Alfalfa Gene Editing Database
Alfalfa Gene Editing Database
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0296280 | XP_003596535.2 | 93.151 | 146 | 10 | 0 | 2 | 147 | 128 | 273 | 1.46e-95 | 287 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0296280 | sp|P21745|EA30_VICFA | 53.623 | 138 | 63 | 1 | 3 | 139 | 127 | 264 | 3.53e-48 | 159 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0296280 | G7ITL0 | 93.151 | 146 | 10 | 0 | 2 | 147 | 128 | 273 | 6.99e-96 | 287 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0217080 | Msa0296280 | 0.854771 | 9.859421e-62 | -8.615850e-47 |
| Msa0217090 | Msa0296280 | 0.936605 | 1.328199e-97 | -8.615850e-47 |
| Msa0256960 | Msa0296280 | 0.936322 | 2.090271e-97 | -8.615850e-47 |
| Msa0296270 | Msa0296280 | 0.850898 | 1.260957e-60 | -8.615850e-47 |
| Msa0296280 | Msa0334650 | 0.916311 | 2.075300e-85 | -8.615850e-47 |
| Msa0296280 | Msa0891010 | 0.816441 | 5.521596e-52 | -8.615850e-47 |
| Msa0296280 | Msa0990920 | 0.818802 | 1.620313e-52 | -8.615850e-47 |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0296280 | MtrunA17_Chr2g0318901 | 93.151 | 146 | 10 | 0 | 2 | 147 | 128 | 273 | 1.35e-99 | 287 |
| Msa0296280 | MtrunA17_Chr2g0318871 | 89.726 | 146 | 15 | 0 | 2 | 147 | 128 | 273 | 7.95e-95 | 275 |
| Msa0296280 | MtrunA17_Chr2g0318931 | 77.037 | 135 | 29 | 1 | 3 | 135 | 138 | 272 | 5.28e-72 | 217 |
| Msa0296280 | MtrunA17_Chr8g0355841 | 57.143 | 140 | 60 | 0 | 3 | 142 | 379 | 518 | 4.77e-59 | 191 |
| Msa0296280 | MtrunA17_Chr8g0355311 | 55.474 | 137 | 61 | 0 | 3 | 139 | 60 | 196 | 4.31e-58 | 179 |
| Msa0296280 | MtrunA17_Chr8g0355321 | 58.333 | 132 | 55 | 0 | 3 | 134 | 172 | 303 | 7.60e-58 | 182 |
| Msa0296280 | MtrunA17_Chr8g0355861 | 56.061 | 132 | 58 | 0 | 3 | 134 | 130 | 261 | 9.86e-57 | 178 |
| Msa0296280 | MtrunA17_Chr8g0355331 | 51.449 | 138 | 67 | 0 | 3 | 140 | 291 | 428 | 1.46e-54 | 177 |
| Msa0296280 | MtrunA17_Chr8g0355871 | 53.435 | 131 | 61 | 0 | 3 | 133 | 92 | 222 | 6.13e-53 | 167 |
| Msa0296280 | MtrunA17_Chr8g0355831 | 59.848 | 132 | 53 | 0 | 3 | 134 | 221 | 352 | 7.52e-53 | 171 |
| Msa0296280 | MtrunA17_Chr1g0168781 | 51.825 | 137 | 65 | 1 | 3 | 138 | 128 | 264 | 2.36e-47 | 154 |
| Msa0296280 | MtrunA17_Chr1g0146631 | 46.043 | 139 | 67 | 5 | 1 | 132 | 186 | 323 | 1.46e-36 | 127 |
| Msa0296280 | MtrunA17_Chr1g0147331 | 46.043 | 139 | 67 | 5 | 1 | 132 | 186 | 323 | 1.66e-36 | 127 |
| Msa0296280 | MtrunA17_Chr3g0139431 | 42.361 | 144 | 73 | 5 | 1 | 134 | 179 | 322 | 2.29e-34 | 122 |
