AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene21404

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21404.t1 MTR_1g090697 92.308 156 12 0 1 156 1 156 1.21e-102 291
MS.gene21404.t1 MTR_1g090710 72.611 157 42 1 1 156 1 157 2.56e-79 232
MS.gene21404.t1 MTR_5g047580 60.000 155 62 0 1 155 1 155 5.94e-64 193
MS.gene21404.t1 MTR_1g090783 62.338 154 58 0 3 156 2 155 1.44e-63 192
MS.gene21404.t1 MTR_1g084950 63.871 155 56 0 1 155 1 155 1.88e-61 187
MS.gene21404.t1 MTR_1g077390 57.419 155 66 0 1 155 1 155 7.34e-60 182
MS.gene21404.t1 MTR_1g077320 61.290 155 60 0 1 155 1 155 9.74e-60 182
MS.gene21404.t1 MTR_4g028720 60.000 155 62 0 1 155 1 155 3.39e-57 176
MS.gene21404.t1 MTR_7g011950 60.000 155 62 0 1 155 1 155 4.65e-57 176
MS.gene21404.t1 MTR_1g077300 56.129 155 66 1 1 155 1 153 4.16e-48 153
MS.gene21404.t1 MTR_5g047560 50.968 155 60 1 1 155 1 139 2.41e-47 150
MS.gene21404.t1 MTR_3g466830 43.226 155 87 1 3 156 2 156 1.14e-37 126
MS.gene21404.t1 MTR_3g466890 41.935 155 89 1 3 156 2 156 1.00e-35 121
MS.gene21404.t1 MTR_4g032620 36.709 158 98 2 1 156 1 158 4.47e-35 122
MS.gene21404.t1 MTR_3g466980 35.065 154 99 1 1 153 1 154 1.84e-32 115
MS.gene21404.t1 MTR_3g065100 41.026 156 91 1 1 155 1 156 2.03e-32 115
MS.gene21404.t1 MTR_2g016210 41.667 156 89 2 1 154 1 156 1.02e-31 114
MS.gene21404.t1 MTR_4g031910 41.772 158 90 2 1 156 1 158 4.13e-31 112
MS.gene21404.t1 MTR_5g075380 36.306 157 99 1 1 156 1 157 4.89e-31 109
MS.gene21404.t1 MTR_8g036130 35.625 160 99 3 1 156 1 160 1.04e-29 108
MS.gene21404.t1 MTR_4g063790 34.615 156 96 3 1 152 1 154 6.04e-28 102
MS.gene21404.t1 MTR_2g035610 42.975 121 68 1 1 120 1 121 5.08e-27 98.6
MS.gene21404.t1 MTR_3g031240 33.544 158 103 2 1 156 1 158 3.97e-26 97.8
MS.gene21404.t1 MTR_3g466900 40.476 126 74 1 32 156 2 127 1.03e-25 95.5
MS.gene21404.t1 MTR_4g032260 39.744 156 92 2 1 154 1 156 3.50e-25 94.7
MS.gene21404.t1 MTR_3g031100 33.758 157 102 2 1 155 1 157 7.61e-25 96.3
MS.gene21404.t1 MTR_3g466930 38.095 126 77 1 32 156 2 127 1.71e-23 89.7
MS.gene21404.t1 MTR_4g032290 39.241 158 94 2 1 156 1 158 9.15e-23 90.5
MS.gene21404.t1 MTR_4g028800 50.000 72 34 1 1 72 1 70 1.48e-21 82.8
MS.gene21404.t1 MTR_3g467080 29.936 157 108 2 1 155 1 157 1.24e-20 83.2
MS.gene21404.t1 MTR_2g035580 29.032 155 109 1 1 154 1 155 1.12e-17 75.5
MS.gene21404.t1 MTR_1g033930 46.809 94 49 1 64 156 22 115 3.36e-17 73.2
MS.gene21404.t1 MTR_4g019670 28.834 163 98 4 1 145 1 163 2.22e-16 75.5
MS.gene21404.t1 MTR_7g106510 29.878 164 95 6 1 145 1 163 5.50e-16 74.3
MS.gene21404.t1 MTR_3g093900 29.032 155 109 1 3 156 6 160 2.28e-15 72.4
MS.gene21404.t1 MTR_3g465410 29.688 128 84 3 29 152 1 126 3.11e-14 65.9
MS.gene21404.t1 MTR_1g033370 39.362 94 56 1 64 156 28 121 4.12e-14 65.1
MS.gene21404.t1 MTR_1g033790 43.617 94 52 1 64 156 22 115 7.01e-14 64.7
MS.gene21404.t1 MTR_7g055800 28.814 118 57 2 1 118 1 91 2.34e-12 59.7
MS.gene21404.t1 MTR_6g005450 30.469 128 76 4 1 115 1 128 4.43e-12 62.8
MS.gene21404.t1 MTR_6g018920 24.224 161 109 4 1 155 1 154 1.98e-11 60.8
MS.gene21404.t1 MTR_7g075850 31.373 153 86 4 1 148 1 139 5.46e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21404.t1 AT1G65300 37.013 154 96 1 3 155 2 155 4.72e-32 115
MS.gene21404.t1 AT3G05860 41.611 149 86 1 1 148 1 149 5.40e-32 113
MS.gene21404.t1 AT3G05860 41.611 149 86 1 1 148 1 149 2.56e-31 113
MS.gene21404.t1 AT3G05860 41.611 149 86 1 1 148 1 149 2.98e-31 113
MS.gene21404.t1 AT5G48670 42.949 156 88 1 1 155 1 156 5.66e-30 111
MS.gene21404.t1 AT1G65330 37.013 154 96 1 3 155 2 155 1.79e-29 108
MS.gene21404.t1 AT5G26630 38.462 156 95 1 1 155 1 156 4.13e-29 106
MS.gene21404.t1 AT1G22590 39.241 158 90 3 1 156 1 154 7.17e-29 104
MS.gene21404.t1 AT5G26650 35.948 153 97 1 4 155 2 154 1.77e-25 100
MS.gene21404.t1 AT1G31640 36.667 150 93 2 3 151 2 150 2.74e-25 100
MS.gene21404.t1 AT1G31630 31.788 151 101 2 3 152 2 151 9.60e-25 97.8
MS.gene21404.t1 AT5G27960 34.641 153 99 1 4 155 2 154 9.53e-24 94.7
MS.gene21404.t1 AT2G28700 33.858 127 77 2 1 123 1 124 1.55e-20 86.3
MS.gene21404.t1 AT5G27810 39.583 96 57 1 29 123 1 96 5.13e-19 77.8
MS.gene21404.t1 AT5G06500 34.459 148 91 3 1 145 1 145 1.28e-17 77.0
MS.gene21404.t1 AT5G26580 30.968 155 94 2 1 155 1 142 9.60e-17 75.9
MS.gene21404.t1 AT2G40210 32.143 140 89 3 1 137 1 137 5.20e-11 60.1

