AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene050090

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene050090.t1 MTR_4g057810 90.435 115 11 0 1 115 1 115 1.82e-73 214
MS.gene050090.t1 MTR_4g057800 81.818 110 18 1 1 108 1 110 7.96e-62 185
MS.gene050090.t1 MTR_2g095430 56.190 105 40 2 5 107 16 116 7.21e-38 124
MS.gene050090.t1 MTR_1g063300 43.956 91 51 0 13 103 14 104 1.33e-21 82.8
MS.gene050090.t1 MTR_1g063290 41.758 91 53 0 13 103 14 104 4.09e-21 81.3
MS.gene050090.t1 MTR_1g063340 43.182 88 47 1 17 101 8 95 1.46e-20 79.7
MS.gene050090.t1 MTR_1g063280 51.429 70 34 0 34 103 38 107 5.26e-20 79.0
MS.gene050090.t1 MTR_1g063330 42.045 88 48 1 17 101 8 95 7.34e-20 77.8
MS.gene050090.t1 MTR_7g101890 38.947 95 58 0 12 106 26 120 4.10e-19 76.6
MS.gene050090.t1 MTR_1g063260 48.571 70 36 0 34 103 37 106 7.68e-19 75.5
MS.gene050090.t1 MTR_7g101920 39.535 86 51 1 22 106 18 103 1.09e-17 72.8
MS.gene050090.t1 MTR_1g063310 39.535 86 49 1 16 101 7 89 5.11e-17 70.9
MS.gene050090.t1 MTR_8g076040 38.667 75 44 1 25 99 28 100 9.92e-14 62.4
MS.gene050090.t1 MTR_7g118010 43.750 64 36 0 36 99 21 84 1.20e-13 62.4
MS.gene050090.t1 MTR_3g092220 39.062 64 39 0 36 99 31 94 1.68e-13 62.0
MS.gene050090.t1 MTR_4g072910 40.217 92 45 4 6 96 10 92 3.33e-13 60.8
MS.gene050090.t1 MTR_8g026730 42.188 64 37 0 36 99 25 88 5.03e-13 60.8
MS.gene050090.t1 MTR_0388s0020 43.750 64 35 1 37 99 74 137 3.11e-12 59.7
MS.gene050090.t1 MTR_5g021820 37.313 67 40 1 25 91 27 91 7.13e-12 57.8
MS.gene050090.t1 MTR_3g117610 44.643 56 29 1 37 92 44 97 9.40e-12 57.4
MS.gene050090.t1 MTR_4g072190 42.857 63 34 1 37 99 35 95 1.02e-11 57.0
MS.gene050090.t1 MTR_4g072160 39.175 97 53 3 4 100 7 97 1.20e-11 57.8
MS.gene050090.t1 MTR_4g025830 39.394 66 39 1 35 99 76 141 1.25e-11 58.5
MS.gene050090.t1 MTR_4g072570 37.349 83 45 3 18 99 9 85 1.44e-11 56.6
