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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0396240 | RHN65700.1 | 89.189 | 74 | 8 | 0 | 1 | 74 | 1 | 74 | 1.85e-39 | 134 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0396240 | A0A396IKD3 | 89.189 | 74 | 8 | 0 | 1 | 74 | 1 | 74 | 8.85e-40 | 134 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0168310 | Msa0396240 | 0.809974 | 1.451171e-50 | -8.615850e-47 |
| Msa0396240 | Msa0396290 | 0.810337 | 1.212078e-50 | -8.615850e-47 |
| Msa0396240 | Msa0545050 | 0.810578 | 1.074922e-50 | -8.615850e-47 |
| Msa0396240 | Msa1170490 | 0.816769 | 4.661096e-52 | -8.615850e-47 |
| Msa0396240 | Msa1175100 | 0.809342 | 1.983909e-50 | -8.615850e-47 |
| Msa0349280 | Msa0396240 | 0.885794 | 5.980166e-72 | -8.615850e-47 |
| Msa0349340 | Msa0396240 | 0.903452 | 3.418726e-79 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0396240 | MtrunA17_Chr3g0082801 | 89.189 | 74 | 8 | 0 | 1 | 74 | 1 | 74 | 1.70e-43 | 134 |
| Msa0396240 | MtrunA17_Chr3g0082851 | 68.254 | 63 | 16 | 3 | 4 | 66 | 1 | 59 | 3.26e-20 | 75.9 |
| Msa0396240 | MtrunA17_Chr3g0082821 | 56.452 | 62 | 22 | 3 | 4 | 64 | 1 | 58 | 8.00e-15 | 62.4 |
| Msa0396240 | MtrunA17_Chr3g0082831 | 52.459 | 61 | 23 | 3 | 4 | 64 | 1 | 55 | 5.78e-12 | 55.1 |
| 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 45 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| GTTTGCCATTCTTATGATTC+TGG | 0.176754 | 3_2:+14123967 | None:intergenic |
| CTTAGTACTAAGTTAATTCT+AGG | 0.225492 | 3_2:-14123810 | Msa0396240:three_prime_UTR |
| TTTCTCCAATATGAGATATA+TGG | 0.266388 | 3_2:-14124348 | Msa0396240:exon |
| GGTTCAATAATAATCTTTCT+TGG | 0.296803 | 3_2:-14124426 | Msa0396240:five_prime_UTR |
| CAACGGCAAGGGTACCATTA+TGG | 0.329834 | 3_2:-14124256 | Msa0396240:CDS |
| GAGGAGGCACAGCATAGTTA+TGG | 0.405206 | 3_2:+14124022 | None:intergenic |
| AGAAGCCATATATCTCATAT+TGG | 0.420251 | 3_2:+14124343 | None:intergenic |
| CATTCTGTTGGTGTTAATGA+TGG | 0.424860 | 3_2:-14124054 | Msa0396240:CDS |
| GTACTAAGTTAATTCTAGGT+TGG | 0.428778 | 3_2:-14123806 | Msa0396240:three_prime_UTR |
| AGGAGGCACAGCATAGTTAT+GGG | 0.448878 | 3_2:+14124023 | None:intergenic |
| CTGATTGGTGCAGGAGGAGG+AGG | 0.483631 | 3_2:+14124006 | None:intergenic |
| CATGCTTCTTTGTGATGATG+AGG | 0.488670 | 3_2:+14124224 | None:intergenic |
| CAACTGATTGGTGCAGGAGG+AGG | 0.506888 | 3_2:+14124003 | None:intergenic |
| AAGAATCAACTGATTGGTGC+AGG | 0.527694 | 3_2:+14123997 | None:intergenic |
| TAGTACTAAGTCATAGTACT+TGG | 0.544103 | 3_2:+14123823 | None:intergenic |
| TAAGAGTGTTATGTTAAACC+TGG | 0.557492 | 3_2:-14124318 | Msa0396240:CDS |
| AGAATGGCAAACAAGTATGT+TGG | 0.557736 | 3_2:-14123956 | Msa0396240:three_prime_UTR |
| GAGCACCAGAATCATAAGAA+TGG | 0.560588 | 3_2:-14123972 | Msa0396240:three_prime_UTR |
| GTCAATGAAAGTAGAAGCAA+CGG | 0.562863 | 3_2:-14124273 | Msa0396240:CDS |
| ATGTTTAGTACAAAATATAA+CGG | 0.563114 | 3_2:+14123778 | None:intergenic |
| GGACGCCTACTTCATTCTGT+TGG | 0.568175 | 3_2:-14124066 | Msa0396240:CDS |
