AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043301

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043301.t1 MTR_7g009070 90.299 134 10 1 1 131 1 134 1.89e-79 230
MS.gene043301.t1 MTR_5g037950 55.385 130 54 1 1 130 1 126 9.14e-41 132
MS.gene043301.t1 MTR_5g037930 56.034 116 51 0 15 130 12 127 7.71e-39 127
MS.gene043301.t1 MTR_5g037890 54.701 117 53 0 14 130 9 125 8.19e-39 127
MS.gene043301.t1 MTR_1g023140 48.214 112 58 0 19 130 2 113 1.71e-38 126
MS.gene043301.t1 MTR_3g112410 46.847 111 59 0 19 129 2 112 1.19e-35 119
MS.gene043301.t1 MTR_5g021180 46.018 113 61 0 19 131 4 116 1.00e-34 117
MS.gene043301.t1 MTR_8g107460 42.574 101 58 0 29 129 260 360 1.55e-26 101
MS.gene043301.t1 MTR_7g073680 38.095 105 65 0 22 126 23 127 2.39e-25 93.6
MS.gene043301.t1 MTR_8g005320 35.238 105 68 0 22 126 25 129 2.01e-24 91.3
MS.gene043301.t1 MTR_2g010750 37.143 105 66 0 23 127 9 113 5.75e-24 89.7
MS.gene043301.t1 MTR_4g081380 36.697 109 69 0 18 126 5 113 9.89e-24 89.4
MS.gene043301.t1 MTR_8g006685 35.238 105 68 0 22 126 94 198 1.76e-23 90.9
MS.gene043301.t1 MTR_8g006560 35.238 105 68 0 22 126 94 198 1.76e-23 90.9
MS.gene043301.t1 MTR_2g082590 35.398 113 73 0 14 126 1 113 2.84e-23 87.8
MS.gene043301.t1 MTR_2g082590 39.806 103 60 1 24 126 26 126 6.31e-23 87.4
MS.gene043301.t1 MTR_1g098660 35.955 89 55 2 41 127 74 162 1.53e-18 77.0
MS.gene043301.t1 MTR_1g114290 38.298 94 53 3 35 127 77 166 1.25e-17 75.1
MS.gene043301.t1 MTR_3g089065 36.082 97 55 4 38 129 78 172 1.34e-17 74.7
MS.gene043301.t1 MTR_2g079420 36.145 83 51 2 48 128 89 171 1.57e-16 72.0
MS.gene043301.t1 MTR_7g102130 29.508 122 82 2 8 129 10 127 5.91e-16 69.3
MS.gene043301.t1 MTR_7g080250 35.484 124 69 5 2 122 57 172 1.55e-15 69.7
MS.gene043301.t1 MTR_8g059015 34.343 99 60 4 32 128 79 174 1.74e-15 69.3
MS.gene043301.t1 MTR_4g094690 31.707 82 54 1 49 128 85 166 4.98e-15 67.8
MS.gene043301.t1 MTR_4g085880 36.842 76 47 1 48 122 84 159 3.58e-14 65.9
MS.gene043301.t1 MTR_2g079340 32.955 88 57 2 44 129 51 138 4.10e-14 65.5
MS.gene043301.t1 MTR_4g088905 35.000 80 52 0 49 128 25 104 3.26e-12 62.4
MS.gene043301.t1 MTR_1g053160 32.468 77 51 1 43 118 425 501 2.87e-11 59.7
MS.gene043301.t1 MTR_3g112400 56.098 41 18 0 79 119 41 81 4.58e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043301.t1 AT5G39950 59.398 133 52 1 1 131 1 133 1.06e-56 173
MS.gene043301.t1 AT1G45145 52.475 101 48 0 29 129 11 111 8.86e-36 119
MS.gene043301.t1 AT3G51030 46.018 113 61 0 19 131 2 114 2.65e-34 115
MS.gene043301.t1 AT1G59730 42.748 131 71 2 1 130 1 128 6.50e-34 115
MS.gene043301.t1 AT1G19730 46.429 112 59 1 19 129 2 113 1.90e-33 113
MS.gene043301.t1 AT1G69880 51.546 97 47 0 33 129 47 143 2.96e-33 114
