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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0396850 | XP_024629238.1 | 66.667 | 108 | 27 | 3 | 3 | 101 | 39 | 146 | 1.18e-37 | 134 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0396850 | sp|Q8RYD1|REM16_ARATH | 42.169 | 83 | 46 | 2 | 4 | 84 | 39 | 121 | 4.23e-13 | 66.6 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0396850 | B7FNG4 | 64.486 | 107 | 29 | 2 | 4 | 101 | 46 | 152 | 2.48e-35 | 129 |
| Gene ID | Type | Classification |
|---|---|---|
| Msa0396850 | TF | B3 |
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0396850 | MtrunA17_Chr1g0154191 | 65.741 | 108 | 28 | 2 | 3 | 101 | 37 | 144 | 3.52e-38 | 131 |
| Msa0396850 | MtrunA17_Chr1g0154131 | 64.815 | 108 | 29 | 2 | 3 | 101 | 40 | 147 | 4.26e-38 | 132 |
| Msa0396850 | MtrunA17_Chr1g0154131 | 64.815 | 108 | 29 | 3 | 3 | 101 | 197 | 304 | 8.02e-38 | 132 |
| Msa0396850 | MtrunA17_Chr1g0154211 | 62.963 | 108 | 31 | 2 | 3 | 101 | 37 | 144 | 6.70e-38 | 130 |
| Msa0396850 | MtrunA17_Chr1g0154171 | 63.889 | 108 | 30 | 2 | 3 | 101 | 37 | 144 | 6.30e-37 | 127 |
| Msa0396850 | MtrunA17_Chr1g0154241 | 63.810 | 105 | 29 | 3 | 3 | 98 | 36 | 140 | 5.80e-36 | 123 |
| Msa0396850 | MtrunA17_Chr1g0154111 | 62.037 | 108 | 32 | 3 | 3 | 101 | 41 | 148 | 2.81e-35 | 126 |
| Msa0396850 | MtrunA17_Chr1g0154111 | 84.507 | 71 | 10 | 1 | 3 | 72 | 368 | 438 | 4.14e-34 | 122 |
| Msa0396850 | MtrunA17_Chr1g0154161 | 72.619 | 84 | 22 | 1 | 3 | 85 | 45 | 128 | 1.13e-34 | 120 |
| Msa0396850 | MtrunA17_Chr1g0154101 | 72.619 | 84 | 22 | 1 | 3 | 85 | 40 | 123 | 4.54e-34 | 123 |
| Msa0396850 | MtrunA17_Chr1g0154101 | 62.037 | 108 | 32 | 3 | 3 | 101 | 197 | 304 | 5.46e-34 | 123 |
| Msa0396850 | MtrunA17_Chr1g0154071 | 70.238 | 84 | 24 | 1 | 3 | 85 | 42 | 125 | 2.25e-31 | 114 |
| Msa0396850 | MtrunA17_Chr1g0154071 | 55.963 | 109 | 37 | 3 | 3 | 101 | 170 | 277 | 5.26e-29 | 108 |
| Msa0396850 | MtrunA17_Chr1g0154151 | 65.060 | 83 | 28 | 1 | 3 | 84 | 19 | 101 | 3.44e-31 | 112 |
| Msa0396850 | MtrunA17_Chr1g0154251 | 53.043 | 115 | 38 | 3 | 3 | 101 | 41 | 155 | 3.39e-29 | 108 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0396850 | AT4G33280.1 | 42.169 | 83 | 46 | 2 | 4 | 84 | 39 | 121 | 4.30e-14 | 66.6 |
| Msa0396850 | AT4G33280.2 | 42.169 | 83 | 46 | 2 | 4 | 84 | 39 | 121 | 4.38e-14 | 66.2 |
| Msa0396850 | AT4G33280.3 | 42.169 | 83 | 46 | 2 | 4 | 84 | 39 | 121 | 5.49e-14 | 66.2 |
| Msa0396850 | AT4G34400.2 | 29.762 | 84 | 58 | 1 | 3 | 85 | 30 | 113 | 6.12e-11 | 57.8 |
