AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0291640

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0291640 MtrunA17_Chr2g0311601 96.610 59 2 0 1 59 1 59 2.89e-39 127
Msa0291640 MtrunA17_Chr4g0043421 82.143 56 10 0 4 59 6 61 1.67e-31 107
Msa0291640 MtrunA17_Chr3g0114061 74.510 51 13 0 9 59 4 54 3.88e-24 88.6
Msa0291640 MtrunA17_Chr5g0437571 74.510 51 13 0 9 59 2 52 5.93e-24 88.2
Msa0291640 MtrunA17_Chr3g0106101 70.833 48 14 0 12 59 6 53 5.04e-23 86.3
Msa0291640 MtrunA17_Chr6g0449641 72.917 48 13 0 10 57 6 53 6.68e-23 85.1
Msa0291640 MtrunA17_Chr2g0326041 60.345 58 23 0 8 65 28 85 1.33e-22 82.4
Msa0291640 MtrunA17_Chr6g0449651 76.087 46 11 0 12 57 66 111 2.09e-22 85.1
Msa0291640 MtrunA17_Chr7g0227511 67.925 53 16 1 10 61 8 60 1.35e-21 82.4
Msa0291640 MtrunA17_Chr3g0129071 71.429 49 14 0 9 57 43 91 2.19e-21 83.2
Msa0291640 MtrunA17_Chr5g0438091 69.388 49 15 0 9 57 35 83 3.53e-21 81.6
Msa0291640 MtrunA17_Chr5g0432451 64.151 53 19 0 5 57 35 87 4.26e-21 82.4
Msa0291640 MtrunA17_Chr4g0058651 71.739 46 13 0 12 57 10 55 1.82e-20 79.7
Msa0291640 MtrunA17_Chr5g0402611 69.565 46 14 0 12 57 7 52 1.92e-20 82.0
Msa0291640 MtrunA17_Chr3g0117121 71.739 46 13 0 12 57 9 54 4.97e-20 79.0
Msa0291640 MtrunA17_Chr8g0353981 66.667 48 16 0 10 57 4 51 8.60e-20 79.0
Msa0291640 MtrunA17_Chr3g0115431 67.391 46 15 0 12 57 8 53 4.45e-19 77.0
Msa0291640 MtrunA17_Chr7g0260971 58.182 55 22 1 4 57 5 59 9.18e-19 75.9
Msa0291640 MtrunA17_Chr5g0444351 65.217 46 16 0 14 59 6 51 2.90e-18 73.2
Msa0291640 MtrunA17_Chr6g0452661 61.364 44 17 0 14 57 10 53 3.30e-18 75.1
Msa0291640 MtrunA17_Chr7g0225111 62.500 48 18 0 12 59 4 51 3.35e-18 72.0
Msa0291640 MtrunA17_Chr4g0030001 66.000 50 16 1 11 59 22 71 4.44e-18 73.6
Msa0291640 MtrunA17_Chr3g0097221 60.870 46 18 0 12 57 6 51 1.90e-17 73.6
Msa0291640 MtrunA17_Chr3g0113891 60.377 53 21 0 5 57 6 58 2.74e-17 71.6
Msa0291640 MtrunA17_Chr6g0452671 51.786 56 26 1 10 64 8 63 3.04e-17 71.6
Msa0291640 MtrunA17_Chr4g0059901 56.863 51 22 0 7 57 4 54 4.98e-17 72.4
Msa0291640 MtrunA17_Chr5g0437401 58.491 53 22 0 5 57 3 55 6.79e-17 70.5
Msa0291640 MtrunA17_Chr8g0342351 53.571 56 22 1 10 65 9 60 4.66e-16 69.7
Msa0291640 MtrunA17_Chr1g0184281 50.000 56 27 1 3 57 5 60 1.56e-15 67.4
Msa0291640 MtrunA17_Chr8g0351721 54.386 57 25 1 2 57 7 63 2.13e-15 67.0
Msa0291640 MtrunA17_Chr1g0200201 60.870 46 18 0 14 59 73 118 2.36e-15 67.4
Msa0291640 MtrunA17_Chr6g0460951 53.846 52 23 1 6 56 33 84 3.93e-15 66.6
Msa0291640 MtrunA17_Chr6g0452691 59.091 44 18 0 14 57 10 53 3.97e-15 65.9
Msa0291640 MtrunA17_Chr7g0261031 54.000 50 22 1 9 57 4 53 6.38e-15 65.9
Msa0291640 MtrunA17_Chr1g0184271 56.522 46 19 1 13 57 12 57 1.06e-14 65.5
Msa0291640 MtrunA17_Chr5g0435641 56.000 50 21 1 9 57 3 52 2.09e-14 64.3
Msa0291640 MtrunA17_Chr8g0351701 56.250 48 20 1 13 59 23 70 2.46e-14 64.7
Msa0291640 MtrunA17_Chr8g0374581 53.846 52 23 1 11 61 6 57 7.63e-14 63.2
Msa0291640 MtrunA17_Chr4g0040831 47.917 48 25 0 9 56 11 58 7.84e-14 62.8
Msa0291640 MtrunA17_Chr8g0374601 53.191 47 22 0 11 57 24 70 8.36e-14 63.5
Msa0291640 MtrunA17_Chr7g0245871 58.696 46 18 1 13 57 27 72 1.23e-13 62.8
