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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0048800 | XP_039690646.1 | 90.179 | 112 | 11 | 0 | 1 | 112 | 1 | 112 | 1.26e-63 | 207 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0048800 | sp|Q9M8K2|REM21_ARATH | 29.221 | 154 | 94 | 2 | 6 | 159 | 23 | 161 | 6.99e-15 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0048800 | A0A072VGJ6 | 90.179 | 112 | 11 | 0 | 1 | 112 | 1 | 112 | 2.38e-63 | 207 |
| Gene ID | Type | Classification |
|---|---|---|
| Msa0048800 | TF | B3 |
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0048800 | MtrunA17_Chr1g0169081 | 90.179 | 112 | 11 | 0 | 1 | 112 | 1 | 112 | 4.59e-67 | 207 |
| Msa0048800 | MtrunA17_Chr1g0169161 | 78.704 | 108 | 23 | 0 | 2 | 109 | 5 | 112 | 4.68e-56 | 179 |
| Msa0048800 | MtrunA17_Chr3g0125161 | 72.034 | 118 | 33 | 0 | 2 | 119 | 16 | 133 | 6.71e-56 | 173 |
| Msa0048800 | MtrunA17_Chr1g0169171 | 71.910 | 89 | 25 | 0 | 31 | 119 | 1 | 89 | 1.74e-38 | 133 |
| Msa0048800 | MtrunA17_Chr1g0154191 | 23.864 | 176 | 124 | 4 | 9 | 177 | 22 | 194 | 8.52e-12 | 62.4 |
| Msa0048800 | MtrunA17_Chr1g0154111 | 31.000 | 100 | 65 | 2 | 9 | 106 | 26 | 123 | 4.76e-11 | 60.5 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0048800 | AT3G06160.5 | 29.221 | 154 | 94 | 2 | 6 | 159 | 8 | 146 | 6.10e-16 | 74.3 |
| Msa0048800 | AT3G06160.4 | 29.221 | 154 | 94 | 2 | 6 | 159 | 8 | 146 | 6.10e-16 | 74.3 |
| Msa0048800 | AT3G06160.3 | 29.221 | 154 | 94 | 2 | 6 | 159 | 8 | 146 | 6.10e-16 | 74.3 |
| Msa0048800 | AT3G06160.1 | 29.221 | 154 | 94 | 2 | 6 | 159 | 23 | 161 | 7.11e-16 | 74.3 |
| Msa0048800 | AT3G06160.2 | 29.221 | 154 | 94 | 2 | 6 | 159 | 67 | 205 | 1.54e-15 | 73.6 |
| Msa0048800 | AT3G18960.1 | 38.614 | 101 | 58 | 3 | 8 | 107 | 30 | 127 | 2.81e-12 | 62.8 |
| Msa0048800 | AT3G18960.2 | 38.614 | 101 | 58 | 3 | 8 | 107 | 30 | 127 | 4.23e-12 | 62.0 |
| Msa0048800 | AT3G18960.3 | 38.824 | 85 | 49 | 2 | 23 | 107 | 9 | 90 | 3.52e-11 | 59.3 |
| Msa0048800 | AT4G01580.1 | 36.364 | 99 | 59 | 3 | 8 | 105 | 30 | 125 | 3.91e-11 | 59.3 |
| Msa0048800 | AT5G57720.1 | 26.087 | 138 | 93 | 3 | 3 | 133 | 8 | 143 | 5.29e-11 | 60.5 |
| Msa0048800 | AT3G53310.1 | 33.735 | 83 | 53 | 1 | 5 | 87 | 8 | 88 | 6.73e-11 | 60.1 |
| Msa0048800 | AT3G06220.1 | 28.049 | 164 | 96 | 4 | 6 | 166 | 8 | 152 | 6.74e-11 | 58.5 |
Find 29 sgRNAs with CRISPR-Local
Find 45 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| ATCAAGTTCATAAAAGCATT+TGG | 0.283969 | 1_2:+1590963 | None:intergenic |
| TAGAGAAGAAAATTCTTTAG+AGG | 0.312899 | 1_2:-1590820 | Msa0048800:CDS |
| TGCTGCTGATGATGATATTA+TGG | 0.325258 | 1_2:-1590604 | Msa0048800:CDS |
| CGAGAATGAAAGAATGTATA+AGG | 0.343428 | 1_2:-1590535 | Msa0048800:CDS |
| TGAACTTGATGCGTTCAAAA+AGG | 0.345818 | 1_2:-1590950 | Msa0048800:CDS |
| GAGATCGCAGGGGAAGATAT+TGG | 0.394933 | 1_2:-1590902 | Msa0048800:CDS |
| ATCTTCCCCTGCGATCTCTT+AGG | 0.396615 | 1_2:+1590907 | None:intergenic |
| TCAAGTTCATAAAAGCATTT+GGG | 0.400504 | 1_2:+1590964 | None:intergenic |
| ATATTGAAAACAACAAATTC+AGG | 0.439326 | 1_2:-1590773 | Msa0048800:CDS |
