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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1314730 | XP_003627282.1 | 93.220 | 118 | 8 | 0 | 1 | 118 | 243 | 360 | 3.50e-70 | 224 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1314730 | sp|Q9SPV4|SAMT_CLABR | 53.659 | 123 | 52 | 1 | 1 | 118 | 236 | 358 | 4.48e-38 | 134 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1314730 | G7L6V4 | 93.220 | 118 | 8 | 0 | 1 | 118 | 243 | 360 | 1.67e-70 | 224 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0016670 | Msa1314730 | 0.820871 | 5.454101e-53 | -8.615850e-47 |
| Msa0017510 | Msa1314730 | 0.809295 | 2.030865e-50 | -8.615850e-47 |
| Msa0026130 | Msa1314730 | 0.810454 | 1.143477e-50 | -8.615850e-47 |
| Msa0110970 | Msa1314730 | 0.814643 | 1.387960e-51 | -8.615850e-47 |
| Msa0118570 | Msa1314730 | 0.805882 | 1.076907e-49 | -8.615850e-47 |
| Msa0669520 | Msa1314730 | 0.801450 | 8.952545e-49 | -8.615850e-47 |
| Msa0157290 | Msa1314730 | 0.810015 | 1.421697e-50 | -8.615850e-47 |
| Msa0166590 | Msa1314730 | 0.809488 | 1.846403e-50 | -8.615850e-47 |
| Msa0168500 | Msa1314730 | 0.800029 | 1.745414e-48 | -8.615850e-47 |
| Msa1234170 | Msa1314730 | 0.821986 | 3.015541e-53 | -8.615850e-47 |
| Msa1314730 | Msa1319000 | 0.815298 | 9.933797e-52 | -8.615850e-47 |
| Msa0395820 | Msa1314730 | 0.803181 | 3.939861e-49 | -8.615850e-47 |
| Msa0461720 | Msa1314730 | 0.806870 | 6.667698e-50 | -8.615850e-47 |
| Msa0469030 | Msa1314730 | 0.808736 | 2.675552e-50 | -8.615850e-47 |
| Msa0255090 | Msa1314730 | 0.805959 | 1.037594e-49 | -8.615850e-47 |
| Msa0259380 | Msa1314730 | 0.802492 | 5.469294e-49 | -8.615850e-47 |
| Msa0292400 | Msa1314730 | 0.838757 | 2.378150e-57 | -8.615850e-47 |
| Msa0300690 | Msa1314730 | 0.812250 | 4.658973e-51 | -8.615850e-47 |
| Msa0316810 | Msa1314730 | 0.800359 | 1.495951e-48 | -8.615850e-47 |
| Msa1124110 | Msa1314730 | 0.804770 | 1.841892e-49 | -8.615850e-47 |
| Msa0504480 | Msa1314730 | 0.801414 | 9.104515e-49 | -8.615850e-47 |
| Msa0861870 | Msa1314730 | 0.805127 | 1.551068e-49 | -8.615850e-47 |
| Msa0880140 | Msa1314730 | 0.809278 | 2.047609e-50 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1314730 | MtrunA17_Chr8g0343971 | 93.220 | 118 | 8 | 0 | 1 | 118 | 243 | 360 | 3.22e-74 | 224 |
| Msa1314730 | MtrunA17_Chr8g0343981 | 62.712 | 118 | 41 | 1 | 1 | 118 | 243 | 357 | 7.12e-46 | 151 |
| Msa1314730 | MtrunA17_Chr3g0107591 | 56.250 | 128 | 45 | 1 | 1 | 117 | 241 | 368 | 2.33e-44 | 147 |
| Msa1314730 | MtrunA17_Chr4g0008111 | 55.932 | 118 | 52 | 0 | 1 | 118 | 242 | 359 | 1.19e-43 | 145 |
