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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0847990 | XP_003613091.1 | 94.915 | 177 | 3 | 1 | 1 | 171 | 1 | 177 | 1.27e-115 | 335 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0847990 | G7JXR4 | 94.915 | 177 | 3 | 1 | 1 | 171 | 1 | 177 | 6.05e-116 | 335 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0012440 | Msa0847990 | 0.813596 | 2.362253e-51 | -8.615850e-47 |
| Msa0057240 | Msa0847990 | 0.820523 | 6.557939e-53 | -8.615850e-47 |
| Msa0619980 | Msa0847990 | 0.820849 | 5.518727e-53 | -8.615850e-47 |
| Msa0663090 | Msa0847990 | 0.815510 | 8.908205e-52 | -8.615850e-47 |
| Msa0706370 | Msa0847990 | 0.840620 | 7.791651e-58 | -8.615850e-47 |
| Msa0810020 | Msa0847990 | 0.809473 | 1.859809e-50 | -8.615850e-47 |
| Msa0149560 | Msa0847990 | 0.823920 | 1.068246e-53 | -8.615850e-47 |
| Msa0219190 | Msa0847990 | 0.805344 | 1.396888e-49 | -8.615850e-47 |
| Msa0426330 | Msa0847990 | 0.802665 | 5.037580e-49 | -8.615850e-47 |
| Msa0847990 | Msa0862100 | 0.809137 | 2.195533e-50 | -8.615850e-47 |
| Msa0847990 | Msa1374440 | 0.800965 | 1.125302e-48 | -8.615850e-47 |
| Msa0847990 | Msa1379990 | 0.822525 | 2.261563e-53 | -8.615850e-47 |
| Msa0847990 | Msa1419010 | 0.812270 | 4.613615e-51 | -8.615850e-47 |
| Msa0847990 | Msa1420060 | 0.818825 | 1.601030e-52 | -8.615850e-47 |
| Msa0847990 | Msa1429420 | 0.816513 | 5.319553e-52 | -8.615850e-47 |
| Msa0847990 | Msa1465370 | 0.825222 | 5.273125e-54 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0847990 | MtrunA17_Chr5g0412491 | 95.210 | 167 | 2 | 1 | 11 | 171 | 1 | 167 | 2.97e-110 | 311 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0847990 | AT1G26290.1 | 42.982 | 114 | 56 | 3 | 1 | 110 | 1 | 109 | 1.91e-16 | 72.4 |
Find 39 sgRNAs with CRISPR-Local
Find 44 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| TCTTACTATGCCTATTATAT+TGG | 0.159642 | 5_4:+32124199 | Msa0847990:three_prime_UTR |
| CTTACTATGCCTATTATATT+GGG | 0.208100 | 5_4:+32124200 | Msa0847990:three_prime_UTR |
| TAACAAAGAAACAAATAAAA+AGG | 0.218969 | 5_4:+32123924 | Msa0847990:CDS |
| AGAATTAGAAGAGGAGATTA+AGG | 0.231798 | 5_4:+32123750 | Msa0847990:CDS |
| AAAATTTACCCCAATATAAT+AGG | 0.309509 | 5_4:-32124209 | None:intergenic |
| CACTTTCTGAGGTGATTATA+AGG | 0.320343 | 5_4:+32123860 | Msa0847990:CDS |
| AAGAAGTGAAGAAGATTGAT+TGG | 0.358796 | 5_4:+32123989 | Msa0847990:CDS |