| Msa0296280 | MtrunA17_Chr1g0147301 | 42.143 | 140 | 72 | 5 | 1 | 132 | 145 | 283 | 1.56e-33 | 119 |
| Msa0296280 | MtrunA17_Chr1g0147271 | 42.446 | 139 | 73 | 3 | 1 | 132 | 245 | 383 | 2.78e-33 | 120 |
| Msa0296280 | MtrunA17_Chr1g0147291 | 42.143 | 140 | 72 | 5 | 1 | 132 | 127 | 265 | 5.07e-33 | 117 |
| Msa0296280 | MtrunA17_Chr1g0147261 | 41.606 | 137 | 73 | 5 | 1 | 131 | 162 | 297 | 1.10e-32 | 117 |
| Msa0296280 | MtrunA17_Chr1g0147311 | 42.143 | 140 | 72 | 5 | 1 | 132 | 216 | 354 | 2.06e-32 | 117 |
| Msa0296280 | MtrunA17_Chr1g0147321 | 41.727 | 139 | 72 | 5 | 1 | 131 | 98 | 235 | 3.13e-32 | 115 |
| Msa0296280 | MtrunA17_Chr1g0147251 | 38.971 | 136 | 78 | 3 | 1 | 131 | 105 | 240 | 3.67e-30 | 109 |
| Msa0296280 | MtrunA17_Chr1g0147241 | 38.971 | 136 | 78 | 4 | 1 | 131 | 175 | 310 | 1.57e-28 | 106 |
| Msa0296280 | MtrunA17_Chr3g0144421 | 35.211 | 142 | 83 | 5 | 1 | 133 | 161 | 302 | 1.85e-21 | 87.8 |
| Msa0296280 | MtrunA17_Chr4g0034821 | 35.172 | 145 | 84 | 6 | 1 | 135 | 149 | 293 | 1.91e-19 | 82.4 |
| Msa0296280 | MtrunA17_Chr3g0138231 | 32.414 | 145 | 88 | 4 | 1 | 135 | 124 | 268 | 1.23e-18 | 79.7 |
| Msa0296280 | MtrunA17_Chr3g0144391 | 34.507 | 142 | 83 | 5 | 2 | 133 | 364 | 505 | 2.30e-17 | 77.8 |
| Msa0296280 | MtrunA17_Chr3g0144451 | 33.793 | 145 | 86 | 5 | 1 | 135 | 133 | 277 | 3.39e-17 | 75.9 |
| Msa0296280 | MtrunA17_Chr3g0144411 | 34.507 | 142 | 83 | 5 | 2 | 133 | 397 | 538 | 1.51e-16 | 75.1 |
| Msa0296280 | MtrunA17_Chr4g0034451 | 32.192 | 146 | 85 | 6 | 1 | 133 | 382 | 526 | 2.79e-15 | 71.6 |
| Msa0296280 | MtrunA17_Chr4g0034731 | 32.414 | 145 | 86 | 6 | 1 | 133 | 288 | 432 | 6.14e-15 | 70.5 |
| Msa0296280 | MtrunA17_Chr4g0034721 | 33.793 | 145 | 84 | 7 | 1 | 133 | 432 | 576 | 1.20e-14 | 69.7 |
| Msa0296280 | MtrunA17_Chr4g0076231 | 27.338 | 139 | 92 | 4 | 2 | 131 | 18 | 156 | 2.43e-12 | 60.8 |
| Msa0296280 | MtrunA17_Chr5g0413591 | 26.812 | 138 | 93 | 4 | 2 | 131 | 489 | 626 | 6.97e-11 | 58.9 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0296280 | AT5G25610.1 | 40.288 | 139 | 75 | 5 | 1 | 131 | 251 | 389 | 1.48e-29 | 110 |
| Msa0296280 | AT1G49320.1 | 34.694 | 147 | 81 | 5 | 1 | 132 | 132 | 278 | 7.10e-18 | 78.2 |
Find 26 sgRNAs with CRISPR-Local
Find 31 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| CTGCTTTCTCTCCAAGATTT+TGG | 0.104089 | 2_3:-49381482 | None:intergenic |
| GAAATTGCAAATCCAATTAA+TGG | 0.208388 | 2_3:-49381384 | None:intergenic |
| AAATCCTTAGGACCATTAAT+TGG | 0.239448 | 2_3:+49381372 | Msa0296280:CDS |
