Alfalfa Gene Editing Database
Alfalfa Gene Editing Database
Nr:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene50949.t1 | RHN65932.1 | 95.7 | 187 | 8 | 0 | 1 | 187 | 1 | 187 | 3.50E-96 | 360.9 |
Swissprot:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene50949.t1 | Q9SS03 | 46.1 | 178 | 90 | 2 | 13 | 186 | 14 | 189 | 1.0e-35 | 151.4 |
Trembl:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene50949.t1 | A0A396IK46 | 95.7 | 187 | 8 | 0 | 1 | 187 | 1 | 187 | 2.5e-96 | 360.9 |
TFs/TRs:
| Gene ID | Type | Classification |
|---|
Protein Kinases:
| Gene ID | Type | Classification |
|---|
Network:
Co-expression Network:
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| MS.gene049821 | MS.gene50949 | 0.824232 | 9.03E-54 | -1.69E-46 |
| MS.gene050020 | MS.gene50949 | 0.812345 | 4.44E-51 | -1.69E-46 |
| MS.gene050807 | MS.gene50949 | 0.850701 | 1.43E-60 | -1.69E-46 |
| MS.gene050808 | MS.gene50949 | 0.829436 | 5.15E-55 | -1.69E-46 |
| MS.gene051719 | MS.gene50949 | 0.852384 | 4.78E-61 | -1.69E-46 |
| MS.gene051720 | MS.gene50949 | 0.838918 | 2.16E-57 | -1.69E-46 |
| MS.gene052133 | MS.gene50949 | 0.826589 | 2.50E-54 | -1.69E-46 |
| MS.gene052665 | MS.gene50949 | 0.821397 | 4.13E-53 | -1.69E-46 |
| MS.gene052673 | MS.gene50949 | -0.825199 | 5.34E-54 | -1.69E-46 |
| MS.gene053563 | MS.gene50949 | 0.801259 | 9.80E-49 | -1.69E-46 |
| MS.gene053581 | MS.gene50949 | 0.852147 | 5.58E-61 | -1.69E-46 |
| MS.gene055465 | MS.gene50949 | 0.817594 | 3.04E-52 | -1.69E-46 |
| MS.gene055466 | MS.gene50949 | 0.805835 | 1.10E-49 | -1.69E-46 |
| MS.gene055468 | MS.gene50949 | 0.813343 | 2.69E-51 | -1.69E-46 |
| MS.gene055469 | MS.gene50949 | 0.809419 | 1.91E-50 | -1.69E-46 |
| MS.gene056136 | MS.gene50949 | 0.806687 | 7.29E-50 | -1.69E-46 |
| MS.gene058852 | MS.gene50949 | 0.829936 | 3.89E-55 | -1.69E-46 |
PPI:
| Gene1 | Gene2 | Type |
|---|
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene50949.t1 | MTR_4g078885 | 61.326 | 181 | 63 | 2 | 8 | 186 | 9 | 184 | 3.26e-77 | 229 |
| MS.gene50949.t1 | MTR_3g034030 | 60.000 | 185 | 67 | 2 | 4 | 186 | 5 | 184 | 4.27e-76 | 226 |
| MS.gene50949.t1 | MTR_1g056370 | 46.196 | 184 | 90 | 4 | 10 | 186 | 4 | 185 | 2.22e-50 | 161 |
| MS.gene50949.t1 | MTR_4g013350 | 47.305 | 167 | 79 | 2 | 29 | 186 | 30 | 196 | 8.01e-48 | 155 |
