AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene48711

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene48711.t1 MTR_4g031910 71.368 234 50 2 1 222 1 229 3.19e-111 318
MS.gene48711.t1 MTR_4g032290 69.262 244 40 2 1 222 1 231 4.46e-108 310
MS.gene48711.t1 MTR_4g032620 56.277 231 92 1 1 222 1 231 3.28e-92 270
MS.gene48711.t1 MTR_8g036130 56.275 247 83 4 1 222 1 247 1.68e-86 256
MS.gene48711.t1 MTR_4g032260 80.255 157 31 0 1 157 1 157 3.05e-81 239
MS.gene48711.t1 MTR_3g065100 46.058 241 105 4 1 219 1 238 2.10e-59 187
MS.gene48711.t1 MTR_3g466980 54.545 154 69 1 1 154 1 153 1.61e-57 181
MS.gene48711.t1 MTR_2g035610 70.492 122 36 0 1 122 1 122 1.43e-49 158
MS.gene48711.t1 MTR_5g075380 45.806 155 83 1 1 155 1 154 4.20e-43 143
MS.gene48711.t1 MTR_3g466830 46.358 151 80 1 3 153 2 151 1.11e-42 142
MS.gene48711.t1 MTR_4g063790 38.889 180 96 1 1 180 1 166 3.59e-42 140
MS.gene48711.t1 MTR_4g032270 53.285 137 49 2 94 222 2 131 1.44e-41 138
MS.gene48711.t1 MTR_3g467080 40.385 156 93 0 1 156 1 156 8.85e-40 134
MS.gene48711.t1 MTR_5g047580 44.231 156 85 2 1 156 1 154 4.09e-39 132
MS.gene48711.t1 MTR_3g466890 47.619 126 66 0 3 128 2 127 1.56e-37 129
MS.gene48711.t1 MTR_1g077390 41.026 156 90 2 1 156 1 154 1.30e-36 126
MS.gene48711.t1 MTR_3g031100 36.571 175 110 1 1 175 1 174 3.28e-36 127
MS.gene48711.t1 MTR_2g016210 37.209 172 107 1 1 171 1 172 5.58e-36 127
MS.gene48711.t1 MTR_1g090710 38.961 154 93 1 1 154 1 153 8.71e-34 119
MS.gene48711.t1 MTR_1g077320 43.590 156 86 2 1 156 1 154 3.43e-33 117
MS.gene48711.t1 MTR_7g011950 42.949 156 87 2 1 156 1 154 9.34e-33 116
MS.gene48711.t1 MTR_3g465410 38.158 152 80 1 29 180 1 138 1.74e-32 115
MS.gene48711.t1 MTR_1g090783 38.312 154 93 2 3 156 2 153 3.26e-32 115
MS.gene48711.t1 MTR_4g028720 42.308 156 88 2 1 156 1 154 9.55e-32 114
MS.gene48711.t1 MTR_1g090697 40.000 150 88 2 1 150 1 148 1.05e-31 113
MS.gene48711.t1 MTR_1g077300 42.949 156 85 2 1 156 1 152 1.34e-31 113
MS.gene48711.t1 MTR_1g084950 42.949 156 87 2 1 156 1 154 2.66e-31 112
MS.gene48711.t1 MTR_4g028800 74.286 70 16 1 1 70 1 68 2.37e-30 107
MS.gene48711.t1 MTR_7g055800 49.573 117 31 2 1 117 1 89 1.13e-28 103
MS.gene48711.t1 MTR_3g031240 38.938 113 69 0 1 113 1 113 2.77e-27 103
MS.gene48711.t1 MTR_7g055790 52.252 111 35 1 1 111 59 151 5.33e-26 99.0
MS.gene48711.t1 MTR_3g466900 39.024 123 74 1 32 154 2 123 6.11e-26 98.2
