AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0088580

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0088580 MtrunA17_Chr1g0205811 91.803 122 10 0 1 122 1 122 3.74e-78 226
Msa0088580 MtrunA17_Chr1g0205801 67.327 101 31 1 1 101 1 99 3.27e-45 142
Msa0088580 MtrunA17_Chr1g0205821 66.250 80 27 0 14 93 13 92 6.99e-31 108
Msa0088580 MtrunA17_Chr1g0205821 56.410 78 34 0 12 89 97 174 1.74e-25 94.4
Msa0088580 MtrunA17_Chr1g0205831 53.271 107 46 2 17 122 76 179 7.47e-28 100
Msa0088580 MtrunA17_Chr1g0205831 58.571 70 29 0 14 83 2 71 1.39e-23 89.7
Msa0088580 MtrunA17_Chr5g0415031 53.409 88 41 0 4 91 33 120 4.59e-24 95.9
Msa0088580 MtrunA17_Chr8g0364231 49.474 95 47 1 9 102 37 131 3.80e-22 90.5
Msa0088580 MtrunA17_Chr3g0077881 49.485 97 43 2 9 99 3 99 3.63e-20 80.9
Msa0088580 MtrunA17_Chr6g0452001 46.512 86 46 0 4 89 53 138 1.02e-19 83.6
Msa0088580 MtrunA17_Chr1g0206781 49.351 77 39 0 15 91 12 88 1.23e-19 77.8
Msa0088580 MtrunA17_Chr3g0077891 46.218 119 58 2 9 121 3 121 3.10e-19 78.6
Msa0088580 MtrunA17_Chr3g0077891 48.052 77 39 1 14 89 99 175 3.47e-14 65.1
Msa0088580 MtrunA17_Chr6g0452021 45.055 91 49 1 9 99 38 127 1.09e-18 80.5
Msa0088580 MtrunA17_Chr3g0077911 48.276 87 42 1 13 99 7 90 3.47e-18 75.5
Msa0088580 MtrunA17_Chr3g0077911 53.521 71 32 1 14 83 90 160 7.89e-15 66.6
Msa0088580 MtrunA17_Chr4g0075971 54.286 70 32 0 17 86 175 244 5.62e-17 75.5
Msa0088580 MtrunA17_Chr4g0075971 41.935 93 54 0 7 99 82 174 1.98e-15 71.2
Msa0088580 MtrunA17_Chr3g0077941 45.370 108 46 2 9 115 3 98 1.00e-16 72.0
Msa0088580 MtrunA17_Chr1g0205861 50.725 69 34 0 14 82 16 84 1.20e-16 70.1
Msa0088580 MtrunA17_Chr4g0075861 43.956 91 51 0 9 99 84 174 2.44e-16 73.6
Msa0088580 MtrunA17_Chr4g0075861 54.286 70 32 0 17 86 175 244 5.61e-16 72.4
Msa0088580 MtrunA17_Chr1g0206771 50.000 72 36 0 15 86 17 88 1.16e-15 69.3
Msa0088580 MtrunA17_Chr1g0206771 49.275 69 35 0 14 82 95 163 6.01e-14 64.7
Msa0088580 MtrunA17_Chr3g0077861 47.126 87 43 1 13 99 7 90 1.67e-15 68.6
Msa0088580 MtrunA17_Chr3g0077861 52.113 71 33 1 14 83 90 160 3.49e-14 65.1
Msa0088580 MtrunA17_Chr8g0364021 41.053 95 54 1 1 95 31 123 3.49e-15 68.9
Msa0088580 MtrunA17_Chr3g0077811 45.570 79 42 1 7 85 8 85 5.64e-15 65.9