| MS.gene50949.t1 | MTR_4g013345 | 45.509 | 167 | 82 | 2 | 29 | 186 | 29 | 195 | 2.47e-46 | 151 |
| MS.gene50949.t1 | MTR_4g013330 | 44.379 | 169 | 83 | 2 | 29 | 186 | 30 | 198 | 7.64e-46 | 150 |
| MS.gene50949.t1 | MTR_4g013320 | 44.311 | 167 | 84 | 2 | 29 | 186 | 32 | 198 | 3.23e-44 | 145 |
| MS.gene50949.t1 | MTR_4g013335 | 48.993 | 149 | 74 | 1 | 40 | 186 | 47 | 195 | 3.30e-44 | 145 |
| MS.gene50949.t1 | MTR_7g093820 | 50.336 | 149 | 69 | 2 | 43 | 186 | 45 | 193 | 1.06e-42 | 141 |
| MS.gene50949.t1 | MTR_7g070390 | 43.011 | 186 | 98 | 3 | 7 | 186 | 8 | 191 | 1.27e-42 | 141 |
| MS.gene50949.t1 | MTR_4g013325 | 47.917 | 144 | 71 | 1 | 47 | 186 | 55 | 198 | 3.99e-42 | 140 |
| MS.gene50949.t1 | MTR_1g054525 | 48.649 | 148 | 70 | 3 | 43 | 186 | 46 | 191 | 6.47e-42 | 139 |
| MS.gene50949.t1 | MTR_7g093850 | 50.336 | 149 | 69 | 2 | 43 | 186 | 45 | 193 | 9.91e-42 | 139 |
| MS.gene50949.t1 | MTR_7g093790 | 47.651 | 149 | 73 | 2 | 43 | 186 | 42 | 190 | 3.93e-41 | 137 |
| MS.gene50949.t1 | MTR_7g093830 | 47.651 | 149 | 73 | 2 | 43 | 186 | 44 | 192 | 3.12e-40 | 135 |
| MS.gene50949.t1 | MTR_4g073950 | 42.208 | 154 | 82 | 2 | 38 | 186 | 40 | 191 | 4.63e-40 | 135 |
| MS.gene50949.t1 | MTR_4g013385 | 40.816 | 147 | 84 | 1 | 43 | 186 | 43 | 189 | 1.32e-38 | 131 |
| MS.gene50949.t1 | MTR_0433s0040 | 40.816 | 147 | 84 | 1 | 43 | 186 | 43 | 189 | 1.32e-38 | 131 |
| MS.gene50949.t1 | MTR_4g013310 | 45.161 | 155 | 77 | 3 | 34 | 184 | 44 | 194 | 1.53e-38 | 131 |
| MS.gene50949.t1 | MTR_5g096120 | 38.919 | 185 | 105 | 2 | 10 | 186 | 4 | 188 | 6.93e-35 | 121 |
| MS.gene50949.t1 | MTR_3g105630 | 42.384 | 151 | 80 | 2 | 43 | 186 | 38 | 188 | 1.44e-33 | 118 |
| MS.gene50949.t1 | MTR_4g013770 | 41.781 | 146 | 80 | 1 | 46 | 186 | 45 | 190 | 4.59e-33 | 117 |
| MS.gene50949.t1 | MTR_3g105640 | 42.384 | 151 | 79 | 3 | 43 | 186 | 38 | 187 | 4.74e-33 | 117 |
| MS.gene50949.t1 | MTR_7g093870 | 44.156 | 154 | 75 | 5 | 43 | 186 | 40 | 192 | 4.62e-31 | 112 |
| MS.gene50949.t1 | MTR_4g013355 | 36.129 | 155 | 85 | 2 | 36 | 186 | 34 | 178 | 2.86e-26 | 99.4 |
| MS.gene50949.t1 | MTR_4g049570 | 30.519 | 154 | 103 | 1 | 38 | 187 | 25 | 178 | 1.00e-19 | 82.0 |
| MS.gene50949.t1 | MTR_4g122130 | 30.851 | 188 | 110 | 3 | 3 | 186 | 8 | 179 | 1.36e-19 | 82.0 |
| MS.gene50949.t1 | MTR_4g049550 | 31.544 | 149 | 98 | 1 | 43 | 187 | 30 | 178 | 4.18e-19 | 80.5 |