MS.gene043301.t1 AT5G42980 47.059 102 54 0 29 130 11 112 2.45e-31 108
MS.gene043301.t1 AT3G17880 40.000 105 63 0 25 129 265 369 9.69e-26 99.8
MS.gene043301.t1 AT3G17880 40.000 105 63 0 25 129 272 376 1.20e-25 99.8
MS.gene043301.t1 AT3G08710 39.062 128 74 2 1 126 1 126 2.11e-24 91.3
MS.gene043301.t1 AT3G08710 39.062 128 74 2 1 126 1 126 2.11e-24 91.3
MS.gene043301.t1 AT3G08710 39.062 128 74 2 1 126 1 126 2.11e-24 91.3
MS.gene043301.t1 AT3G56420 38.298 94 58 0 33 126 50 143 2.69e-24 91.7
MS.gene043301.t1 AT3G56420 38.298 94 58 0 33 126 50 143 2.69e-24 91.7
MS.gene043301.t1 AT3G56420 38.298 94 58 0 33 126 50 143 2.69e-24 91.7
MS.gene043301.t1 AT2G40790 38.298 94 58 0 33 126 50 143 1.30e-21 84.7
MS.gene043301.t1 AT2G40790 38.298 94 58 0 33 126 50 143 1.30e-21 84.7
MS.gene043301.t1 AT1G11530 38.144 97 60 0 30 126 9 105 2.41e-21 82.8
MS.gene043301.t1 AT1G43560 36.697 109 66 3 12 117 41 149 8.58e-20 80.1
MS.gene043301.t1 AT1G76760 39.744 78 46 1 41 117 77 154 6.32e-19 78.2
MS.gene043301.t1 AT1G50320 44.286 70 38 1 43 111 85 154 4.12e-17 73.6
MS.gene043301.t1 AT3G02730 36.782 87 54 1 46 131 88 174 5.82e-17 73.2
MS.gene043301.t1 AT3G15360 32.673 101 63 4 30 128 92 189 1.83e-16 72.4
MS.gene043301.t1 AT1G03680 36.145 83 51 2 48 128 95 177 5.47e-16 70.9
MS.gene043301.t1 AT4G03520 36.620 71 44 1 48 117 101 171 1.60e-15 69.7
MS.gene043301.t1 AT3G53220 26.549 113 81 1 17 129 15 125 1.60e-15 68.2
MS.gene043301.t1 AT1G31020 30.000 110 75 1 21 128 47 156 4.20e-15 67.8
MS.gene043301.t1 AT2G35010 34.146 82 52 1 49 128 110 191 4.82e-15 68.6
MS.gene043301.t1 AT2G35010 34.146 82 52 1 49 128 110 191 4.82e-15 68.6
MS.gene043301.t1 AT5G16400 32.184 87 58 1 46 131 98 184 1.66e-14 67.0
MS.gene043301.t1 AT4G04950 33.645 107 67 1 22 128 2 104 4.32e-14 67.8
MS.gene043301.t1 AT4G32580 31.868 91 62 0 38 128 14 104 4.53e-14 65.1
MS.gene043301.t1 AT1G52990 32.632 95 63 1 36 129 218 312 1.48e-13 65.9
MS.gene043301.t1 AT4G26160 32.292 96 61 2 38 129 105 200 2.25e-12 62.0
MS.gene043301.t1 AT2G41680 28.889 90 62 2 43 130 440 529 1.07e-11 61.2

Find 26 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGATGTGGCACAAGAGTTTA+AGG 0.257673 7.2:+88591326 MS.gene043301:intron
AATCGATGTTGATGAATTAT+CGG 0.348841 7.2:+88590719 MS.gene043301:CDS
AAAGAGGTTGATAAGGTTGT+TGG 0.418770 7.2:+88591387 MS.gene043301:CDS
TTAGCCATGGCTTGAAGAAT+CGG 0.442279 7.2:-88590669 None:intergenic
CGTTTGTGTTGTTGAAGAAT+GGG 0.453169 7.2:+88591364 MS.gene043301:CDS
ACGTTTGTGTTGTTGAAGAA+TGG 0.456074 7.2:+88591363 MS.gene043301:CDS
TTCTCCTCCTTAGTCGGCAG+TGG 0.459284 7.2:+88590388 MS.gene043301:CDS
TAAGGTTGTTGGAGCAAAGA+AGG 0.462298 7.2:+88591398 MS.gene043301:CDS
TACGGGGCCACTGCCGACTA+AGG 0.463959 7.2:-88590395 None:intergenic