| GACAATAAAATACAACCTTT+TGG | 0.266567 | 2_3:-49381527 | None:intergenic |
| TTGTCATTTCCTAGGAAATA+AGG | 0.268344 | 2_3:+49381704 | Msa0296280:CDS |
| TGGTGCCAATGTTGCTGTTT+AGG | 0.323507 | 2_3:+49381767 | Msa0296280:CDS |
| ATAAAATAGCCTTATTTCCT+AGG | 0.361639 | 2_3:-49381713 | None:intergenic |
| GCATTGTCCAAACCTAAATT+AGG | 0.363667 | 2_3:-49381741 | None:intergenic |
| GTTTGTCATGCTGATACTTC+AGG | 0.375794 | 2_3:+49381624 | Msa0296280:CDS |
| GGATTTGCAATTTCAAAACT+TGG | 0.388201 | 2_3:+49381393 | Msa0296280:CDS |
| AAACCTGTTTGTCATTTCCT+AGG | 0.419287 | 2_3:+49381696 | Msa0296280:CDS |
| ATGGGTACCTAATTTAGGTT+TGG | 0.424424 | 2_3:+49381734 | Msa0296280:CDS |
| ATAGAGTCAGTCCAAAATCT+TGG | 0.433215 | 2_3:+49381471 | Msa0296280:CDS |
| AGAAAGCAGTGATGTGTCAT+AGG | 0.434072 | 2_3:+49381496 | Msa0296280:CDS |
| TTGTTCATGCTTATCAATGA+AGG | 0.454114 | 2_3:-49381442 | None:intergenic |
| TTTCCTAGGAAATGACAAAC+AGG | 0.459958 | 2_3:-49381699 | None:intergenic |
| GTTCCATCATTTGCCACCAA+TGG | 0.478916 | 2_3:-49381582 | None:intergenic |
| TTAGGTTTGGACAATGCCTA+TGG | 0.494021 | 2_3:+49381747 | Msa0296280:CDS |
| GTTCCATTGGTGGCAAATGA+TGG | 0.508291 | 2_3:+49381579 | Msa0296280:CDS |
| AAATCCAATTAATGGTCCTA+AGG | 0.512590 | 2_3:-49381376 | None:intergenic |
| TCATAGGTTGAATTTCCAAA+AGG | 0.512621 | 2_3:+49381512 | Msa0296280:CDS |
| CAGATTATGAAAGCTGATCC+AGG | 0.521758 | 2_3:+49381669 | Msa0296280:CDS |
| AACAGCAACATTGGCACCAT+AGG | 0.567015 | 2_3:-49381763 | None:intergenic |
| TGACAAACAGGTTTACTACC+TGG | 0.588938 | 2_3:-49381687 | None:intergenic |
| GTACACCTAAACAGCAACAT+TGG | 0.590624 | 2_3:-49381772 | None:intergenic |
| GTAAAGAAAGGTCCAATGAA+GGG | 0.630060 | 2_3:+49381330 | None:intergenic |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | TTTTATTGTCATGAAATTCA+TGG | + | chr2_3:49381540-49381559 | Msa0296280:CDS | 20.0% |
| !! | AAATTTTGTGCAAAATCCTT+AGG | + | chr2_3:49381360-49381379 | Msa0296280:CDS | 25.0% |
| ! | GAAATTGCAAATCCAATTAA+TGG | - | chr2_3:49381387-49381406 | None:intergenic | 25.0% |
| !! | GACAATAAAATACAACCTTT+TGG | - | chr2_3:49381530-49381549 | None:intergenic | 25.0% |
| !!! | ATAAAATAGCCTTATTTCCT+AGG | - | chr2_3:49381716-49381735 | None:intergenic | 25.0% |
| !!! | TAGGAAATAAGGCTATTTTA+TGG | + | chr2_3:49381715-49381734 | Msa0296280:CDS | 25.0% |
| !!! | AGGAAATAAGGCTATTTTAT+GGG | + | chr2_3:49381716-49381735 | Msa0296280:CDS | 25.0% |
| !! | ATTTTATGGGTACCTAATTT+AGG | + | chr2_3:49381729-49381748 | Msa0296280:CDS | 25.0% |
| AAATCCTTAGGACCATTAAT+TGG | + | chr2_3:49381372-49381391 | Msa0296280:CDS | 30.0% | |
