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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0039200 | XP_002510790.1 | 89.474 | 76 | 8 | 0 | 1 | 76 | 1 | 76 | 1.07e-34 | 125 |
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0000220 | Msa0039200 | 0.871325 | 7.448788e-67 | -8.615850e-47 |
| Msa0001460 | Msa0039200 | 0.803413 | 3.528563e-49 | -8.615850e-47 |
| Msa0003470 | Msa0039200 | 0.820265 | 7.515846e-53 | -8.615850e-47 |
| Msa0005160 | Msa0039200 | 0.838220 | 3.272524e-57 | -8.615850e-47 |
| Msa0005690 | Msa0039200 | 0.809481 | 1.852623e-50 | -8.615850e-47 |
| Msa0006700 | Msa0039200 | 0.851363 | 9.316136e-61 | -8.615850e-47 |
| Msa0006820 | Msa0039200 | 0.831031 | 2.101608e-55 | -8.615850e-47 |
| Msa0007160 | Msa0039200 | 0.838724 | 2.426256e-57 | -8.615850e-47 |
| Msa0007230 | Msa0039200 | 0.838152 | 3.407906e-57 | -8.615850e-47 |
| Msa0008330 | Msa0039200 | 0.839982 | 1.143961e-57 | -8.615850e-47 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0039200 | MtrunA17_Chr1g0203261 | 100.000 | 73 | 0 | 0 | 1 | 73 | 1 | 73 | 6.74e-34 | 112 |
| Msa0039200 | MtrunA17_Chr6g0471211 | 87.671 | 73 | 9 | 0 | 4 | 76 | 3 | 75 | 4.46e-26 | 93.2 |
| Msa0039200 | MtrunA17_Chr8g0387471 | 52.113 | 71 | 33 | 1 | 5 | 75 | 3 | 72 | 8.43e-18 | 72.8 |
| Msa0039200 | MtrunA17_Chr6g0469651 | 50.704 | 71 | 34 | 1 | 3 | 73 | 1 | 70 | 3.09e-17 | 71.2 |
| Msa0039200 | MtrunA17_Chr6g0469541 | 45.333 | 75 | 40 | 1 | 5 | 79 | 3 | 76 | 1.33e-15 | 66.6 |
| Msa0039200 | MtrunA17_Chr6g0469671 | 47.297 | 74 | 38 | 1 | 3 | 76 | 1 | 73 | 6.02e-15 | 65.1 |
| Msa0039200 | MtrunA17_Chr7g0233181 | 44.000 | 75 | 41 | 1 | 5 | 79 | 3 | 76 | 2.86e-14 | 63.2 |
| Msa0039200 | MtrunA17_Chr1g0202561 | 47.945 | 73 | 37 | 1 | 3 | 75 | 1 | 72 | 3.69e-14 | 63.5 |
| Msa0039200 | MtrunA17_Chr6g0469571 | 47.826 | 69 | 35 | 1 | 5 | 73 | 3 | 70 | 4.81e-14 | 63.2 |
| Msa0039200 | MtrunA17_Chr1g0202541 | 47.945 | 73 | 37 | 1 | 3 | 75 | 1 | 72 | 5.21e-14 | 63.2 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0039200 | AT5G23760.1 | 86.301 | 73 | 10 | 0 | 4 | 76 | 3 | 75 | 3.57e-24 | 88.6 |
| Msa0039200 | AT5G23760.2 | 84.375 | 64 | 10 | 0 | 13 | 76 | 1 | 64 | 2.97e-18 | 73.2 |
| Msa0039200 | AT5G52740.1 | 47.887 | 71 | 34 | 2 | 3 | 73 | 1 | 68 | 4.50e-11 | 55.5 |
| Msa0039200 | AT1G01490.1 | 44.118 | 102 | 43 | 3 | 3 | 91 | 1 | 101 | 6.59e-11 | 56.2 |
| Msa0039200 | AT1G01490.2 | 44.118 | 102 | 43 | 3 | 3 | 91 | 1 | 101 | 6.59e-11 | 56.2 |
| Msa0039200 | AT1G01490.4 | 45.000 | 100 | 41 | 3 | 5 | 91 | 30 | 128 | 6.98e-11 | 56.6 |
Find 25 sgRNAs with CRISPR-Local
Find 126 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| AACAAGGAAGATGAGAATGA+AGG | 0.549514 | 1_1:-68756585 | None:intergenic |
| AAGGTAGATATAATATCAGT+TGG | 0.509973 | 1_1:+68757301 | Msa0039200:CDS |
| AATGAAGGCTTGAGAAGTTG+TGG | 0.614445 | 1_1:-68756570 | None:intergenic |
| AATGGAACCAAAGTACATAA+AGG | 0.376879 | 1_1:+68757641 | Msa0039200:three_prime_UTR |
| ACAATATAAGGTAAGGCGTG+CGG | 0.680766 | 1_1:-68756539 | None:intergenic |
