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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0446010 | GAU48222.1 | 82.143 | 140 | 18 | 1 | 1 | 133 | 133 | 272 | 7.37e-79 | 249 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0446010 | A0A2Z6PEX1 | 82.143 | 140 | 18 | 1 | 1 | 133 | 133 | 272 | 3.52e-79 | 249 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0446010 | Msa0466760 | 0.871966 | 4.568486e-67 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0446010 | MtrunA17_Chr5g0414621 | 81.061 | 132 | 25 | 0 | 1 | 132 | 792 | 923 | 4.80e-72 | 233 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|
Find 31 sgRNAs with CRISPR-Local
Find 38 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| GATGAAGGATGAGTTATTTA+AGG | 0.188373 | 3_3:-21145396 | Msa0446010:CDS |
| TCTGACTTCTTCCTCCATTC+TGG | 0.224365 | 3_3:+21145056 | None:intergenic |
| TACTTCTGTCTTCATTCCTT+TGG | 0.256359 | 3_3:+21145109 | None:intergenic |
| TGAGTTATTTAAGGAATTTA+TGG | 0.280166 | 3_3:-21145387 | Msa0446010:intron |
| ACTTCTGTCTTCATTCCTTT+GGG | 0.322275 | 3_3:+21145110 | None:intergenic |
| AAGGAATGAAGACAGAAGTA+TGG | 0.343317 | 3_3:-21145106 | Msa0446010:CDS |
| ATCAGACTATGATCGAAATA+TGG | 0.356084 | 3_3:-21145252 | Msa0446010:CDS |
| TGTTGAGTTCACTTGTCTTA+AGG | 0.376477 | 3_3:+21145160 | None:intergenic |
| AACAAATTTGCTCGACACTA+AGG | 0.398046 | 3_3:-21145141 | Msa0446010:CDS |
| TAATCTTTCCACTTCTCAGC+TGG | 0.414586 | 3_3:+21145428 | None:intergenic |
| GGGATGGCTTGGTCGACATT+TGG | 0.420534 | 3_3:-21145085 | Msa0446010:CDS |
| TCTTCATTCCTTTGGGACCA+TGG | 0.421977 | 3_3:+21145117 | None:intergenic |
| CCAGTGTGCAATACTGCATC+AGG | 0.443322 | 3_3:+21145005 | None:intergenic |
| GACAGAAGTATGGGATGGCT+TGG | 0.489800 | 3_3:-21145096 | Msa0446010:CDS |
| ACAAATTTGCTCGACACTAA+GGG | 0.523362 | 3_3:-21145140 | Msa0446010:CDS |
| AGATTACAATGCTGAGATGA+AGG | 0.528777 | 3_3:-21145411 | Msa0446010:CDS |
| TGTGTGGGAAAGAACATGTT+TGG | 0.530860 | 3_3:-21145222 | Msa0446010:CDS |
| GTGCAATACTGCATCAGGTA+AGG | 0.537765 | 3_3:+21145010 | None:intergenic |
| AGGAATGAAGACAGAAGTAT+GGG | 0.548649 | 3_3:-21145105 | Msa0446010:CDS |
| ACATTTGGTTGAAACCAGAA+TGG | 0.549163 | 3_3:-21145070 | Msa0446010:CDS |
| ATATTTCGATCATAGTCTGA+TGG | 0.556584 | 3_3:+21145254 | None:intergenic |
| TGCCTACTCCAGCTGAGAAG+TGG | 0.566811 | 3_3:-21145436 | Msa0446010:CDS |
| TTCCACTTCTCAGCTGGAGT+AGG | 0.583500 | 3_3:+21145434 | None:intergenic |
| AAATATGGCAAGAACTGTGT+GGG | 0.586246 | 3_3:-21145237 | Msa0446010:CDS |
| TTGCTCGACACTAAGGGCCA+TGG | 0.609906 | 3_3:-21145134 | Msa0446010:CDS |
| ACTAAGGGCCATGGTCCCAA+AGG | 0.614121 | 3_3:-21145125 | Msa0446010:CDS |
| TTTGGTTGAAACCAGAATGG+AGG | 0.619563 | 3_3:-21145067 | Msa0446010:CDS |
| ATGAAGACAGAAGTATGGGA+TGG | 0.652799 | 3_3:-21145101 | Msa0446010:CDS |
| GAAATATGGCAAGAACTGTG+TGG | 0.655421 | 3_3:-21145238 | Msa0446010:CDS |
| CCTGATGCAGTATTGCACAC+TGG | 0.670209 | 3_3:-21145005 | Msa0446010:CDS |
| GATGCAGTATTGCACACTGG+AGG | 0.691912 | 3_3:-21145002 | Msa0446010:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | TGAGTTATTTAAGGAATTTA+TGG | - | chr3_3:21145006-21145025 | Msa0446010:CDS | 20.0% |
| !! | AAACTAAAATATAAGACTAG+AGG | + | chr3_3:21145046-21145065 | None:intergenic | 20.0% |
| !!! | TTTTTAAATGATCAGGATAT+CGG | + | chr3_3:21145198-21145217 | None:intergenic | 20.0% |
| ! | ATGATATACTATAACAACGT+AGG | - | chr3_3:21145102-21145121 | Msa0446010:CDS | 25.0% |
| ! | TGATATACTATAACAACGTA+GGG | - | chr3_3:21145103-21145122 | Msa0446010:CDS | 25.0% |
| !!! | CTTGCATTTTTTAAATGATC+AGG | + | chr3_3:21145205-21145224 | None:intergenic | 25.0% |
