Alfalfa Gene Editing Database
Alfalfa Gene Editing Database
Nr:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene049540.t1 | KEH34477.1 | 86.5 | 133 | 18 | 0 | 1 | 133 | 29 | 161 | 2.50E-56 | 228 |
Swissprot:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene049540.t1 | Q9FJK3 | 44.1 | 127 | 70 | 1 | 1 | 127 | 29 | 154 | 9.2e-23 | 107.8 |
Trembl:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene049540.t1 | A0A072UY35 | 86.5 | 133 | 18 | 0 | 1 | 133 | 29 | 161 | 1.8e-56 | 228.0 |
TFs/TRs:
| Gene ID | Type | Classification |
|---|---|---|
| MS.gene049540.t1 | TF | MADS-M-type |
Protein Kinases:
| Gene ID | Type | Classification |
|---|
Network:
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene049540.t1 | MTR_3g467080 | 86.466 | 133 | 18 | 0 | 1 | 133 | 29 | 161 | 9.72e-83 | 239 |
| MS.gene049540.t1 | MTR_4g063790 | 77.444 | 133 | 30 | 0 | 1 | 133 | 29 | 161 | 6.95e-71 | 210 |
| MS.gene049540.t1 | MTR_3g465410 | 75.188 | 133 | 33 | 0 | 1 | 133 | 1 | 133 | 2.57e-69 | 205 |
| MS.gene049540.t1 | MTR_3g466980 | 52.756 | 127 | 57 | 2 | 1 | 126 | 29 | 153 | 3.52e-40 | 134 |
| MS.gene049540.t1 | MTR_3g031100 | 44.697 | 132 | 73 | 0 | 1 | 132 | 29 | 160 | 1.05e-33 | 118 |
| MS.gene049540.t1 | MTR_3g065100 | 45.528 | 123 | 66 | 1 | 4 | 126 | 32 | 153 | 3.44e-33 | 116 |
| MS.gene049540.t1 | MTR_3g031240 | 45.736 | 129 | 70 | 0 | 1 | 129 | 29 | 157 | 2.07e-31 | 110 |
| MS.gene049540.t1 | MTR_4g032290 | 42.308 | 130 | 75 | 0 | 4 | 133 | 32 | 161 | 2.23e-30 | 109 |
| MS.gene049540.t1 | MTR_2g035580 | 45.600 | 125 | 67 | 1 | 2 | 126 | 30 | 153 | 4.86e-29 | 103 |
| MS.gene049540.t1 | MTR_4g032260 | 39.024 | 123 | 75 | 0 | 6 | 128 | 34 | 156 | 6.04e-29 | 103 |
| MS.gene049540.t1 | MTR_2g016210 | 40.152 | 132 | 79 | 0 | 1 | 132 | 29 | 160 | 7.00e-29 | 105 |
| MS.gene049540.t1 | MTR_4g031910 | 40.800 | 125 | 74 | 0 | 4 | 128 | 32 | 156 | 4.88e-28 | 103 |
| MS.gene049540.t1 | MTR_4g032620 | 36.508 | 126 | 80 | 0 | 1 | 126 | 29 | 154 | 5.86e-27 | 100 |
| MS.gene049540.t1 | MTR_2g035610 | 48.352 | 91 | 47 | 0 | 4 | 94 | 32 | 122 | 4.54e-26 | 95.1 |
| MS.gene049540.t1 | MTR_5g075380 | 36.508 | 126 | 79 | 1 | 1 | 126 | 29 | 153 | 1.04e-25 | 95.5 |
| MS.gene049540.t1 | MTR_8g036130 | 39.695 | 131 | 77 | 1 | 1 | 129 | 29 | 159 | 8.99e-25 | 95.1 |
| MS.gene049540.t1 | MTR_3g466830 | 40.000 | 125 | 74 | 1 | 1 | 125 | 28 | 151 | 1.37e-23 | 89.7 |
| MS.gene049540.t1 | MTR_3g466900 | 34.921 | 126 | 81 | 1 | 4 | 129 | 2 | 126 | 3.86e-20 | 80.1 |
| MS.gene049540.t1 | MTR_1g077320 | 33.858 | 127 | 80 | 3 | 4 | 129 | 32 | 155 | 6.72e-19 | 77.8 |
| MS.gene049540.t1 | MTR_3g466890 | 36.000 | 125 | 79 | 1 | 2 | 126 | 29 | 152 | 1.79e-18 | 76.6 |
| MS.gene049540.t1 | MTR_3g466930 | 35.772 | 123 | 78 | 1 | 4 | 126 | 2 | 123 | 2.71e-18 | 75.5 |
