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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0687730 | XP_013456276.1 | 59.542 | 131 | 39 | 2 | 1 | 117 | 189 | 319 | 7.22e-37 | 137 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0687730 | A0A072UKT5 | 59.542 | 131 | 39 | 2 | 1 | 117 | 189 | 319 | 3.45e-37 | 137 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0687730 | Msa1037900 | 0.809033 | 2.310521e-50 | -8.615850e-47 |
| Msa0687730 | Msa1081570 | 0.804635 | 1.965372e-49 | -8.615850e-47 |
| Msa0687730 | Msa1129960 | 0.810597 | 1.065207e-50 | -8.615850e-47 |
| Msa0687730 | Msa1421550 | 0.805049 | 1.609959e-49 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0687730 | MtrunA17_Chr4g0033391 | 59.542 | 131 | 39 | 2 | 1 | 117 | 189 | 319 | 6.64e-41 | 137 |
| Msa0687730 | MtrunA17_Chr2g0307141 | 58.824 | 136 | 39 | 2 | 1 | 119 | 225 | 360 | 8.30e-40 | 135 |
| Msa0687730 | MtrunA17_Chr2g0307131 | 59.259 | 135 | 38 | 2 | 1 | 118 | 221 | 355 | 1.04e-39 | 135 |
| Msa0687730 | MtrunA17_Chr4g0033291 | 59.398 | 133 | 40 | 2 | 1 | 119 | 197 | 329 | 1.37e-39 | 134 |
| Msa0687730 | MtrunA17_Chr6g0468491 | 55.882 | 136 | 43 | 2 | 1 | 119 | 179 | 314 | 6.67e-38 | 129 |
| Msa0687730 | MtrunA17_Chr4g0033281 | 56.154 | 130 | 44 | 2 | 1 | 117 | 195 | 324 | 9.56e-35 | 122 |
| Msa0687730 | MtrunA17_Chr4g0054581 | 54.286 | 140 | 43 | 4 | 1 | 119 | 240 | 379 | 1.45e-33 | 120 |
| Msa0687730 | MtrunA17_Chr4g0054621 | 46.923 | 130 | 57 | 3 | 1 | 119 | 214 | 342 | 9.36e-26 | 98.6 |
| Msa0687730 | MtrunA17_Chr7g0225901 | 49.550 | 111 | 39 | 2 | 1 | 94 | 130 | 240 | 9.35e-25 | 94.4 |
| Msa0687730 | MtrunA17_Chr5g0400621 | 46.667 | 135 | 55 | 3 | 1 | 118 | 199 | 333 | 4.53e-23 | 91.3 |
| Msa0687730 | MtrunA17_Chr5g0400641 | 45.455 | 121 | 41 | 4 | 1 | 100 | 40 | 156 | 4.36e-20 | 80.1 |
| Msa0687730 | MtrunA17_Chr4g0002831 | 46.667 | 75 | 36 | 1 | 41 | 111 | 127 | 201 | 7.41e-15 | 67.4 |
| Msa0687730 | MtrunA17_Chr6g0468461 | 44.898 | 98 | 49 | 2 | 1 | 94 | 215 | 311 | 1.27e-14 | 68.6 |
| Msa0687730 | MtrunA17_Chr4g0002851 | 33.628 | 113 | 66 | 2 | 4 | 112 | 87 | 194 | 1.22e-12 | 61.6 |
| Msa0687730 | MtrunA17_Chr4g0002781 | 32.847 | 137 | 68 | 3 | 1 | 115 | 216 | 350 | 1.85e-12 | 62.4 |
| Msa0687730 | MtrunA17_Chr4g0002801 | 37.143 | 105 | 60 | 2 | 15 | 115 | 229 | 331 | 2.27e-12 | 62.0 |
| Msa0687730 | MtrunA17_Chr4g0054561 | 35.433 | 127 | 61 | 4 | 1 | 109 | 197 | 320 | 4.16e-12 | 61.2 |
| Msa0687730 | MtrunA17_Chr2g0333541 | 45.946 | 74 | 37 | 1 | 41 | 111 | 192 | 265 | 5.70e-12 | 60.5 |