MS.gene48711.t1 MTR_3g466930 43.333 90 51 0 32 121 2 91 4.55e-24 93.2
MS.gene48711.t1 MTR_7g106510 39.370 127 77 0 3 129 6 132 4.60e-24 99.8
MS.gene48711.t1 MTR_4g019670 40.157 127 76 0 3 129 6 132 5.65e-24 99.4
MS.gene48711.t1 MTR_2g035580 35.032 157 101 1 1 157 1 156 2.88e-23 92.0
MS.gene48711.t1 MTR_7g055940 48.113 106 27 2 1 106 1 78 4.00e-23 89.0
MS.gene48711.t1 MTR_5g047560 41.026 117 52 2 1 117 1 100 7.48e-22 87.8
MS.gene48711.t1 MTR_3g093900 34.646 127 83 0 3 129 6 132 6.47e-21 90.9
MS.gene48711.t1 MTR_2g035590 60.494 81 32 0 74 154 1 81 2.94e-19 79.7
MS.gene48711.t1 MTR_1g114730 30.088 113 72 3 1 107 1 112 1.55e-12 65.9
MS.gene48711.t1 MTR_6g018920 31.858 113 70 4 1 107 1 112 1.57e-12 65.9
MS.gene48711.t1 MTR_6g005450 33.333 114 67 4 1 107 1 112 2.48e-12 65.5
MS.gene48711.t1 MTR_4g084780 36.937 111 54 2 74 168 1 111 4.71e-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.gene48711.t1 AT5G48670 52.597 154 72 1 1 154 1 153 1.82e-43 149
MS.gene48711.t1 AT1G65330 43.452 168 85 2 3 161 2 168 1.10e-39 137
MS.gene48711.t1 AT1G65300 44.079 152 84 1 3 154 2 152 4.94e-39 136
MS.gene48711.t1 AT5G26630 42.365 203 106 2 1 193 1 202 4.49e-38 132
MS.gene48711.t1 AT5G27960 41.667 168 87 3 5 162 3 169 6.61e-37 131
MS.gene48711.t1 AT5G26650 37.981 208 110 5 5 202 3 201 6.83e-37 132
MS.gene48711.t1 AT1G31630 35.714 168 97 3 3 161 2 167 1.12e-32 121
MS.gene48711.t1 AT1G31640 38.411 151 91 2 3 153 2 150 6.75e-31 118
MS.gene48711.t1 AT2G28700 36.364 176 107 2 1 174 1 173 1.76e-30 115
MS.gene48711.t1 AT5G27810 53.763 93 43 0 29 121 1 93 2.05e-30 109
MS.gene48711.t1 AT3G05860 39.669 121 73 0 1 121 1 121 2.14e-28 106
MS.gene48711.t1 AT3G05860 39.669 121 73 0 1 121 1 121 6.05e-28 106
MS.gene48711.t1 AT3G05860 39.669 121 73 0 1 121 1 121 7.73e-28 106
MS.gene48711.t1 AT5G26580 34.884 172 85 5 1 161 1 156 6.24e-25 100
MS.gene48711.t1 AT1G22590 30.864 162 108 1 1 162 1 158 3.09e-24 94.7
MS.gene48711.t1 AT5G06500 33.758 157 102 2 1 157 1 155 4.11e-20 85.9
MS.gene48711.t1 AT2G40210 40.310 129 76 1 1 129 1 128 9.63e-20 86.7
MS.gene48711.t1 AT5G58890 37.795 127 68 5 6 123 6 130 2.98e-15 73.6
MS.gene48711.t1 AT5G55690 41.026 78 39 2 1 71 1 78 1.35e-12 65.9
MS.gene48711.t1 AT5G55690 41.026 78 39 2 1 71 1 78 1.35e-12 65.9

Find 58 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCCTTCAAGGTAGTAAATT+AGG 0.161446 4.4:+71792762 None:intergenic