Find 25 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATACCTCTCAATTACCTTCT+TGG 0.215921 1.4:+71852439 None:intergenic
TGCCTTCCTTGCCGCGTTAT+CGG 0.274204 1.4:+71852595 None:intergenic
GACAACACTTTGTGATATTC+CGG 0.300516 1.4:-71852525 MS.gene21404:CDS
TCTGCATAATGTATCTTTCA+TGG 0.373491 1.4:+71852378 None:intergenic
TTCTTGGCTTCTTCTAGATT+CGG 0.376844 1.4:+71852455 None:intergenic
TGCCGCGTTATCGGAGATAA+AGG 0.416769 1.4:+71852604 None:intergenic
TTGATTCTCAGACCGAGGTT+TGG 0.445696 1.4:-71852478 MS.gene21404:CDS
CTCCGATAACGCGGCAAGGA+AGG 0.449540 1.4:-71852597 MS.gene21404:CDS
AAGCTACAATAAAAGAAAGA+AGG 0.492405 1.4:-71852573 MS.gene21404:CDS
TTTCACCTTCCTTCTCGTCA+TGG 0.513068 1.4:+71852631 None:intergenic
TTCTAGATTCGGCCAAACCT+CGG 0.514603 1.4:+71852466 None:intergenic
ACCTCGGTCTGAGAATCAAA+AGG 0.517136 1.4:+71852482 None:intergenic
GCATGTTGAGAAGAAGTTGA+AGG 0.520532 1.4:-71852213 MS.gene21404:CDS
TGCAGATGATTGCTAAAGCA+AGG 0.534319 1.4:-71852361 MS.gene21404:CDS
GGTCTGAGAATCAAAAGGAC+TGG 0.551947 1.4:+71852487 None:intergenic
AAAGAAGGGTCTCATAAAGA+AGG 0.555375 1.4:-71852558 MS.gene21404:CDS
AGCTACAATAAAAGAAAGAA+GGG 0.567899 1.4:-71852572 MS.gene21404:CDS
TGTTGAGAAGAAGTTGAAGG+AGG 0.578028 1.4:-71852210 MS.gene21404:CDS
TGCAACCATGACGAGAAGGA+AGG 0.595441 1.4:-71852636 None:intergenic
GAATCTAGAAGAAGCCAAGA+AGG 0.598410 1.4:-71852453 MS.gene21404:CDS
TGCCTTTATCTCCGATAACG+CGG 0.615017 1.4:-71852606 MS.gene21404:CDS
TTATCTCCGATAACGCGGCA+AGG 0.616944 1.4:-71852601 MS.gene21404:CDS
CTGGAAATTATAGCACAAGC+CGG 0.619015 1.4:+71852506 None:intergenic
AAGCCAAGAAGGTAATTGAG+AGG 0.625836 1.4:-71852442 MS.gene21404:CDS
GCAGATGATTGCTAAAGCAA+GGG 0.627505 1.4:-71852360 MS.gene21404:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGCTACAATAAAAGAAAGA+AGG - chr1.4:71852237-71852256 MS.gene21404:CDS 25.0%
! AGCTACAATAAAAGAAAGAA+GGG - chr1.4:71852238-71852257 MS.gene21404:CDS 25.0%
TCTGCATAATGTATCTTTCA+TGG + chr1.4:71852435-71852454 None:intergenic 30.0%
! AGCTGAATCTTTTTATGCTA+CGG - chr1.4:71852512-71852531 MS.gene21404:CDS 30.0%
AAAGAAGGGTCTCATAAAGA+AGG - chr1.4:71852252-71852271 MS.gene21404:CDS 35.0%
ATACCTCTCAATTACCTTCT+TGG + chr1.4:71852374-71852393 None:intergenic 35.0%
GACAACACTTTGTGATATTC+CGG - chr1.4:71852285-71852304 MS.gene21404:CDS 35.0%
TTCTTGGCTTCTTCTAGATT+CGG + chr1.4:71852358-71852377 None:intergenic 35.0%
! TTTTCAGTTCTTCAGCAGTT+AGG + chr1.4:71852567-71852586 None:intergenic 35.0%
AAGCCAAGAAGGTAATTGAG+AGG - chr1.4:71852368-71852387 MS.gene21404:CDS 40.0%
CTGGAAATTATAGCACAAGC+CGG + chr1.4:71852307-71852326 None:intergenic 40.0%
GAATCTAGAAGAAGCCAAGA+AGG - chr1.4:71852357-71852376 MS.gene21404:CDS 40.0%
GCAGATGATTGCTAAAGCAA+GGG - chr1.4:71852450-71852469 MS.gene21404:CDS 40.0%
GCATGTTGAGAAGAAGTTGA+AGG - chr1.4:71852597-71852616 MS.gene21404:CDS 40.0%
TGCAGATGATTGCTAAAGCA+AGG - chr1.4:71852449-71852468 MS.gene21404:CDS 40.0%
TGTTGAGAAGAAGTTGAAGG+AGG - chr1.4:71852600-71852619 MS.gene21404:CDS 40.0%
ACCTCGGTCTGAGAATCAAA+AGG + chr1.4:71852331-71852350 None:intergenic 45.0%
GGTCTGAGAATCAAAAGGAC+TGG + chr1.4:71852326-71852345 None:intergenic 45.0%
TGCCTTTATCTCCGATAACG+CGG - chr1.4:71852204-71852223 MS.gene21404:CDS 45.0%
TTCTAGATTCGGCCAAACCT+CGG + chr1.4:71852347-71852366 None:intergenic 45.0%
TTGATTCTCAGACCGAGGTT+TGG - chr1.4:71852332-71852351 MS.gene21404:CDS 45.0%
!! TCCTTTTGATTCTCAGACCG+AGG - chr1.4:71852327-71852346 MS.gene21404:CDS 45.0%
TGCCGCGTTATCGGAGATAA+AGG + chr1.4:71852209-71852228 None:intergenic 50.0%
TTATCTCCGATAACGCGGCA+AGG - chr1.4:71852209-71852228 MS.gene21404:CDS 50.0%
TGCCTTCCTTGCCGCGTTAT+CGG + chr1.4:71852218-71852237 None:intergenic 55.0%
CTCCGATAACGCGGCAAGGA+AGG - chr1.4:71852213-71852232 MS.gene21404:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 71852181 71852651 71852181 ID=MS.gene21404
chr1.4 mRNA 71852181 71852651 71852181 ID=MS.gene21404.t1;Parent=MS.gene21404
chr1.4 exon 71852181 71852651 71852181 ID=MS.gene21404.t1.exon1;Parent=MS.gene21404.t1
chr1.4 CDS 71852181 71852651 71852181 ID=cds.MS.gene21404.t1;Parent=MS.gene21404.t1
Gene Sequence

