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.gene012816.t1 | XP_003603145.1 | 95 | 140 | 7 | 0 | 1 | 140 | 91 | 230 | 4.70E-72 | 280.4 |
Swissprot:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene012816.t1 | Q9LVS0 | 70.3 | 64 | 16 | 1 | 2 | 65 | 97 | 157 | 2.3e-19 | 96.7 |
Trembl:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene012816.t1 | G7J7M5 | 95.0 | 140 | 7 | 0 | 1 | 140 | 91 | 230 | 3.4e-72 | 280.4 |
TFs/TRs:
| Gene ID | Type | Classification |
|---|---|---|
| MS.gene012816.t1 | TF | MYB-related |
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.gene012816.t1 | MTR_3g104370 | 95.000 | 140 | 7 | 0 | 1 | 140 | 91 | 230 | 1.41e-95 | 275 |
| MS.gene012816.t1 | MTR_4g100630 | 54.545 | 88 | 36 | 2 | 2 | 88 | 96 | 180 | 8.51e-26 | 99.8 |
| MS.gene012816.t1 | MTR_6g092540 | 58.333 | 84 | 31 | 2 | 1 | 83 | 97 | 177 | 2.34e-25 | 97.8 |
| MS.gene012816.t1 | MTR_8g101650 | 61.111 | 72 | 25 | 1 | 1 | 72 | 105 | 173 | 2.13e-24 | 95.1 |
| MS.gene012816.t1 | MTR_2g100930 | 66.154 | 65 | 19 | 1 | 1 | 65 | 109 | 170 | 1.42e-23 | 94.4 |
| MS.gene012816.t1 | MTR_5g069710 | 49.485 | 97 | 42 | 2 | 1 | 97 | 132 | 221 | 2.91e-23 | 92.8 |
| MS.gene012816.t1 | MTR_3g462790 | 56.410 | 78 | 27 | 2 | 1 | 78 | 147 | 217 | 1.70e-21 | 88.2 |
| MS.gene012816.t1 | MTR_7g067080 | 67.797 | 59 | 19 | 0 | 1 | 59 | 140 | 198 | 1.74e-21 | 88.2 |
| MS.gene012816.t1 | MTR_4g111975 | 57.353 | 68 | 26 | 1 | 1 | 68 | 138 | 202 | 2.95e-21 | 87.4 |
| MS.gene012816.t1 | MTR_1g111830 | 69.492 | 59 | 16 | 1 | 2 | 60 | 125 | 181 | 3.31e-21 | 86.3 |
| MS.gene012816.t1 | MTR_4g107230 | 74.468 | 47 | 12 | 0 | 1 | 47 | 84 | 130 | 5.34e-21 | 86.3 |
| MS.gene012816.t1 | MTR_5g037080 | 75.000 | 48 | 12 | 0 | 1 | 48 | 102 | 149 | 6.21e-21 | 86.7 |
| MS.gene012816.t1 | MTR_5g081860 | 70.370 | 54 | 16 | 0 | 1 | 54 | 125 | 178 | 1.04e-20 | 85.5 |
| MS.gene012816.t1 | MTR_5g027570 | 51.316 | 76 | 36 | 1 | 3 | 78 | 94 | 168 | 4.85e-20 | 82.8 |
| MS.gene012816.t1 | MTR_5g088010 | 50.000 | 70 | 35 | 0 | 3 | 72 | 62 | 131 | 5.54e-20 | 83.2 |
| MS.gene012816.t1 | MTR_2g090305 | 59.322 | 59 | 24 | 0 | 1 | 59 | 28 | 86 | 1.51e-19 | 80.5 |
| MS.gene012816.t1 | MTR_1g048660 | 71.739 | 46 | 13 | 0 | 2 | 47 | 13 | 58 | 1.64e-19 | 77.8 |
| MS.gene012816.t1 | MTR_5g088060 | 54.688 | 64 | 29 | 0 | 3 | 66 | 274 | 337 | 3.52e-19 | 82.8 |
