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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0274830 | XP_004506244.1 | 63.934 | 61 | 18 | 2 | 9 | 66 | 215 | 274 | 8.44e-13 | 74.3 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0274830 | sp|Q8VWF6|SSL3_ARATH | 52.459 | 61 | 25 | 2 | 9 | 66 | 201 | 260 | 5.75e-11 | 60.8 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0274830 | A0A1S2YL19 | 63.934 | 61 | 18 | 2 | 9 | 66 | 215 | 274 | 4.03e-13 | 74.3 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0274830 | Msa1455100 | 0.815864 | 7.429866e-52 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0274830 | MtrunA17_Chr4g0025341 | 58.333 | 60 | 23 | 1 | 9 | 66 | 203 | 262 | 2.33e-15 | 70.1 |
| Msa0274830 | MtrunA17_Chr2g0322241 | 59.016 | 61 | 21 | 2 | 9 | 66 | 207 | 266 | 1.44e-14 | 67.8 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0274830 | AT5G22020.3 | 50.000 | 66 | 29 | 2 | 2 | 64 | 200 | 264 | 3.26e-13 | 64.7 |
| Msa0274830 | AT5G22020.1 | 50.000 | 66 | 29 | 2 | 2 | 64 | 200 | 264 | 3.26e-13 | 64.7 |
| Msa0274830 | AT5G22020.2 | 50.000 | 66 | 29 | 2 | 2 | 64 | 200 | 264 | 3.26e-13 | 64.7 |
| Msa0274830 | AT1G08470.1 | 52.459 | 61 | 25 | 2 | 9 | 66 | 201 | 260 | 5.85e-12 | 60.8 |
Find 31 sgRNAs with CRISPR-Local
Find 42 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| AAGGTTTCTTTCTGCATAAT+AGG | 0.246528 | 2_3:-6686649 | Msa0274830:CDS |
| TCATTCAGCTGACAGTTTCT+AGG | 0.266378 | 2_3:-6686969 | Msa0274830:CDS |
| CCACCACAATGTGGTGGTTT+AGG | 0.297275 | 2_3:-6686562 | Msa0274830:CDS |
| ATGAAACTGTGATTCATAAT+TGG | 0.312607 | 2_3:-6686615 | Msa0274830:CDS |
| CATCCCTGGGAAATGCCATT+TGG | 0.363615 | 2_3:+6686871 | None:intergenic |
| ATCCCTGGGAAATGCCATTT+GGG | 0.367832 | 2_3:+6686872 | None:intergenic |
| AGGTTTCTTTCTGCATAATA+GGG | 0.386437 | 2_3:-6686648 | Msa0274830:CDS |
| GAAATGCAACCATGTCACTA+TGG | 0.413836 | 2_3:-6686926 | Msa0274830:CDS |
| CATTCAGCTGACAGTTTCTA+GGG | 0.432738 | 2_3:-6686968 | Msa0274830:CDS |
| TTTGTGAAGGTGCTATTGGC+AGG | 0.459800 | 2_3:-6686834 | Msa0274830:intron |
| CAAATGGCATTTCCCAGGGA+TGG | 0.482525 | 2_3:-6686870 | Msa0274830:CDS |
| ATTCCCAAATGGCATTTCCC+AGG | 0.485931 | 2_3:-6686875 | Msa0274830:CDS |
| TAATTGGACGTGTGTGGAGG+AGG | 0.502458 | 2_3:-6686599 | Msa0274830:CDS |
| TTGGACGTGTGTGGAGGAGG+AGG | 0.504412 | 2_3:-6686596 | Msa0274830:CDS |
| ACAGTTTCTAGGGATGATAC+TGG | 0.531686 | 2_3:-6686958 | Msa0274830:CDS |
| TTTCCCAGGGATGGTTCTAT+CGG | 0.534560 | 2_3:-6686861 | Msa0274830:CDS |
| AGGAACATTCAATTCCCAAA+TGG | 0.553727 | 2_3:-6686886 | Msa0274830:CDS |
| TTCTAGGGATGATACTGGCA+AGG | 0.554718 | 2_3:-6686953 | Msa0274830:CDS |
| TTCCCAAATGGCATTTCCCA+GGG | 0.561785 | 2_3:-6686874 | Msa0274830:CDS |
| AAGACCGATAGAACCATCCC+TGG | 0.574574 | 2_3:+6686857 | None:intergenic |
