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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0349280 | RHN65700.1 | 90.541 | 74 | 7 | 0 | 1 | 74 | 1 | 74 | 1.27e-40 | 137 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0349280 | A0A396IKD3 | 90.541 | 74 | 7 | 0 | 1 | 74 | 1 | 74 | 6.07e-41 | 137 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0349280 | Msa0349340 | 0.910066 | 2.837428e-82 | -8.615850e-47 |
| Msa0349280 | Msa0396240 | 0.885794 | 5.980166e-72 | -8.615850e-47 |
| Msa0349280 | Msa1170490 | 0.937814 | 1.876966e-98 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0349280 | MtrunA17_Chr3g0082801 | 90.541 | 74 | 7 | 0 | 1 | 74 | 1 | 74 | 1.17e-44 | 137 |
| Msa0349280 | MtrunA17_Chr3g0082851 | 66.667 | 63 | 17 | 3 | 4 | 66 | 1 | 59 | 4.78e-19 | 73.2 |
| Msa0349280 | MtrunA17_Chr3g0082821 | 56.452 | 62 | 22 | 3 | 4 | 64 | 1 | 58 | 2.81e-14 | 61.2 |
| Msa0349280 | MtrunA17_Chr3g0082831 | 52.459 | 61 | 23 | 3 | 4 | 64 | 1 | 55 | 2.53e-11 | 53.1 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|
Find 30 sgRNAs with CRISPR-Local
Find 44 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| GTTTGCCATTCTTATGATTC+TGG | 0.176754 | 3_1:+12762502 | None:intergenic |
| CTTAGTACTAAGTTAATTCT+AGG | 0.225492 | 3_1:-12762343 | Msa0349280:three_prime_UTR |
| TTTCTCCAATATGAGATATA+TGG | 0.266388 | 3_1:-12762883 | Msa0349280:exon |
| CAACGGCAAGGGTACCGTTA+TGG | 0.409172 | 3_1:-12762791 | Msa0349280:CDS |
| AGAAGCCATATATCTCATAT+TGG | 0.420251 | 3_1:+12762878 | None:intergenic |
| CATTCTGTTGGTGTTAATGA+TGG | 0.424860 | 3_1:-12762589 | Msa0349280:CDS |
| GTACTAAGTTAATTCTAGGT+TGG | 0.428778 | 3_1:-12762339 | Msa0349280:three_prime_UTR |
| GAGGAGGCACAGCATAGTTA+TGG | 0.458701 | 3_1:+12762557 | None:intergenic |
| CTGATTGGTGCAGGAGGAGG+AGG | 0.483631 | 3_1:+12762541 | None:intergenic |
| CATGCTTCTTTGTGATGATG+AGG | 0.488670 | 3_1:+12762759 | None:intergenic |
| CAACTGATTGGTGCAGGAGG+AGG | 0.506888 | 3_1:+12762538 | None:intergenic |
| GGTTCAATAATAATCTTTCG+TGG | 0.515123 | 3_1:-12762961 | Msa0349280:five_prime_UTR |
| AAGAATCAACTGATTGGTGC+AGG | 0.527694 | 3_1:+12762532 | None:intergenic |
| TAGTACTAAGTCATAGTACT+TGG | 0.544103 | 3_1:+12762356 | None:intergenic |
| TAAGAGTGTTATGTTAAACC+TGG | 0.557492 | 3_1:-12762853 | Msa0349280:CDS |
| AGAATGGCAAACAAGTATGT+TGG | 0.557736 | 3_1:-12762491 | Msa0349280:three_prime_UTR |
| GAGCACCAGAATCATAAGAA+TGG | 0.560588 | 3_1:-12762507 | Msa0349280:three_prime_UTR |
| GTCAATGAAAGTAGAAGCAA+CGG | 0.562863 | 3_1:-12762808 | Msa0349280:CDS |
| ATGTTTAGTACAAAATATAA+CGG | 0.563114 | 3_1:+12762311 | None:intergenic |
| GGACGCCTACTTCATTCTGT+TGG | 0.568175 | 3_1:-12762601 | Msa0349280:CDS |
| GCTCTGAAGAATCAACTGAT+TGG | 0.569246 | 3_1:+12762526 | None:intergenic |
| TAACACCAACAGAATGAAGT+AGG | 0.577968 | 3_1:+12762596 | None:intergenic |