| MS.gene012816.t1 | MTR_5g488160 | 54.688 | 64 | 29 | 0 | 3 | 66 | 274 | 337 | 3.52e-19 | 82.8 |
| MS.gene012816.t1 | MTR_0036s0260 | 59.322 | 59 | 24 | 0 | 1 | 59 | 28 | 86 | 4.27e-19 | 79.7 |
| MS.gene012816.t1 | MTR_8g063600 | 52.703 | 74 | 34 | 1 | 1 | 74 | 106 | 178 | 8.10e-17 | 75.1 |
| MS.gene012816.t1 | MTR_5g027550 | 65.217 | 46 | 16 | 0 | 3 | 48 | 79 | 124 | 1.67e-16 | 73.6 |
| MS.gene012816.t1 | MTR_4g015130 | 62.745 | 51 | 19 | 0 | 9 | 59 | 1 | 51 | 2.01e-16 | 69.7 |
| MS.gene012816.t1 | MTR_8g063870 | 50.000 | 68 | 32 | 1 | 3 | 68 | 94 | 161 | 1.80e-15 | 71.2 |
| MS.gene012816.t1 | MTR_1g083180 | 49.231 | 65 | 32 | 1 | 3 | 67 | 63 | 126 | 2.91e-14 | 66.6 |
| MS.gene012816.t1 | MTR_3g070110 | 48.571 | 70 | 32 | 1 | 3 | 68 | 97 | 166 | 4.46e-13 | 63.9 |
| MS.gene012816.t1 | MTR_5g075790 | 64.583 | 48 | 16 | 1 | 3 | 50 | 115 | 161 | 7.32e-13 | 63.5 |
| MS.gene012816.t1 | MTR_5g075760 | 64.583 | 48 | 16 | 1 | 3 | 50 | 107 | 153 | 8.38e-13 | 63.5 |
| MS.gene012816.t1 | MTR_7g110040 | 78.378 | 37 | 7 | 1 | 14 | 50 | 11 | 46 | 1.06e-12 | 59.3 |
| MS.gene012816.t1 | MTR_1g033620 | 48.438 | 64 | 30 | 1 | 16 | 79 | 20 | 80 | 1.49e-12 | 63.2 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene012816.t1 | AT5G56840 | 46.617 | 133 | 67 | 2 | 1 | 133 | 91 | 219 | 2.68e-25 | 96.7 |
| MS.gene012816.t1 | AT5G47390 | 55.952 | 84 | 25 | 2 | 2 | 85 | 97 | 168 | 5.50e-25 | 98.2 |
| MS.gene012816.t1 | AT2G38090 | 66.102 | 59 | 20 | 0 | 1 | 59 | 141 | 199 | 5.00e-22 | 89.4 |
| MS.gene012816.t1 | AT5G58900 | 66.102 | 59 | 20 | 0 | 1 | 59 | 141 | 199 | 5.51e-22 | 89.0 |
| MS.gene012816.t1 | AT5G01200 | 64.407 | 59 | 21 | 0 | 1 | 59 | 146 | 204 | 1.16e-21 | 87.8 |
| MS.gene012816.t1 | AT5G61620 | 60.000 | 70 | 25 | 1 | 2 | 71 | 109 | 175 | 1.17e-21 | 88.6 |
| MS.gene012816.t1 | AT1G70000 | 78.723 | 47 | 10 | 0 | 2 | 48 | 99 | 145 | 1.83e-21 | 87.4 |
| MS.gene012816.t1 | AT1G70000 | 78.723 | 47 | 10 | 0 | 2 | 48 | 99 | 145 | 1.83e-21 | 87.4 |
| MS.gene012816.t1 | AT1G49010 | 60.294 | 68 | 24 | 2 | 1 | 68 | 134 | 198 | 2.65e-21 | 87.8 |
| MS.gene012816.t1 | AT3G16350 | 75.000 | 48 | 12 | 0 | 1 | 48 | 137 | 184 | 4.49e-21 | 87.8 |
| MS.gene012816.t1 | AT5G04760 | 53.750 | 80 | 31 | 2 | 2 | 77 | 100 | 177 | 2.12e-20 | 83.6 |
| MS.gene012816.t1 | AT5G08520 | 57.353 | 68 | 26 | 2 | 1 | 68 | 118 | 182 | 3.65e-20 | 84.3 |
| MS.gene012816.t1 | AT3G11280 | 64.407 | 59 | 21 | 0 | 1 | 59 | 127 | 185 | 1.11e-19 | 82.4 |