| GCTCTGAAGAATCAACTGAT+TGG | 0.569246 | 3_2:+14123991 | None:intergenic |
| TAACACCAACAGAATGAAGT+AGG | 0.577968 | 3_2:+14124061 | None:intergenic |
| GAATCATAAACAGAAAAGCC+AGG | 0.588758 | 3_2:+14124300 | None:intergenic |
| TGAAAGTAGAAGCAACGGCA+AGG | 0.589324 | 3_2:-14124268 | Msa0396240:CDS |
| ATGTTGGCAAAGAATAAACA+TGG | 0.605178 | 3_2:-14123940 | Msa0396240:three_prime_UTR |
| GAAAGTAGAAGCAACGGCAA+GGG | 0.621106 | 3_2:-14124267 | Msa0396240:CDS |
| AATCAACTGATTGGTGCAGG+AGG | 0.632665 | 3_2:+14124000 | None:intergenic |
| TTGGAAAAGGAAAAGGGAGA+CGG | 0.660028 | 3_2:-14124466 | None:intergenic |
| ACAGCATAGTTATGGGAGCG+TGG | 0.670795 | 3_2:+14124030 | None:intergenic |
| TGTTGGCAAAGAATAAACAT+GGG | 0.690833 | 3_2:-14123939 | Msa0396240:three_prime_UTR |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | ATAAAAATATATATAGTGGT+TGG | + | chr3_2:14124343-14124362 | None:intergenic | 15.0% |
| !! | ATGTTTAGTACAAAATATAA+CGG | + | chr3_2:14124430-14124449 | None:intergenic | 15.0% |
| !!! | ATTATTAAACAAGTTTTGCT+AGG | + | chr3_2:14124306-14124325 | None:intergenic | 20.0% |
| ! | ATTGAACCTTAAAAAGTAGT+AGG | + | chr3_2:14123767-14123786 | None:intergenic | 25.0% |
| ! | GGTTCAATAATAATCTTTCT+TGG | - | chr3_2:14123779-14123798 | Msa0396240:three_prime_UTR | 25.0% |
| ! | TTTCTCCAATATGAGATATA+TGG | - | chr3_2:14123857-14123876 | Msa0396240:three_prime_UTR | 25.0% |
| !!! | GCATGTAAGTAATTTTTTGT+AGG | - | chr3_2:14123999-14124018 | Msa0396240:exon | 25.0% |
| !! | TTTTCCATTAAAATTGTGCA+TGG | - | chr3_2:14124060-14124079 | Msa0396240:CDS | 25.0% |
| !! | TAAACCATGCACAATTTTAA+TGG | + | chr3_2:14124067-14124086 | None:intergenic | 25.0% |
| ! | CTTAGTACTAAGTTAATTCT+AGG | - | chr3_2:14124395-14124414 | Msa0396240:five_prime_UTR | 25.0% |
| AGAAGCCATATATCTCATAT+TGG | + | chr3_2:14123865-14123884 | None:intergenic | 30.0% | |
| !! | TAAGAGTGTTATGTTAAACC+TGG | - | chr3_2:14123887-14123906 | Msa0396240:three_prime_UTR | 30.0% |
| ! | TGAGGCTTAATTTTCCATAA+TGG | + | chr3_2:14123966-14123985 | None:intergenic | 30.0% |
| ATGTTGGCAAAGAATAAACA+TGG | - | chr3_2:14124265-14124284 | Msa0396240:CDS | 30.0% | |
| TGTTGGCAAAGAATAAACAT+GGG | - | chr3_2:14124266-14124285 | Msa0396240:CDS | 30.0% | |
| TAGTACTAAGTCATAGTACT+TGG | + | chr3_2:14124385-14124404 | None:intergenic | 30.0% | |
| GTACTAAGTTAATTCTAGGT+TGG | - | chr3_2:14124399-14124418 | Msa0396240:five_prime_UTR | 30.0% | |
| GAATCATAAACAGAAAAGCC+AGG | + | chr3_2:14123908-14123927 | None:intergenic | 35.0% | |
| GTCAATGAAAGTAGAAGCAA+CGG | - | chr3_2:14123932-14123951 | Msa0396240:three_prime_UTR | 35.0% | |
| AAACATGGCAACAACATGAA+GGG | + | chr3_2:14124100-14124119 | None:intergenic | 35.0% | |
| ATGTTGTTGCCATGTTTGTT+TGG | - | chr3_2:14124103-14124122 | Msa0396240:intron | 35.0% | |
| TGTTGTTGCCATGTTTGTTT+GGG | - | chr3_2:14124104-14124123 | Msa0396240:intron | 35.0% | |
| TTGAGATTCCCAAACAAACA+TGG | + | chr3_2:14124115-14124134 | None:intergenic | 35.0% | |