| Msa0687730 | MtrunA17_Chr7g0233441 | 38.961 | 77 | 43 | 1 | 40 | 112 | 118 | 194 | 1.11e-11 | 58.9 |
| Msa0687730 | MtrunA17_Chr4g0049331 | 31.655 | 139 | 68 | 4 | 1 | 117 | 177 | 310 | 1.66e-11 | 59.3 |
| Msa0687730 | MtrunA17_Chr2g0280161 | 30.370 | 135 | 76 | 2 | 1 | 117 | 219 | 353 | 2.60e-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 |
|---|
Find 22 sgRNAs with CRISPR-Local
Find 46 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| AAAAGCAATGTCTTATCTTT+TGG | 0.203496 | 4_4:-52709790 | Msa0687730:CDS |
| CATGTGGAAGCAAGGGTGTT+AGG | 0.291400 | 4_4:-52709907 | Msa0687730:CDS |
| ATCCCTTGCACTTCTGAGAT+TGG | 0.311626 | 4_4:+52709863 | None:intergenic |
| GAGAACATTGAAGGTGTTAT+TGG | 0.322532 | 4_4:-52709940 | Msa0687730:CDS |
| TAGGGAAAGATATGTTGATT+TGG | 0.374148 | 4_4:-52709888 | Msa0687730:CDS |
| GAAAGAACTTGGAGAGCCTT+TGG | 0.390032 | 4_4:-52710057 | Msa0687730:CDS |
| ACCCTTGCTTCCACATGAAA+TGG | 0.403044 | 4_4:+52709913 | None:intergenic |
| ATGTGGAAGCAAGGGTGTTA+GGG | 0.446382 | 4_4:-52709906 | Msa0687730:CDS |
| TCATTTGATGAGAACATTGA+AGG | 0.468182 | 4_4:-52709949 | Msa0687730:CDS |
| CACCATTTCATGTGGAAGCA+AGG | 0.482800 | 4_4:-52709915 | Msa0687730:CDS |
| ATCAAATACATGAAAGAACT+TGG | 0.484281 | 4_4:-52710068 | Msa0687730:exon |
| AATCCCTACCTGAGTAATGA+TGG | 0.502166 | 4_4:+52709759 | None:intergenic |
| TGTTCTTCTAAAACTTCCAA+AGG | 0.524143 | 4_4:+52710041 | None:intergenic |
| AGGCAACAACTTGAGCATAA+AGG | 0.528487 | 4_4:-52709445 | Msa0687730:CDS |
| CCAAACCTCTGCAGCAATGA+CGG | 0.528577 | 4_4:-52709979 | Msa0687730:intron |
| ACCATTTCATGTGGAAGCAA+GGG | 0.554925 | 4_4:-52709914 | Msa0687730:CDS |
| TATTGGTTCACCATTTCATG+TGG | 0.603150 | 4_4:-52709923 | Msa0687730:CDS |
| ACTTCAATGTTGTCATGCGT+AGG | 0.604852 | 4_4:+52709409 | None:intergenic |
| AGACATTACCATCATTACTC+AGG | 0.612640 | 4_4:-52709767 | Msa0687730:intron |
| GATCCAATCTCAGAAGTGCA+AGG | 0.613626 | 4_4:-52709866 | Msa0687730:CDS |
| ATCCAATCTCAGAAGTGCAA+GGG | 0.627063 | 4_4:-52709865 | Msa0687730:CDS |
| AATGTTCTCATCAAATGACG+AGG | 0.702664 | 4_4:+52709954 | None:intergenic |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | AATCTTTTTTTAGTTATTAT+TGG | - | chr4_4:52709797-52709816 | Msa0687730:CDS | 10.0% |
| !!! | TAAAATAAATATTTTGTTCT+AGG | - | chr4_4:52709864-52709883 | Msa0687730:CDS | 10.0% |
| !! | AAGATTGATATTAAATATAA+TGG | + | chr4_4:52709969-52709988 | None:intergenic | 10.0% |
| !!! | TTTTTTTTTGAAGTAGTTAT+TGG | - | chr4_4:52709824-52709843 | Msa0687730:CDS | 15.0% |
