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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0002060 | XP_003590003.1 | 81.043 | 422 | 14 | 5 | 1 | 361 | 1 | 417 | 0.0 | 663 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0002060 | sp|P0A9T5|TAS_SHIFL | 40.000 | 360 | 144 | 8 | 57 | 359 | 1 | 345 | 2.22e-78 | 247 |
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0000220 | Msa0002060 | 0.840633 | 7.729297e-58 | -8.615850e-47 |
| Msa0001510 | Msa0002060 | 0.851030 | 1.156755e-60 | -8.615850e-47 |
| Msa0001540 | Msa0002060 | 0.861238 | 1.180182e-63 | -8.615850e-47 |
| Msa0002060 | Msa0002690 | 0.812167 | 4.857786e-51 | -8.615850e-47 |
| Msa0002060 | Msa0002700 | 0.804745 | 1.863825e-49 | -8.615850e-47 |
| Msa0002060 | Msa0003470 | 0.801935 | 7.119924e-49 | -8.615850e-47 |
| Msa0002060 | Msa0004180 | 0.809030 | 2.314394e-50 | -8.615850e-47 |
| Msa0002060 | Msa0006580 | 0.800083 | 1.702145e-48 | -8.615850e-47 |
| Msa0002060 | Msa0007570 | 0.806228 | 9.110270e-50 | -8.615850e-47 |
| Msa0002060 | Msa0009210 | 0.853814 | 1.862934e-61 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0002060 | MtrunA17_Chr1g0167421 | 81.043 | 422 | 14 | 5 | 1 | 361 | 1 | 417 | 0.0 | 663 |
| Msa0002060 | MtrunA17_Chr8g0380261 | 49.065 | 214 | 99 | 5 | 66 | 276 | 48 | 254 | 1.60e-63 | 207 |
| Msa0002060 | MtrunA17_Chr4g0005881 | 83.929 | 56 | 6 | 1 | 180 | 235 | 21 | 73 | 3.05e-28 | 105 |
| Msa0002060 | MtrunA17_Chr7g0274071 | 26.689 | 296 | 157 | 12 | 62 | 354 | 18 | 256 | 1.65e-14 | 73.9 |
| Msa0002060 | MtrunA17_Chr7g0274061 | 28.514 | 249 | 134 | 11 | 62 | 306 | 16 | 224 | 4.42e-13 | 69.7 |
| Msa0002060 | MtrunA17_Chr7g0274041 | 27.189 | 217 | 118 | 7 | 61 | 275 | 11 | 189 | 1.54e-12 | 67.8 |
| Msa0002060 | MtrunA17_Chr1g0204651 | 26.007 | 273 | 144 | 13 | 61 | 326 | 9 | 230 | 3.02e-12 | 67.0 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0002060 | AT1G04420.1 | 64.267 | 389 | 74 | 7 | 33 | 361 | 29 | 412 | 3.38e-169 | 478 |
| Msa0002060 | AT1G10810.2 | 26.923 | 260 | 143 | 11 | 61 | 317 | 11 | 226 | 1.31e-11 | 64.7 |
| Msa0002060 | AT1G60690.1 | 28.111 | 217 | 115 | 9 | 61 | 275 | 11 | 188 | 4.23e-11 | 63.9 |
Find 80 sgRNAs with CRISPR-Local
Find 275 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| AACAACGTGTTTGTATTGTG+TGG | 0.687492 | 1_1:+3929625 | Msa0002060:five_prime_UTR |
| AACAATGCAACGTAGCGATC+TGG | 0.476923 | 1_1:-3931985 | None:intergenic |
| AACTATTAAGTATCTTGAGT+TGG | 0.528848 | 1_1:+3933824 | Msa0002060:CDS |
| AATATCAGTGAAATCACTCT+TGG | 0.502115 | 1_1:+3929876 | Msa0002060:CDS |
| AATCCAAGCGCGAGCTGAAC+AGG | 0.376331 | 1_1:-3933867 | None:intergenic |
| AATGTTTCAGATGACCTTTG+GGG | 0.691458 | 1_1:+3930924 | Msa0002060:intron |