Msa0291640 MtrunA17_Chr8g0374591 53.191 47 22 0 11 57 6 52 1.35e-13 60.8
Msa0291640 MtrunA17_Chr5g0439111 52.273 44 21 0 14 57 10 53 1.72e-13 62.4
Msa0291640 MtrunA17_Chr4g0055441 56.818 44 19 0 14 57 3 46 8.84e-13 59.3
Msa0291640 MtrunA17_Chr2g0330201 46.939 49 26 0 9 57 15 63 1.31e-12 60.5
Msa0291640 MtrunA17_Chr6g0460941 53.333 45 20 1 13 56 7 51 1.42e-11 54.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0291640 AT1G31320.1 77.966 59 13 0 1 59 1 59 7.46e-31 106
Msa0291640 AT2G30130.1 81.250 48 9 0 12 59 7 54 4.38e-25 92.0
Msa0291640 AT1G16530.1 72.131 61 15 2 1 59 1 61 1.18e-24 90.5
Msa0291640 AT2G40470.1 75.000 48 12 0 10 57 42 89 1.06e-22 86.7
Msa0291640 AT2G40470.2 75.000 48 12 0 10 57 17 64 2.59e-22 85.1
Msa0291640 AT2G30340.2 67.925 53 17 0 5 57 45 97 3.40e-22 86.3
Msa0291640 AT2G30340.1 67.925 53 17 0 5 57 44 96 4.00e-22 86.3
Msa0291640 AT3G27650.1 72.917 48 13 0 10 57 36 83 6.91e-22 83.2
Msa0291640 AT5G63090.4 73.913 46 12 0 12 57 10 55 4.08e-21 81.6
Msa0291640 AT5G63090.3 73.913 46 12 0 12 57 10 55 4.08e-21 81.6
Msa0291640 AT5G63090.2 73.913 46 12 0 12 57 10 55 4.08e-21 81.6
Msa0291640 AT5G63090.1 73.913 46 12 0 12 57 10 55 4.08e-21 81.6
Msa0291640 AT1G65620.1 70.833 48 14 0 10 57 6 53 5.58e-21 81.6
Msa0291640 AT1G65620.4 70.833 48 14 0 10 57 6 53 5.58e-21 81.6
Msa0291640 AT1G65620.3 70.833 48 14 0 10 57 6 53 5.58e-21 81.6
Msa0291640 AT1G65620.5 70.833 48 14 0 10 57 6 53 5.58e-21 81.6
Msa0291640 AT1G65620.2 70.833 48 14 0 10 57 6 53 5.58e-21 81.6
Msa0291640 AT5G66870.1 71.739 46 13 0 12 57 6 51 1.55e-20 82.4
Msa0291640 AT3G26660.1 66.667 51 15 1 11 59 1 51 8.99e-20 76.6
Msa0291640 AT3G26620.1 66.667 51 15 1 11 59 1 51 1.07e-19 76.6
Msa0291640 AT2G28500.1 63.265 49 18 0 11 59 53 101 2.06e-19 78.2
Msa0291640 AT2G23660.2 67.391 46 15 0 12 57 4 49 3.15e-19 79.0
Msa0291640 AT2G23660.3 67.391 46 15 0 12 57 4 49 3.15e-19 79.0
Msa0291640 AT2G23660.1 67.391 46 15 0 12 57 4 49 3.15e-19 79.0
Msa0291640 AT1G07900.1 63.265 49 18 0 11 59 31 79 1.99e-18 75.1
Msa0291640 AT2G42430.1 57.407 54 22 1 5 57 7 60 4.63e-18 75.1
Msa0291640 AT3G47870.1 54.902 51 23 0 7 57 30 80 1.57e-15 68.9
Msa0291640 AT3G11090.1 54.717 53 24 0 5 57 3 55 1.79e-15 66.6
Msa0291640 AT4G00210.1 55.556 54 23 1 5 57 3 56 2.18e-15 67.4
Msa0291640 AT3G50510.1 62.791 43 16 0 12 54 11 53 3.42e-15 66.6
Msa0291640 AT3G50510.2 62.791 43 16 0 12 54 11 53 3.42e-15 66.6
Msa0291640 AT2G42440.1 56.000 50 21 1 9 57 3 52 6.59e-15 66.6
Msa0291640 AT3G03760.1 57.447 47 19 1 12 57 50 96 2.81e-14 65.1
Msa0291640 AT5G06080.1 58.696 46 18 1 12 56 6 51 3.23e-14 63.9
Msa0291640 AT3G58190.1 58.696 46 18 1 13 57 11 56 9.85e-14 63.2
Msa0291640 AT1G72980.1 51.020 49 24 0 9 57 9 57 1.11e-13 63.2
Msa0291640 AT2G31310.1 54.000 50 22 1 9 57 3 52 2.84e-13 61.6
Msa0291640 AT3G13850.1 56.818 44 19 0 14 57 37 80 4.27e-13 62.0
Msa0291640 AT2G45410.1 62.791 43 15 1 16 57 19 61 8.79e-13 60.1
Msa0291640 AT1G06280.1 52.273 44 21 0 14 57 25 68 1.35e-12 60.1
Msa0291640 AT2G19820.1 45.455 55 30 0 3 57 2 56 5.22e-12 57.0
Msa0291640 AT4G00220.1 55.814 43 18 1 16 57 20 62 1.70e-11 57.4
Msa0291640 AT2G45420.1 55.814 43 18 1 16 57 40 82 2.23e-11 57.4