| MS.gene50949.t1 | MTR_4g122110 | 32.414 | 145 | 94 | 1 | 46 | 186 | 35 | 179 | 4.90e-19 | 80.5 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene50949.t1 | AT1G65870 | 48.734 | 158 | 77 | 1 | 33 | 186 | 32 | 189 | 2.01e-46 | 151 |
| MS.gene50949.t1 | AT5G42500 | 45.399 | 163 | 83 | 2 | 28 | 186 | 25 | 185 | 4.75e-46 | 150 |
| MS.gene50949.t1 | AT2G21100 | 42.763 | 152 | 83 | 1 | 39 | 186 | 36 | 187 | 4.82e-42 | 140 |
| MS.gene50949.t1 | AT2G21100 | 42.763 | 152 | 83 | 1 | 39 | 186 | 36 | 187 | 4.82e-42 | 140 |
| MS.gene50949.t1 | AT1G22900 | 43.558 | 163 | 86 | 2 | 28 | 186 | 33 | 193 | 4.88e-42 | 140 |
| MS.gene50949.t1 | AT5G42510 | 44.375 | 160 | 83 | 3 | 31 | 186 | 25 | 182 | 3.54e-41 | 137 |
| MS.gene50949.t1 | AT1G55210 | 44.595 | 148 | 81 | 1 | 40 | 186 | 39 | 186 | 1.83e-38 | 130 |
| MS.gene50949.t1 | AT1G55210 | 44.595 | 148 | 81 | 1 | 40 | 186 | 39 | 186 | 1.83e-38 | 130 |
| MS.gene50949.t1 | AT3G13650 | 44.138 | 145 | 80 | 1 | 43 | 186 | 41 | 185 | 2.86e-38 | 130 |
| MS.gene50949.t1 | AT1G58170 | 37.368 | 190 | 109 | 2 | 1 | 186 | 1 | 184 | 1.25e-37 | 128 |
| MS.gene50949.t1 | AT5G49040 | 43.624 | 149 | 78 | 3 | 43 | 186 | 43 | 190 | 9.02e-37 | 126 |
| MS.gene50949.t1 | AT5G49030 | 47.656 | 128 | 63 | 1 | 43 | 166 | 43 | 170 | 4.26e-34 | 127 |
| MS.gene50949.t1 | AT3G13662 | 46.400 | 125 | 66 | 1 | 43 | 166 | 40 | 164 | 8.92e-33 | 115 |
| MS.gene50949.t1 | AT3G58090 | 52.336 | 107 | 51 | 0 | 80 | 186 | 165 | 271 | 8.85e-32 | 115 |
| MS.gene50949.t1 | AT4G38700 | 42.857 | 154 | 78 | 3 | 43 | 186 | 36 | 189 | 1.39e-31 | 113 |
| MS.gene50949.t1 | AT2G21110 | 32.086 | 187 | 106 | 3 | 9 | 186 | 11 | 185 | 3.51e-29 | 107 |
| MS.gene50949.t1 | AT3G13660 | 38.710 | 124 | 76 | 0 | 63 | 186 | 1 | 124 | 1.41e-25 | 95.9 |
| MS.gene50949.t1 | AT4G11210 | 29.032 | 186 | 123 | 5 | 1 | 184 | 1 | 179 | 4.02e-17 | 75.5 |
| MS.gene50949.t1 | AT4G23690 | 33.858 | 127 | 77 | 4 | 43 | 163 | 38 | 163 | 1.19e-11 | 60.8 |
| MS.gene50949.t1 | AT4G11190 | 28.750 | 160 | 106 | 4 | 27 | 184 | 26 | 179 | 3.44e-11 | 59.7 |
Find 36 sgRNAs with CRISPR-Local
Find 43 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| ATGCTACTGCTAAGAGTGTT+TGG | 0.319714 | 3.3:+13592383 | MS.gene50949:CDS |
| TTGGCGGCACCGGCGTGTTT+AGG | 0.334517 | 3.3:+13592347 | MS.gene50949:CDS |