| Msa1314730 | MtrunA17_Chr8g0372671 | 54.545 | 121 | 52 | 1 | 1 | 118 | 242 | 362 | 1.86e-42 | 142 |
| Msa1314730 | MtrunA17_Chr5g0404631 | 56.250 | 128 | 45 | 1 | 1 | 117 | 253 | 380 | 4.93e-42 | 142 |
| Msa1314730 | MtrunA17_Chr8g0372821 | 51.181 | 127 | 51 | 1 | 1 | 116 | 242 | 368 | 5.46e-38 | 131 |
| Msa1314730 | MtrunA17_Chr6g0475241 | 56.410 | 117 | 48 | 2 | 1 | 117 | 243 | 356 | 1.36e-36 | 127 |
| Msa1314730 | MtrunA17_Chr6g0475221 | 50.000 | 124 | 51 | 2 | 1 | 117 | 234 | 353 | 5.83e-34 | 120 |
| Msa1314730 | MtrunA17_Chr1g0155451 | 38.843 | 121 | 70 | 2 | 1 | 117 | 96 | 216 | 9.74e-25 | 93.6 |
| Msa1314730 | MtrunA17_Chr1g0155471 | 39.316 | 117 | 68 | 2 | 4 | 117 | 8 | 124 | 1.49e-24 | 90.5 |
| Msa1314730 | MtrunA17_Chr3g0107871 | 39.167 | 120 | 69 | 3 | 1 | 116 | 221 | 340 | 2.55e-18 | 78.6 |
| Msa1314730 | MtrunA17_Chr6g0455081 | 31.452 | 124 | 77 | 1 | 3 | 118 | 8 | 131 | 3.58e-18 | 74.3 |
| Msa1314730 | MtrunA17_Chr7g0252501 | 33.871 | 124 | 73 | 2 | 1 | 116 | 106 | 228 | 1.52e-17 | 75.1 |
| Msa1314730 | MtrunA17_Chr5g0419851 | 32.759 | 116 | 75 | 1 | 1 | 116 | 308 | 420 | 2.16e-17 | 76.3 |
| Msa1314730 | MtrunA17_Chr3g0144871 | 30.952 | 126 | 79 | 1 | 1 | 118 | 244 | 369 | 1.67e-15 | 70.9 |
| Msa1314730 | MtrunA17_Chr7g0252361 | 30.081 | 123 | 79 | 2 | 1 | 116 | 241 | 363 | 3.49e-13 | 64.3 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1314730 | AT4G36470.1 | 36.752 | 117 | 74 | 0 | 1 | 117 | 254 | 370 | 1.66e-22 | 90.5 |
| Msa1314730 | AT3G11480.1 | 35.043 | 117 | 76 | 0 | 1 | 117 | 263 | 379 | 6.54e-19 | 80.9 |
| Msa1314730 | AT5G04380.2 | 35.246 | 122 | 74 | 1 | 1 | 117 | 197 | 318 | 1.57e-18 | 79.3 |
| Msa1314730 | AT5G04380.3 | 35.246 | 122 | 74 | 1 | 1 | 117 | 268 | 389 | 2.57e-18 | 79.3 |
| Msa1314730 | AT5G66430.1 | 36.290 | 124 | 72 | 1 | 1 | 117 | 231 | 354 | 2.15e-17 | 76.3 |
| Msa1314730 | AT2G14060.1 | 36.800 | 125 | 68 | 4 | 4 | 117 | 248 | 372 | 7.50e-17 | 75.1 |
| Msa1314730 | AT5G04370.3 | 36.134 | 119 | 74 | 2 | 1 | 117 | 277 | 395 | 9.73e-17 | 74.7 |
| Msa1314730 | AT5G04370.1 | 36.134 | 119 | 74 | 2 | 1 | 117 | 272 | 390 | 1.02e-16 | 74.7 |
| Msa1314730 | AT5G04370.2 | 36.134 | 119 | 74 | 2 | 1 | 117 | 291 | 409 | 1.08e-16 | 74.7 |
| Msa1314730 | AT5G38020.2 | 35.606 | 132 | 70 | 4 | 1 | 117 | 198 | 329 | 2.63e-16 | 73.2 |
| Msa1314730 | AT5G38020.1 | 35.606 | 132 | 70 | 4 | 1 | 117 | 237 | 368 | 3.09e-16 | 73.2 |
| Msa1314730 | AT5G04380.1 | 36.607 | 112 | 66 | 1 | 11 | 117 | 267 | 378 | 7.75e-16 | 72.4 |
| Msa1314730 | AT3G21950.2 | 34.848 | 132 | 71 | 4 | 1 | 117 | 269 | 400 | 8.87e-15 | 69.3 |