| AATTATCGGTGCAACATCTG+TGG | 0.606607 | 1_1:+3933920 | Msa0002060:CDS |
| ACTCCTGTTCAGCTCGCGCT+TGG | 0.430695 | 1_1:+3933864 | Msa0002060:CDS |
| AGAAAAGTCTTAAGCGTCTC+GGG | 0.484155 | 1_1:+3931692 | Msa0002060:CDS |
| AGAAATGGCAACAACGTCGG+AGG | 0.648860 | 1_1:-3929697 | None:intergenic |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| AATATCAGTGAAATCACTCT+TGG | + | chr1_1:3929876-3929895 | Msa0002060:CDS | 30.0% | |
| TTAGACAAGTTAGACTCAAT+AGG | - | chr1_1:3929997-3930016 | None:intergenic | 30.0% | |
| CTTTACTTTCAACTCACTTT+CGG | - | chr1_1:3930088-3930107 | None:intergenic | 30.0% | |
| CCTGAACATAAGTTTATAAG+TGG | - | chr1_1:3930575-3930594 | None:intergenic | 30.0% | |
| CCACTTATAAACTTATGTTC+AGG | + | chr1_1:3930572-3930591 | Msa0002060:intron | 30.0% | |
| AATCAAGATTGTTAAAGTCC+CGG | - | chr1_1:3930613-3930632 | None:intergenic | 30.0% | |
| GTATTAGTTATTCAGGAGTT+TGG | + | chr1_1:3931424-3931443 | Msa0002060:intron | 30.0% | |
| TTATAATCTATGCACAAAGG+GGG | - | chr1_1:3931573-3931592 | None:intergenic | 30.0% | |
| GACAAATATCAAAGAAAGTG+TGG | + | chr1_1:3931669-3931688 | Msa0002060:CDS | 30.0% | |
| TTTGTTGCAAATTCATTGGT+GGG | + | chr1_1:3931729-3931748 | Msa0002060:intron | 30.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr1_1 | gene | 3929521 | 3934339 | 3929521 | ID=Msa0002060;Name=Msa0002060 |
| chr1_1 | mRNA | 3929521 | 3934339 | 3929521 | ID=Msa0002060-mRNA-1;Parent=Msa0002060;Name=Msa0002060-mRNA-1;_AED=0.17;_eAED=0.17;_QI=154|0.44|0.7|0.8|1|1|10|281|361 |
| chr1_1 | exon | 3929521 | 3929902 | 3929521 | ID=Msa0002060-mRNA-1:exon:1162;Parent=Msa0002060-mRNA-1 |
| chr1_1 | exon | 3930770 | 3930775 | 3930770 | ID=Msa0002060-mRNA-1:exon:1163;Parent=Msa0002060-mRNA-1 |
| chr1_1 | exon | 3930934 | 3931029 | 3930934 | ID=Msa0002060-mRNA-1:exon:1164;Parent=Msa0002060-mRNA-1 |
| chr1_1 | exon | 3931340 | 3931423 | 3931340 | ID=Msa0002060-mRNA-1:exon:1165;Parent=Msa0002060-mRNA-1 |
| chr1_1 | exon | 3931586 | 3931746 | 3931586 | ID=Msa0002060-mRNA-1:exon:1166;Parent=Msa0002060-mRNA-1 |
| chr1_1 | exon | 3931885 | 3931893 | 3931885 | ID=Msa0002060-mRNA-1:exon:1167;Parent=Msa0002060-mRNA-1 |
| chr1_1 | exon | 3931984 | 3932101 | 3931984 | ID=Msa0002060-mRNA-1:exon:1168;Parent=Msa0002060-mRNA-1 |
| chr1_1 | exon | 3932473 | 3932608 | 3932473 | ID=Msa0002060-mRNA-1:exon:1169;Parent=Msa0002060-mRNA-1 |
| chr1_1 | exon | 3933379 | 3933386 | 3933379 | ID=Msa0002060-mRNA-1:exon:1170;Parent=Msa0002060-mRNA-1 |
| chr1_1 | exon | 3933819 | 3934339 | 3933819 | ID=Msa0002060-mRNA-1:exon:1171;Parent=Msa0002060-mRNA-1 |
| chr1_1 | five_prime_UTR | 3929521 | 3929674 | 3929521 | ID=Msa0002060-mRNA-1:five_prime_utr;Parent=Msa0002060-mRNA-1 |