| GATGAAGGATGAGTTATTTA+AGG | - | chr3_3:21144997-21145016 | Msa0446010:CDS | 30.0% | |
| ATATTTCGATCATAGTCTGA+TGG | + | chr3_3:21145142-21145161 | None:intergenic | 30.0% | |
| ATCAGACTATGATCGAAATA+TGG | - | chr3_3:21145141-21145160 | Msa0446010:CDS | 30.0% | |
| GCTTCATTGAACATAAAAAG+AGG | - | chr3_3:21145422-21145441 | Msa0446010:CDS | 30.0% | |
| CATTGAACATAAAAAGAGGA+TGG | - | chr3_3:21145426-21145445 | Msa0446010:CDS | 30.0% | |
| AGATTACAATGCTGAGATGA+AGG | - | chr3_3:21144982-21145001 | Msa0446010:CDS | 35.0% | |
| AAATATGGCAAGAACTGTGT+GGG | - | chr3_3:21145156-21145175 | Msa0446010:CDS | 35.0% | |
| TGTTGAGTTCACTTGTCTTA+AGG | + | chr3_3:21145236-21145255 | None:intergenic | 35.0% | |
| ! | AACAAATTTGCTCGACACTA+AGG | - | chr3_3:21145252-21145271 | Msa0446010:CDS | 35.0% |
| ! | ACAAATTTGCTCGACACTAA+GGG | - | chr3_3:21145253-21145272 | Msa0446010:CDS | 35.0% |
| ACTTCTGTCTTCATTCCTTT+GGG | + | chr3_3:21145286-21145305 | None:intergenic | 35.0% | |
| TACTTCTGTCTTCATTCCTT+TGG | + | chr3_3:21145287-21145306 | None:intergenic | 35.0% | |
| AAGGAATGAAGACAGAAGTA+TGG | - | chr3_3:21145287-21145306 | Msa0446010:intron | 35.0% | |
| ! | AGGAATGAAGACAGAAGTAT+GGG | - | chr3_3:21145288-21145307 | Msa0446010:intron | 35.0% |
| ACATTTGGTTGAAACCAGAA+TGG | - | chr3_3:21145323-21145342 | Msa0446010:intron | 35.0% | |
| TAATCTTTCCACTTCTCAGC+TGG | + | chr3_3:21144968-21144987 | None:intergenic | 40.0% | |
| GAAATATGGCAAGAACTGTG+TGG | - | chr3_3:21145155-21145174 | Msa0446010:CDS | 40.0% | |
| TGTGTGGGAAAGAACATGTT+TGG | - | chr3_3:21145171-21145190 | Msa0446010:CDS | 40.0% | |
| ! | ATGAAGACAGAAGTATGGGA+TGG | - | chr3_3:21145292-21145311 | Msa0446010:intron | 40.0% |
| TTTGGTTGAAACCAGAATGG+AGG | - | chr3_3:21145326-21145345 | Msa0446010:intron | 40.0% | |
| !! | TCTTCATTCCTTTGGGACCA+TGG | + | chr3_3:21145279-21145298 | None:intergenic | 45.0% |
| TCTGACTTCTTCCTCCATTC+TGG | + | chr3_3:21145340-21145359 | None:intergenic | 45.0% | |
| GTGCAATACTGCATCAGGTA+AGG | + | chr3_3:21145386-21145405 | None:intergenic | 45.0% | |
| TTCCACTTCTCAGCTGGAGT+AGG | + | chr3_3:21144962-21144981 | None:intergenic | 50.0% | |
| ! | GACAGAAGTATGGGATGGCT+TGG | - | chr3_3:21145297-21145316 | Msa0446010:intron | 50.0% |
| CCAGTGTGCAATACTGCATC+AGG | + | chr3_3:21145391-21145410 | None:intergenic | 50.0% | |
| CCTGATGCAGTATTGCACAC+TGG | - | chr3_3:21145388-21145407 | Msa0446010:CDS | 50.0% | |
| GATGCAGTATTGCACACTGG+AGG | - | chr3_3:21145391-21145410 | Msa0446010:CDS | 50.0% | |
| TGCCTACTCCAGCTGAGAAG+TGG | - | chr3_3:21144957-21144976 | Msa0446010:CDS | 55.0% | |
| TTGCTCGACACTAAGGGCCA+TGG | - | chr3_3:21145259-21145278 | Msa0446010:CDS | 55.0% | |
| ACTAAGGGCCATGGTCCCAA+AGG | - | chr3_3:21145268-21145287 | Msa0446010:CDS | 55.0% | |
| !! | GGGATGGCTTGGTCGACATT+TGG | - | chr3_3:21145308-21145327 | Msa0446010:intron | 55.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3_3 | gene | 21144956 | 21145459 | 21144956 | ID=Msa0446010;Name=Msa0446010 |
| chr3_3 | mRNA | 21144956 | 21145459 | 21144956 | ID=Msa0446010-mRNA-1;Parent=Msa0446010;Name=Msa0446010-mRNA-1;_AED=0.55;_eAED=0.55;_QI=0|0|0|0.5|1|0.5|2|0|135 |
| chr3_3 | exon | 21145388 | 21145459 | 21145388 | ID=Msa0446010-mRNA-1:exon:4441;Parent=Msa0446010-mRNA-1 |
| chr3_3 | exon | 21144956 | 21145291 | 21144956 | ID=Msa0446010-mRNA-1:exon:4440;Parent=Msa0446010-mRNA-1 |
| chr3_3 | CDS | 21145388 | 21145459 | 21145388 | ID=Msa0446010-mRNA-1:cds;Parent=Msa0446010-mRNA-1 |
| chr3_3 | CDS | 21144956 | 21145291 | 21144956 | ID=Msa0446010-mRNA-1:cds;Parent=Msa0446010-mRNA-1 |
| Gene Sequence |
| Protein sequence |