TGATTGATTTCTCTGCTACA+TGG 0.471205 7.2:+88590622 MS.gene043301:CDS
TGATGATTCTGATGACTGTA+CGG 0.487264 7.2:-88590413 None:intergenic
GAATGGGAAAGAGGTTGATA+AGG 0.491854 7.2:+88591380 MS.gene043301:CDS
GATGATTCTGATGACTGTAC+GGG 0.500909 7.2:-88590412 None:intergenic
GATTTCTCTGCTACATGGTG+TGG 0.519111 7.2:+88590627 MS.gene043301:CDS
GGCACAAGAGTTTAAGGTGC+AGG 0.519916 7.2:+88591332 MS.gene043301:CDS
ATCAGTGAATTCATTAGCCA+TGG 0.533887 7.2:-88590682 None:intergenic
GTGTGGACCTTGTAAAATGA+TGG 0.541235 7.2:+88590644 MS.gene043301:CDS
CCTTCCACTCATCTGCTCGC+TGG 0.549073 7.2:+88590455 MS.gene043301:CDS
GTTGTTGAAGAATGGGAAAG+AGG 0.553595 7.2:+88591371 MS.gene043301:CDS
AGATGAGTGGAAGGTCTTGA+CGG 0.570930 7.2:-88590446 None:intergenic
GGGGCCACTGCCGACTAAGG+AGG 0.594415 7.2:-88590392 None:intergenic
GTTGCCAGCGAGCAGATGAG+TGG 0.605035 7.2:-88590459 None:intergenic
TTCTTCAACAACACAAACGT+TGG 0.610426 7.2:-88591360 None:intergenic
CCAGCGAGCAGATGAGTGGA+AGG 0.627549 7.2:-88590455 None:intergenic
GGAACCGATTCTTCAAGCCA+TGG 0.630372 7.2:+88590665 MS.gene043301:CDS
ATGATTCTGATGACTGTACG+GGG 0.715538 7.2:-88590411 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAAAAAATAGAAAAATAAAA+TGG - chr7.2:88590557-88590576 None:intergenic 10.0%
!!! CATTTTATTTTTCTATTTTT+TGG + chr7.2:88590555-88590574 MS.gene043301:intron 10.0%
!!! TCATTTTTACAAATTATTAT+CGG + chr7.2:88591220-88591239 MS.gene043301:intron 10.0%
!!! TGATAATAGTAAATTTTAAA+AGG - chr7.2:88591053-88591072 None:intergenic 10.0%
!!! AATTATACAAAAAGCATTTA+AGG + chr7.2:88591008-88591027 MS.gene043301:intron 15.0%
!!! AGTAAATTTTAAAAGGAAAA+AGG - chr7.2:88591046-88591065 None:intergenic 15.0%
!!! ATAATGTTTTAATTTTTGTG+TGG + chr7.2:88591284-88591303 MS.gene043301:intron 15.0%
!!! ATTTTAAAAGGAAAAAGGTT+AGG - chr7.2:88591041-88591060 None:intergenic 20.0%
!!! TTAATTTTTGTGTGGTTTTT+TGG + chr7.2:88591292-88591311 MS.gene043301:intron 20.0%
! ATTGAGATCTAAAGAGATAT+GGG - chr7.2:88590526-88590545 None:intergenic 25.0%
! TATTGAGATCTAAAGAGATA+TGG - chr7.2:88590527-88590546 None:intergenic 25.0%
! TTCACAAACAGAAAATCAAA+AGG - chr7.2:88590597-88590616 None:intergenic 25.0%
! TTCTCAAAGTTTATTATAGC+AGG - chr7.2:88590966-88590985 None:intergenic 25.0%
!! AATCGATGTTGATGAATTAT+CGG + chr7.2:88590719-88590738 MS.gene043301:CDS 25.0%
!! AATTCTGTTATTTGTTGCAA+TGG + chr7.2:88590876-88590895 MS.gene043301:intron 25.0%
!! TGAATCAATTTTTGACCATA+CGG - chr7.2:88591094-88591113 None:intergenic 25.0%
!!! TTTTGATTTTCTGTTTGTGA+AGG + chr7.2:88590596-88590615 MS.gene043301:intron 25.0%
AACACAACAGTTCATCAAAT+TGG - chr7.2:88590759-88590778 None:intergenic 30.0%
ACACAACAGTTCATCAAATT+GGG - chr7.2:88590758-88590777 None:intergenic 30.0%
GAAGGATGAACTTAAAAACA+AGG + chr7.2:88591416-88591435 MS.gene043301:CDS 30.0%