Find 11 sgRNAs with CRISPR-Local

Find 13 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTGATGAACCTCACAAATT+TGG 0.273735 2_3:+40311534 Msa0291640:CDS
GGTTCATCAGCTGGAAAGTA+TGG 0.370523 2_3:-40311522 None:intergenic
GAAGGATGGTGGTAGAAAAC+AGG 0.392084 2_3:+40311431 Msa0291640:CDS
CTGCATGCAAGCTTCTTAGA+AGG 0.457783 2_3:+40311472 Msa0291640:CDS
AATTTGTGAGGTTCATCAGC+TGG 0.500821 2_3:-40311531 None:intergenic
TGGAGGAACATGAAGGATGG+TGG 0.550713 2_3:+40311420 None:intergenic
AATTGGAGGAACATGAAGGA+TGG 0.564311 2_3:+40311417 None:intergenic
CAATGTGAACAAAATGTCAC+AGG 0.579259 2_3:+40311584 Msa0291640:CDS
AGAAGCTTGCATGCAGCACA+TGG 0.590179 2_3:-40311465 None:intergenic
TGGACACTGCCAAATTTGTG+AGG 0.657276 2_3:-40311543 None:intergenic
AAGGATGGTGGTAGAAAACA+GGG 0.667923 2_3:+40311432 Msa0291640:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAATGTGAACAAAATGTCAC+AGG + chr2_3:40311584-40311603 Msa0291640:CDS 35.0%
! AAGGATGGTGGTAGAAAACA+GGG + chr2_3:40311432-40311451 Msa0291640:CDS 40.0%
AATTTGTGAGGTTCATCAGC+TGG - chr2_3:40311534-40311553 None:intergenic 40.0%
GCTGATGAACCTCACAAATT+TGG + chr2_3:40311534-40311553 Msa0291640:CDS 40.0%
! GCAGTGTCCACAAGATTTTT+GGG + chr2_3:40311556-40311575 Msa0291640:CDS 40.0%
! CAGTGTCCACAAGATTTTTG+GGG + chr2_3:40311557-40311576 Msa0291640:CDS 40.0%
! GAAGGATGGTGGTAGAAAAC+AGG + chr2_3:40311431-40311450 Msa0291640:CDS 45.0%
CTGCATGCAAGCTTCTTAGA+AGG + chr2_3:40311472-40311491 Msa0291640:CDS 45.0%
GGTTCATCAGCTGGAAAGTA+TGG - chr2_3:40311525-40311544 None:intergenic 45.0%
TGGACACTGCCAAATTTGTG+AGG - chr2_3:40311546-40311565 None:intergenic 45.0%
! GGCAGTGTCCACAAGATTTT+TGG + chr2_3:40311555-40311574 Msa0291640:CDS 45.0%
TGCTAGCCCCAAAAATCTTG+TGG - chr2_3:40311566-40311585 None:intergenic 45.0%
AGAAGCTTGCATGCAGCACA+TGG - chr2_3:40311468-40311487 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 40311429 40311647 40311429 ID=Msa0291640;Name=Msa0291640
chr2_3 mRNA 40311429 40311647 40311429 ID=Msa0291640-mRNA-1;Parent=Msa0291640;Name=Msa0291640-mRNA-1;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|1|1|0|72
chr2_3 exon 40311429 40311647 40311429 ID=Msa0291640-mRNA-1:exon:12959;Parent=Msa0291640-mRNA-1
chr2_3 CDS 40311429 40311647 40311429 ID=Msa0291640-mRNA-1:cds;Parent=Msa0291640-mRNA-1
Gene Sequence

>Msa0291640

ATGAAGGATGGTGGTAGAAAACAGGGTACAATGTCACCATGTGCTGCATGCAAGCTTCTTAGAAGGAGATGTGCTAAAGATTGTGTGTTTGCTCCATACTTTCCAGCTGATGAACCTCACAAATTTGGCAGTGTCCACAAGATTTTTGGGGCTAGCAATGTGAACAAAATGTCACAGGTTCAAATTAAATTCATGCACTATCATGTTATCATCACCTGA
Protein sequence

>Msa0291640

MKDGGRKQGTMSPCAACKLLRRRCAKDCVFAPYFPADEPHKFGSVHKIFGASNVNKMSQVQIKFMHYHVIIT*