| TCAGTGCTTTGTTGATTTGT+TGG | 0.368171 | 3.3:-13592007 | None:intergenic |
| CTGCCTATTGTTGGCGGCAC+CGG | 0.371881 | 3.3:+13592337 | MS.gene50949:CDS |
| CCATCAAATACAGTTGGGTT+TGG | 0.383222 | 3.3:+13592106 | MS.gene50949:CDS |
| CCGGCGTGTTTAGGTTTGCT+AGG | 0.384387 | 3.3:+13592356 | MS.gene50949:CDS |
| AGCTCAAGGGATGTTTGGTT+TGG | 0.396536 | 3.3:+13592195 | MS.gene50949:CDS |
| ACGCCGGTGCCGCCAACAAT+AGG | 0.397084 | 3.3:-13592340 | None:intergenic |
| CCAAACCCAACTGTATTTGA+TGG | 0.400788 | 3.3:-13592106 | None:intergenic |
| TCTCTAACCGTGTCTTGAAC+AGG | 0.414606 | 3.3:-13592313 | None:intergenic |
| TGCTACTGCTAAGAGTGTTT+GGG | 0.423437 | 3.3:+13592384 | MS.gene50949:CDS |
| GCTCTTGTCCTTCAGTTAAG+AGG | 0.424118 | 3.3:-13592150 | None:intergenic |
| GGTAGAGCTCAAGGGATGTT+TGG | 0.428431 | 3.3:+13592190 | MS.gene50949:CDS |
| CGGCGTGTTTAGGTTTGCTA+GGG | 0.449156 | 3.3:+13592357 | MS.gene50949:CDS |
| TCAATAATTTGTACAACCGT+TGG | 0.456883 | 3.3:-13592082 | None:intergenic |
| GGTAGTACTCTTAGTATGCT+TGG | 0.469670 | 3.3:+13592283 | MS.gene50949:CDS |
| TAACATGATGTTGAATTGTT+CGG | 0.474733 | 3.3:-13591984 | None:intergenic |
| GTTAGAGAACTGCCTATTGT+TGG | 0.476698 | 3.3:+13592328 | MS.gene50949:CDS |
| ATTAATCTTGCTTTCACCGA+TGG | 0.478192 | 3.3:+13592250 | MS.gene50949:CDS |
| ATTGATCCATCAAATACAGT+TGG | 0.481548 | 3.3:+13592100 | MS.gene50949:CDS |
| TTGATCCATCAAATACAGTT+GGG | 0.483436 | 3.3:+13592101 | MS.gene50949:CDS |
| AAACCTGTCGGTAGAGCTCA+AGG | 0.523725 | 3.3:+13592181 | MS.gene50949:CDS |
| GTTTGGAGCAAGTTACATGA+TGG | 0.529133 | 3.3:+13592123 | MS.gene50949:CDS |
| AGAGAACTGCCTATTGTTGG+CGG | 0.541168 | 3.3:+13592331 | MS.gene50949:CDS |
| ATCCCTTGAGCTCTACCGAC+AGG | 0.544812 | 3.3:-13592184 | None:intergenic |
| GTACTCTTAGTATGCTTGGA+AGG | 0.545035 | 3.3:+13592287 | MS.gene50949:CDS |
| TTGTTCGGAGAACACTCCAT+TGG | 0.582295 | 3.3:-13591969 | None:intergenic |
| ATGGACAACCTCTTAACTGA+AGG | 0.591801 | 3.3:+13592142 | MS.gene50949:CDS |
| TTGGCATCTTTGCATGATCG+TGG | 0.594187 | 3.3:+13592214 | MS.gene50949:CDS |
| ATCTTTGCATGATCGTGGAA+TGG | 0.599273 | 3.3:+13592219 | MS.gene50949:CDS |
| GAGCTAACATCAAAACCTGT+CGG | 0.634037 | 3.3:+13592169 | MS.gene50949:CDS |
| GGCGTGTTTAGGTTTGCTAG+GGG | 0.673525 | 3.3:+13592358 | MS.gene50949:CDS |