MS.gene050090.t1 MTR_4g072370 37.662 77 45 2 21 96 6 80 1.96e-11 56.2
MS.gene050090.t1 MTR_3g113310 39.683 63 36 1 37 99 41 101 2.60e-11 56.2
MS.gene050090.t1 MTR_4g072330 36.842 76 45 2 22 96 7 80 3.32e-11 55.5
MS.gene050090.t1 MTR_2g043960 36.250 80 43 2 37 110 75 152 3.43e-11 57.4
MS.gene050090.t1 MTR_4g124750 33.673 98 58 3 5 100 37 129 4.11e-11 57.0
MS.gene050090.t1 MTR_3g117640 43.284 67 36 2 37 102 33 98 4.99e-11 55.5
MS.gene050090.t1 MTR_8g461210 35.227 88 52 3 17 101 11 96 7.94e-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.gene050090.t1 AT2G28085 47.222 108 50 3 4 104 16 123 8.78e-25 91.3
MS.gene050090.t1 AT3G09870 46.575 73 39 0 29 101 36 108 2.69e-17 72.0
MS.gene050090.t1 AT3G61900 35.238 105 64 2 16 116 5 109 1.16e-15 68.2
MS.gene050090.t1 AT5G53590 45.588 68 34 1 37 101 45 112 1.38e-13 63.2
MS.gene050090.t1 AT2G46690 36.585 82 51 1 19 99 5 86 2.61e-13 62.0
MS.gene050090.t1 AT4G34800 43.421 76 41 2 27 100 10 85 7.54e-13 60.1
MS.gene050090.t1 AT4G34770 35.294 85 54 1 16 99 13 97 3.09e-12 58.5
MS.gene050090.t1 AT2G21220 47.273 55 27 1 37 91 39 91 3.75e-12 58.5
MS.gene050090.t1 AT4G34810 39.759 83 46 3 27 105 36 118 8.15e-12 57.8
MS.gene050090.t1 AT4G34790 45.000 60 32 1 38 96 39 98 8.54e-12 57.8
MS.gene050090.t1 AT1G19830 38.356 73 43 1 37 109 47 117 2.82e-11 56.6
MS.gene050090.t1 AT4G34760 42.857 63 34 1 37 99 42 102 3.13e-11 56.2
MS.gene050090.t1 AT5G66260 40.625 64 36 1 38 101 34 95 3.38e-11 55.8
MS.gene050090.t1 AT4G12410 39.683 63 37 1 38 99 76 138 4.22e-11 57.0
MS.gene050090.t1 AT4G00880 40.323 62 37 0 38 99 28 89 4.71e-11 56.2
MS.gene050090.t1 AT4G34780 43.548 62 33 2 37 96 27 88 4.75e-11 55.8
MS.gene050090.t1 AT5G20810 36.364 88 51 2 30 114 71 156 6.02e-11 56.6
MS.gene050090.t1 AT1G75580 47.273 55 27 1 37 91 43 95 7.31e-11 55.1
MS.gene050090.t1 AT5G20810 36.471 85 49 2 30 111 71 153 9.82e-11 56.6