| TATGATGGAGGATGAGGAAG+AGG | 0.443474 | 1_2:-1590682 | Msa0048800:CDS |
| CATGTCAAAGCTCATCGTAT+TGG | 0.475966 | 1_2:-1590879 | Msa0048800:CDS |
| GAAGAAGTCTGGGTAATCCT+TGG | 0.492866 | 1_2:+1591237 | None:intergenic |
| TAATAATATGATGGAGGATG+AGG | 0.497070 | 1_2:-1590688 | Msa0048800:CDS |
| AGAAGAAAATTCTTTAGAGG+AGG | 0.500908 | 1_2:-1590817 | Msa0048800:CDS |
| GGAGGAAAATAATAATATGA+TGG | 0.518357 | 1_2:-1590697 | Msa0048800:CDS |
| ATCAATGTGTGAAAAGAAGA+AGG | 0.520397 | 1_2:-1590730 | Msa0048800:CDS |
| AGAGAAGCACGCTGAAAGAA+TGG | 0.532134 | 1_2:-1591200 | Msa0048800:intron |
| GATGAGGAAGAGGACGATGA+TGG | 0.534431 | 1_2:-1590672 | Msa0048800:CDS |
| GGAAAATAATAATATGATGG+AGG | 0.559551 | 1_2:-1590694 | Msa0048800:CDS |
| GCCGTCATCACCATCACCAT+TGG | 0.574672 | 1_2:+1590560 | None:intergenic |
| GAAGAAGGTAAGTGACGTGG+AGG | 0.599885 | 1_2:-1590715 | Msa0048800:CDS |
| AATTGTAACTAAGATGGCCA+AGG | 0.605912 | 1_2:-1591254 | None:intergenic |
| ACCAATGGTGATGGTGATGA+CGG | 0.607997 | 1_2:-1590561 | Msa0048800:CDS |
| GAAGAACATCATGATACCAA+TGG | 0.623557 | 1_2:-1590576 | Msa0048800:CDS |
| TGATGATGATATTATGGCAG+AGG | 0.627493 | 1_2:-1590598 | Msa0048800:CDS |
| TCTTTCAGCGTGCTTCTCTG+AGG | 0.632246 | 1_2:+1591204 | None:intergenic |
| CATCATGATACCAATGGTGA+TGG | 0.638805 | 1_2:-1590570 | Msa0048800:CDS |
| AAAGAAGAAGGTAAGTGACG+TGG | 0.663180 | 1_2:-1590718 | Msa0048800:CDS |
| TTTATCCTAAGAGATCGCAG+GGG | 0.779931 | 1_2:-1590912 | Msa0048800:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | TAGAAAAAAAAAATAATTGG+AGG | + | chr1_2:1590614-1590633 | None:intergenic | 15.0% |
| !!! | TTTTGATAAAAAAACCAGTT+TGG | - | chr1_2:1590637-1590656 | Msa0048800:CDS | 20.0% |
| !! | TTTCAATATGTGTAAAAACA+AGG | + | chr1_2:1590975-1590994 | None:intergenic | 20.0% |
| !! | ATATTGAAAACAACAAATTC+AGG | - | chr1_2:1590986-1591005 | Msa0048800:intron | 20.0% |
| !! | AAAAAACTTTGAAGAAGTCT+GGG | + | chr1_2:1590535-1590554 | None:intergenic | 25.0% |
| ! | AAAAATAATTGGAGGAAGAA+TGG | + | chr1_2:1590606-1590625 | None:intergenic | 25.0% |
| !!! | TCAAGTTCATAAAAGCATTT+GGG | + | chr1_2:1590798-1590817 | None:intergenic | 25.0% |
| !!! | ATCAAGTTCATAAAAGCATT+TGG | + | chr1_2:1590799-1590818 | None:intergenic | 25.0% |
| ! | TTCAAAAAGGAAGGTAATAA+AGG | - | chr1_2:1590822-1590841 | Msa0048800:CDS | 25.0% |
| ! | TAGAGAAGAAAATTCTTTAG+AGG | - | chr1_2:1590939-1590958 | Msa0048800:CDS | 25.0% |
| ! | GGAGGAAAATAATAATATGA+TGG | - | chr1_2:1591062-1591081 | Msa0048800:intron | 25.0% |
| ! | GGAAAATAATAATATGATGG+AGG | - | chr1_2:1591065-1591084 | Msa0048800:intron | 25.0% |
| ! | GAAAAAACTTTGAAGAAGTC+TGG | + | chr1_2:1590536-1590555 | None:intergenic | 30.0% |
| TATATCTTTGCATACCAAAC+TGG | + | chr1_2:1590654-1590673 | None:intergenic | 30.0% | |
| !!! | GATGAGCTTTATTTTGATGA+TGG | - | chr1_2:1590904-1590923 | Msa0048800:CDS | 30.0% |
| !!! | AGCTTTATTTTGATGATGGT+TGG | - | chr1_2:1590908-1590927 | Msa0048800:CDS | 30.0% |
| ! | AGAAGAAAATTCTTTAGAGG+AGG | - | chr1_2:1590942-1590961 | Msa0048800:CDS | 30.0% |
| ATCAATGTGTGAAAAGAAGA+AGG | - | chr1_2:1591029-1591048 | Msa0048800:intron | 30.0% | |