| MS.gene049540.t1 | MTR_5g047580 | 33.333 | 129 | 84 | 2 | 1 | 129 | 29 | 155 | 2.48e-17 | 73.6 |
| MS.gene049540.t1 | MTR_1g077300 | 30.769 | 130 | 86 | 2 | 4 | 133 | 32 | 157 | 5.84e-17 | 72.8 |
| MS.gene049540.t1 | MTR_4g028720 | 31.746 | 126 | 84 | 2 | 4 | 129 | 32 | 155 | 6.65e-17 | 72.8 |
| MS.gene049540.t1 | MTR_7g011950 | 30.952 | 126 | 85 | 2 | 4 | 129 | 32 | 155 | 9.46e-17 | 72.4 |
| MS.gene049540.t1 | MTR_1g090783 | 30.233 | 129 | 88 | 2 | 1 | 129 | 28 | 154 | 1.70e-16 | 71.6 |
| MS.gene049540.t1 | MTR_7g055800 | 41.667 | 84 | 34 | 1 | 3 | 86 | 18 | 86 | 3.55e-16 | 68.9 |
| MS.gene049540.t1 | MTR_1g077390 | 34.848 | 132 | 78 | 4 | 1 | 129 | 29 | 155 | 4.45e-16 | 70.5 |
| MS.gene049540.t1 | MTR_1g084950 | 29.921 | 127 | 85 | 3 | 4 | 129 | 32 | 155 | 1.62e-15 | 68.9 |
| MS.gene049540.t1 | MTR_7g055940 | 40.789 | 76 | 30 | 1 | 3 | 78 | 18 | 78 | 9.74e-14 | 62.4 |
| MS.gene049540.t1 | MTR_1g090697 | 29.134 | 127 | 86 | 3 | 1 | 126 | 29 | 152 | 3.86e-13 | 62.8 |
| MS.gene049540.t1 | MTR_1g090710 | 28.906 | 128 | 86 | 3 | 1 | 126 | 29 | 153 | 2.87e-12 | 60.5 |
| MS.gene049540.t1 | MTR_4g084780 | 53.704 | 54 | 25 | 0 | 46 | 99 | 1 | 54 | 9.11e-12 | 58.9 |
| MS.gene049540.t1 | MTR_4g028800 | 48.889 | 45 | 23 | 0 | 1 | 45 | 27 | 71 | 1.90e-11 | 56.2 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene049540.t1 | AT5G48670 | 44.000 | 125 | 67 | 2 | 4 | 127 | 32 | 154 | 1.80e-28 | 106 |
| MS.gene049540.t1 | AT5G27810 | 51.685 | 89 | 43 | 0 | 1 | 89 | 1 | 89 | 1.44e-27 | 99.0 |
| MS.gene049540.t1 | AT1G65300 | 38.636 | 132 | 79 | 2 | 2 | 133 | 29 | 158 | 2.29e-22 | 89.4 |
| MS.gene049540.t1 | AT1G65330 | 37.705 | 122 | 75 | 1 | 1 | 122 | 28 | 148 | 2.18e-19 | 81.6 |
| MS.gene049540.t1 | AT3G05860 | 38.710 | 124 | 71 | 2 | 1 | 122 | 29 | 149 | 3.21e-19 | 79.7 |
| MS.gene049540.t1 | AT3G05860 | 45.161 | 93 | 47 | 1 | 1 | 89 | 29 | 121 | 8.14e-19 | 79.7 |
| MS.gene049540.t1 | AT3G05860 | 47.191 | 89 | 43 | 1 | 1 | 85 | 29 | 117 | 9.77e-19 | 79.7 |
| MS.gene049540.t1 | AT5G26650 | 32.558 | 129 | 86 | 1 | 1 | 129 | 27 | 154 | 3.50e-16 | 73.6 |
| MS.gene049540.t1 | AT5G26630 | 31.405 | 121 | 82 | 1 | 6 | 126 | 34 | 153 | 8.18e-16 | 71.2 |
| MS.gene049540.t1 | AT1G31640 | 35.606 | 132 | 71 | 4 | 2 | 127 | 29 | 152 | 1.59e-14 | 69.3 |
| MS.gene049540.t1 | AT5G27960 | 30.233 | 129 | 89 | 1 | 1 | 129 | 27 | 154 | 3.84e-14 | 67.8 |
| MS.gene049540.t1 | AT5G26865 | 45.455 | 66 | 35 | 1 | 2 | 66 | 8 | 73 | 2.80e-12 | 59.7 |
| MS.gene049540.t1 | AT2G28700 | 30.328 | 122 | 84 | 1 | 1 | 122 | 29 | 149 | 3.60e-12 | 62.4 |
| MS.gene049540.t1 | AT1G22590 | 28.788 | 132 | 77 | 2 | 1 | 129 | 29 | 146 | 2.47e-11 | 58.2 |
| MS.gene049540.t1 | AT5G06500 | 34.146 | 82 | 50 | 1 | 1 | 82 | 29 | 106 | 7.55e-11 | 58.2 |
Find 28 sgRNAs with CRISPR-Local