| AAGGAATCCTGTTCAAGACA+CGG | 0.674439 | 3.3:+13592306 | MS.gene50949:CDS |
| ACTACCAGCAAAATCACCAT+CGG | 0.683340 | 3.3:-13592266 | None:intergenic |
| AACCTGTCGGTAGAGCTCAA+GGG | 0.694023 | 3.3:+13592182 | MS.gene50949:CDS |
| CCTAGCAAACCTAAACACGC+CGG | 0.714305 | 3.3:-13592356 | None:intergenic |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| ! | TAACATGATGTTGAATTGTT+CGG | - | chr3.3:13591987-13592006 | None:intergenic | 25.0% |
| !! | ATGGTAAAAAAAGTGCAAAT+GGG | - | chr3.3:13592041-13592060 | None:intergenic | 25.0% |
| ATTGATCCATCAAATACAGT+TGG | + | chr3.3:13592100-13592119 | MS.gene50949:CDS | 30.0% | |
| CTTAGAAGGTAAAAATCCAA+CGG | + | chr3.3:13592066-13592085 | MS.gene50949:CDS | 30.0% | |
| TTGATCCATCAAATACAGTT+GGG | + | chr3.3:13592101-13592120 | MS.gene50949:CDS | 30.0% | |
| ! | CATGGTAAAAAAAGTGCAAA+TGG | - | chr3.3:13592042-13592061 | None:intergenic | 30.0% |
| ! | TCAATAATTTGTACAACCGT+TGG | - | chr3.3:13592085-13592104 | None:intergenic | 30.0% |
| ! | TTTTACCATGACATCTTAGA+AGG | + | chr3.3:13592052-13592071 | MS.gene50949:CDS | 30.0% |
| !!! | TTTTACCTTCTAAGATGTCA+TGG | - | chr3.3:13592060-13592079 | None:intergenic | 30.0% |
| ATTAATCTTGCTTTCACCGA+TGG | + | chr3.3:13592250-13592269 | MS.gene50949:CDS | 35.0% | |
| ! | GCTCAATTTTTCACTACCAA+TGG | + | chr3.3:13591953-13591972 | MS.gene50949:CDS | 35.0% |
| !! | TCAGTGCTTTGTTGATTTGT+TGG | - | chr3.3:13592010-13592029 | None:intergenic | 35.0% |
| AAGGAATCCTGTTCAAGACA+CGG | + | chr3.3:13592306-13592325 | MS.gene50949:CDS | 40.0% | |
| ACTACCAGCAAAATCACCAT+CGG | - | chr3.3:13592269-13592288 | None:intergenic | 40.0% | |
| ATCTTTGCATGATCGTGGAA+TGG | + | chr3.3:13592219-13592238 | MS.gene50949:CDS | 40.0% | |
| ATGGACAACCTCTTAACTGA+AGG | + | chr3.3:13592142-13592161 | MS.gene50949:CDS | 40.0% | |
| CCAAACCCAACTGTATTTGA+TGG | - | chr3.3:13592109-13592128 | None:intergenic | 40.0% | |
| CCATCAAATACAGTTGGGTT+TGG | + | chr3.3:13592106-13592125 | MS.gene50949:CDS | 40.0% | |
| GAGCTAACATCAAAACCTGT+CGG | + | chr3.3:13592169-13592188 | MS.gene50949:CDS | 40.0% | |
| GGTAGTACTCTTAGTATGCT+TGG | + | chr3.3:13592283-13592302 | MS.gene50949:CDS | 40.0% | |
| GTACTCTTAGTATGCTTGGA+AGG | + | chr3.3:13592287-13592306 | MS.gene50949:CDS | 40.0% | |
| GTTAGAGAACTGCCTATTGT+TGG | + | chr3.3:13592328-13592347 | MS.gene50949:CDS | 40.0% | |