Msa0088580 MtrunA17_Chr7g0256011 47.826 69 36 0 14 82 16 84 8.91e-15 65.5
Msa0088580 MtrunA17_Chr7g0218891 40.964 83 45 2 4 84 5 85 2.80e-13 64.3
Msa0088580 MtrunA17_Chr7g0218891 41.429 70 41 0 20 89 193 262 2.67e-12 61.6
Msa0088580 MtrunA17_Chr7g0218911 49.206 63 32 0 22 84 6 68 2.25e-12 59.3
Msa0088580 MtrunA17_Chr2g0328701 40.909 88 46 2 5 89 17 101 5.03e-12 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0088580 AT3G01320.1 47.959 98 51 0 5 102 48 145 9.28e-22 89.7
Msa0088580 AT3G01320.2 47.959 98 51 0 5 102 48 145 9.46e-22 89.7
Msa0088580 AT1G70060.2 54.321 81 37 0 9 89 9 89 2.19e-20 85.9
Msa0088580 AT1G70060.1 54.321 81 37 0 9 89 9 89 2.19e-20 85.9
Msa0088580 AT1G24190.3 53.086 81 38 0 9 89 9 89 7.66e-20 84.3
Msa0088580 AT1G24190.2 53.086 81 38 0 9 89 9 89 8.36e-20 84.0
Msa0088580 AT1G24190.1 53.086 81 38 0 9 89 9 89 8.86e-20 84.0
Msa0088580 AT5G15020.1 50.667 75 37 0 9 83 47 121 1.30e-17 77.8
Msa0088580 AT5G15020.2 50.667 75 37 0 9 83 47 121 1.38e-17 77.8
Msa0088580 AT5G15025.1 47.143 70 37 0 14 83 47 116 3.59e-16 69.3
Msa0088580 AT1G10450.3 44.186 86 47 1 14 99 84 168 1.32e-15 72.0
Msa0088580 AT1G10450.2 44.186 86 47 1 14 99 33 117 1.41e-15 72.0
Msa0088580 AT1G10450.1 44.186 86 47 1 14 99 33 117 1.41e-15 72.0
Msa0088580 AT1G59890.3 45.455 77 42 0 13 89 44 120 1.73e-15 71.6
Msa0088580 AT1G59890.2 45.455 77 42 0 13 89 44 120 1.75e-15 71.6
Msa0088580 AT1G59890.1 45.455 77 42 0 13 89 44 120 1.82e-15 71.6
Msa0088580 AT1G59890.4 45.455 77 42 0 13 89 44 120 1.89e-15 71.6
Msa0088580 AT1G70030.3 45.455 77 42 0 7 83 15 91 1.33e-14 65.5
Msa0088580 AT1G70030.2 41.489 94 54 1 7 100 15 107 4.28e-14 64.7
Msa0088580 AT1G70030.1 44.444 81 45 0 7 87 4 84 4.44e-14 65.1
Msa0088580 AT5G15040.1 46.053 76 39 1 13 88 2 75 1.09e-13 62.0
Msa0088580 AT5G15040.3 46.053 76 39 1 13 88 2 75 1.09e-13 62.0
Msa0088580 AT5G15040.2 46.053 76 39 1 13 88 2 75 1.09e-13 62.0
Msa0088580 AT1G24200.1 46.377 69 37 0 14 82 14 82 1.69e-13 64.3
Msa0088580 AT5G35610.1 40.000 95 54 1 8 102 4 95 2.18e-13 63.2
Msa0088580 AT1G27220.1 42.029 69 40 0 14 82 14 82 5.90e-12 60.1
Msa0088580 AT1G23810.1 36.782 87 54 1 14 100 109 194 8.48e-11 57.4

