AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0082450

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0082450 MtrunA17_Chr1g0185861 100.000 147 0 0 1 147 1 147 6.11e-103 301
Msa0082450 MtrunA17_Chr7g0259501 87.075 147 15 1 1 147 1 143 2.27e-73 225
Msa0082450 MtrunA17_Chr5g0440341 78.261 115 25 0 33 147 23 137 9.13e-65 203
Msa0082450 MtrunA17_Chr7g0254001 79.464 112 23 0 36 147 13 124 5.26e-63 199
Msa0082450 MtrunA17_Chr4g0002921 66.972 109 36 0 39 147 23 131 7.87e-49 160
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0082450 AT3G06190.2 73.759 141 33 1 7 147 2 138 1.10e-67 207
Msa0082450 AT3G06190.4 73.759 141 33 1 7 147 2 138 1.57e-67 207
Msa0082450 AT3G06190.3 73.759 141 33 1 7 147 2 138 1.57e-67 207
Msa0082450 AT3G06190.5 73.759 141 33 1 7 147 2 138 2.42e-67 208
Msa0082450 AT3G03740.1 78.571 126 23 1 22 147 31 152 6.09e-67 210
Msa0082450 AT3G06190.1 73.759 141 33 1 7 147 2 138 8.24e-67 208
Msa0082450 AT5G21010.1 67.669 133 43 0 15 147 2 134 1.37e-62 197
Msa0082450 AT3G43700.3 67.910 134 41 1 16 147 8 141 1.77e-61 193
Msa0082450 AT3G43700.2 67.910 134 41 1 16 147 8 141 2.27e-61 193
Msa0082450 AT3G43700.1 67.910 134 41 1 16 147 8 141 6.65e-61 193
Msa0082450 AT2G39760.4 69.421 121 36 1 27 147 11 130 3.03e-59 187
Msa0082450 AT2G39760.3 69.421 121 36 1 27 147 11 130 3.03e-59 187
Msa0082450 AT2G39760.2 69.421 121 36 1 27 147 11 130 3.22e-59 187
Msa0082450 AT5G19000.1 77.778 108 24 0 40 147 32 139 4.13e-59 189
Msa0082450 AT5G19000.3 77.778 108 24 0 40 147 32 139 4.13e-59 189
Msa0082450 AT2G39760.1 69.421 121 36 1 27 147 11 130 5.66e-59 188
Msa0082450 AT5G19000.2 77.778 108 24 0 40 147 32 139 1.04e-58 188