| ! | TAATAATATGATGGAGGATG+AGG | - | chr1_2:1591071-1591090 | Msa0048800:intron | 30.0% |
| CGAGAATGAAAGAATGTATA+AGG | - | chr1_2:1591224-1591243 | Msa0048800:CDS | 30.0% | |
| CTGAGGAGATAACATTACTT+GGG | + | chr1_2:1590683-1590702 | None:intergenic | 35.0% | |
| TCTGAGGAGATAACATTACT+TGG | + | chr1_2:1590684-1590703 | None:intergenic | 35.0% | |
| AATACACTTCTTAGACTCTG+AGG | + | chr1_2:1590700-1590719 | None:intergenic | 35.0% | |
| TGAACTTGATGCGTTCAAAA+AGG | - | chr1_2:1590809-1590828 | Msa0048800:CDS | 35.0% | |
| ! | ATTTTATCCTAAGAGATCGC+AGG | - | chr1_2:1590845-1590864 | Msa0048800:CDS | 35.0% |
| ! | TTTTATCCTAAGAGATCGCA+GGG | - | chr1_2:1590846-1590865 | Msa0048800:CDS | 35.0% |
| ! | TGCTGCTGATGATGATATTA+TGG | - | chr1_2:1591155-1591174 | Msa0048800:intron | 35.0% |
| ! | TGATGATGATATTATGGCAG+AGG | - | chr1_2:1591161-1591180 | Msa0048800:intron | 35.0% |
| GAAGAACATCATGATACCAA+TGG | - | chr1_2:1591183-1591202 | Msa0048800:intron | 35.0% | |
| CTTGATGCGTTCAAAAAGGA+AGG | - | chr1_2:1590813-1590832 | Msa0048800:CDS | 40.0% | |
| TTTATCCTAAGAGATCGCAG+GGG | - | chr1_2:1590847-1590866 | Msa0048800:CDS | 40.0% | |
| CATGTCAAAGCTCATCGTAT+TGG | - | chr1_2:1590880-1590899 | Msa0048800:CDS | 40.0% | |
| AAAGAAGAAGGTAAGTGACG+TGG | - | chr1_2:1591041-1591060 | Msa0048800:intron | 40.0% | |
| CATCATGATACCAATGGTGA+TGG | - | chr1_2:1591189-1591208 | Msa0048800:intron | 40.0% | |
| GAAGAAGTCTGGGTAATCCT+TGG | + | chr1_2:1590525-1590544 | None:intergenic | 45.0% | |
| ! | AGAGAAGCACGCTGAAAGAA+TGG | - | chr1_2:1590559-1590578 | Msa0048800:CDS | 45.0% |
| ! | TATGATGGAGGATGAGGAAG+AGG | - | chr1_2:1591077-1591096 | Msa0048800:intron | 45.0% |
| !! | ACCAATGGTGATGGTGATGA+CGG | - | chr1_2:1591198-1591217 | Msa0048800:intron | 45.0% |
| !! | AAATAGAAAAAAAAAATAAT+TGG | + | chr1_2:1590617-1590636 | None:intergenic | 5.0% |
| TCTTTCAGCGTGCTTCTCTG+AGG | + | chr1_2:1590558-1590577 | None:intergenic | 50.0% | |
| ATCTTCCCCTGCGATCTCTT+AGG | + | chr1_2:1590855-1590874 | None:intergenic | 50.0% | |
| GAGATCGCAGGGGAAGATAT+TGG | - | chr1_2:1590857-1590876 | Msa0048800:CDS | 50.0% | |
| GAAGAAGGTAAGTGACGTGG+AGG | - | chr1_2:1591044-1591063 | Msa0048800:intron | 50.0% | |
| GATGAGGAAGAGGACGATGA+TGG | - | chr1_2:1591087-1591106 | Msa0048800:intron | 50.0% | |
| GCCGTCATCACCATCACCAT+TGG | + | chr1_2:1591202-1591221 | None:intergenic | 55.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr1_2 | gene | 1590518 | 1591263 | 1590518 | ID=Msa0048800;Name=Msa0048800 |
| chr1_2 | mRNA | 1590518 | 1591263 | 1590518 | ID=Msa0048800-mRNA-1;Parent=Msa0048800;Name=Msa0048800-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0|0|1|1|1|2|0|178 |
| chr1_2 | exon | 1591201 | 1591263 | 1591201 | ID=Msa0048800-mRNA-1:exon:338;Parent=Msa0048800-mRNA-1 |
| chr1_2 | exon | 1590518 | 1590991 | 1590518 | ID=Msa0048800-mRNA-1:exon:337;Parent=Msa0048800-mRNA-1 |
| chr1_2 | CDS | 1591201 | 1591263 | 1591201 | ID=Msa0048800-mRNA-1:cds;Parent=Msa0048800-mRNA-1 |
| chr1_2 | CDS | 1590518 | 1590991 | 1590518 | ID=Msa0048800-mRNA-1:cds;Parent=Msa0048800-mRNA-1 |
| Gene Sequence |
| Protein sequence |