| AAATCCAATTAATGGTCCTA+AGG | - | chr2_3:49381379-49381398 | None:intergenic | 30.0% | |
| GGATTTGCAATTTCAAAACT+TGG | + | chr2_3:49381393-49381412 | Msa0296280:CDS | 30.0% | |
| TTGTTCATGCTTATCAATGA+AGG | - | chr2_3:49381445-49381464 | None:intergenic | 30.0% | |
| ! | TCATAGGTTGAATTTCCAAA+AGG | + | chr2_3:49381512-49381531 | Msa0296280:CDS | 30.0% |
| ! | TTGTCATTTCCTAGGAAATA+AGG | + | chr2_3:49381704-49381723 | Msa0296280:CDS | 30.0% |
| ATAGAGTCAGTCCAAAATCT+TGG | + | chr2_3:49381471-49381490 | Msa0296280:CDS | 35.0% | |
| ! | TCATGGAACAACAGCTTTTA+TGG | + | chr2_3:49381557-49381576 | Msa0296280:CDS | 35.0% |
| ! | AACAGCTTTTATGGTTCCAT+TGG | + | chr2_3:49381566-49381585 | Msa0296280:CDS | 35.0% |
| ! | AAACCTGTTTGTCATTTCCT+AGG | + | chr2_3:49381696-49381715 | Msa0296280:CDS | 35.0% |
| TTTCCTAGGAAATGACAAAC+AGG | - | chr2_3:49381702-49381721 | None:intergenic | 35.0% | |
| ! | ATGGGTACCTAATTTAGGTT+TGG | + | chr2_3:49381734-49381753 | Msa0296280:CDS | 35.0% |
| GCATTGTCCAAACCTAAATT+AGG | - | chr2_3:49381744-49381763 | None:intergenic | 35.0% | |
| ! | CTGCTTTCTCTCCAAGATTT+TGG | - | chr2_3:49381485-49381504 | None:intergenic | 40.0% |
| AGAAAGCAGTGATGTGTCAT+AGG | + | chr2_3:49381496-49381515 | Msa0296280:CDS | 40.0% | |
| ! | AGCTTTTATGGTTCCATTGG+TGG | + | chr2_3:49381569-49381588 | Msa0296280:CDS | 40.0% |
| GTTTGTCATGCTGATACTTC+AGG | + | chr2_3:49381624-49381643 | Msa0296280:CDS | 40.0% | |
| CAGATTATGAAAGCTGATCC+AGG | + | chr2_3:49381669-49381688 | Msa0296280:CDS | 40.0% | |
| TGACAAACAGGTTTACTACC+TGG | - | chr2_3:49381690-49381709 | None:intergenic | 40.0% | |
| TTAGGTTTGGACAATGCCTA+TGG | + | chr2_3:49381747-49381766 | Msa0296280:CDS | 40.0% | |
| ! | GTTCCATTGGTGGCAAATGA+TGG | + | chr2_3:49381579-49381598 | Msa0296280:CDS | 45.0% |
| GTTCCATCATTTGCCACCAA+TGG | - | chr2_3:49381585-49381604 | None:intergenic | 45.0% | |
| AACAGCAACATTGGCACCAT+AGG | - | chr2_3:49381766-49381785 | None:intergenic | 45.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr2_3 | gene | 49381345 | 49381788 | 49381345 | ID=Msa0296280;Name=Msa0296280 |
| chr2_3 | mRNA | 49381345 | 49381788 | 49381345 | ID=Msa0296280-mRNA-1;Parent=Msa0296280;Name=Msa0296280-mRNA-1;_AED=0.38;_eAED=0.38;_QI=0|-1|0|1|-1|1|1|0|147 |
| chr2_3 | exon | 49381345 | 49381788 | 49381345 | ID=Msa0296280-mRNA-1:exon:15537;Parent=Msa0296280-mRNA-1 |
| chr2_3 | CDS | 49381345 | 49381788 | 49381345 | ID=Msa0296280-mRNA-1:cds;Parent=Msa0296280-mRNA-1 |
| Gene Sequence |
| Protein sequence |