| Msa0396850 | AT4G34400.1 | 29.762 | 84 | 58 | 1 | 3 | 85 | 30 | 113 | 6.12e-11 | 57.8 |
Find 17 sgRNAs with CRISPR-Local
Find 28 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| CAATGGTGAATCACTCTTTA+AGG | 0.159419 | 3_2:+15710338 | Msa0396850:CDS |
| CCAGAAAATGTGAACATTAA+AGG | 0.276269 | 3_2:+15710189 | Msa0396850:CDS |
| AGTGGAGTTGTGTGGGATAT+AGG | 0.336475 | 3_2:+15710216 | Msa0396850:CDS |
| GAATCGTTGCCAGCCATTCA+TGG | 0.382363 | 3_2:-15710268 | None:intergenic |
| GTGGAGTTGTGTGGGATATA+GGG | 0.433125 | 3_2:+15710217 | Msa0396850:CDS |
| CTGTTTACTCCATGAATGGC+TGG | 0.479854 | 3_2:+15710259 | Msa0396850:CDS |
| TTCCTTGTCTTTAAGTACAA+TGG | 0.496096 | 3_2:+15710321 | Msa0396850:CDS |
| GATACTGTTTACTCCATGAA+TGG | 0.535022 | 3_2:+15710255 | Msa0396850:CDS |
| CACCATTGTACTTAAAGACA+AGG | 0.554483 | 3_2:-15710323 | None:intergenic |
| ATATCCCACACAACTCCACT+AGG | 0.558401 | 3_2:-15710213 | None:intergenic |
| AAGGTCCTAGTGGAGTTGTG+TGG | 0.588466 | 3_2:+15710208 | Msa0396850:CDS |
| AGGTCCTAGTGGAGTTGTGT+GGG | 0.591978 | 3_2:+15710209 | Msa0396850:CDS |
| GTGAACATTAAAGGTCCTAG+TGG | 0.611800 | 3_2:+15710198 | Msa0396850:CDS |
| TGGGAATGCTCAAAAGAACA+AGG | 0.623231 | 3_2:+15710422 | Msa0396850:CDS |
| GGAATGCTCAAAAGAACAAG+GGG | 0.657421 | 3_2:+15710424 | Msa0396850:CDS |
| GGGAATGCTCAAAAGAACAA+GGG | 0.680489 | 3_2:+15710423 | Msa0396850:CDS |
| GAATGCTCAAAAGAACAAGG+GGG | 0.812726 | 3_2:+15710425 | Msa0396850:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | AAAATATAAATTTCCTTCTG+AGG | - | chr3_2:15710120-15710139 | None:intergenic | 20.0% |
| !!! | AAATTGTCTGAAAATGTTTT+AGG | - | chr3_2:15710159-15710178 | None:intergenic | 20.0% |
| !!! | TTTAAGGTTTTAATCTTTGA+TGG | + | chr3_2:15710354-15710373 | Msa0396850:intron | 20.0% |
| !!! | TCTTATTTTGTTGGAAAATG+TGG | + | chr3_2:15710402-15710421 | Msa0396850:CDS | 25.0% |
| !!! | CTTATTTTGTTGGAAAATGT+GGG | + | chr3_2:15710403-15710422 | Msa0396850:CDS | 25.0% |
| ! | ATGTATCTTTTAACCTCAGA+AGG | + | chr3_2:15710104-15710123 | Msa0396850:intron | 30.0% |
| ! | CCTTTAATGTTCACATTTTC+TGG | - | chr3_2:15710192-15710211 | None:intergenic | 30.0% |
| CCAGAAAATGTGAACATTAA+AGG | + | chr3_2:15710189-15710208 | Msa0396850:CDS | 30.0% | |
| TTCCTTGTCTTTAAGTACAA+TGG | + | chr3_2:15710321-15710340 | Msa0396850:CDS | 30.0% | |
| !!! | AAAGCAGCTTCTTATTTTGT+TGG | + | chr3_2:15710393-15710412 | Msa0396850:CDS | 30.0% |
| GATACTGTTTACTCCATGAA+TGG | + | chr3_2:15710255-15710274 | Msa0396850:CDS | 35.0% | |