Find 37 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTCAAAAGGGATTGGAAT+TGG 0.250201 1_2:+61309577 Msa0082450:CDS
CGAGTGAAGGGACTGATGTT+AGG 0.326194 1_2:+61309719 Msa0082450:CDS
GAACCTATGTGAGCCTTTGA+TGG 0.352408 1_2:-61309536 None:intergenic
CCACGATATTTCAACGTATA+AGG 0.352677 1_2:-61309829 None:intergenic
TCACATAGGTTCAAGATAAC+GGG 0.392891 1_2:+61309547 Msa0082450:CDS
TCTCAAAAGGGATTGGAATT+GGG 0.424168 1_2:+61309578 Msa0082450:CDS
GATGTTGAGGAGGTTGTTGA+TGG 0.428183 1_2:-61309502 None:intergenic
CACCGTTGGTGGGTACGAAT+GGG 0.437086 1_2:+61309624 Msa0082450:CDS
TCACCGTTGGTGGGTACGAA+TGG 0.438080 1_2:+61309623 Msa0082450:CDS
ACGGGGTATTCACTCTCAAA+AGG 0.441675 1_2:+61309565 Msa0082450:CDS
TTCATCGCGCTTGCGAGTGA+AGG 0.449539 1_2:+61309706 Msa0082450:CDS
CTCACATAGGTTCAAGATAA+CGG 0.449878 1_2:+61309546 Msa0082450:CDS
TATTCACTCTCAAAAGGGAT+TGG 0.480986 1_2:+61309571 Msa0082450:CDS
GAGGTTGTTGATGGAATTGA+GGG 0.492292 1_2:-61309493 None:intergenic
GAGTGAAGGGACTGATGTTA+GGG 0.509324 1_2:+61309720 Msa0082450:CDS
AGATGATGATGATGAATTTG+AGG 0.513479 1_2:-61309455 None:intergenic
GGAGGTTGTTGATGGAATTG+AGG 0.515360 1_2:-61309494 None:intergenic
CGGGGTATTCACTCTCAAAA+GGG 0.521264 1_2:+61309566 Msa0082450:CDS
TCATCGCGCTTGCGAGTGAA+GGG 0.522765 1_2:+61309707 Msa0082450:CDS
GATGGAATTGAGGGTGGTGA+TGG 0.542993 1_2:-61309484 None:intergenic
GAGTGGGAAAGAGAGGCATA+AGG 0.552695 1_2:+61309771 Msa0082450:CDS
TGGATCAGAGTGGGAAAGAG+AGG 0.559531 1_2:+61309764 Msa0082450:CDS
TTTGATAGGACGTTGGAGAG+TGG 0.581385 1_2:+61309805 Msa0082450:CDS
ATGTGAGCCTTTGATGGTGT+CGG 0.584850 1_2:-61309530 None:intergenic
GTTGTTGATGGAATTGAGGG+TGG 0.596454 1_2:-61309490 None:intergenic
TGAAATATCGTGGTAGCATG+TGG 0.600425 1_2:+61309839 Msa0082450:CDS
TCGATAACCGACACCATCAA+AGG 0.601387 1_2:+61309523 Msa0082450:CDS
CGCCCATTCGTACCCACCAA+CGG 0.616095 1_2:-61309626 None:intergenic
GATGATGATGAATTTGAGGA+TGG 0.626655 1_2:-61309451 None:intergenic
CCTTATACGTTGAAATATCG+TGG 0.627057 1_2:+61309829 Msa0082450:CDS
ACACCATCAAAGGCTCACAT+AGG 0.632820 1_2:+61309533 Msa0082450:CDS
GTCGGTTATCGATGTTGAGG+AGG 0.637096 1_2:-61309512 None:intergenic
CACATAGGTTCAAGATAACG+GGG 0.658135 1_2:+61309548 Msa0082450:CDS
CCCTGATGGGAAAAGCGTGG+AGG 0.667337 1_2:+61309660 Msa0082450:CDS
TTACCCTGATGGGAAAAGCG+TGG 0.670712 1_2:+61309657 Msa0082450:CDS
AGATTCTTCGCGAAACAACG+AGG 0.699126 1_2:+61309428 Msa0082450:CDS
GGTGTCGGTTATCGATGTTG+AGG 0.707765 1_2:-61309515 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGATGATGATGATGAATTTG+AGG - chr1_2:61309458-61309477 None:intergenic 30.0%
!!! CGATTTATTTTTACCCTGAT+GGG + chr1_2:61309647-61309666 Msa0082450:CDS 30.0%
! GCTTTTTGAATTAACGCTTT+TGG + chr1_2:61309744-61309763 Msa0082450:CDS 30.0%
!! AGGTTCATAGTCATTTTGAT+AGG + chr1_2:61309791-61309810 Msa0082450:CDS 30.0%
! GATGATGATGAATTTGAGGA+TGG - chr1_2:61309454-61309473 None:intergenic 35.0%
CTCACATAGGTTCAAGATAA+CGG + chr1_2:61309546-61309565 Msa0082450:CDS 35.0%
TCACATAGGTTCAAGATAAC+GGG + chr1_2:61309547-61309566 Msa0082450:CDS 35.0%
TATTCACTCTCAAAAGGGAT+TGG + chr1_2:61309571-61309590 Msa0082450:CDS 35.0%
TCTCAAAAGGGATTGGAATT+GGG + chr1_2:61309578-61309597 Msa0082450:CDS 35.0%
!!! GCGATTTATTTTTACCCTGA+TGG + chr1_2:61309646-61309665 Msa0082450:CDS 35.0%
!! TAGTCATTTTGATAGGACGT+TGG + chr1_2:61309798-61309817 Msa0082450:CDS 35.0%
CCACGATATTTCAACGTATA+AGG - chr1_2:61309832-61309851 None:intergenic 35.0%
CCTTATACGTTGAAATATCG+TGG + chr1_2:61309829-61309848 Msa0082450:CDS 35.0%
! GAGGTTGTTGATGGAATTGA+GGG - chr1_2:61309496-61309515 None:intergenic 40.0%
CACATAGGTTCAAGATAACG+GGG + chr1_2:61309548-61309567 Msa0082450:CDS 40.0%
CTCTCAAAAGGGATTGGAAT+TGG + chr1_2:61309577-61309596 Msa0082450:CDS 40.0%
! TTAACGCTTTTGGATCAGAG+TGG + chr1_2:61309754-61309773 Msa0082450:CDS 40.0%
! TAACGCTTTTGGATCAGAGT+GGG + chr1_2:61309755-61309774 Msa0082450:CDS 40.0%
TGAAATATCGTGGTAGCATG+TGG + chr1_2:61309839-61309858 Msa0082450:CDS 40.0%
AGATTCTTCGCGAAACAACG+AGG + chr1_2:61309428-61309447 Msa0082450:CDS 45.0%
! GTTGTTGATGGAATTGAGGG+TGG - chr1_2:61309493-61309512 None:intergenic 45.0%
! GGAGGTTGTTGATGGAATTG+AGG - chr1_2:61309497-61309516 None:intergenic 45.0%
GATGTTGAGGAGGTTGTTGA+TGG - chr1_2:61309505-61309524 None:intergenic 45.0%
TCGATAACCGACACCATCAA+AGG + chr1_2:61309523-61309542 Msa0082450:CDS 45.0%
!! ATGTGAGCCTTTGATGGTGT+CGG - chr1_2:61309533-61309552 None:intergenic 45.0%
ACACCATCAAAGGCTCACAT+AGG + chr1_2:61309533-61309552 Msa0082450:CDS 45.0%
GAACCTATGTGAGCCTTTGA+TGG - chr1_2:61309539-61309558 None:intergenic 45.0%
! ACGGGGTATTCACTCTCAAA+AGG + chr1_2:61309565-61309584 Msa0082450:CDS 45.0%
! CGGGGTATTCACTCTCAAAA+GGG + chr1_2:61309566-61309585 Msa0082450:CDS 45.0%
!! GCATCTGAGATTTTCACCGT+TGG + chr1_2:61309610-61309629 Msa0082450:CDS 45.0%
!! TCTGAGATTTTCACCGTTGG+TGG + chr1_2:61309613-61309632 Msa0082450:CDS 45.0%
! CTGAGATTTTCACCGTTGGT+GGG + chr1_2:61309614-61309633 Msa0082450:CDS 45.0%
GAGTGAAGGGACTGATGTTA+GGG + chr1_2:61309720-61309739 Msa0082450:CDS 45.0%
TTTGATAGGACGTTGGAGAG+TGG + chr1_2:61309805-61309824 Msa0082450:CDS 45.0%
GATGGAATTGAGGGTGGTGA+TGG - chr1_2:61309487-61309506 None:intergenic 50.0%
GTCGGTTATCGATGTTGAGG+AGG - chr1_2:61309515-61309534 None:intergenic 50.0%
!! GGTGTCGGTTATCGATGTTG+AGG - chr1_2:61309518-61309537 None:intergenic 50.0%
TTACCCTGATGGGAAAAGCG+TGG + chr1_2:61309657-61309676 Msa0082450:CDS 50.0%
CGAGTGAAGGGACTGATGTT+AGG + chr1_2:61309719-61309738 Msa0082450:CDS 50.0%
TGGATCAGAGTGGGAAAGAG+AGG + chr1_2:61309764-61309783 Msa0082450:CDS 50.0%
! GAGTGGGAAAGAGAGGCATA+AGG + chr1_2:61309771-61309790 Msa0082450:CDS 50.0%
! TCACCGTTGGTGGGTACGAA+TGG + chr1_2:61309623-61309642 Msa0082450:CDS 55.0%
! CACCGTTGGTGGGTACGAAT+GGG + chr1_2:61309624-61309643 Msa0082450:CDS 55.0%
! CCTCCACGCTTTTCCCATCA+GGG - chr1_2:61309663-61309682 None:intergenic 55.0%
! TCCTCCACGCTTTTCCCATC+AGG - chr1_2:61309664-61309683 None:intergenic 55.0%
TTCATCGCGCTTGCGAGTGA+AGG + chr1_2:61309706-61309725 Msa0082450:CDS 55.0%
TCATCGCGCTTGCGAGTGAA+GGG + chr1_2:61309707-61309726 Msa0082450:CDS 55.0%
CGCCCATTCGTACCCACCAA+CGG - chr1_2:61309629-61309648 None:intergenic 60.0%
! CCCTGATGGGAAAAGCGTGG+AGG + chr1_2:61309660-61309679 Msa0082450:CDS 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 61309421 61309888 61309421 ID=Msa0082450;Name=Msa0082450
chr1_2 mRNA 61309421 61309888 61309421 ID=Msa0082450-mRNA-1;Parent=Msa0082450;Name=Msa0082450-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|-1|0|1|-1|1|1|0|155
chr1_2 exon 61309421 61309888 61309421 ID=Msa0082450-mRNA-1:exon:20294;Parent=Msa0082450-mRNA-1
chr1_2 CDS 61309421 61309888 61309421 ID=Msa0082450-mRNA-1:cds;Parent=Msa0082450-mRNA-1
Gene Sequence

