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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0462260 | RHN65700.1 | 86.486 | 74 | 10 | 0 | 1 | 74 | 1 | 74 | 1.77e-36 | 127 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0462260 | A0A396IKD3 | 86.486 | 74 | 10 | 0 | 1 | 74 | 1 | 74 | 8.47e-37 | 127 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0462260 | Msa1170490 | 0.810416 | 1.165314e-50 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0462260 | MtrunA17_Chr3g0082801 | 86.486 | 74 | 10 | 0 | 1 | 74 | 1 | 74 | 1.63e-40 | 127 |
| Msa0462260 | MtrunA17_Chr3g0082851 | 66.667 | 63 | 17 | 3 | 4 | 66 | 1 | 59 | 1.76e-18 | 71.6 |
| Msa0462260 | MtrunA17_Chr3g0082821 | 50.000 | 62 | 26 | 3 | 4 | 64 | 1 | 58 | 9.93e-12 | 54.7 |
| Msa0462260 | MtrunA17_Chr3g0082831 | 50.820 | 61 | 24 | 3 | 4 | 64 | 1 | 55 | 4.87e-11 | 52.4 |
| 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_3:-61047013 | None:intergenic |
| CTTAGTACTAAGTTAATTCT+AGG | 0.225492 | 3_3:+61047172 | Msa0462260:three_prime_UTR |
| TTTCTCCAATATGAGATATA+TGG | 0.266388 | 3_3:+61046622 | Msa0462260:exon |
| AGAAGCCATATATCTCATAT+TGG | 0.420251 | 3_3:-61046627 | None:intergenic |
| CATTCTGTTGGTGTTAATGA+TGG | 0.424860 | 3_3:+61046926 | Msa0462260:CDS |
| GTACTAAGTTAATTCTAGGT+TGG | 0.428778 | 3_3:+61047176 | Msa0462260:three_prime_UTR |
| CATGCTTCTTTGTGAGGAAG+AGG | 0.456230 | 3_3:-61046746 | None:intergenic |
| GAGGAGGCACAGCATAGTTA+TGG | 0.458701 | 3_3:-61046958 | None:intergenic |
| CTGATTGGTGCAGGAGGAGG+AGG | 0.483631 | 3_3:-61046974 | None:intergenic |
| CAACTGATTGGTGCAGGAGG+AGG | 0.506888 | 3_3:-61046977 | None:intergenic |
| CAACGGCAAGGGTACCATCA+TGG | 0.520766 | 3_3:+61046714 | Msa0462260:CDS |
| AAGAATCAACTGATTGGTGC+AGG | 0.527694 | 3_3:-61046983 | None:intergenic |
| TAGTACTAAGTCATAGTACT+TGG | 0.544103 | 3_3:-61047159 | None:intergenic |
| TACTTACATGCTTCTTTGTG+AGG | 0.549537 | 3_3:-61046752 | None:intergenic |
| AGAATGGCAAACAAGTATGT+TGG | 0.557736 | 3_3:+61047024 | Msa0462260:three_prime_UTR |
| TAAGAGTATTATGTTAAACC+TGG | 0.559931 | 3_3:+61046652 | Msa0462260:CDS |
| GAGCACCAGAATCATAAGAA+TGG | 0.560588 | 3_3:+61047008 | Msa0462260:three_prime_UTR |
| ATGTTTAGTACAAAATATAA+CGG | 0.563114 | 3_3:-61047204 | None:intergenic |
| GGACGCCTACTTCATTCTGT+TGG | 0.568175 | 3_3:+61046914 | Msa0462260:CDS |
| GCTCTGAAGAATCAACTGAT+TGG | 0.569246 | 3_3:-61046989 | None:intergenic |
| TAACACCAACAGAATGAAGT+AGG | 0.577968 | 3_3:-61046919 | None:intergenic |
| TGAAAGTAGAAGCAACGGCA+AGG | 0.589324 | 3_3:+61046702 | Msa0462260:CDS |
| GTCAATGAAAGTAGAAGCAA+CGG | 0.589839 | 3_3:+61046697 | Msa0462260:CDS |
| GAATCATAAACAGAAAAGCC+AGG | 0.595790 | 3_3:-61046670 | None:intergenic |
| ATGTTGGCAAAGAATAAACA+TGG | 0.605178 | 3_3:+61047040 | Msa0462260:three_prime_UTR |