AGAAACAAAGAAAAGAAAAT+AGG 0.231520 4.4:-71793109 MS.gene48711:CDS
CCCTTTGGTGAGATCAATTC+TGG 0.238779 4.4:-71792792 MS.gene48711:CDS
TACCAATGTCCTTCAAATTA+TGG 0.254451 4.4:+71792982 None:intergenic
GAGTGAAGAAATGGCAATTA+TGG 0.305887 4.4:-71792913 MS.gene48711:CDS
AAGAAAGGGTCTATTGAAAA+AGG 0.312767 4.4:-71793342 MS.gene48711:CDS
ATCTCTGGCGGAGGCTCATA+AGG 0.326033 4.4:+71793266 None:intergenic
ATGAGCCTCCGCCAGAGATT+TGG 0.368469 4.4:-71793262 MS.gene48711:CDS
GCCCTAATTTACTACCTTGA+AGG 0.380748 4.4:-71792764 None:intergenic
TCCTTCAAGGTAGTAAATTA+GGG 0.396741 4.4:+71792763 None:intergenic
GAAGGACATTGGTAGACGTT+TGG 0.410243 4.4:-71792973 MS.gene48711:CDS
GAAACAAAGAAAAGAAAATA+GGG 0.419680 4.4:-71793108 MS.gene48711:CDS
TCTGGTGAAGGCCAAATCTC+TGG 0.421178 4.4:+71793251 None:intergenic
GATGCTGCTGGAGGTGGTGG+TGG 0.431714 4.4:+71792939 None:intergenic
GTTGAATGACCATAATTTGA+AGG 0.445081 4.4:-71792991 MS.gene48711:CDS
CTAGATGCTGCTGGAGGTGG+TGG 0.448669 4.4:+71792936 None:intergenic
CTCCTAGATGCTGCTGGAGG+TGG 0.449911 4.4:+71792933 None:intergenic
AGCATCTAGGAGTGAAGAAA+TGG 0.457574 4.4:-71792922 MS.gene48711:CDS
CACAACCATGGCTAGAAGTA+AGG 0.461347 4.4:-71793420 None:intergenic
CTCATAAGGGCCATACACTA+TGG 0.468858 4.4:+71793280 None:intergenic
ATCATACAAGAAAAGAAGAA+AGG 0.473094 4.4:-71793357 MS.gene48711:CDS
TCAATTATTGATAGACTCAA+TGG 0.473888 4.4:-71792841 MS.gene48711:CDS
TCTTCACTCCTAGATGCTGC+TGG 0.474575 4.4:+71792927 None:intergenic
CTTGACACAAAGGGTTCTGA+AGG 0.478789 4.4:-71793147 MS.gene48711:CDS
TAGATTTGAGTTATCTTACT+TGG 0.479037 4.4:-71793013 MS.gene48711:CDS
GCGCAAGAGACAGTGCCCTT+TGG 0.496623 4.4:-71792807 MS.gene48711:CDS
TGCGGCATCATTGACAATGA+AGG 0.507200 4.4:+71793388 None:intergenic
AGAGACTTTCTTGACACAAA+GGG 0.517022 4.4:-71793156 MS.gene48711:CDS
GACCATAATTTGAAGGACAT+TGG 0.519945 4.4:-71792984 MS.gene48711:CDS
GGACATTGGTAGACGTTTGG+CGG 0.524285 4.4:-71792970 MS.gene48711:CDS
CACCACCTCCAGCAGCATCT+AGG 0.525577 4.4:-71792935 MS.gene48711:CDS
TTTGTGTCAAGAAAGTCTCT+TGG 0.525855 4.4:+71793159 None:intergenic
TCATACAAGAAAAGAAGAAA+GGG 0.526600 4.4:-71793356 MS.gene48711:CDS
TCTCTGGCGGAGGCTCATAA+GGG 0.528514 4.4:+71793267 None:intergenic
TTTAACCTTACTTCTAGCCA+TGG 0.533701 4.4:+71793415 None:intergenic
ATGTCTCATTGTCTCAATGA+AGG 0.542205 4.4:-71793065 MS.gene48711:CDS