| Msa1314730 | AT1G19640.1 | 32.812 | 128 | 74 | 2 | 1 | 116 | 260 | 387 | 1.19e-14 | 68.9 |
| Msa1314730 | AT3G21950.1 | 34.848 | 132 | 71 | 4 | 1 | 117 | 237 | 368 | 1.44e-14 | 68.6 |
| Msa1314730 | AT1G68040.1 | 33.333 | 117 | 74 | 2 | 4 | 117 | 248 | 363 | 2.07e-14 | 68.2 |
| Msa1314730 | AT1G15125.1 | 37.634 | 93 | 52 | 2 | 1 | 92 | 233 | 320 | 2.18e-12 | 62.4 |
Find 32 sgRNAs with CRISPR-Local
Find 42 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| CATTATATGTTGTTTATTAA+TGG | 0.128488 | 8_4:-13779529 | Msa1314730:three_prime_UTR |
| TCATGCAGTTCTTATTATAT+TGG | 0.263360 | 8_4:+13779420 | None:intergenic |
| GGCTACTGCTCTTAATGATA+TGG | 0.272144 | 8_4:-13780001 | Msa1314730:exon |
| GATGAAAGTGATTCTGAAAA+TGG | 0.278441 | 8_4:-13779742 | Msa1314730:CDS |
| GTATGCTACAGGGGATTATA+AGG | 0.298506 | 8_4:-13779900 | Msa1314730:intron |
| TGGAATATTGTTGCGACGAT+TGG | 0.341844 | 8_4:-13780032 | Msa1314730:five_prime_UTR |
| AAACAACTCCATGTGATTGA+TGG | 0.354713 | 8_4:+13779789 | None:intergenic |
| TCTTAATGATATGGTGTTGC+AGG | 0.360149 | 8_4:-13779992 | Msa1314730:intron |
| AACGGAATTCATTCTCTCCT+TGG | 0.389981 | 8_4:+13779600 | None:intergenic |
| GGAATATTGTTGCGACGATT+GGG | 0.395406 | 8_4:-13780031 | Msa1314730:five_prime_UTR |
| CAATGATATGGTAACATTAA+CGG | 0.422223 | 8_4:+13779582 | None:intergenic |
| ATTGAAAGTTGTTGTGGTAC+TGG | 0.422598 | 8_4:-13779498 | Msa1314730:three_prime_UTR |
| GAAAATGGATATGATGTTGC+AGG | 0.441689 | 8_4:-13779727 | Msa1314730:CDS |
| ACTTCCAACTCCACTTCATT+CGG | 0.444785 | 8_4:+13779832 | None:intergenic |
| CCTTTGCTAGTTAGTCACTT+TGG | 0.468922 | 8_4:-13779682 | Msa1314730:CDS |
| AACACAACAACGCAGACAAT+TGG | 0.469150 | 8_4:+13779377 | None:intergenic |
| AAATAAATTGAAAGTTGTTG+TGG | 0.493939 | 8_4:-13779504 | Msa1314730:three_prime_UTR |
| CAACAATATTCCACGTCACA+TGG | 0.526509 | 8_4:+13780042 | None:intergenic |
| TATGCTACAGGGGATTATAA+GGG | 0.539471 | 8_4:-13779899 | Msa1314730:intron |
| TGGTGAAGCTATCATTGAAG+AGG | 0.568437 | 8_4:-13779662 | Msa1314730:CDS |
| ATTGATTGATCAAATATCCA+AGG | 0.570539 | 8_4:-13779617 | Msa1314730:CDS |
| AACTCCACTTCATTCGGAGA+CGG | 0.584106 | 8_4:+13779838 | None:intergenic |
| CAATCAATAATTCCTTGTAA+CGG | 0.589742 | 8_4:+13779632 | None:intergenic |
| CCAAAGTGACTAACTAGCAA+AGG | 0.593693 | 8_4:+13779682 | None:intergenic |
| ATCGTTTGCCATCAATCACA+TGG | 0.595409 | 8_4:-13779797 | Msa1314730:CDS |
| GAGTTGGAAGTTCTCAATGA+AGG | 0.596864 | 8_4:-13779820 | Msa1314730:CDS |
| TTATCCGTCTCCGAATGAAG+TGG | 0.599970 | 8_4:-13779842 | Msa1314730:CDS |
| TGCAGGGTGCATTAGAGCTG+TGG | 0.607342 | 8_4:-13779710 | Msa1314730:CDS |