| TATGATCCTTTCACAGGAAC+AGG | 0.362440 | 5_4:-32124039 | None:intergenic |
| TTCAACTCCTCTGCTGAAAC+AGG | 0.402447 | 5_4:-32123694 | None:intergenic |
| ATCTTGCTCGTCGATTGCTT+CGG | 0.414612 | 5_4:+32123785 | Msa0847990:CDS |
| GGATAAGAAGCTACTTCAAT+TGG | 0.436350 | 5_4:+32124116 | Msa0847990:CDS |
| AGGAACTAAAATTGAAATCA+AGG | 0.471855 | 5_4:+32123897 | Msa0847990:CDS |
| TTAGAAGAGGAGATTAAGGA+AGG | 0.474485 | 5_4:+32123754 | Msa0847990:CDS |
| GGTGATTATAAGGATGAGAA+TGG | 0.489148 | 5_4:+32123870 | Msa0847990:CDS |
| TTGATTGGGAAAAGAGTTTG+AGG | 0.494350 | 5_4:+32124004 | Msa0847990:CDS |
| AAAGGATAAAATAATGATGA+GGG | 0.497614 | 5_4:+32124077 | Msa0847990:CDS |
| AGAAGTGAAGAAGATTGATT+GGG | 0.510525 | 5_4:+32123990 | Msa0847990:CDS |
| GCTACTTCAATTGGTGTGGA+AGG | 0.513216 | 5_4:+32124125 | Msa0847990:CDS |
| TGAGGTTCCTGTTTCAGCAG+AGG | 0.528276 | 5_4:+32123687 | Msa0847990:CDS |
| ATTATAAGGATGAGAATGGA+AGG | 0.528677 | 5_4:+32123874 | Msa0847990:CDS |
| TCAAGCCCTGTTCCTGTGAA+AGG | 0.530825 | 5_4:+32124033 | Msa0847990:CDS |
| AATAATAACATGGATCATCA+TGG | 0.531079 | 5_4:+32123529 | None:intergenic |
| ATATGTTAGATCAAAGCAAA+AGG | 0.536682 | 5_4:+32124059 | Msa0847990:CDS |
| TTACTATGCCTATTATATTG+GGG | 0.540322 | 5_4:+32124201 | Msa0847990:three_prime_UTR |
| TTGGTGTGGAAGGTTTAAAG+TGG | 0.548941 | 5_4:+32124135 | Msa0847990:exon |
| ATATAATAGGCATAGTAAGA+AGG | 0.558419 | 5_4:-32124196 | None:intergenic |
| CTAACATATGATCCTTTCAC+AGG | 0.563019 | 5_4:-32124045 | None:intergenic |
| TGATTGGGAAAAGAGTTTGA+GGG | 0.564884 | 5_4:+32124005 | Msa0847990:CDS |
| AAAAGGATAAAATAATGATG+AGG | 0.564917 | 5_4:+32124076 | Msa0847990:CDS |
| CAAAATTAGAGCACTTTCTG+AGG | 0.566466 | 5_4:+32123849 | Msa0847990:CDS |
| GATTGAAAGAGAATTAGAAG+AGG | 0.571961 | 5_4:+32123741 | Msa0847990:CDS |
| GAGGGGAAAGAATGCAAGTG+AGG | 0.574468 | 5_4:+32124095 | Msa0847990:CDS |
| AGAAGCTACTTCAATTGGTG+TGG | 0.577937 | 5_4:+32124121 | Msa0847990:CDS |
| TGGGAAAAGAGTTTGAGGGC+AGG | 0.600710 | 5_4:+32124009 | Msa0847990:CDS |
| ATAAGGATGAGAATGGAAGG+AGG | 0.636221 | 5_4:+32123877 | Msa0847990:CDS |
| ATGATCCTTTCACAGGAACA+GGG | 0.639503 | 5_4:-32124038 | None:intergenic |
| AAGGATAAAATAATGATGAG+GGG | 0.646560 | 5_4:+32124078 | Msa0847990:CDS |
| CATCATGGAATGTACACCAA+AGG | 0.652781 | 5_4:+32123544 | Msa0847990:CDS |
| AACTAAAATTGAAATCAAGG+AGG | 0.721284 | 5_4:+32123900 | Msa0847990:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | TAACAAAGAAACAAATAAAA+AGG | + | chr5_4:32123924-32123943 | Msa0847990:CDS | 15.0% |