| !! | AATATATCAAGCAAAAATAA+TGG | + | chr4_4:52709897-52709916 | None:intergenic | 15.0% |
| !!! | ATTTTGTTGTCTTTTTATTT+TGG | - | chr4_4:52709918-52709937 | Msa0687730:CDS | 15.0% |
| !!! | AATCTTAATTATTTTAGAGT+TGG | - | chr4_4:52709983-52710002 | Msa0687730:intron | 15.0% |
| !!! | ATCTTAATTATTTTAGAGTT+GGG | - | chr4_4:52709984-52710003 | Msa0687730:intron | 15.0% |
| !!! | GGGATTTTTAGTTAAAATTA+TGG | - | chr4_4:52709610-52709629 | Msa0687730:intron | 20.0% |
| ! | ATCAAATACATGAAAGAACT+TGG | - | chr4_4:52709387-52709406 | Msa0687730:exon | 25.0% |
| !! | AAAAGCAATGTCTTATCTTT+TGG | - | chr4_4:52709665-52709684 | Msa0687730:intron | 25.0% |
| !! | TGTTCTTCTAAAACTTCCAA+AGG | + | chr4_4:52709417-52709436 | None:intergenic | 30.0% |
| TCATTTGATGAGAACATTGA+AGG | - | chr4_4:52709506-52709525 | Msa0687730:intron | 30.0% | |
| ! | TAGGGAAAGATATGTTGATT+TGG | - | chr4_4:52709567-52709586 | Msa0687730:intron | 30.0% |
| !!! | ATTATTTTAGAGTTGGGTGA+AGG | - | chr4_4:52709990-52710009 | Msa0687730:intron | 30.0% |
| ACAAAAATAGAGTCACGTAG+AGG | - | chr4_4:52709439-52709458 | Msa0687730:CDS | 35.0% | |
| AATGTTCTCATCAAATGACG+AGG | + | chr4_4:52709504-52709523 | None:intergenic | 35.0% | |
| !! | GAGAACATTGAAGGTGTTAT+TGG | - | chr4_4:52709515-52709534 | Msa0687730:intron | 35.0% |
| !! | TATTGGTTCACCATTTCATG+TGG | - | chr4_4:52709532-52709551 | Msa0687730:intron | 35.0% |
| AGACATTACCATCATTACTC+AGG | - | chr4_4:52709688-52709707 | Msa0687730:intron | 35.0% | |
| ATTACCATCATTACTCAGGT+AGG | - | chr4_4:52709692-52709711 | Msa0687730:intron | 35.0% | |
| TTACCATCATTACTCAGGTA+GGG | - | chr4_4:52709693-52709712 | Msa0687730:intron | 35.0% | |
| !!! | CAGGTAGGGATTTCTTTTTT+TGG | - | chr4_4:52709707-52709726 | Msa0687730:intron | 35.0% |
| !! | TTTTTGGTCAAGTAGACTAG+TGG | - | chr4_4:52709723-52709742 | Msa0687730:intron | 35.0% |
| ! | TTTTGGTCAAGTAGACTAGT+GGG | - | chr4_4:52709724-52709743 | Msa0687730:intron | 35.0% |
| ACCATTTCATGTGGAAGCAA+GGG | - | chr4_4:52709541-52709560 | Msa0687730:intron | 40.0% | |
| ! | ATCCAATCTCAGAAGTGCAA+GGG | - | chr4_4:52709590-52709609 | Msa0687730:intron | 40.0% |
| AATCCCTACCTGAGTAATGA+TGG | + | chr4_4:52709699-52709718 | None:intergenic | 40.0% | |
| TTTGGTCAAGTAGACTAGTG+GGG | - | chr4_4:52709725-52709744 | Msa0687730:intron | 40.0% | |
| AGGCAACAACTTGAGCATAA+AGG | - | chr4_4:52710010-52710029 | Msa0687730:intron | 40.0% | |
| ACTTCAATGTTGTCATGCGT+AGG | + | chr4_4:52710049-52710068 | None:intergenic | 40.0% | |
| GAAAGAACTTGGAGAGCCTT+TGG | - | chr4_4:52709398-52709417 | Msa0687730:CDS | 45.0% | |