| ACTGGATCCATAGCAAAAGG+TGG | 0.684112 | 1_1:+68756989 | Msa0039200:intron |
| AGTGATAATATCTATGACTT+CGG | 0.540904 | 1_1:+68757537 | Msa0039200:three_prime_UTR |
| ATACCTGAGCCATTGTCACA+GGG | 0.655527 | 1_1:-68756622 | None:intergenic |
| ATAGAAAATGAATCTTAGTA+GGG | 0.499112 | 1_1:-68757613 | None:intergenic |
| ATAGCAAAAGGTGGTGTTAA+AGG | 0.319190 | 1_1:+68756998 | Msa0039200:intron |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| AAAATGAATATATGCGCACA+TGG | - | chr1_1:68756707-68756726 | None:intergenic | 30.0% | |
| ATCTATCTCTTGAGGTTATA+AGG | + | chr1_1:68756843-68756862 | Msa0039200:intron | 30.0% | |
| ACATAAGAGGATAGAAAAAG+TGG | - | chr1_1:68756947-68756966 | None:intergenic | 30.0% | |
| CATATTGAGACAAACATAAG+AGG | - | chr1_1:68756960-68756979 | None:intergenic | 30.0% | |
| ATTCCATTAATGTGTTTCCA+GGG | - | chr1_1:68757145-68757164 | None:intergenic | 30.0% | |
| TATTCCATTAATGTGTTTCC+AGG | - | chr1_1:68757146-68757165 | None:intergenic | 30.0% | |
| AAATTCATCTGTGTAACTGT+TGG | + | chr1_1:68757166-68757185 | Msa0039200:intron | 30.0% | |
| GAACAGAAGTTAACAGTTAT+TGG | + | chr1_1:68757232-68757251 | Msa0039200:CDS | 30.0% | |
| AAAGAAGGAAGAGAAAAAAG+AGG | + | chr1_1:68757375-68757394 | Msa0039200:CDS | 30.0% | |
| ATGTCACAAAAATGGGTAAA+AGG | + | chr1_1:68757574-68757593 | Msa0039200:three_prime_UTR | 30.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr1_1 | gene | 68756494 | 68757664 | 68756494 | ID=Msa0039200;Name=Msa0039200 |
| chr1_1 | mRNA | 68756494 | 68757664 | 68756494 | ID=Msa0039200-mRNA-1;Parent=Msa0039200;Name=Msa0039200-mRNA-1;_AED=0.18;_eAED=0.18;_QI=138|1|1|1|1|1|3|244|102 |
| chr1_1 | exon | 68756494 | 68756640 | 68756494 | ID=Msa0039200-mRNA-1:exon:22485;Parent=Msa0039200-mRNA-1 |
| chr1_1 | exon | 68757002 | 68757083 | 68757002 | ID=Msa0039200-mRNA-1:exon:22486;Parent=Msa0039200-mRNA-1 |
| chr1_1 | exon | 68757203 | 68757664 | 68757203 | ID=Msa0039200-mRNA-1:exon:22487;Parent=Msa0039200-mRNA-1 |
| chr1_1 | five_prime_UTR | 68756494 | 68756631 | 68756494 | ID=Msa0039200-mRNA-1:five_prime_utr;Parent=Msa0039200-mRNA-1 |
| chr1_1 | CDS | 68756632 | 68756640 | 68756632 | ID=Msa0039200-mRNA-1:cds;Parent=Msa0039200-mRNA-1 |
| chr1_1 | CDS | 68757002 | 68757083 | 68757002 | ID=Msa0039200-mRNA-1:cds;Parent=Msa0039200-mRNA-1 |
| chr1_1 | CDS | 68757203 | 68757420 | 68757203 | ID=Msa0039200-mRNA-1:cds;Parent=Msa0039200-mRNA-1 |
| chr1_1 | three_prime_UTR | 68757421 | 68757664 | 68757421 | ID=Msa0039200-mRNA-1:three_prime_utr;Parent=Msa0039200-mRNA-1 |
| Gene Sequence |
>Msa0039200 ATGGCTCAGCAAAAGGTGGTGTTAAAGGTTCTCACTATGACAGATGACAAAACAAAGAAGAAAGCAATAGAAGCAGTTGCTGATATCTATGGAGTTGATTCAATCGCTACAGATGTGAACGAACAGAAGTTAACAGTTATTGGCGAAATGGATACAGTTGCAGTAGTGAAGAAGCTGAAGAAAGTAGGGAAGGTAGATATAATATCAGTTGGACCTGCCAAAGAAGAGAAAAAAGAAGAAAAGAAAGACGAAAGTAAAGACGAAAAGAAGGAAGAGAAAAAAGAGGAGAAACAAGAGGAGAAAAAATAA |
| Protein sequence |
>Msa0039200 MAQQKVVLKVLTMTDDKTKKKAIEAVADIYGVDSIATDVNEQKLTVIGEMDTVAVVKKLKKVGKVDIISVGPAKEEKKEEKKDESKDEKKEEKKEEKQEEKK* |