TTGATAGACTCAATGGTGGC+TGG 0.550677 4.4:-71792834 MS.gene48711:CDS
CCAGAATTGATCTCACCAAA+GGG 0.554343 4.4:+71792792 None:intergenic
GAAGCCTGTGCCATAGTGTA+TGG 0.559714 4.4:-71793290 MS.gene48711:CDS
GAAGGCCAAATCTCTGGCGG+AGG 0.565437 4.4:+71793257 None:intergenic
CATTAATAGATATGCCAACA+TGG 0.579766 4.4:+71792883 None:intergenic
GAGATTTGGCCTTCACCAGA+GGG 0.580805 4.4:-71793248 MS.gene48711:CDS
AGAGATTTGGCCTTCACCAG+AGG 0.583520 4.4:-71793249 MS.gene48711:CDS
TCCAGAATTGATCTCACCAA+AGG 0.590517 4.4:+71792791 None:intergenic
GATTTGGCCTTCACCAGAGG+GGG 0.601928 4.4:-71793246 MS.gene48711:CDS
CTTGTATGATTCTTTCCTTG+CGG 0.605657 4.4:+71793370 None:intergenic
AAGAGACTTTCTTGACACAA+AGG 0.607804 4.4:-71793157 MS.gene48711:CDS
ACAGGCTTCAATGCCACAGA+GGG 0.611791 4.4:+71793304 None:intergenic
ATTATGGATCATAGCCATGT+TGG 0.623360 4.4:-71792897 MS.gene48711:CDS
AGGGCCATACACTATGGCAC+AGG 0.641363 4.4:+71793286 None:intergenic
TCACTCCTAGATGCTGCTGG+AGG 0.645942 4.4:+71792930 None:intergenic
GGTGAAGGCCAAATCTCTGG+CGG 0.646852 4.4:+71793254 None:intergenic
TCATTGTCAATGATGCCGCA+AGG 0.664783 4.4:-71793385 MS.gene48711:CDS
ATTATTGATAGACTCAATGG+TGG 0.675374 4.4:-71792838 MS.gene48711:CDS
GCTGAACTTAACACCCTCTG+TGG 0.691245 4.4:-71793317 MS.gene48711:CDS
TGTGCACGACAATATGTCAA+CGG 0.691955 4.4:-71793036 MS.gene48711:CDS
CACAGGCTTCAATGCCACAG+AGG 0.696692 4.4:+71793303 None:intergenic
AGATTTGGCCTTCACCAGAG+GGG 0.703414 4.4:-71793247 MS.gene48711:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAACAAAGAAAAGAAAAT+AGG - chr4.4:71793071-71793090 MS.gene48711:CDS 20.0%
!! GAAACAAAGAAAAGAAAATA+GGG - chr4.4:71793072-71793091 MS.gene48711:CDS 20.0%
! ATCATACAAGAAAAGAAGAA+AGG - chr4.4:71792823-71792842 MS.gene48711:CDS 25.0%
! TCAATTATTGATAGACTCAA+TGG - chr4.4:71793339-71793358 MS.gene48711:CDS 25.0%
! TCATACAAGAAAAGAAGAAA+GGG - chr4.4:71792824-71792843 MS.gene48711:CDS 25.0%
!! TAGATTTGAGTTATCTTACT+TGG - chr4.4:71793167-71793186 MS.gene48711:CDS 25.0%
AAGAAAGGGTCTATTGAAAA+AGG - chr4.4:71792838-71792857 MS.gene48711:CDS 30.0%
ATTATTGATAGACTCAATGG+TGG - chr4.4:71793342-71793361 MS.gene48711:CDS 30.0%
CATTAATAGATATGCCAACA+TGG + chr4.4:71793300-71793319 None:intergenic 30.0%
GTTGAATGACCATAATTTGA+AGG - chr4.4:71793189-71793208 MS.gene48711:CDS 30.0%
TACCAATGTCCTTCAAATTA+TGG + chr4.4:71793201-71793220 None:intergenic 30.0%
AAGAGACTTTCTTGACACAA+AGG - chr4.4:71793023-71793042 MS.gene48711:CDS 35.0%