| GAATCATAAACAGAAAAGCC+AGG | 0.588758 | 3_1:+12762835 | None:intergenic |
| TGAAAGTAGAAGCAACGGCA+AGG | 0.589324 | 3_1:-12762803 | Msa0349280:CDS |
| ATGTTGGCAAAGAATAAACA+TGG | 0.605178 | 3_1:-12762475 | Msa0349280:three_prime_UTR |
| GAAAGTAGAAGCAACGGCAA+GGG | 0.621106 | 3_1:-12762802 | Msa0349280:CDS |
| AATCAACTGATTGGTGCAGG+AGG | 0.632665 | 3_1:+12762535 | None:intergenic |
| TTGGAAAAGGAAAAGGGAGA+CGG | 0.660028 | 3_1:-12763001 | None:intergenic |
| ACAGCATAGTTATGGAAGCG+TGG | 0.675066 | 3_1:+12762565 | None:intergenic |
| TGTTGGCAAAGAATAAACAT+GGG | 0.690833 | 3_1:-12762474 | Msa0349280:three_prime_UTR |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | AAAAATATATATATAGTGGT+TGG | + | chr3_1:12762876-12762895 | None:intergenic | 15.0% |
| !! | ATGTTTAGTACAAAATATAA+CGG | + | chr3_1:12762965-12762984 | None:intergenic | 15.0% |
| !!! | ATTATTAAACAAGTTTTGCT+AGG | + | chr3_1:12762839-12762858 | None:intergenic | 20.0% |
| ! | ATTGAACCTTAAAAAGTAGT+AGG | + | chr3_1:12762300-12762319 | None:intergenic | 25.0% |
| ! | TTTCTCCAATATGAGATATA+TGG | - | chr3_1:12762390-12762409 | Msa0349280:three_prime_UTR | 25.0% |
| !!! | GCATGTAAGTAATTTTTTGT+AGG | - | chr3_1:12762532-12762551 | Msa0349280:exon | 25.0% |
| !! | TTTTCCATTAAAATTGTGCA+TGG | - | chr3_1:12762593-12762612 | Msa0349280:CDS | 25.0% |
| !! | TAAACCATGCACAATTTTAA+TGG | + | chr3_1:12762600-12762619 | None:intergenic | 25.0% |
| ! | CTTAGTACTAAGTTAATTCT+AGG | - | chr3_1:12762930-12762949 | Msa0349280:five_prime_UTR | 25.0% |
| GGTTCAATAATAATCTTTCG+TGG | - | chr3_1:12762312-12762331 | Msa0349280:three_prime_UTR | 30.0% | |
| AGAAGCCATATATCTCATAT+TGG | + | chr3_1:12762398-12762417 | None:intergenic | 30.0% | |
| !! | TAAGAGTGTTATGTTAAACC+TGG | - | chr3_1:12762420-12762439 | Msa0349280:three_prime_UTR | 30.0% |
| ! | TGAGGCTTAATTTTCCATAA+CGG | + | chr3_1:12762499-12762518 | None:intergenic | 30.0% |
| ATGTTGGCAAAGAATAAACA+TGG | - | chr3_1:12762798-12762817 | Msa0349280:CDS | 30.0% | |
| TGTTGGCAAAGAATAAACAT+GGG | - | chr3_1:12762799-12762818 | Msa0349280:CDS | 30.0% | |
| TAGTACTAAGTCATAGTACT+TGG | + | chr3_1:12762920-12762939 | None:intergenic | 30.0% | |
| GTACTAAGTTAATTCTAGGT+TGG | - | chr3_1:12762934-12762953 | Msa0349280:five_prime_UTR | 30.0% | |
| GAATCATAAACAGAAAAGCC+AGG | + | chr3_1:12762441-12762460 | None:intergenic | 35.0% | |
| GTCAATGAAAGTAGAAGCAA+CGG | - | chr3_1:12762465-12762484 | Msa0349280:three_prime_UTR | 35.0% | |
| AAACATGGCAACAACATGAA+GGG | + | chr3_1:12762633-12762652 | None:intergenic | 35.0% | |
| ATGTTGTTGCCATGTTTGTT+TGG | - | chr3_1:12762636-12762655 | Msa0349280:intron | 35.0% | |
| TGTTGTTGCCATGTTTGTTT+GGG | - | chr3_1:12762637-12762656 | Msa0349280:intron | 35.0% | |
| TTGAGATTCCCAAACAAACA+TGG | + | chr3_1:12762648-12762667 | None:intergenic | 35.0% | |
| TTGTTTGGGAATCTCAAAGA+TGG | - | chr3_1:12762651-12762670 | Msa0349280:intron | 35.0% | |