Find 17 sgRNAs with CRISPR-Local

Find 17 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCTTCTGTATCAATTCTT+TGG 0.241773 1_2:-69654318 None:intergenic
TGCTTCAGCTTCACCAATCT+TGG 0.305827 1_2:-69654206 None:intergenic
AGAACTTCTGAAAGATTTCA+AGG 0.359735 1_2:+69654294 Msa0088580:CDS
ACCAATCTTGGCATTTACTC+TGG 0.415002 1_2:-69654194 None:intergenic
AGCTGTGAAAGAAGGAGTTA+TGG 0.477622 1_2:+69654336 Msa0088580:CDS
TCCAGAGTAAATGCCAAGAT+TGG 0.492118 1_2:+69654193 Msa0088580:CDS
ACATGAAATCTCACTTCCAT+TGG 0.500530 1_2:+69654417 Msa0088580:CDS
CAGAATGATGATGAACTTCA+AGG 0.516640 1_2:+69654484 Msa0088580:CDS
GATACAGAAGCTGTGAAAGA+AGG 0.535981 1_2:+69654328 Msa0088580:CDS
TTCAACATCTTCATGCCACC+AGG 0.561140 1_2:+69654394 Msa0088580:CDS
GATGATCAACAACAAGGTGA+TGG 0.565922 1_2:+69654442 Msa0088580:CDS
TGTTGTTGATCATCATCCAA+TGG 0.574340 1_2:-69654433 None:intergenic
GATGATGAACTTCAAGGTGA+TGG 0.578269 1_2:+69654490 Msa0088580:CDS
TGAACTTCAAGGTGATGGAT+TGG 0.587737 1_2:+69654495 Msa0088580:CDS
GGAAGTGAGATTTCATGTCC+TGG 0.614261 1_2:-69654412 None:intergenic
TTGGATGATGATCAACAACA+AGG 0.710928 1_2:+69654436 Msa0088580:CDS
AGTGAGATTTCATGTCCTGG+TGG 0.738423 1_2:-69654409 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAACTTCTGAAAGATTTCA+AGG + chr1_2:69654294-69654313 Msa0088580:CDS 30.0%
CAGCTTCTGTATCAATTCTT+TGG - chr1_2:69654321-69654340 None:intergenic 35.0%
ACATGAAATCTCACTTCCAT+TGG + chr1_2:69654417-69654436 Msa0088580:CDS 35.0%
TGTTGTTGATCATCATCCAA+TGG - chr1_2:69654436-69654455 None:intergenic 35.0%
TTGGATGATGATCAACAACA+AGG + chr1_2:69654436-69654455 Msa0088580:CDS 35.0%
! CAGAATGATGATGAACTTCA+AGG + chr1_2:69654484-69654503 Msa0088580:CDS 35.0%
TCCAGAGTAAATGCCAAGAT+TGG + chr1_2:69654193-69654212 Msa0088580:CDS 40.0%
ACCAATCTTGGCATTTACTC+TGG - chr1_2:69654197-69654216 None:intergenic 40.0%
GATACAGAAGCTGTGAAAGA+AGG + chr1_2:69654328-69654347 Msa0088580:CDS 40.0%
AGCTGTGAAAGAAGGAGTTA+TGG + chr1_2:69654336-69654355 Msa0088580:CDS 40.0%
GATGATCAACAACAAGGTGA+TGG + chr1_2:69654442-69654461 Msa0088580:CDS 40.0%
GATGATGAACTTCAAGGTGA+TGG + chr1_2:69654490-69654509 Msa0088580:CDS 40.0%
!! TGAACTTCAAGGTGATGGAT+TGG + chr1_2:69654495-69654514 Msa0088580:CDS 40.0%
TGCTTCAGCTTCACCAATCT+TGG - chr1_2:69654209-69654228 None:intergenic 45.0%
TTCAACATCTTCATGCCACC+AGG + chr1_2:69654394-69654413 Msa0088580:CDS 45.0%
AGTGAGATTTCATGTCCTGG+TGG - chr1_2:69654412-69654431 None:intergenic 45.0%
GGAAGTGAGATTTCATGTCC+TGG - chr1_2:69654415-69654434 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 69654184 69654552 69654184 ID=Msa0088580;Name=Msa0088580
chr1_2 mRNA 69654184 69654552 69654184 ID=Msa0088580-mRNA-1;Parent=Msa0088580;Name=Msa0088580-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|-1|0|1|-1|1|1|0|122
chr1_2 exon 69654184 69654552 69654184 ID=Msa0088580-mRNA-1:exon:23958;Parent=Msa0088580-mRNA-1
chr1_2 CDS 69654184 69654552 69654184 ID=Msa0088580-mRNA-1:cds;Parent=Msa0088580-mRNA-1
Gene Sequence

>Msa0088580

ATGAGAAGATCCAGAGTAAATGCCAAGATTGGTGAAGCTGAAGCACTTGCGTTTATAATGAAAGTGAAATATGCGTTTCAAGATAAGAGAGAAAAGTATGAAGAATTTTTAGAACTTCTGAAAGATTTCAAGGTCCAAAGAATTGATACAGAAGCTGTGAAAGAAGGAGTTATGGAGTTGTTTAAAGAACATCAATATTTGATTTCAAGATTCAACATCTTCATGCCACCAGGACATGAAATCTCACTTCCATTGGATGATGATCAACAACAAGGTGATGGATTAGAGTTCAAAGATGAACAGAATGATGATGAACTTCAAGGTGATGGATTGGCACTCAAAGATGAGCAGAAAAATGATGAAGAATAA
Protein sequence

>Msa0088580

MRRSRVNAKIGEAEALAFIMKVKYAFQDKREKYEEFLELLKDFKVQRIDTEAVKEGVMELFKEHQYLISRFNIFMPPGHEISLPLDDDQQQGDGLEFKDEQNDDELQGDGLALKDEQKNDEE*