AGAGACTTTCTTGACACAAA+GGG - chr4.4:71793024-71793043 MS.gene48711:CDS 35.0%
ATGTCTCATTGTCTCAATGA+AGG - chr4.4:71793115-71793134 MS.gene48711:CDS 35.0%
ATTATGGATCATAGCCATGT+TGG - chr4.4:71793283-71793302 MS.gene48711:CDS 35.0%
CTTGTATGATTCTTTCCTTG+CGG + chr4.4:71792813-71792832 None:intergenic 35.0%
GACCATAATTTGAAGGACAT+TGG - chr4.4:71793196-71793215 MS.gene48711:CDS 35.0%
GAGTGAAGAAATGGCAATTA+TGG - chr4.4:71793267-71793286 MS.gene48711:CDS 35.0%
TTTGTGTCAAGAAAGTCTCT+TGG + chr4.4:71793024-71793043 None:intergenic 35.0%
AGCATCTAGGAGTGAAGAAA+TGG - chr4.4:71793258-71793277 MS.gene48711:CDS 40.0%
CCAGAATTGATCTCACCAAA+GGG + chr4.4:71793391-71793410 None:intergenic 40.0%
TCCAGAATTGATCTCACCAA+AGG + chr4.4:71793392-71793411 None:intergenic 40.0%
TGTGCACGACAATATGTCAA+CGG - chr4.4:71793144-71793163 MS.gene48711:CDS 40.0%
!! CGTCATGAATTTTGAGAGCA+CGG + chr4.4:71792966-71792985 None:intergenic 40.0%
!! TGAATTTTGAGAGCACGGAT+TGG + chr4.4:71792961-71792980 None:intergenic 40.0%
CCCTTTGGTGAGATCAATTC+TGG - chr4.4:71793388-71793407 MS.gene48711:CDS 45.0%
CTCATAAGGGCCATACACTA+TGG + chr4.4:71792903-71792922 None:intergenic 45.0%
GAAGGACATTGGTAGACGTT+TGG - chr4.4:71793207-71793226 MS.gene48711:CDS 45.0%
TCATTGTCAATGATGCCGCA+AGG - chr4.4:71792795-71792814 MS.gene48711:CDS 45.0%
TGCGGCATCATTGACAATGA+AGG + chr4.4:71792795-71792814 None:intergenic 45.0%
TTGATAGACTCAATGGTGGC+TGG - chr4.4:71793346-71793365 MS.gene48711:CDS 45.0%
! CTTGACACAAAGGGTTCTGA+AGG - chr4.4:71793033-71793052 MS.gene48711:CDS 45.0%
ACAGGCTTCAATGCCACAGA+GGG + chr4.4:71792879-71792898 None:intergenic 50.0%
GAAGCCTGTGCCATAGTGTA+TGG - chr4.4:71792890-71792909 MS.gene48711:CDS 50.0%
GCTGAACTTAACACCCTCTG+TGG - chr4.4:71792863-71792882 MS.gene48711:CDS 50.0%
GGACATTGGTAGACGTTTGG+CGG - chr4.4:71793210-71793229 MS.gene48711:CDS 50.0%
TCTGGTGAAGGCCAAATCTC+TGG + chr4.4:71792932-71792951 None:intergenic 50.0%
TCTTCACTCCTAGATGCTGC+TGG + chr4.4:71793256-71793275 None:intergenic 50.0%
! AGAGATTTGGCCTTCACCAG+AGG - chr4.4:71792931-71792950 MS.gene48711:CDS 50.0%
! AGATTTGGCCTTCACCAGAG+GGG - chr4.4:71792933-71792952 MS.gene48711:CDS 50.0%
! GAGATTTGGCCTTCACCAGA+GGG - chr4.4:71792932-71792951 MS.gene48711:CDS 50.0%
AGGGCCATACACTATGGCAC+AGG + chr4.4:71792897-71792916 None:intergenic 55.0%
ATCTCTGGCGGAGGCTCATA+AGG + chr4.4:71792917-71792936 None:intergenic 55.0%