| ! | GTTTGGAGCAAGTTACATGA+TGG | + | chr3.3:13592123-13592142 | MS.gene50949:CDS | 40.0% |
| !! | ATGCTACTGCTAAGAGTGTT+TGG | + | chr3.3:13592383-13592402 | MS.gene50949:CDS | 40.0% |
| !! | TGCTACTGCTAAGAGTGTTT+GGG | + | chr3.3:13592384-13592403 | MS.gene50949:CDS | 40.0% |
| AGAGAACTGCCTATTGTTGG+CGG | + | chr3.3:13592331-13592350 | MS.gene50949:CDS | 45.0% | |
| AGCTCAAGGGATGTTTGGTT+TGG | + | chr3.3:13592195-13592214 | MS.gene50949:CDS | 45.0% | |
| GCTCTTGTCCTTCAGTTAAG+AGG | - | chr3.3:13592153-13592172 | None:intergenic | 45.0% | |
| TCTCTAACCGTGTCTTGAAC+AGG | - | chr3.3:13592316-13592335 | None:intergenic | 45.0% | |
| TTGGCATCTTTGCATGATCG+TGG | + | chr3.3:13592214-13592233 | MS.gene50949:CDS | 45.0% | |
| TTGTTCGGAGAACACTCCAT+TGG | - | chr3.3:13591972-13591991 | None:intergenic | 45.0% | |
| ! | TTCACCGATGGTGATTTTGC+TGG | + | chr3.3:13592262-13592281 | MS.gene50949:CDS | 45.0% |
| AAACCTGTCGGTAGAGCTCA+AGG | + | chr3.3:13592181-13592200 | MS.gene50949:CDS | 50.0% | |
| AACCTGTCGGTAGAGCTCAA+GGG | + | chr3.3:13592182-13592201 | MS.gene50949:CDS | 50.0% | |
| CCTAGCAAACCTAAACACGC+CGG | - | chr3.3:13592359-13592378 | None:intergenic | 50.0% | |
| GGTAGAGCTCAAGGGATGTT+TGG | + | chr3.3:13592190-13592209 | MS.gene50949:CDS | 50.0% | |
| !! | CGGCGTGTTTAGGTTTGCTA+GGG | + | chr3.3:13592357-13592376 | MS.gene50949:CDS | 50.0% |
| !! | GGCGTGTTTAGGTTTGCTAG+GGG | + | chr3.3:13592358-13592377 | MS.gene50949:CDS | 50.0% |
| ATCCCTTGAGCTCTACCGAC+AGG | - | chr3.3:13592187-13592206 | None:intergenic | 55.0% | |
| ! | CCGGCGTGTTTAGGTTTGCT+AGG | + | chr3.3:13592356-13592375 | MS.gene50949:CDS | 55.0% |
| CTGCCTATTGTTGGCGGCAC+CGG | + | chr3.3:13592337-13592356 | MS.gene50949:CDS | 60.0% | |
| !! | ACGCCGGTGCCGCCAACAAT+AGG | - | chr3.3:13592343-13592362 | None:intergenic | 65.0% |
| !! | TTGGCGGCACCGGCGTGTTT+AGG | + | chr3.3:13592347-13592366 | MS.gene50949:CDS | 65.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3.3 | gene | 13591902 | 13592465 | 13591902 | ID=MS.gene50949 |
| chr3.3 | mRNA | 13591902 | 13592465 | 13591902 | ID=MS.gene50949.t1;Parent=MS.gene50949 |
| chr3.3 | exon | 13591902 | 13592465 | 13591902 | ID=MS.gene50949.t1.exon1;Parent=MS.gene50949.t1 |
| chr3.3 | CDS | 13591902 | 13592465 | 13591902 | ID=cds.MS.gene50949.t1;Parent=MS.gene50949.t1 |
| Gene Sequence |
| Protein sequence |