TTAAAAGGAAAAAGGTTAGG+TGG - chr7.2:88591038-88591057 None:intergenic 30.0%
! TGGTCAAAAATTGATTCACT+CGG + chr7.2:88591096-88591115 MS.gene043301:intron 30.0%
! TTCTTTAGATGTTTTTCGTG+TGG + chr7.2:88590915-88590934 MS.gene043301:intron 30.0%
!! ATTTTTGTGTGGTTTTTTGG+TGG + chr7.2:88591295-88591314 MS.gene043301:intron 30.0%
!! TTTTTGTGTGGTTTTTTGGT+GGG + chr7.2:88591296-88591315 MS.gene043301:intron 30.0%
ATCAGTGAATTCATTAGCCA+TGG - chr7.2:88590685-88590704 None:intergenic 35.0%
CACAACAGTTCATCAAATTG+GGG - chr7.2:88590757-88590776 None:intergenic 35.0%
TGATGATTCTGATGACTGTA+CGG - chr7.2:88590416-88590435 None:intergenic 35.0%
TTCTTCAACAACACAAACGT+TGG - chr7.2:88591363-88591382 None:intergenic 35.0%
! ACGTTTGTGTTGTTGAAGAA+TGG + chr7.2:88591363-88591382 MS.gene043301:CDS 35.0%
! CGTTTGTGTTGTTGAAGAAT+GGG + chr7.2:88591364-88591383 MS.gene043301:CDS 35.0%
! CTGTTATTTGTTGCAATGGA+TGG + chr7.2:88590880-88590899 MS.gene043301:intron 35.0%
! TGATTGATTTCTCTGCTACA+TGG + chr7.2:88590622-88590641 MS.gene043301:CDS 35.0%
! TGATTTTCTGTTTGTGAAGG+TGG + chr7.2:88590599-88590618 MS.gene043301:intron 35.0%
!! AAAGAGGTTGATAAGGTTGT+TGG + chr7.2:88591387-88591406 MS.gene043301:CDS 35.0%
!! ATCGGTTCCATCATTTTACA+AGG - chr7.2:88590654-88590673 None:intergenic 35.0%
!! TCATTTTTCTCCTCCTTAGT+CGG + chr7.2:88590382-88590401 MS.gene043301:CDS 35.0%
!!! GGTTTTTTGGTGGGAATTAT+AGG + chr7.2:88591305-88591324 MS.gene043301:intron 35.0%
AAAATTTCGCACCCACACTT+CGG + chr7.2:88590793-88590812 MS.gene043301:intron 40.0%
ATGATTCTGATGACTGTACG+GGG - chr7.2:88590414-88590433 None:intergenic 40.0%
GATGATTCTGATGACTGTAC+GGG - chr7.2:88590415-88590434 None:intergenic 40.0%
GTGTGGACCTTGTAAAATGA+TGG + chr7.2:88590644-88590663 MS.gene043301:CDS 40.0%
GTTGTTGAAGAATGGGAAAG+AGG + chr7.2:88591371-88591390 MS.gene043301:CDS 40.0%
TAAGGTTGTTGGAGCAAAGA+AGG + chr7.2:88591398-88591417 MS.gene043301:CDS 40.0%
TTAGCCATGGCTTGAAGAAT+CGG - chr7.2:88590672-88590691 None:intergenic 40.0%
TTGGTGGGAATTATAGGATG+TGG + chr7.2:88591311-88591330 MS.gene043301:intron 40.0%
TTTGACCATACGGTCTAACA+TGG - chr7.2:88591084-88591103 None:intergenic 40.0%
!! GAATGGGAAAGAGGTTGATA+AGG + chr7.2:88591380-88591399 MS.gene043301:CDS 40.0%
AGATGAGTGGAAGGTCTTGA+CGG - chr7.2:88590449-88590468 None:intergenic 45.0%
CTTGTCCATGTTAGACCGTA+TGG + chr7.2:88591076-88591095 MS.gene043301:intron 45.0%
GATTTCTCTGCTACATGGTG+TGG + chr7.2:88590627-88590646 MS.gene043301:CDS 45.0%
GGATGTGGCACAAGAGTTTA+AGG + chr7.2:88591326-88591345 MS.gene043301:intron 45.0%
! GATATGGGTTTTACGAGACG+AGG - chr7.2:88590511-88590530 None:intergenic 45.0%
AAGCCTTCTCTCCGAAGTGT+GGG - chr7.2:88590807-88590826 None:intergenic 50.0%
TAAGCCTTCTCTCCGAAGTG+TGG - chr7.2:88590808-88590827 None:intergenic 50.0%