| TAACACCAACAGAATGAAGT+AGG | + | chr3_1:12762680-12762699 | None:intergenic | 35.0% | |
| !! | CATTCTGTTGGTGTTAATGA+TGG | - | chr3_1:12762684-12762703 | Msa0349280:intron | 35.0% |
| GTTTGCCATTCTTATGATTC+TGG | + | chr3_1:12762774-12762793 | None:intergenic | 35.0% | |
| AGAATGGCAAACAAGTATGT+TGG | - | chr3_1:12762782-12762801 | Msa0349280:CDS | 35.0% | |
| !!! | ACGGTGCCTACTACTTTTTA+AGG | - | chr3_1:12762291-12762310 | Msa0349280:three_prime_UTR | 40.0% |
| ! | CATGCTTCTTTGTGATGATG+AGG | + | chr3_1:12762517-12762536 | None:intergenic | 40.0% |
| CAAACATGGCAACAACATGA+AGG | + | chr3_1:12762634-12762653 | None:intergenic | 40.0% | |
| AAGAATCAACTGATTGGTGC+AGG | + | chr3_1:12762744-12762763 | None:intergenic | 40.0% | |
| !! | GCTCTGAAGAATCAACTGAT+TGG | + | chr3_1:12762750-12762769 | None:intergenic | 40.0% |
| GAGCACCAGAATCATAAGAA+TGG | - | chr3_1:12762766-12762785 | Msa0349280:CDS | 40.0% | |
| TGAAAGTAGAAGCAACGGCA+AGG | - | chr3_1:12762470-12762489 | Msa0349280:three_prime_UTR | 45.0% | |
| GAAAGTAGAAGCAACGGCAA+GGG | - | chr3_1:12762471-12762490 | Msa0349280:three_prime_UTR | 45.0% | |
| ACAGCATAGTTATGGAAGCG+TGG | + | chr3_1:12762711-12762730 | None:intergenic | 45.0% | |
| AATCAACTGATTGGTGCAGG+AGG | + | chr3_1:12762741-12762760 | None:intergenic | 45.0% | |
| !! | AAATAAAAATATATATATAG+TGG | + | chr3_1:12762880-12762899 | None:intergenic | 5.0% |
| GGACGCCTACTTCATTCTGT+TGG | - | chr3_1:12762672-12762691 | Msa0349280:intron | 50.0% | |
| ! | GAGGAGGCACAGCATAGTTA+TGG | + | chr3_1:12762719-12762738 | None:intergenic | 50.0% |
| !! | CAACGGCAAGGGTACCGTTA+TGG | - | chr3_1:12762482-12762501 | Msa0349280:three_prime_UTR | 55.0% |
| CAACTGATTGGTGCAGGAGG+AGG | + | chr3_1:12762738-12762757 | None:intergenic | 55.0% | |
| CTGATTGGTGCAGGAGGAGG+AGG | + | chr3_1:12762735-12762754 | None:intergenic | 60.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3_1 | gene | 12762284 | 12763011 | 12762284 | ID=Msa0349280;Name=Msa0349280 |
| chr3_1 | mRNA | 12762284 | 12763011 | 12762284 | ID=Msa0349280-mRNA-1;Parent=Msa0349280;Name=Msa0349280-mRNA-1;_AED=0.38;_eAED=0.38;_QI=116|1|1|1|1|1|2|253|74 |
| chr3_1 | exon | 12762284 | 12762625 | 12762284 | ID=Msa0349280-mRNA-1:exon:3287;Parent=Msa0349280-mRNA-1 |
| chr3_1 | exon | 12762760 | 12763011 | 12762760 | ID=Msa0349280-mRNA-1:exon:3286;Parent=Msa0349280-mRNA-1 |
| chr3_1 | five_prime_UTR | 12762896 | 12763011 | 12762896 | ID=Msa0349280-mRNA-1:five_prime_utr;Parent=Msa0349280-mRNA-1 |
| chr3_1 | CDS | 12762760 | 12762895 | 12762760 | ID=Msa0349280-mRNA-1:cds;Parent=Msa0349280-mRNA-1 |
| chr3_1 | CDS | 12762537 | 12762625 | 12762537 | ID=Msa0349280-mRNA-1:cds;Parent=Msa0349280-mRNA-1 |
| chr3_1 | three_prime_UTR | 12762284 | 12762536 | 12762284 | ID=Msa0349280-mRNA-1:three_prime_utr;Parent=Msa0349280-mRNA-1 |
| Gene Sequence |
| Protein sequence |