>MS.gene21404

ATGACGAGAAGGAAGGTGAAACTTGCCTTTATCTCCGATAACGCGGCAAGGAAGGCAAGCTACAATAAAAGAAAGAAGGGTCTCATAAAGAAGGTAACTGAACTGACAACACTTTGTGATATTCCGGCTTGTGCTATAATTTCCAGTCCTTTTGATTCTCAGACCGAGGTTTGGCCGAATCTAGAAGAAGCCAAGAAGGTAATTGAGAGGTATCAAAGTTATTCTTTGATAGACGAAAACAAGAATGTGAGCCATGAAAGATACATTATGCAGATGATTGCTAAAGCAAGGGACAAACTAAGAAAGTTGAAGCATGAGAATCGTGAGCAAGAGCTGAATCTTTTTATGCTACGGAACTTGAAAAATAACAACTTGTATGAAGACCTAACTGCTGAAGAACTGAAAAATCTTGCTAAGCATGTTGAGAAGAAGTTGAAGGAGGTTGATGACAAGATTGATACACTTGATTGA
Protein sequence

>MS.gene21404.t1

MTRRKVKLAFISDNAARKASYNKRKKGLIKKVTELTTLCDIPACAIISSPFDSQTEVWPNLEEAKKVIERYQSYSLIDENKNVSHERYIMQMIAKARDKLRKLKHENREQELNLFMLRNLKNNNLYEDLTAEELKNLAKHVEKKLKEVDDKIDTLD