Find 32 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| ATTGGTCATTTCCTGCTTTC+TGG | 0.066665 | 3.2:-57737979 | None:intergenic |
| ATTCATACCACAGAATTTAA+TGG | 0.196701 | 3.2:+57738017 | MS.gene049540:CDS |
| CAGGTTTGGCCATCAGATTC+AGG | 0.232242 | 3.2:+57737822 | MS.gene049540:CDS |
| GTTCAAGAGTTTGCATGAAC+TGG | 0.380322 | 3.2:+57737866 | MS.gene049540:CDS |
| GATGAAATTAGCACTCTTTG+TGG | 0.382102 | 3.2:+57737753 | MS.gene049540:CDS |
| AATGAAATGATGAATGATAT+TGG | 0.442815 | 3.2:-57737997 | None:intergenic |
| ACAATCCTCAAGTACAGGTT+TGG | 0.465441 | 3.2:+57737808 | MS.gene049540:CDS |
| GAGGACAAATCATTAAGATC+AGG | 0.474701 | 3.2:-57738056 | None:intergenic |
| TATTCTTGAGGCAAACCATT+GGG | 0.481117 | 3.2:+57737919 | MS.gene049540:CDS |
| AGGTTTGGCCATCAGATTCA+GGG | 0.491311 | 3.2:+57737823 | MS.gene049540:CDS |
| GGGTTAGAAGTGTGATATCC+AGG | 0.506627 | 3.2:+57737844 | MS.gene049540:CDS |
| AAGGAAGGAAACCAGAAAGC+AGG | 0.520416 | 3.2:+57737968 | MS.gene049540:CDS |
| CAAATTCTCAGCAATAAAAG+AGG | 0.520681 | 3.2:-57738075 | None:intergenic |
| CTATTCTTGAGGCAAACCAT+TGG | 0.534098 | 3.2:+57737918 | MS.gene049540:CDS |
| TAAATATCCATTAAATTCTG+TGG | 0.554522 | 3.2:-57738024 | None:intergenic |
| TTGCTCGTAAATTATTGCAC+CGG | 0.562136 | 3.2:-57737784 | None:intergenic |
| GCAAAACAATCCTCAAGTAC+AGG | 0.563776 | 3.2:+57737803 | MS.gene049540:CDS |
| CTGCTCATAGACTTTCCCAA+TGG | 0.579151 | 3.2:-57737934 | None:intergenic |
| TTCATGCAAACTCTTGAACC+TGG | 0.581655 | 3.2:-57737862 | None:intergenic |
| ACTCTTTGTGGAATAGAAGC+CGG | 0.588115 | 3.2:+57737765 | MS.gene049540:CDS |
| GAGGTCGATCAAAAGATGAA+AGG | 0.605953 | 3.2:+57738101 | MS.gene049540:CDS |
| CTTCTAACCCCTGAATCTGA+TGG | 0.608216 | 3.2:-57737831 | None:intergenic |
| GATGGCCAAACCTGTACTTG+AGG | 0.609083 | 3.2:-57737813 | None:intergenic |
| ATGAGCAGATGATGAAACAA+AGG | 0.611511 | 3.2:+57737949 | MS.gene049540:CDS |
| GGTTTGGCCATCAGATTCAG+GGG | 0.628974 | 3.2:+57737824 | MS.gene049540:CDS |
| TATTGCTGAGAATTTGAGGG+AGG | 0.639350 | 3.2:+57738082 | MS.gene049540:CDS |
| GCAGATGATGAAACAAAGGA+AGG | 0.642572 | 3.2:+57737953 | MS.gene049540:CDS |
| TGGATCAAGAGCTATTCTTG+AGG | 0.708311 | 3.2:+57737907 | MS.gene049540:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | AATGAAATGATGAATGATAT+TGG | - | chr3.2:57738000-57738019 | None:intergenic | 20.0% |
| !! | TAAATATCCATTAAATTCTG+TGG | - | chr3.2:57738027-57738046 | None:intergenic | 20.0% |
| ! | ATTCATACCACAGAATTTAA+TGG | + | chr3.2:57738017-57738036 | MS.gene049540:CDS | 25.0% |
| !! | TTTTATTGCTGAGAATTTGA+GGG | + | chr3.2:57738079-57738098 | MS.gene049540:CDS | 25.0% |
| ACTGGAACAAAGTAAAAAGA+TGG | + | chr3.2:57737884-57737903 | MS.gene049540:CDS | 30.0% | |
| CAAATTCTCAGCAATAAAAG+AGG | - | chr3.2:57738078-57738097 | None:intergenic | 30.0% | |