| chr1_1 | CDS | 3929675 | 3929902 | 3929675 | ID=Msa0002060-mRNA-1:cds;Parent=Msa0002060-mRNA-1 |
| chr1_1 | CDS | 3930770 | 3930775 | 3930770 | ID=Msa0002060-mRNA-1:cds;Parent=Msa0002060-mRNA-1 |
| chr1_1 | CDS | 3930934 | 3931029 | 3930934 | ID=Msa0002060-mRNA-1:cds;Parent=Msa0002060-mRNA-1 |
| chr1_1 | CDS | 3931340 | 3931423 | 3931340 | ID=Msa0002060-mRNA-1:cds;Parent=Msa0002060-mRNA-1 |
| chr1_1 | CDS | 3931586 | 3931746 | 3931586 | ID=Msa0002060-mRNA-1:cds;Parent=Msa0002060-mRNA-1 |
| chr1_1 | CDS | 3931885 | 3931893 | 3931885 | ID=Msa0002060-mRNA-1:cds;Parent=Msa0002060-mRNA-1 |
| chr1_1 | CDS | 3931984 | 3932101 | 3931984 | ID=Msa0002060-mRNA-1:cds;Parent=Msa0002060-mRNA-1 |
| chr1_1 | CDS | 3932473 | 3932608 | 3932473 | ID=Msa0002060-mRNA-1:cds;Parent=Msa0002060-mRNA-1 |
| chr1_1 | CDS | 3933379 | 3933386 | 3933379 | ID=Msa0002060-mRNA-1:cds;Parent=Msa0002060-mRNA-1 |
| chr1_1 | CDS | 3933819 | 3934058 | 3933819 | ID=Msa0002060-mRNA-1:cds;Parent=Msa0002060-mRNA-1 |
| chr1_1 | three_prime_UTR | 3934059 | 3934339 | 3934059 | ID=Msa0002060-mRNA-1:three_prime_utr;Parent=Msa0002060-mRNA-1 |
| Gene Sequence |
>Msa0002060 ATGGCCGGTGTCTGCTCTTTCTCCTCCGACGTTGTTGCCATTTCTCATTCTCTCACACAATCACTGTCTCTCAACAATACTACACTTTCAACAACAAGTAGAAGAAGATGCATTTTGAGGAGGACGAGAACTGTGAGGCCTCTTGTTTGTGCCGCCATCAACAATCCATTGCAGTACCGGAAACTTGGTGACTCTGATCTTAATATCAGTGAAATCACTCTTGGTACTGGTAAAATGACCTTTGGGGAGCAAAACACAGAAAAAGAATCTCATGACATACTCAATTATGCATTCGAGAACGGCATTAATGCTCTTGATACTGCTGAGGCTTACCCGATTCCAATGAAGAAAGAGACACAAGGAAAAACTGATCTCTATATAGCTAGCTGGCTGAAATCTCAATCTCGTGACAAGATTATAATAGCAACAAAAGTTTGCGGTTATTCTGAGAGATCGAGTTACTTACGGGACAATGCAGACATTTTGCGGGTTGATGCGACAAATATCAAAGAAAGTGTGGAGAAAAGTCTTAAGCGTCTCGGGACTGATTATATTGATTTGTTGCAAATTCATTGGAATCATAAGCCAGATCGCTACGTTGCATTGTTTGGTGAATATTCCTATGATCCTTCAAAATGGAGGCCTAGTGTGCCGTTTGTTGAACAGTTGCAAGCTTTTCAAGAACTTATCAATGAAGGAAAGGTACGTTACATAGGTGTTTCAAATGAGACTTCATATGGAGTGATGGAATTCGTCCATGCAGCTAAAGTTGAGGGACTTCCAAAGATTGTCAGTATCCAGAACAGCTATAGCTTGCTTGTAAGAAGTCGTTTTGAAGTTGATCTCGAAGCAACTATTAAGTATCTTGAGTTGGCCAAGAAACATGGTTTAACTCCTGTTCAGCTCGCGCTTGGATTTGTGAGAGATCGTCCATTCATGGCGAGTTCAATTATCGGTGCAACATCTGTGGACCAACTAAAAGAAGACATTGATGCTTTTACAACAACTGAACGGCCTTTACCAGCAGAAGTCATGACAGGAATTGAAGCTATCTTCAAGAGATACAAAGATCCTAGCATCCTTTAA |
| Protein sequence |
>Msa0002060 MAGVCSFSSDVVAISHSLTQSLSLNNTTLSTTSRRRCILRRTRTVRPLVCAAINNPLQYRKLGDSDLNISEITLGTGKMTFGEQNTEKESHDILNYAFENGINALDTAEAYPIPMKKETQGKTDLYIASWLKSQSRDKIIIATKVCGYSERSSYLRDNADILRVDATNIKESVEKSLKRLGTDYIDLLQIHWNHKPDRYVALFGEYSYDPSKWRPSVPFVEQLQAFQELINEGKVRYIGVSNETSYGVMEFVHAAKVEGLPKIVSIQNSYSLLVRSRFEVDLEATIKYLELAKKHGLTPVQLALGFVRDRPFMASSIIGATSVDQLKEDIDAFTTTERPLPAEVMTGIEAIFKRYKDPSIL* |