| MS.gene012816.t1 | AT3G11280 | 64.407 | 59 | 21 | 0 | 1 | 59 | 127 | 185 | 1.11e-19 | 82.4 |
| MS.gene012816.t1 | AT5G05790 | 64.407 | 59 | 21 | 0 | 1 | 59 | 131 | 189 | 2.14e-19 | 82.0 |
| MS.gene012816.t1 | AT5G05790 | 64.407 | 59 | 21 | 0 | 1 | 59 | 131 | 189 | 2.14e-19 | 82.0 |
| MS.gene012816.t1 | AT1G74840 | 70.213 | 47 | 14 | 0 | 1 | 47 | 96 | 142 | 3.29e-19 | 80.9 |
| MS.gene012816.t1 | AT4G09450 | 51.899 | 79 | 35 | 2 | 1 | 77 | 91 | 168 | 4.47e-19 | 79.7 |
| MS.gene012816.t1 | AT1G74840 | 70.213 | 47 | 14 | 0 | 1 | 47 | 96 | 142 | 4.66e-19 | 80.9 |
| MS.gene012816.t1 | AT1G19000 | 70.213 | 47 | 14 | 0 | 1 | 47 | 102 | 148 | 7.56e-19 | 80.5 |
| MS.gene012816.t1 | AT1G19000 | 70.213 | 47 | 14 | 0 | 1 | 47 | 102 | 148 | 7.56e-19 | 80.5 |
| MS.gene012816.t1 | AT3G10580 | 53.030 | 66 | 26 | 1 | 1 | 66 | 95 | 155 | 2.12e-18 | 79.0 |
| MS.gene012816.t1 | AT3G10580 | 53.030 | 66 | 26 | 1 | 1 | 66 | 95 | 155 | 3.11e-18 | 79.0 |
| MS.gene012816.t1 | AT3G10590 | 41.758 | 91 | 52 | 1 | 2 | 91 | 112 | 202 | 2.83e-13 | 64.7 |
| MS.gene012816.t1 | AT5G23650 | 63.830 | 47 | 17 | 0 | 1 | 47 | 120 | 166 | 4.03e-13 | 65.5 |
Find 34 sgRNAs with CRISPR-Local
Find 42 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| AGAAGCTTGGGAAGGGTAAC+TGG | 0.328316 | 3.3:+85853841 | MS.gene012816:CDS |
| CATGCCTCTGTTAGCTCTAA+TGG | 0.334233 | 3.3:-85854304 | None:intergenic |
| CTTATGCAGCTGATATCATT+TGG | 0.348494 | 3.3:-85854133 | None:intergenic |
| TTTGTGCATGACTAGCTACC+TGG | 0.362976 | 3.3:-85853905 | None:intergenic |
| TTTGGAGTCAAATTTATTCC+TGG | 0.373119 | 3.3:-85854115 | None:intergenic |
| AATTTCTACTTCCACTTAGT+TGG | 0.375503 | 3.3:-85854156 | None:intergenic |
| CTCAACATTCAATACTGAAA+TGG | 0.409371 | 3.3:+85854203 | MS.gene012816:CDS |
| CTTAGAGGACTTGAGAAGCT+TGG | 0.418302 | 3.3:+85853828 | MS.gene012816:CDS |
| TCCGTTGATGTTGAAGAGTT+AGG | 0.422454 | 3.3:-85854226 | None:intergenic |
| TTAGAGGACTTGAGAAGCTT+GGG | 0.428690 | 3.3:+85853829 | MS.gene012816:CDS |
| GCAAGTTTGAGTTCTAAATC+AGG | 0.432705 | 3.3:-85854271 | None:intergenic |
| GAGCACATGATATTTCTTAG+AGG | 0.438938 | 3.3:+85853813 | MS.gene012816:CDS |
| CTCTGTTAGCTCTAATGGCA+TGG | 0.487511 | 3.3:-85854299 | None:intergenic |
| TTACATAATGGAGGCTAAGA+TGG | 0.500282 | 3.3:-85853977 | None:intergenic |
| AAATCAGGTGCTGCACTATG+AGG | 0.523156 | 3.3:-85854256 | None:intergenic |