| CTGCATAATAGGGAGTAAAG+AGG | 0.575401 | 2_3:-6686638 | Msa0274830:CDS |
| CAATGGTTTCCATAGTGACA+TGG | 0.582340 | 2_3:+6686917 | None:intergenic |
| AATGTTCCTCACAAGAACAA+TGG | 0.587303 | 2_3:+6686900 | None:intergenic |
| TGGAAACCATTGTTCTTGTG+AGG | 0.606117 | 2_3:-6686906 | Msa0274830:CDS |
| CAACCTAAACCACCACATTG+TGG | 0.637474 | 2_3:+6686559 | None:intergenic |
| GATTCATAATTGGACGTGTG+TGG | 0.639963 | 2_3:-6686605 | Msa0274830:CDS |
| CCTAAACCACCACATTGTGG+TGG | 0.645933 | 2_3:+6686562 | None:intergenic |
| AGACCGATAGAACCATCCCT+GGG | 0.664371 | 2_3:+6686858 | None:intergenic |
| AATTGTCCACCACAATGTGG+TGG | 0.667141 | 2_3:-6686568 | Msa0274830:CDS |
| TCATAATTGGACGTGTGTGG+AGG | 0.669833 | 2_3:-6686602 | Msa0274830:CDS |
| GTAAATTGTCCACCACAATG+TGG | 0.754301 | 2_3:-6686571 | Msa0274830:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | AAAATTAAGATTAGATAAAA+AGG | + | chr2_3:6686836-6686855 | None:intergenic | 10.0% |
| !! | TATGAAATAAATTCTGTTAC+AGG | - | chr2_3:6686635-6686654 | Msa0274830:CDS | 20.0% |
| !! | TAAGATTAGATAAAAAGGTA+AGG | + | chr2_3:6686831-6686850 | None:intergenic | 20.0% |
| ! | TTTCATAATTCAGAACTTCA+AGG | + | chr2_3:6686580-6686599 | None:intergenic | 25.0% |
| ! | GAATTATGAAATTCTGATAC+TGG | - | chr2_3:6686589-6686608 | Msa0274830:CDS | 25.0% |
| ! | ATGAAACTGTGATTCATAAT+TGG | - | chr2_3:6687016-6687035 | Msa0274830:intron | 25.0% |
| ATTAACATCAGTTCAGACAT+AGG | + | chr2_3:6686909-6686928 | None:intergenic | 30.0% | |
| TGACAATGCTTTGATAAAAG+AGG | + | chr2_3:6686942-6686961 | None:intergenic | 30.0% | |
| !!! | AAAAGTGCTGATAGTTTTGA+AGG | - | chr2_3:6686963-6686982 | Msa0274830:CDS | 30.0% |
| AAGGTTTCTTTCTGCATAAT+AGG | - | chr2_3:6686982-6687001 | Msa0274830:intron | 30.0% | |
| AGGTTTCTTTCTGCATAATA+GGG | - | chr2_3:6686983-6687002 | Msa0274830:intron | 30.0% | |
| AATGTTCCTCACAAGAACAA+TGG | + | chr2_3:6686734-6686753 | None:intergenic | 35.0% | |
| AGGAACATTCAATTCCCAAA+TGG | - | chr2_3:6686745-6686764 | Msa0274830:intron | 35.0% | |
| ! | TTCTATCGGTCTTTTTGTGA+AGG | - | chr2_3:6686784-6686803 | Msa0274830:intron | 35.0% |
| !!! | TCTTTTTGTGAAGGTGCTAT+TGG | - | chr2_3:6686793-6686812 | Msa0274830:intron | 35.0% |
| CAGACATAGGAACGTAATAT+AGG | + | chr2_3:6686896-6686915 | None:intergenic | 35.0% | |
| TCATTCAGCTGACAGTTTCT+AGG | - | chr2_3:6686662-6686681 | Msa0274830:CDS | 40.0% | |
| CATTCAGCTGACAGTTTCTA+GGG | - | chr2_3:6686663-6686682 | Msa0274830:CDS | 40.0% | |
| ! | ACAGTTTCTAGGGATGATAC+TGG | - | chr2_3:6686673-6686692 | Msa0274830:CDS | 40.0% |
| GAAATGCAACCATGTCACTA+TGG | - | chr2_3:6686705-6686724 | Msa0274830:intron | 40.0% | |
| CAATGGTTTCCATAGTGACA+TGG | + | chr2_3:6686717-6686736 | None:intergenic | 40.0% | |