>Msa0082450

ATGGGTAAGATTCTTCGCGAAACAACGAGGCCATCCTCAAATTCATCATCATCATCTTCATCACCATCACCACCCTCAATTCCATCAACAACCTCCTCAACATCGATAACCGACACCATCAAAGGCTCACATAGGTTCAAGATAACGGGGTATTCACTCTCAAAAGGGATTGGAATTGGGAAATACATAGCATCTGAGATTTTCACCGTTGGTGGGTACGAATGGGCGATTTATTTTTACCCTGATGGGAAAAGCGTGGAGGATAATGCTACGTATGTGTCGCTTTTCATCGCGCTTGCGAGTGAAGGGACTGATGTTAGGGCGCTTTTTGAATTAACGCTTTTGGATCAGAGTGGGAAAGAGAGGCATAAGGTTCATAGTCATTTTGATAGGACGTTGGAGAGTGGACCTTATACGTTGAAATATCGTGGTAGCATGTGGTTAGTTTTCAGTTATCATTTAGTTTAA
Protein sequence

>Msa0082450

MGKILRETTRPSSNSSSSSSSPSPPSIPSTTSSTSITDTIKGSHRFKITGYSLSKGIGIGKYIASEIFTVGGYEWAIYFYPDGKSVEDNATYVSLFIALASEGTDVRALFELTLLDQSGKERHKVHSHFDRTLESGPYTLKYRGSMWLVFSYHLV*