ATGAGCCTCCGCCAGAGATT+TGG - chr4.4:71792918-71792937 MS.gene48711:CDS 55.0%
CACAGGCTTCAATGCCACAG+AGG + chr4.4:71792880-71792899 None:intergenic 55.0%
GGTGAAGGCCAAATCTCTGG+CGG + chr4.4:71792929-71792948 None:intergenic 55.0%
TCACTCCTAGATGCTGCTGG+AGG + chr4.4:71793253-71793272 None:intergenic 55.0%
TCTCTGGCGGAGGCTCATAA+GGG + chr4.4:71792916-71792935 None:intergenic 55.0%
! GATTTGGCCTTCACCAGAGG+GGG - chr4.4:71792934-71792953 MS.gene48711:CDS 55.0%
CACCACCTCCAGCAGCATCT+AGG - chr4.4:71793245-71793264 MS.gene48711:CDS 60.0%
CTAGATGCTGCTGGAGGTGG+TGG + chr4.4:71793247-71793266 None:intergenic 60.0%
CTCCTAGATGCTGCTGGAGG+TGG + chr4.4:71793250-71793269 None:intergenic 60.0%
GAAGGCCAAATCTCTGGCGG+AGG + chr4.4:71792926-71792945 None:intergenic 60.0%
GATTGGACCCCCTCTGGTGA+AGG + chr4.4:71792944-71792963 None:intergenic 60.0%
GCGCAAGAGACAGTGCCCTT+TGG - chr4.4:71793373-71793392 MS.gene48711:CDS 60.0%
! GATGCTGCTGGAGGTGGTGG+TGG + chr4.4:71793244-71793263 None:intergenic 65.0%
!! AGCACGGATTGGACCCCCTC+TGG + chr4.4:71792950-71792969 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 71792767 71793435 71792767 ID=MS.gene48711
chr4.4 mRNA 71792767 71793435 71792767 ID=MS.gene48711.t1;Parent=MS.gene48711
chr4.4 exon 71792767 71793435 71792767 ID=MS.gene48711.t1.exon1;Parent=MS.gene48711.t1
chr4.4 CDS 71792767 71793435 71792767 ID=cds.MS.gene48711.t1;Parent=MS.gene48711.t1
Gene Sequence

>MS.gene48711

ATGGCTAGAAGTAAGGTTAAACTTGCCTTCATTGTCAATGATGCCGCAAGGAAAGAATCATACAAGAAAAGAAGAAAGGGTCTATTGAAAAAGGTTGCTGAACTTAACACCCTCTGTGGCATTGAAGCCTGTGCCATAGTGTATGGCCCTTATGAGCCTCCGCCAGAGATTTGGCCTTCACCAGAGGGGGTCCAATCCGTGCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATAATGAACCAAGAGACTTTCTTGACACAAAGGGTTCTGAAGGCTGAAGAGAAATTGAAGAAACAAAGAAAAGAAAATAGGGAGCAAGAGATGACAATACTCATGTCTCATTGTCTCAATGAAGGTAGAGTTGTGCACGACAATATGTCAACGGTAGATTTGAGTTATCTTACTTGGTTGAATGACCATAATTTGAAGGACATTGGTAGACGTTTGGCGGCAACAGTGCCACCACCACCTCCAGCAGCATCTAGGAGTGAAGAAATGGCAATTATGGATCATAGCCATGTTGGCATATCTATTAATGATGATGACATTATTCAAAGTCAATTATTGATAGACTCAATGGTGGCTGGTAATGCGCAAGAGACAGTGCCCTTTGGTGAGATCAATTCTGGAGTTTGCCCTAATTTACTACCTTGA
Protein sequence

>MS.gene48711.t1

MARSKVKLAFIVNDAARKESYKKRRKGLLKKVAELNTLCGIEACAIVYGPYEPPPEIWPSPEGVQSVLSKFMTMHEFQKCKKIMNQETFLTQRVLKAEEKLKKQRKENREQEMTILMSHCLNEGRVVHDNMSTVDLSYLTWLNDHNLKDIGRRLAATVPPPPPAASRSEEMAIMDHSHVGISINDDDIIQSQLLIDSMVAGNAQETVPFGEINSGVCPNLLP