| TTCGGAGACGGATAATAGTG+AGG | 0.637717 | 8_4:+13779850 | None:intergenic |
| TCGGAGACGGATAATAGTGA+GGG | 0.639677 | 8_4:+13779851 | None:intergenic |
| AAATGAAGATCCATGTGACG+TGG | 0.640046 | 8_4:-13780052 | Msa1314730:five_prime_UTR |
| AAAATGGATATGATGTTGCA+GGG | 0.702180 | 8_4:-13779726 | Msa1314730:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | ATATAACTCATTTTTCATAT+AGG | + | chr8_4:13779463-13779482 | None:intergenic | 15.0% |
| !! | ATATGAAAAATGAGTTATAT+AGG | - | chr8_4:13779463-13779482 | Msa1314730:three_prime_UTR | 15.0% |
| !!! | CATTATATGTTGTTTATTAA+TGG | - | chr8_4:13779885-13779904 | Msa1314730:CDS | 15.0% |
| !! | AAATAAATTGAAAGTTGTTG+TGG | - | chr8_4:13779910-13779929 | Msa1314730:intron | 20.0% |
| ! | CAATCAATAATTCCTTGTAA+CGG | + | chr8_4:13779785-13779804 | None:intergenic | 25.0% |
| ! | ATTGATTGATCAAATATCCA+AGG | - | chr8_4:13779797-13779816 | Msa1314730:CDS | 25.0% |
| ! | CAATGATATGGTAACATTAA+CGG | + | chr8_4:13779835-13779854 | None:intergenic | 25.0% |
| !!! | TGATTTTCTAGTCAATGATA+TGG | + | chr8_4:13779847-13779866 | None:intergenic | 25.0% |
| ! | TCATGCAGTTCTTATTATAT+TGG | + | chr8_4:13779997-13780016 | None:intergenic | 25.0% |
| TCCTTAATATTGTATGCTAC+AGG | - | chr8_4:13779503-13779522 | Msa1314730:three_prime_UTR | 30.0% | |
| CCTTAATATTGTATGCTACA+GGG | - | chr8_4:13779504-13779523 | Msa1314730:three_prime_UTR | 30.0% | |
| CTTAATATTGTATGCTACAG+GGG | - | chr8_4:13779505-13779524 | Msa1314730:three_prime_UTR | 30.0% | |
| ! | GATGAAAGTGATTCTGAAAA+TGG | - | chr8_4:13779672-13779691 | Msa1314730:CDS | 30.0% |
| AAAATGGATATGATGTTGCA+GGG | - | chr8_4:13779688-13779707 | Msa1314730:CDS | 30.0% | |
| !! | TCTTAATGATATGGTGTTGC+AGG | - | chr8_4:13779422-13779441 | Msa1314730:three_prime_UTR | 35.0% |
| CCCTGTAGCATACAATATTA+AGG | + | chr8_4:13779507-13779526 | None:intergenic | 35.0% | |
| TATGCTACAGGGGATTATAA+GGG | - | chr8_4:13779515-13779534 | Msa1314730:three_prime_UTR | 35.0% | |
| AAACAACTCCATGTGATTGA+TGG | + | chr8_4:13779628-13779647 | None:intergenic | 35.0% | |
| GAAAATGGATATGATGTTGC+AGG | - | chr8_4:13779687-13779706 | Msa1314730:CDS | 35.0% | |
| ATTGAAAGTTGTTGTGGTAC+TGG | - | chr8_4:13779916-13779935 | Msa1314730:intron | 35.0% | |
| AAATGAAGATCCATGTGACG+TGG | - | chr8_4:13779362-13779381 | Msa1314730:three_prime_UTR | 40.0% | |
| CAACAATATTCCACGTCACA+TGG | + | chr8_4:13779375-13779394 | None:intergenic | 40.0% | |
| TGGAATATTGTTGCGACGAT+TGG | - | chr8_4:13779382-13779401 | Msa1314730:three_prime_UTR | 40.0% | |
| GGAATATTGTTGCGACGATT+GGG | - | chr8_4:13779383-13779402 | Msa1314730:three_prime_UTR | 40.0% | |