| GAAAGTAGAAGCAACGGCAA+GGG | 0.621106 | 3_3:+61046703 | Msa0462260:CDS |
| AATCAACTGATTGGTGCAGG+AGG | 0.632665 | 3_3:-61046980 | None:intergenic |
| TTTGAAAAGGAAAAGGGAGA+CGG | 0.666203 | 3_3:+61046517 | None:intergenic |
| ACAGCATAGTTATGGAAGCG+TGG | 0.675066 | 3_3:-61046950 | None:intergenic |
| TGTTGGCAAAGAATAAACAT+GGG | 0.690833 | 3_3:+61047041 | Msa0462260:three_prime_UTR |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | AAAAATATATATATAGTGGT+TGG | - | chr3_3:61047118-61047137 | None:intergenic | 15.0% |
| !! | ATGTTTAGTACAAAATATAA+CGG | - | chr3_3:61047207-61047226 | None:intergenic | 15.0% |
| !!! | AAGAAAGATTTTTAAGTAGT+AGG | - | chr3_3:61046545-61046564 | None:intergenic | 20.0% |
| !! | TACTACTTAAAAATCTTTCT+TGG | + | chr3_3:61046544-61046563 | Msa0462260:five_prime_UTR | 20.0% |
| !!! | ATTATTAAACAAGTTTTGCT+AGG | - | chr3_3:61047081-61047100 | None:intergenic | 20.0% |
| ! | TTTCTCCAATATGAGATATA+TGG | + | chr3_3:61046622-61046641 | Msa0462260:exon | 25.0% |
| !!! | TAAGAGTATTATGTTAAACC+TGG | + | chr3_3:61046652-61046671 | Msa0462260:CDS | 25.0% |
| !! | TTTTCCATTAAAATTGTGCA+TGG | + | chr3_3:61046835-61046854 | Msa0462260:intron | 25.0% |
| !! | TTAACCATGCACAATTTTAA+TGG | - | chr3_3:61046842-61046861 | None:intergenic | 25.0% |
| ! | CTTAGTACTAAGTTAATTCT+AGG | + | chr3_3:61047172-61047191 | Msa0462260:three_prime_UTR | 25.0% |
| AGAAGCCATATATCTCATAT+TGG | - | chr3_3:61046630-61046649 | None:intergenic | 30.0% | |
| ! | GCATGTAAGTAACTTTTTGT+AGG | + | chr3_3:61046764-61046783 | Msa0462260:intron | 30.0% |
| ATGTTGGCAAAGAATAAACA+TGG | + | chr3_3:61047040-61047059 | Msa0462260:three_prime_UTR | 30.0% | |
| TGTTGGCAAAGAATAAACAT+GGG | + | chr3_3:61047041-61047060 | Msa0462260:three_prime_UTR | 30.0% | |
| TAGTACTAAGTCATAGTACT+TGG | - | chr3_3:61047162-61047181 | None:intergenic | 30.0% | |
| GTACTAAGTTAATTCTAGGT+TGG | + | chr3_3:61047176-61047195 | Msa0462260:three_prime_UTR | 30.0% | |
| GAATCATAAACAGAAAAGCC+AGG | - | chr3_3:61046673-61046692 | None:intergenic | 35.0% | |
| GTCAATGAAAGTAGAAGCAA+CGG | + | chr3_3:61046697-61046716 | Msa0462260:CDS | 35.0% | |
| ! | AGAGGCTTAATTTTCCATGA+TGG | - | chr3_3:61046731-61046750 | None:intergenic | 35.0% |
| TACTTACATGCTTCTTTGTG+AGG | - | chr3_3:61046755-61046774 | None:intergenic | 35.0% | |
| AAACATGGCAACAAGATGAA+GGG | - | chr3_3:61046875-61046894 | None:intergenic | 35.0% | |
| ATCTTGTTGCCATGTTTGTT+TGG | + | chr3_3:61046878-61046897 | Msa0462260:intron | 35.0% | |
| TCTTGTTGCCATGTTTGTTT+GGG | + | chr3_3:61046879-61046898 | Msa0462260:intron | 35.0% | |
| TTGAGATTCCCAAACAAACA+TGG | - | chr3_3:61046890-61046909 | None:intergenic | 35.0% | |
| TTGTTTGGGAATCTCAAAGA+TGG | + | chr3_3:61046893-61046912 | Msa0462260:intron | 35.0% | |