| !! | AACAAAGAAACAAATAAAAA+GGG | + | chr5_4:32123925-32123944 | Msa0847990:CDS | 15.0% |
| !!! | TATTTTCTTGCTTTTTTAAT+TGG | + | chr5_4:32124161-32124180 | Msa0847990:three_prime_UTR | 15.0% |
| !!! | ACTTCTTTCAAACATTTTTT+GGG | - | chr5_4:32123976-32123995 | None:intergenic | 20.0% |
| !! | AAAAGGATAAAATAATGATG+AGG | + | chr5_4:32124076-32124095 | Msa0847990:CDS | 20.0% |
| !! | AAAGGATAAAATAATGATGA+GGG | + | chr5_4:32124077-32124096 | Msa0847990:CDS | 20.0% |
| ! | GTCAAATAAAAATGTTCTTG+AGG | + | chr5_4:32123669-32123688 | Msa0847990:CDS | 25.0% |
| ! | AGGAACTAAAATTGAAATCA+AGG | + | chr5_4:32123897-32123916 | Msa0847990:CDS | 25.0% |
| ! | AACTAAAATTGAAATCAAGG+AGG | + | chr5_4:32123900-32123919 | Msa0847990:CDS | 25.0% |
| !!! | CATTTTTTGGGTCTAAAATT+TGG | - | chr5_4:32123964-32123983 | None:intergenic | 25.0% |
| !!! | CACTTCTTTCAAACATTTTT+TGG | - | chr5_4:32123977-32123996 | None:intergenic | 25.0% |
| ! | ATATGTTAGATCAAAGCAAA+AGG | + | chr5_4:32124059-32124078 | Msa0847990:CDS | 25.0% |
| ! | AAGGATAAAATAATGATGAG+GGG | + | chr5_4:32124078-32124097 | Msa0847990:CDS | 25.0% |
| ! | ATATAATAGGCATAGTAAGA+AGG | - | chr5_4:32124199-32124218 | None:intergenic | 25.0% |
| GATTGAAAGAGAATTAGAAG+AGG | + | chr5_4:32123741-32123760 | Msa0847990:CDS | 30.0% | |
| AGAATTAGAAGAGGAGATTA+AGG | + | chr5_4:32123750-32123769 | Msa0847990:CDS | 30.0% | |
| ATTATAAGGATGAGAATGGA+AGG | + | chr5_4:32123874-32123893 | Msa0847990:CDS | 30.0% | |
| AAGAAGTGAAGAAGATTGAT+TGG | + | chr5_4:32123989-32124008 | Msa0847990:CDS | 30.0% | |
| AGAAGTGAAGAAGATTGATT+GGG | + | chr5_4:32123990-32124009 | Msa0847990:CDS | 30.0% | |
| CTAGAATTTCACTTCACCTT+TGG | - | chr5_4:32123563-32123582 | None:intergenic | 35.0% | |
| CAAAGGTGAAGTGAAATTCT+AGG | + | chr5_4:32123561-32123580 | Msa0847990:intron | 35.0% | |
| TTAGAAGAGGAGATTAAGGA+AGG | + | chr5_4:32123754-32123773 | Msa0847990:CDS | 35.0% | |
| ! | CAAAATTAGAGCACTTTCTG+AGG | + | chr5_4:32123849-32123868 | Msa0847990:CDS | 35.0% |
| !! | CACTTTCTGAGGTGATTATA+AGG | + | chr5_4:32123860-32123879 | Msa0847990:CDS | 35.0% |
| GGTGATTATAAGGATGAGAA+TGG | + | chr5_4:32123870-32123889 | Msa0847990:CDS | 35.0% | |
| TTGATTGGGAAAAGAGTTTG+AGG | + | chr5_4:32124004-32124023 | Msa0847990:CDS | 35.0% | |
| TGATTGGGAAAAGAGTTTGA+GGG | + | chr5_4:32124005-32124024 | Msa0847990:CDS | 35.0% | |
