:intergenic 50.0%
GCTTTCGGTCCTCCATATTC+CGG + chr5.3:8201609-8201628 None:intergenic 50.0%
GGAATATGGAGGACCGAAAG+CGG - chr5.3:8201608-8201627 MS.gene43521:CDS 50.0%
! CAACCGGAGCCACTCATTTT+CGG + chr5.3:8201794-8201813 None:intergenic 50.0%
! CCCGGTTTTCAACTCTCAAC+CGG + chr5.3:8201720-8201739 None:intergenic 50.0%
! CCGTGAAATCAGAGGCATAG+AGG + chr5.3:8201456-8201475 None:intergenic 50.0%
! TTAGGGCTGGTGGTTTGGAA+GGG + chr5.3:8201526-8201545 None:intergenic 50.0%
ATATGGAGGACCGAAAGCGG+AGG - chr5.3:8201611-8201630 MS.gene43521:CDS 55.0%
CCGGAGCTTGAAGTGAGCTT+AGG + chr5.3:8201544-8201563 None:intergenic 55.0%
CCGGTTGGAACGAACCATGT+TGG - chr5.3:8201807-8201826 MS.gene43521:CDS 55.0%
CGAAAATGAGTGGCTCCGGT+TGG - chr5.3:8201792-8201811 MS.gene43521:CDS 55.0%
CTCACTTCAAGCTCCGGTTC+AGG - chr5.3:8201547-8201566 MS.gene43521:CDS 55.0%
GCTTGAAGTGAGCTTAGGGC+TGG + chr5.3:8201539-8201558 None:intergenic 55.0%
GGATGGCTCGAACCGGAATA+TGG - chr5.3:8201594-8201613 MS.gene43521:CDS 55.0%
TGAAGTGAGCTTAGGGCTGG+TGG + chr5.3:8201536-8201555 None:intergenic 55.0%
TGGCTCGAACCGGAATATGG+AGG - chr5.3:8201597-8201616 MS.gene43521:CDS 55.0%
! CAACTCTCAACCGGTTCACC+TGG + chr5.3:8201711-8201730 None:intergenic 55.0%
! CTTAGGGCTGGTGGTTTGGA+AGG + chr5.3:8201527-8201546 None:intergenic 55.0%
! TGAGCTTAGGGCTGGTGGTT+TGG + chr5.3:8201531-8201550 None:intergenic 55.0%
CGGTCATGGATGGCTCGAAC+CGG - chr5.3:8201587-8201606 MS.gene43521:CDS 60.0%
CGGTTCGAGCCATCCATGAC+CGG + chr5.3:8201589-8201608 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 8201442 8201915 8201442 ID=MS.gene43521
chr5.3 mRNA 8201442 8201915 8201442 ID=MS.gene43521.t1;Parent=MS.gene43521
chr5.3 exon 8201442 8201915 8201442 ID=MS.gene43521.t1.exon1;Parent=MS.gene43521.t1
chr5.3 CDS 8201442 8201915 8201442 ID=cds.MS.gene43521.t1;Parent=MS.gene43521.t1
Gene Sequence

>MS.gene43521

ATGCTCTCTTCCCTCTATGCCTCTGATTTCACGGCATTAGACGAAAGTTTAACGCCGTGGGATTTTTCTAACATTCTGTCACCCTTCCAAACCACCAGCCCTAAGCTCACTTCAAGCTCCGGTTCAGGCGAACCAAATGAAAAACCGGTCATGGATGGCTCGAACCGGAATATGGAGGACCGAAAGCGGAGGAGAATGATATCGAACCGGGAATCAGCAAGAAGATCACGTATGAGAAAACAAAGACATCTTGAGAATTTAAGGAACCAGGTGAACCGGTTGAGAGTTGAAAACCGGGAATTGAACAACGGGTTGCAGTTTTTACTGTATCAATGTAATCGTCTACGAACCGAAAATGAGTGGCTCCGGTTGGAACGAACCATGTTGGGTCAAAAGTTGTCAAACATAAGTCAAAATATGGTTTTTCAACCTTTCTCATCTGCATGGCCATGCAATATTGTCACAGCTGAATAA
Protein sequence

>MS.gene43521.t1

MLSSLYASDFTALDESLTPWDFSNILSPFQTTSPKLTSSSGSGEPNEKPVMDGSNRNMEDRKRRRMISNRESARRSRMRKQRHLENLRNQVNRLRVENRELNNGLQFLLYQCNRLRTENEWLRLERTMLGQKLSNISQNMVFQPFSSAWPCNIVTAE