| ! | ATTGCTGCAGAGGTTTGGTT+TGG | + | chr4_4:52709474-52709493 | None:intergenic | 45.0% |
| CACCATTTCATGTGGAAGCA+AGG | - | chr4_4:52709540-52709559 | Msa0687730:intron | 45.0% | |
| ACCCTTGCTTCCACATGAAA+TGG | + | chr4_4:52709545-52709564 | None:intergenic | 45.0% | |
| !! | ATGTGGAAGCAAGGGTGTTA+GGG | - | chr4_4:52709549-52709568 | Msa0687730:intron | 45.0% |
| ! | GATCCAATCTCAGAAGTGCA+AGG | - | chr4_4:52709589-52709608 | Msa0687730:intron | 45.0% |
| !! | ATCCCTTGCACTTCTGAGAT+TGG | + | chr4_4:52709595-52709614 | None:intergenic | 45.0% |
| CCAAACCTCTGCAGCAATGA+CGG | - | chr4_4:52709476-52709495 | Msa0687730:intron | 50.0% | |
| !! | CATGTGGAAGCAAGGGTGTT+AGG | - | chr4_4:52709548-52709567 | Msa0687730:intron | 50.0% |
| TCCGAGTTCGAACTCAGGTA+GGG | - | chr4_4:52709750-52709769 | Msa0687730:intron | 50.0% | |
| TCCCTACCTGAGTTCGAACT+CGG | + | chr4_4:52709754-52709773 | None:intergenic | 50.0% | |
| CCGTCATTGCTGCAGAGGTT+TGG | + | chr4_4:52709479-52709498 | None:intergenic | 55.0% | |
| AGGAACCGTCATTGCTGCAG+AGG | + | chr4_4:52709484-52709503 | None:intergenic | 55.0% | |
| GTCCGAGTTCGAACTCAGGT+AGG | - | chr4_4:52709749-52709768 | Msa0687730:intron | 55.0% | |
| GGGTGTCCGAGTTCGAACTC+AGG | - | chr4_4:52709745-52709764 | Msa0687730:intron | 60.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr4_4 | gene | 52709376 | 52710101 | 52709376 | ID=Msa0687730;Name=Msa0687730 |
| chr4_4 | mRNA | 52709376 | 52710101 | 52709376 | ID=Msa0687730-mRNA-1;Parent=Msa0687730;Name=Msa0687730-mRNA-1;_AED=0.26;_eAED=0.26;_QI=20|0|0|1|0|0|3|19|119 |
| chr4_4 | exon | 52709376 | 52709475 | 52709376 | ID=Msa0687730-mRNA-1:exon:13931;Parent=Msa0687730-mRNA-1 |
| chr4_4 | exon | 52709768 | 52709987 | 52709768 | ID=Msa0687730-mRNA-1:exon:13930;Parent=Msa0687730-mRNA-1 |
| chr4_4 | exon | 52710023 | 52710101 | 52710023 | ID=Msa0687730-mRNA-1:exon:13929;Parent=Msa0687730-mRNA-1 |
| chr4_4 | five_prime_UTR | 52710082 | 52710101 | 52710082 | ID=Msa0687730-mRNA-1:five_prime_utr;Parent=Msa0687730-mRNA-1 |
| chr4_4 | CDS | 52710023 | 52710081 | 52710023 | ID=Msa0687730-mRNA-1:cds;Parent=Msa0687730-mRNA-1 |
| chr4_4 | CDS | 52709768 | 52709987 | 52709768 | ID=Msa0687730-mRNA-1:cds;Parent=Msa0687730-mRNA-1 |
| chr4_4 | CDS | 52709395 | 52709475 | 52709395 | ID=Msa0687730-mRNA-1:cds;Parent=Msa0687730-mRNA-1 |
| chr4_4 | three_prime_UTR | 52709376 | 52709394 | 52709376 | ID=Msa0687730-mRNA-1:three_prime_utr;Parent=Msa0687730-mRNA-1 |
| Gene Sequence |
| Protein sequence |