| CTAACATATGATCCTTTCAC+AGG | - | chr5_4:32124048-32124067 | None:intergenic | 35.0% | |
| GGATAAGAAGCTACTTCAAT+TGG | + | chr5_4:32124116-32124135 | Msa0847990:CDS | 35.0% | |
| CATCATGGAATGTACACCAA+AGG | + | chr5_4:32123544-32123563 | Msa0847990:CDS | 40.0% | |
| ATAAGGATGAGAATGGAAGG+AGG | + | chr5_4:32123877-32123896 | Msa0847990:CDS | 40.0% | |
| ATGATCCTTTCACAGGAACA+GGG | - | chr5_4:32124041-32124060 | None:intergenic | 40.0% | |
| TATGATCCTTTCACAGGAAC+AGG | - | chr5_4:32124042-32124061 | None:intergenic | 40.0% | |
| AGAAGCTACTTCAATTGGTG+TGG | + | chr5_4:32124121-32124140 | Msa0847990:CDS | 40.0% | |
| TTGGTGTGGAAGGTTTAAAG+TGG | + | chr5_4:32124135-32124154 | Msa0847990:exon | 40.0% | |
| TTCAACTCCTCTGCTGAAAC+AGG | - | chr5_4:32123697-32123716 | None:intergenic | 45.0% | |
| ! | ATCTTGCTCGTCGATTGCTT+CGG | + | chr5_4:32123785-32123804 | Msa0847990:CDS | 45.0% |
| !! | TGCTTCGGATTTTTCAGCAG+AGG | + | chr5_4:32123800-32123819 | Msa0847990:CDS | 45.0% |
| !! | TCGGATTTTTCAGCAGAGGA+AGG | + | chr5_4:32123804-32123823 | Msa0847990:CDS | 45.0% |
| GCTACTTCAATTGGTGTGGA+AGG | + | chr5_4:32124125-32124144 | Msa0847990:CDS | 45.0% | |
| TGAGGTTCCTGTTTCAGCAG+AGG | + | chr5_4:32123687-32123706 | Msa0847990:CDS | 50.0% | |
| TGGGAAAAGAGTTTGAGGGC+AGG | + | chr5_4:32124009-32124028 | Msa0847990:CDS | 50.0% | |
| TCAAGCCCTGTTCCTGTGAA+AGG | + | chr5_4:32124033-32124052 | Msa0847990:CDS | 50.0% | |
| GAGGGGAAAGAATGCAAGTG+AGG | + | chr5_4:32124095-32124114 | Msa0847990:CDS | 50.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr5_4 | gene | 32123538 | 32124220 | 32123538 | ID=Msa0847990;Name=Msa0847990 |
| chr5_4 | mRNA | 32123538 | 32124220 | 32123538 | ID=Msa0847990-mRNA-1;Parent=Msa0847990;Name=Msa0847990-mRNA-1;_AED=0.18;_eAED=0.18;_QI=0|1|0.5|1|0|0.5|2|68|171 |
| chr5_4 | exon | 32123538 | 32123565 | 32123538 | ID=Msa0847990-mRNA-1:exon:11244;Parent=Msa0847990-mRNA-1 |
| chr5_4 | exon | 32123665 | 32124220 | 32123665 | ID=Msa0847990-mRNA-1:exon:11245;Parent=Msa0847990-mRNA-1 |
| chr5_4 | CDS | 32123538 | 32123565 | 32123538 | ID=Msa0847990-mRNA-1:cds;Parent=Msa0847990-mRNA-1 |
| chr5_4 | CDS | 32123665 | 32124152 | 32123665 | ID=Msa0847990-mRNA-1:cds;Parent=Msa0847990-mRNA-1 |
| chr5_4 | three_prime_UTR | 32124153 | 32124220 | 32124153 | ID=Msa0847990-mRNA-1:three_prime_utr;Parent=Msa0847990-mRNA-1 |
| Gene Sequence |
| Protein sequence |