| TCTGTTAGCTCTAATGGCAT+GGG | 0.534114 | 3.3:-85854298 | None:intergenic |
| TGATCAAGCTATTCTGAGAC+TGG | 0.538315 | 3.3:-85853941 | None:intergenic |
| ACACTACTGGTTAGCTTAAG+GGG | 0.538405 | 3.3:-85854329 | None:intergenic |
| TTGTGCATGACTAGCTACCT+GGG | 0.547274 | 3.3:-85853904 | None:intergenic |
| TTAATTTACTTACATAATGG+AGG | 0.564586 | 3.3:-85853986 | None:intergenic |
| GGACTTGAGAAGCTTGGGAA+GGG | 0.571874 | 3.3:+85853834 | MS.gene012816:CDS |
| ATGTGCTCCTCCTCGGTCCA+CGG | 0.572063 | 3.3:-85853798 | None:intergenic |
| GCCTAACTCTTCAACATCAA+CGG | 0.576928 | 3.3:+85854225 | MS.gene012816:CDS |
| CATTTCAGTATTGAATGTTG+AGG | 0.583001 | 3.3:-85854202 | None:intergenic |
| AGCTGCATAAGCCAACTAAG+TGG | 0.584599 | 3.3:+85854145 | MS.gene012816:CDS |
| AAATATCATGTGCTCCTCCT+CGG | 0.585344 | 3.3:-85853805 | None:intergenic |
| AGGACTTGAGAAGCTTGGGA+AGG | 0.598172 | 3.3:+85853833 | MS.gene012816:CDS |
| ATCAGGTATGCCGTGGACCG+AGG | 0.606863 | 3.3:+85853788 | None:intergenic |
| GCATGACTAGCTACCTGGGT+TGG | 0.613754 | 3.3:-85853900 | None:intergenic |
| CTTGGGAAGGGTAACTGGAG+AGG | 0.645821 | 3.3:+85853846 | MS.gene012816:CDS |
| AGGTATGCCGTGGACCGAGG+AGG | 0.665092 | 3.3:+85853791 | None:intergenic |
| TCAAGCTATTCTGAGACTGG+CGG | 0.679211 | 3.3:-85853938 | None:intergenic |
| TGAGGATGAGAAAGCCACTG+AGG | 0.730112 | 3.3:-85854184 | None:intergenic |
| CATGCCATTAGAGCTAACAG+AGG | 0.740508 | 3.3:+85854300 | MS.gene012816:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | AAATTAAATATAGAATAAGA+TGG | - | chr3.3:85854075-85854094 | None:intergenic | 10.0% |
| !! | ATCTTATTCTATATTTAATT+TGG | + | chr3.3:85854074-85854093 | MS.gene012816:intron | 10.0% |
| !!! | ATTTTAATTTACTTACATAA+TGG | - | chr3.3:85853992-85854011 | None:intergenic | 10.0% |
| !!! | AATTAAAGAAGTTTAAAGTA+AGG | - | chr3.3:85854048-85854067 | None:intergenic | 15.0% |
| !! | TTAATTTACTTACATAATGG+AGG | - | chr3.3:85853989-85854008 | None:intergenic | 20.0% |
| !!! | TATTCTATATTTAATTTGGC+AGG | + | chr3.3:85854078-85854097 | MS.gene012816:intron | 20.0% |
| !!! | TGCACGTAACTATTTTTATA+TGG | - | chr3.3:85854021-85854040 | None:intergenic | 25.0% |
| AATTTCTACTTCCACTTAGT+TGG | - | chr3.3:85854159-85854178 | None:intergenic | 30.0% | |
| CTCAACATTCAATACTGAAA+TGG | + | chr3.3:85854203-85854222 | MS.gene012816:CDS | 30.0% | |
| ! | CATTTCAGTATTGAATGTTG+AGG | - | chr3.3:85854205-85854224 | None:intergenic | 30.0% |