Find 17 sgRNAs with CRISPR-Local

Find 19 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCATTTCTTCTCATTAAT+AGG 0.162461 4.2:-45433152 None:intergenic
TCCAAAAGCCTCACAAATAT+TGG 0.177813 4.2:-45433285 None:intergenic
CCCAATATTTGTGAGGCTTT+TGG 0.243458 4.2:+45433284 MS.gene050090:CDS
ATCATTTCTTCTCATTAATA+GGG 0.270249 4.2:-45433151 None:intergenic
TAATGAATTTCAAATGATAT+TGG 0.273211 4.2:+45433368 MS.gene050090:CDS
CCAAAAGCCTCACAAATATT+GGG 0.309347 4.2:-45433284 None:intergenic
AATATCATTTGAAATTCATT+AGG 0.337534 4.2:-45433366 None:intergenic
AATATCCACTAGGTCGTCTA+TGG 0.384725 4.2:-45433412 None:intergenic
GAAATCAAAATGGTTGTTGT+AGG 0.433297 4.2:+45433081 None:intergenic
GGGTTTGTTAAACAACTCAA+TGG 0.477349 4.2:-45433264 None:intergenic
ATCAAAATGGTTGTTGTAGG+TGG 0.492707 4.2:+45433084 None:intergenic
AAATATGGATTTAATGGAGA+TGG 0.550581 4.2:+45433321 MS.gene050090:CDS
GAAGAAATGATAATAAATCA+AGG 0.559372 4.2:+45433163 MS.gene050090:CDS
TAACAAACCCAATATTTGTG+AGG 0.586788 4.2:+45433277 MS.gene050090:CDS
TGAAATTCATTAGGTCGACA+AGG 0.616935 4.2:-45433357 None:intergenic
TTTAACTTGAAATATCCACT+AGG 0.647972 4.2:-45433422 None:intergenic
TGAAGCCATAGACGACCTAG+TGG 0.666615 4.2:+45433407 MS.gene050090:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATGAATTTCAAATGATAT+TGG + chr4.2:45433368-45433387 MS.gene050090:CDS 15.0%
!!! AATATCATTTGAAATTCATT+AGG - chr4.2:45433369-45433388 None:intergenic 15.0%
!! ATCATTTCTTCTCATTAATA+GGG - chr4.2:45433154-45433173 None:intergenic 20.0%
!! GAAGAAATGATAATAAATCA+AGG + chr4.2:45433163-45433182 MS.gene050090:CDS 20.0%
!! TATCATTTCTTCTCATTAAT+AGG - chr4.2:45433155-45433174 None:intergenic 20.0%
! AAATATGGATTTAATGGAGA+TGG + chr4.2:45433321-45433340 MS.gene050090:CDS 25.0%
! GCTGAAAAATATGGATTTAA+TGG + chr4.2:45433315-45433334 MS.gene050090:CDS 25.0%
!!! TTCTCATTAATAGGGTTTTT+TGG - chr4.2:45433146-45433165 None:intergenic 25.0%
GTTGCAAAAGATGTGAAAAA+AGG + chr4.2:45433189-45433208 MS.gene050090:CDS 30.0%
TAACAAACCCAATATTTGTG+AGG + chr4.2:45433277-45433296 MS.gene050090:CDS 30.0%
!! ACATTTTGTTGTGATTGCTA+AGG + chr4.2:45433212-45433231 MS.gene050090:CDS 30.0%
CCAAAAGCCTCACAAATATT+GGG - chr4.2:45433287-45433306 None:intergenic 35.0%
GAAGAAGCAGCTGAAAAATA+TGG + chr4.2:45433306-45433325 MS.gene050090:CDS 35.0%
TCCAAAAGCCTCACAAATAT+TGG - chr4.2:45433288-45433307 None:intergenic 35.0%
TGAAATTCATTAGGTCGACA+AGG - chr4.2:45433360-45433379 None:intergenic 35.0%
!! GGGTTTGTTAAACAACTCAA+TGG - chr4.2:45433267-45433286 None:intergenic 35.0%
AATATCCACTAGGTCGTCTA+TGG - chr4.2:45433415-45433434 None:intergenic 40.0%
! CCCAATATTTGTGAGGCTTT+TGG + chr4.2:45433284-45433303 MS.gene050090:CDS 40.0%
TGAAGCCATAGACGACCTAG+TGG + chr4.2:45433407-45433426 MS.gene050090:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 45433090 45433443 45433090 ID=MS.gene050090
chr4.2 mRNA 45433090 45433443 45433090 ID=MS.gene050090.t1;Parent=MS.gene050090
chr4.2 exon 45433090 45433443 45433090 ID=MS.gene050090.t1.exon1;Parent=MS.gene050090.t1
chr4.2 CDS 45433090 45433443 45433090 ID=cds.MS.gene050090.t1;Parent=MS.gene050090.t1
Gene Sequence

>MS.gene050090

ATGGTTGTTGTAGGTGGAATTTTGAAGCTCAAGAATAATGTCTTCAAAAAGCTCCAAAAAACCCTATTAATGAGAAGAAATGATAATAAATCAAGGTATGTTGCAAAAGATGTGAAAAAAGGACATTTTGTTGTGATTGCTAAGGATGAAGATGAAGCAAAGAGATTTGTTGTGCCATTGAGTTGTTTAACAAACCCAATATTTGTGAGGCTTTTGGAAGAAGCAGCTGAAAAATATGGATTTAATGGAGATGGTGCAATTACTGTTCCTTGTCGACCTAATGAATTTCAAATGATATTGGAGCAGAAAATGCAAGATGAAGCCATAGACGACCTAGTGGATATTTCAAGTTAA
Protein sequence

>MS.gene050090.t1

MVVVGGILKLKNNVFKKLQKTLLMRRNDNKSRYVAKDVKKGHFVVIAKDEDEAKRFVVPLSCLTNPIFVRLLEEAAEKYGFNGDGAITVPCRPNEFQMILEQKMQDEAIDDLVDISS