! GGAACCGATTCTTCAAGCCA+TGG + chr7.2:88590665-88590684 MS.gene043301:CDS 50.0%
! GGCACAAGAGTTTAAGGTGC+AGG + chr7.2:88591332-88591351 MS.gene043301:CDS 50.0%
TTCTCCTCCTTAGTCGGCAG+TGG + chr7.2:88590388-88590407 MS.gene043301:CDS 55.0%
CCAGCGAGCAGATGAGTGGA+AGG - chr7.2:88590458-88590477 None:intergenic 60.0%
CCTTCCACTCATCTGCTCGC+TGG + chr7.2:88590455-88590474 MS.gene043301:CDS 60.0%
GCACCCACACTTCGGAGAGA+AGG + chr7.2:88590801-88590820 MS.gene043301:intron 60.0%
GTTGCCAGCGAGCAGATGAG+TGG - chr7.2:88590462-88590481 None:intergenic 60.0%
! TACGGGGCCACTGCCGACTA+AGG - chr7.2:88590398-88590417 None:intergenic 65.0%
! GGGGCCACTGCCGACTAAGG+AGG - chr7.2:88590395-88590414 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 88590376 88591458 88590376 ID=MS.gene043301
chr7.2 mRNA 88590376 88591458 88590376 ID=MS.gene043301.t1;Parent=MS.gene043301
chr7.2 exon 88590376 88590516 88590376 ID=MS.gene043301.t1.exon1;Parent=MS.gene043301.t1
chr7.2 CDS 88590376 88590516 88590376 ID=cds.MS.gene043301.t1;Parent=MS.gene043301.t1
chr7.2 exon 88590618 88590740 88590618 ID=MS.gene043301.t1.exon2;Parent=MS.gene043301.t1
chr7.2 CDS 88590618 88590740 88590618 ID=cds.MS.gene043301.t1;Parent=MS.gene043301.t1
chr7.2 exon 88591327 88591458 88591327 ID=MS.gene043301.t1.exon3;Parent=MS.gene043301.t1
chr7.2 CDS 88591327 88591458 88591327 ID=cds.MS.gene043301.t1;Parent=MS.gene043301.t1
Gene Sequence

>MS.gene043301

ATGGGATCATTTTTCTCCTCCTTAGTCGGCAGTGGCCCCGTACAGTCATCAGAATCATCAGAGAGTTCTTCCGTCAAGACCTTCCACTCATCTGCTCGCTGGCAACTTCACTTCAACGAACTCAAAGATTCTCCTCGTCTCGTAAAACCCATATCTCTTTAGATCTCAATAATTTTAACCATTTTATTTTTCTATTTTTTGGATCTGAAATTCTGAATCCTTTTGATTTTCTGTTTGTGAAGGTGGTGATTGATTTCTCTGCTACATGGTGTGGACCTTGTAAAATGATGGAACCGATTCTTCAAGCCATGGCTAATGAATTCACTGATGTTGAATTCATCAAAATCGATGTTGATGAATTATCGGTAATAATCTTATCCCCAATTTGATGAACTGTTGTGTTTTTAATTTCTGTAAAAAATTTCGCACCCACACTTCGGAGAGAAGGCTTATCACACTCGTGAGCATCTCATACAACACTTACACATGTGATCACATTCAATTCTGTTATTTGTTGCAATGGATGGAAACTAGTACATTTCTTTAGATGTTTTTCGTGTGGTTCTTAACTAAAAAATACATTTTTGCCTGCTATAATAAACTTTGAGAAAATCATGAGTAGTTTAATTCAGAATTATACAAAAAGCATTTAAGGAAATCCACCTAACCTTTTTCCTTTTAAAATTTACTATTATCATGTCTTGTCCATGTTAGACCGTATGGTCAAAAATTGATTCACTCGGAGTCGATGTGTCATTATTTGCATCAATGCTTTGTAGCATATTTATTACGTGTTTGTATTGTATCATAGTACAATACTAACACATGATTACATTCAATTATGTCATTTTTACAAATTATTATCGGTGTAGATGTGTTAATATGTGTTATTGCTTCTTAGCATATTTATAATGTTTTAATTTTTGTGTGGTTTTTTGGTGGGAATTATAGGATGTGGCACAAGAGTTTAAGGTGCAGGCTATGCCAACGTTTGTGTTGTTGAAGAATGGGAAAGAGGTTGATAAGGTTGTTGGAGCAAAGAAGGATGAACTTAAAAACAAGGTTCAAAAGCACAAAGCGTAG
Protein sequence

>MS.gene043301.t1

MGSFFSSLVGSGPVQSSESSESSSVKTFHSSARWQLHFNELKDSPRLVVIDFSATWCGPCKMMEPILQAMANEFTDVEFIKIDVDELSDVAQEFKVQAMPTFVLLKNGKEVDKVVGAKKDELKNKVQKHKA