| ! | CTTTTATTGCTGAGAATTTG+AGG | + | chr3.2:57738078-57738097 | MS.gene049540:CDS | 30.0% |
| ATGAGCAGATGATGAAACAA+AGG | + | chr3.2:57737949-57737968 | MS.gene049540:CDS | 35.0% | |
| GAGGACAAATCATTAAGATC+AGG | - | chr3.2:57738059-57738078 | None:intergenic | 35.0% | |
| GATGAAATTAGCACTCTTTG+TGG | + | chr3.2:57737753-57737772 | MS.gene049540:CDS | 35.0% | |
| GGAACAAAGTAAAAAGATGG+TGG | + | chr3.2:57737887-57737906 | MS.gene049540:CDS | 35.0% | |
| TATTCTTGAGGCAAACCATT+GGG | + | chr3.2:57737919-57737938 | MS.gene049540:CDS | 35.0% | |
| TTGCTCGTAAATTATTGCAC+CGG | - | chr3.2:57737787-57737806 | None:intergenic | 35.0% | |
| ACAATCCTCAAGTACAGGTT+TGG | + | chr3.2:57737808-57737827 | MS.gene049540:CDS | 40.0% | |
| ACTCTTTGTGGAATAGAAGC+CGG | + | chr3.2:57737765-57737784 | MS.gene049540:CDS | 40.0% | |
| ATTGGTCATTTCCTGCTTTC+TGG | - | chr3.2:57737982-57738001 | None:intergenic | 40.0% | |
| CTATTCTTGAGGCAAACCAT+TGG | + | chr3.2:57737918-57737937 | MS.gene049540:CDS | 40.0% | |
| GAGGTCGATCAAAAGATGAA+AGG | + | chr3.2:57738101-57738120 | MS.gene049540:CDS | 40.0% | |
| GCAAAACAATCCTCAAGTAC+AGG | + | chr3.2:57737803-57737822 | MS.gene049540:CDS | 40.0% | |
| GCAGATGATGAAACAAAGGA+AGG | + | chr3.2:57737953-57737972 | MS.gene049540:CDS | 40.0% | |
| GTTCAAGAGTTTGCATGAAC+TGG | + | chr3.2:57737866-57737885 | MS.gene049540:CDS | 40.0% | |
| TATTGCTGAGAATTTGAGGG+AGG | + | chr3.2:57738082-57738101 | MS.gene049540:CDS | 40.0% | |
| TGGATCAAGAGCTATTCTTG+AGG | + | chr3.2:57737907-57737926 | MS.gene049540:CDS | 40.0% | |
| TTCATGCAAACTCTTGAACC+TGG | - | chr3.2:57737865-57737884 | None:intergenic | 40.0% | |
| AAGGAAGGAAACCAGAAAGC+AGG | + | chr3.2:57737968-57737987 | MS.gene049540:CDS | 45.0% | |
| AGGTTTGGCCATCAGATTCA+GGG | + | chr3.2:57737823-57737842 | MS.gene049540:CDS | 45.0% | |
| CTGCTCATAGACTTTCCCAA+TGG | - | chr3.2:57737937-57737956 | None:intergenic | 45.0% | |
| CTTCTAACCCCTGAATCTGA+TGG | - | chr3.2:57737834-57737853 | None:intergenic | 45.0% | |
| ! | GGGTTAGAAGTGTGATATCC+AGG | + | chr3.2:57737844-57737863 | MS.gene049540:CDS | 45.0% |
| CAGGTTTGGCCATCAGATTC+AGG | + | chr3.2:57737822-57737841 | MS.gene049540:CDS | 50.0% | |
| GATGGCCAAACCTGTACTTG+AGG | - | chr3.2:57737816-57737835 | None:intergenic | 50.0% | |
| GGTTTGGCCATCAGATTCAG+GGG | + | chr3.2:57737824-57737843 | MS.gene049540:CDS | 50.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3.2 | gene | 57737741 | 57738142 | 57737741 | ID=MS.gene049540 |
| chr3.2 | mRNA | 57737741 | 57738142 | 57737741 | ID=MS.gene049540.t1;Parent=MS.gene049540 |
| chr3.2 | exon | 57737741 | 57738142 | 57737741 | ID=MS.gene049540.t1.exon1;Parent=MS.gene049540.t1 |
| chr3.2 | CDS | 57737741 | 57738142 | 57737741 | ID=cds.MS.gene049540.t1;Parent=MS.gene049540.t1 |
| Gene Sequence |
| Protein sequence |