| TTGTTTGGGAATCTCAAAGA+TGG | - | chr3_2:14124118-14124137 | Msa0396240:intron | 35.0% | |
| TAACACCAACAGAATGAAGT+AGG | + | chr3_2:14124147-14124166 | None:intergenic | 35.0% | |
| !! | CATTCTGTTGGTGTTAATGA+TGG | - | chr3_2:14124151-14124170 | Msa0396240:intron | 35.0% |
| GTTTGCCATTCTTATGATTC+TGG | + | chr3_2:14124241-14124260 | None:intergenic | 35.0% | |
| AGAATGGCAAACAAGTATGT+TGG | - | chr3_2:14124249-14124268 | Msa0396240:CDS | 35.0% | |
| !!! | ACGGTGCCTACTACTTTTTA+AGG | - | chr3_2:14123758-14123777 | Msa0396240:three_prime_UTR | 40.0% |
| ! | CATGCTTCTTTGTGATGATG+AGG | + | chr3_2:14123984-14124003 | None:intergenic | 40.0% |
| CAAACATGGCAACAACATGA+AGG | + | chr3_2:14124101-14124120 | None:intergenic | 40.0% | |
| AAGAATCAACTGATTGGTGC+AGG | + | chr3_2:14124211-14124230 | None:intergenic | 40.0% | |
| !! | GCTCTGAAGAATCAACTGAT+TGG | + | chr3_2:14124217-14124236 | None:intergenic | 40.0% |
| GAGCACCAGAATCATAAGAA+TGG | - | chr3_2:14124233-14124252 | Msa0396240:CDS | 40.0% | |
| TGAAAGTAGAAGCAACGGCA+AGG | - | chr3_2:14123937-14123956 | Msa0396240:three_prime_UTR | 45.0% | |
| GAAAGTAGAAGCAACGGCAA+GGG | - | chr3_2:14123938-14123957 | Msa0396240:three_prime_UTR | 45.0% | |
| ! | AGGAGGCACAGCATAGTTAT+GGG | + | chr3_2:14124185-14124204 | None:intergenic | 45.0% |
| AATCAACTGATTGGTGCAGG+AGG | + | chr3_2:14124208-14124227 | None:intergenic | 45.0% | |
| !! | AAAAATAAAAATATATATAG+TGG | + | chr3_2:14124347-14124366 | None:intergenic | 5.0% |
| !! | CAACGGCAAGGGTACCATTA+TGG | - | chr3_2:14123949-14123968 | Msa0396240:three_prime_UTR | 50.0% |
| GGACGCCTACTTCATTCTGT+TGG | - | chr3_2:14124139-14124158 | Msa0396240:intron | 50.0% | |
| ACAGCATAGTTATGGGAGCG+TGG | + | chr3_2:14124178-14124197 | None:intergenic | 50.0% | |
| ! | GAGGAGGCACAGCATAGTTA+TGG | + | chr3_2:14124186-14124205 | None:intergenic | 50.0% |
| CAACTGATTGGTGCAGGAGG+AGG | + | chr3_2:14124205-14124224 | None:intergenic | 55.0% | |
| CTGATTGGTGCAGGAGGAGG+AGG | + | chr3_2:14124202-14124221 | None:intergenic | 60.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3_2 | gene | 14123751 | 14124476 | 14123751 | ID=Msa0396240;Name=Msa0396240 |
| chr3_2 | mRNA | 14123751 | 14124476 | 14123751 | ID=Msa0396240-mRNA-1;Parent=Msa0396240;Name=Msa0396240-mRNA-1;_AED=0.37;_eAED=0.37;_QI=116|1|1|1|1|1|2|251|74 |
| chr3_2 | exon | 14123751 | 14124090 | 14123751 | ID=Msa0396240-mRNA-1:exon:3272;Parent=Msa0396240-mRNA-1 |
| chr3_2 | exon | 14124225 | 14124476 | 14124225 | ID=Msa0396240-mRNA-1:exon:3271;Parent=Msa0396240-mRNA-1 |
| chr3_2 | five_prime_UTR | 14124361 | 14124476 | 14124361 | ID=Msa0396240-mRNA-1:five_prime_utr;Parent=Msa0396240-mRNA-1 |
| chr3_2 | CDS | 14124225 | 14124360 | 14124225 | ID=Msa0396240-mRNA-1:cds;Parent=Msa0396240-mRNA-1 |
| chr3_2 | CDS | 14124002 | 14124090 | 14124002 | ID=Msa0396240-mRNA-1:cds;Parent=Msa0396240-mRNA-1 |
| chr3_2 | three_prime_UTR | 14123751 | 14124001 | 14123751 | ID=Msa0396240-mRNA-1:three_prime_utr;Parent=Msa0396240-mRNA-1 |
| Gene Sequence |
| Protein sequence |