| TGGAAACCATTGTTCTTGTG+AGG | - | chr2_3:6686725-6686744 | Msa0274830:intron | 40.0% | |
| CTGCATAATAGGGAGTAAAG+AGG | - | chr2_3:6686993-6687012 | Msa0274830:intron | 40.0% | |
| GATTCATAATTGGACGTGTG+TGG | - | chr2_3:6687026-6687045 | Msa0274830:intron | 40.0% | |
| GTAAATTGTCCACCACAATG+TGG | - | chr2_3:6687060-6687079 | Msa0274830:intron | 40.0% | |
| ! | TTCTAGGGATGATACTGGCA+AGG | - | chr2_3:6686678-6686697 | Msa0274830:CDS | 45.0% |
| ATTCCCAAATGGCATTTCCC+AGG | - | chr2_3:6686756-6686775 | Msa0274830:intron | 45.0% | |
| TTCCCAAATGGCATTTCCCA+GGG | - | chr2_3:6686757-6686776 | Msa0274830:intron | 45.0% | |
| ! | ATCCCTGGGAAATGCCATTT+GGG | + | chr2_3:6686762-6686781 | None:intergenic | 45.0% |
| ! | TTTCCCAGGGATGGTTCTAT+CGG | - | chr2_3:6686770-6686789 | Msa0274830:intron | 45.0% |
| !! | TTTGTGAAGGTGCTATTGGC+AGG | - | chr2_3:6686797-6686816 | Msa0274830:intron | 45.0% |
| TCATAATTGGACGTGTGTGG+AGG | - | chr2_3:6687029-6687048 | Msa0274830:intron | 45.0% | |
| AATTGTCCACCACAATGTGG+TGG | - | chr2_3:6687063-6687082 | Msa0274830:intron | 45.0% | |
| CAACCTAAACCACCACATTG+TGG | + | chr2_3:6687075-6687094 | None:intergenic | 45.0% | |
| CATCCCTGGGAAATGCCATT+TGG | + | chr2_3:6686763-6686782 | None:intergenic | 50.0% | |
| CAAATGGCATTTCCCAGGGA+TGG | - | chr2_3:6686761-6686780 | Msa0274830:intron | 50.0% | |
| AGACCGATAGAACCATCCCT+GGG | + | chr2_3:6686776-6686795 | None:intergenic | 50.0% | |
| AAGACCGATAGAACCATCCC+TGG | + | chr2_3:6686777-6686796 | None:intergenic | 50.0% | |
| TAATTGGACGTGTGTGGAGG+AGG | - | chr2_3:6687032-6687051 | Msa0274830:intron | 50.0% | |
| CCTAAACCACCACATTGTGG+TGG | + | chr2_3:6687072-6687091 | None:intergenic | 50.0% | |
| CCACCACAATGTGGTGGTTT+AGG | - | chr2_3:6687069-6687088 | Msa0274830:intron | 50.0% | |
| TTGGACGTGTGTGGAGGAGG+AGG | - | chr2_3:6687035-6687054 | Msa0274830:intron | 60.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr2_3 | gene | 6686558 | 6687095 | 6686558 | ID=Msa0274830;Name=Msa0274830 |
| chr2_3 | mRNA | 6686558 | 6687095 | 6686558 | ID=Msa0274830-mRNA-1;Parent=Msa0274830;Name=Msa0274830-mRNA-1;_AED=0.52;_eAED=0.52;_QI=0|0|0|0.66|0|0.33|3|0|109 |
| chr2_3 | exon | 6687070 | 6687095 | 6687070 | ID=Msa0274830-mRNA-1:exon:3211;Parent=Msa0274830-mRNA-1 |
| chr2_3 | exon | 6686835 | 6686996 | 6686835 | ID=Msa0274830-mRNA-1:exon:3210;Parent=Msa0274830-mRNA-1 |
| chr2_3 | exon | 6686558 | 6686699 | 6686558 | ID=Msa0274830-mRNA-1:exon:3209;Parent=Msa0274830-mRNA-1 |
| chr2_3 | CDS | 6687070 | 6687095 | 6687070 | ID=Msa0274830-mRNA-1:cds;Parent=Msa0274830-mRNA-1 |
| chr2_3 | CDS | 6686835 | 6686996 | 6686835 | ID=Msa0274830-mRNA-1:cds;Parent=Msa0274830-mRNA-1 |
| chr2_3 | CDS | 6686558 | 6686699 | 6686558 | ID=Msa0274830-mRNA-1:cds;Parent=Msa0274830-mRNA-1 |
| Gene Sequence |
| Protein sequence |