| !!! | TTGCGACGATTGGGATTTTT+TGG | - | chr8_4:13779392-13779411 | Msa1314730:three_prime_UTR | 40.0% |
| GGCTACTGCTCTTAATGATA+TGG | - | chr8_4:13779413-13779432 | Msa1314730:three_prime_UTR | 40.0% | |
| GTATGCTACAGGGGATTATA+AGG | - | chr8_4:13779514-13779533 | Msa1314730:three_prime_UTR | 40.0% | |
| ACTTCCAACTCCACTTCATT+CGG | + | chr8_4:13779585-13779604 | None:intergenic | 40.0% | |
| GAGTTGGAAGTTCTCAATGA+AGG | - | chr8_4:13779594-13779613 | Msa1314730:CDS | 40.0% | |
| ATCGTTTGCCATCAATCACA+TGG | - | chr8_4:13779617-13779636 | Msa1314730:CDS | 40.0% | |
| CCAAAGTGACTAACTAGCAA+AGG | + | chr8_4:13779735-13779754 | None:intergenic | 40.0% | |
| CCTTTGCTAGTTAGTCACTT+TGG | - | chr8_4:13779732-13779751 | Msa1314730:CDS | 40.0% | |
| TGGTGAAGCTATCATTGAAG+AGG | - | chr8_4:13779752-13779771 | Msa1314730:CDS | 40.0% | |
| !!! | AGAGGTTTTTAGCCGTTACA+AGG | - | chr8_4:13779770-13779789 | Msa1314730:CDS | 40.0% |
| AACGGAATTCATTCTCTCCT+TGG | + | chr8_4:13779817-13779836 | None:intergenic | 40.0% | |
| AACACAACAACGCAGACAAT+TGG | + | chr8_4:13780040-13780059 | None:intergenic | 40.0% | |
| TCGGAGACGGATAATAGTGA+GGG | + | chr8_4:13779566-13779585 | None:intergenic | 45.0% | |
| TTCGGAGACGGATAATAGTG+AGG | + | chr8_4:13779567-13779586 | None:intergenic | 45.0% | |
| TTATCCGTCTCCGAATGAAG+TGG | - | chr8_4:13779572-13779591 | Msa1314730:CDS | 45.0% | |
| AACTCCACTTCATTCGGAGA+CGG | + | chr8_4:13779579-13779598 | None:intergenic | 45.0% | |
| GTCTCCGAATGAAGTGGAGT+TGG | - | chr8_4:13779578-13779597 | Msa1314730:CDS | 50.0% | |
| TGCAGGGTGCATTAGAGCTG+TGG | - | chr8_4:13779704-13779723 | Msa1314730:CDS | 55.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr8_4 | gene | 13779354 | 13780082 | 13779354 | ID=Msa1314730;Name=Msa1314730 |
| chr8_4 | mRNA | 13779354 | 13780082 | 13779354 | ID=Msa1314730-mRNA-1;Parent=Msa1314730;Name=Msa1314730-mRNA-1;_AED=0.00;_eAED=0.00;_QI=78|1|1|1|1|1|2|213|118 |
| chr8_4 | exon | 13779354 | 13779911 | 13779354 | ID=Msa1314730-mRNA-1:exon:5199;Parent=Msa1314730-mRNA-1 |
| chr8_4 | exon | 13779993 | 13780082 | 13779993 | ID=Msa1314730-mRNA-1:exon:5198;Parent=Msa1314730-mRNA-1 |
| chr8_4 | five_prime_UTR | 13780005 | 13780082 | 13780005 | ID=Msa1314730-mRNA-1:five_prime_utr;Parent=Msa1314730-mRNA-1 |
| chr8_4 | CDS | 13779993 | 13780004 | 13779993 | ID=Msa1314730-mRNA-1:cds;Parent=Msa1314730-mRNA-1 |
| chr8_4 | CDS | 13779567 | 13779911 | 13779567 | ID=Msa1314730-mRNA-1:cds;Parent=Msa1314730-mRNA-1 |
| chr8_4 | three_prime_UTR | 13779354 | 13779566 | 13779354 | ID=Msa1314730-mRNA-1:three_prime_utr;Parent=Msa1314730-mRNA-1 |
| Gene Sequence |
| Protein sequence |