| CACCATTGTACTTAAAGACA+AGG | - | chr3_2:15710326-15710345 | None:intergenic | 35.0% | |
| CAATGGTGAATCACTCTTTA+AGG | + | chr3_2:15710338-15710357 | Msa0396850:CDS | 35.0% | |
| AAAAGAACAAGGGGGTAAAA+AGG | + | chr3_2:15710433-15710452 | Msa0396850:CDS | 35.0% | |
| CTGAAGAGCAAAAGAGATGT+TGG | - | chr3_2:15710080-15710099 | None:intergenic | 40.0% | |
| GTGAACATTAAAGGTCCTAG+TGG | + | chr3_2:15710198-15710217 | Msa0396850:CDS | 40.0% | |
| TGGGAATGCTCAAAAGAACA+AGG | + | chr3_2:15710422-15710441 | Msa0396850:CDS | 40.0% | |
| GGGAATGCTCAAAAGAACAA+GGG | + | chr3_2:15710423-15710442 | Msa0396850:CDS | 40.0% | |
| GGAATGCTCAAAAGAACAAG+GGG | + | chr3_2:15710424-15710443 | Msa0396850:CDS | 40.0% | |
| GAATGCTCAAAAGAACAAGG+GGG | + | chr3_2:15710425-15710444 | Msa0396850:CDS | 40.0% | |
| ATATCCCACACAACTCCACT+AGG | - | chr3_2:15710216-15710235 | None:intergenic | 45.0% | |
| AGTGGAGTTGTGTGGGATAT+AGG | + | chr3_2:15710216-15710235 | Msa0396850:CDS | 45.0% | |
| GTGGAGTTGTGTGGGATATA+GGG | + | chr3_2:15710217-15710236 | Msa0396850:CDS | 45.0% | |
| CTGTTTACTCCATGAATGGC+TGG | + | chr3_2:15710259-15710278 | Msa0396850:CDS | 45.0% | |
| ACAAGGGGGTAAAAAGGCAA+AGG | + | chr3_2:15710439-15710458 | Msa0396850:CDS | 45.0% | |
| AAGGTCCTAGTGGAGTTGTG+TGG | + | chr3_2:15710208-15710227 | Msa0396850:CDS | 50.0% | |
| AGGTCCTAGTGGAGTTGTGT+GGG | + | chr3_2:15710209-15710228 | Msa0396850:CDS | 50.0% | |
| GAATCGTTGCCAGCCATTCA+TGG | - | chr3_2:15710271-15710290 | None:intergenic | 50.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3_2 | gene | 15710061 | 15710472 | 15710061 | ID=Msa0396850;Name=Msa0396850 |
| chr3_2 | mRNA | 15710061 | 15710472 | 15710061 | ID=Msa0396850-mRNA-1;Parent=Msa0396850;Name=Msa0396850-mRNA-1;_AED=0.28;_eAED=0.50;_QI=0|0|0|0.66|0|0|3|0|101 |
| chr3_2 | exon | 15710061 | 15710066 | 15710061 | ID=Msa0396850-mRNA-1:exon:3553;Parent=Msa0396850-mRNA-1 |
| chr3_2 | exon | 15710150 | 15710359 | 15710150 | ID=Msa0396850-mRNA-1:exon:3554;Parent=Msa0396850-mRNA-1 |
| chr3_2 | exon | 15710383 | 15710472 | 15710383 | ID=Msa0396850-mRNA-1:exon:3555;Parent=Msa0396850-mRNA-1 |
| chr3_2 | CDS | 15710061 | 15710066 | 15710061 | ID=Msa0396850-mRNA-1:cds;Parent=Msa0396850-mRNA-1 |
| chr3_2 | CDS | 15710150 | 15710359 | 15710150 | ID=Msa0396850-mRNA-1:cds;Parent=Msa0396850-mRNA-1 |
| chr3_2 | CDS | 15710383 | 15710472 | 15710383 | ID=Msa0396850-mRNA-1:cds;Parent=Msa0396850-mRNA-1 |
| Gene Sequence |
| Protein sequence |