| TAACACCAACAGAATGAAGT+AGG | - | chr3_3:61046922-61046941 | None:intergenic | 35.0% | |
| !! | CATTCTGTTGGTGTTAATGA+TGG | + | chr3_3:61046926-61046945 | Msa0462260:CDS | 35.0% |
| GTTTGCCATTCTTATGATTC+TGG | - | chr3_3:61047016-61047035 | None:intergenic | 35.0% | |
| AGAATGGCAAACAAGTATGT+TGG | + | chr3_3:61047024-61047043 | Msa0462260:three_prime_UTR | 35.0% | |
| CAAACATGGCAACAAGATGA+AGG | - | chr3_3:61046876-61046895 | None:intergenic | 40.0% | |
| AAGAATCAACTGATTGGTGC+AGG | - | chr3_3:61046986-61047005 | None:intergenic | 40.0% | |
| !! | GCTCTGAAGAATCAACTGAT+TGG | - | chr3_3:61046992-61047011 | None:intergenic | 40.0% |
| GAGCACCAGAATCATAAGAA+TGG | + | chr3_3:61047008-61047027 | Msa0462260:three_prime_UTR | 40.0% | |
| TGAAAGTAGAAGCAACGGCA+AGG | + | chr3_3:61046702-61046721 | Msa0462260:CDS | 45.0% | |
| GAAAGTAGAAGCAACGGCAA+GGG | + | chr3_3:61046703-61046722 | Msa0462260:CDS | 45.0% | |
| CATGCTTCTTTGTGAGGAAG+AGG | - | chr3_3:61046749-61046768 | None:intergenic | 45.0% | |
| ACAGCATAGTTATGGAAGCG+TGG | - | chr3_3:61046953-61046972 | None:intergenic | 45.0% | |
| AATCAACTGATTGGTGCAGG+AGG | - | chr3_3:61046983-61047002 | None:intergenic | 45.0% | |
| !! | AAATAAAAATATATATATAG+TGG | - | chr3_3:61047122-61047141 | None:intergenic | 5.0% |
| GGACGCCTACTTCATTCTGT+TGG | + | chr3_3:61046914-61046933 | Msa0462260:CDS | 50.0% | |
| ! | GAGGAGGCACAGCATAGTTA+TGG | - | chr3_3:61046961-61046980 | None:intergenic | 50.0% |
| !! | CAACGGCAAGGGTACCATCA+TGG | + | chr3_3:61046714-61046733 | Msa0462260:CDS | 55.0% |
| CAACTGATTGGTGCAGGAGG+AGG | - | chr3_3:61046980-61046999 | None:intergenic | 55.0% | |
| CTGATTGGTGCAGGAGGAGG+AGG | - | chr3_3:61046977-61046996 | None:intergenic | 60.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3_3 | gene | 61046529 | 61047253 | 61046529 | ID=Msa0462260;Name=Msa0462260 |
| chr3_3 | mRNA | 61046529 | 61047253 | 61046529 | ID=Msa0462260-mRNA-1;Parent=Msa0462260;Name=Msa0462260-mRNA-1;_AED=0.36;_eAED=0.36;_QI=103|1|1|1|1|1|2|253|74 |
| chr3_3 | exon | 61046529 | 61046767 | 61046529 | ID=Msa0462260-mRNA-1:exon:12855;Parent=Msa0462260-mRNA-1 |
| chr3_3 | exon | 61046912 | 61047253 | 61046912 | ID=Msa0462260-mRNA-1:exon:12856;Parent=Msa0462260-mRNA-1 |
| chr3_3 | five_prime_UTR | 61046529 | 61046631 | 61046529 | ID=Msa0462260-mRNA-1:five_prime_utr;Parent=Msa0462260-mRNA-1 |
| chr3_3 | CDS | 61046632 | 61046767 | 61046632 | ID=Msa0462260-mRNA-1:cds;Parent=Msa0462260-mRNA-1 |
| chr3_3 | CDS | 61046912 | 61047000 | 61046912 | ID=Msa0462260-mRNA-1:cds;Parent=Msa0462260-mRNA-1 |
| chr3_3 | three_prime_UTR | 61047001 | 61047253 | 61047001 | ID=Msa0462260-mRNA-1:three_prime_utr;Parent=Msa0462260-mRNA-1 |
| Gene Sequence |
| Protein sequence |