| ! | TTTGGAGTCAAATTTATTCC+TGG | - | chr3.3:85854118-85854137 | None:intergenic | 30.0% |
| !! | CTATATTTAATTTGGCAGGT+GGG | + | chr3.3:85854082-85854101 | MS.gene012816:intron | 30.0% |
| !! | TCTATATTTAATTTGGCAGG+TGG | + | chr3.3:85854081-85854100 | MS.gene012816:intron | 30.0% |
| CTTATGCAGCTGATATCATT+TGG | - | chr3.3:85854136-85854155 | None:intergenic | 35.0% | |
| GAGCACATGATATTTCTTAG+AGG | + | chr3.3:85853813-85853832 | MS.gene012816:CDS | 35.0% | |
| ! | GTAGAAATTTTCTTCCTCAG+TGG | + | chr3.3:85854170-85854189 | MS.gene012816:CDS | 35.0% |
| ! | TTACATAATGGAGGCTAAGA+TGG | - | chr3.3:85853980-85853999 | None:intergenic | 35.0% |
| !! | GCAAGTTTGAGTTCTAAATC+AGG | - | chr3.3:85854274-85854293 | None:intergenic | 35.0% |
| AAATATCATGTGCTCCTCCT+CGG | - | chr3.3:85853808-85853827 | None:intergenic | 40.0% | |
| AACAACAAAAACACCAACCC+AGG | + | chr3.3:85853887-85853906 | MS.gene012816:CDS | 40.0% | |
| GCCTAACTCTTCAACATCAA+CGG | + | chr3.3:85854225-85854244 | MS.gene012816:CDS | 40.0% | |
| TCCGTTGATGTTGAAGAGTT+AGG | - | chr3.3:85854229-85854248 | None:intergenic | 40.0% | |
| TTAGAGGACTTGAGAAGCTT+GGG | + | chr3.3:85853829-85853848 | MS.gene012816:CDS | 40.0% | |
| !! | TCTGTTAGCTCTAATGGCAT+GGG | - | chr3.3:85854301-85854320 | None:intergenic | 40.0% |
| !! | TGATCAAGCTATTCTGAGAC+TGG | - | chr3.3:85853944-85853963 | None:intergenic | 40.0% |
| AGCTGCATAAGCCAACTAAG+TGG | + | chr3.3:85854145-85854164 | MS.gene012816:CDS | 45.0% | |
| CATGCCATTAGAGCTAACAG+AGG | + | chr3.3:85854300-85854319 | MS.gene012816:CDS | 45.0% | |
| CTTAGAGGACTTGAGAAGCT+TGG | + | chr3.3:85853828-85853847 | MS.gene012816:CDS | 45.0% | |
| ! | AAATCAGGTGCTGCACTATG+AGG | - | chr3.3:85854259-85854278 | None:intergenic | 45.0% |
| ! | TTGTGCATGACTAGCTACCT+GGG | - | chr3.3:85853907-85853926 | None:intergenic | 45.0% |
| ! | TTTGTGCATGACTAGCTACC+TGG | - | chr3.3:85853908-85853927 | None:intergenic | 45.0% |
| !! | CATGCCTCTGTTAGCTCTAA+TGG | - | chr3.3:85854307-85854326 | None:intergenic | 45.0% |
| !! | CTCTGTTAGCTCTAATGGCA+TGG | - | chr3.3:85854302-85854321 | None:intergenic | 45.0% |
| !! | TCAAGCTATTCTGAGACTGG+CGG | - | chr3.3:85853941-85853960 | None:intergenic | 45.0% |
| AGAAGCTTGGGAAGGGTAAC+TGG | + | chr3.3:85853841-85853860 | MS.gene012816:CDS | 50.0% | |
| AGGACTTGAGAAGCTTGGGA+AGG | + | chr3.3:85853833-85853852 | MS.gene012816:CDS | 50.0% | |
| CAGGTGGGATGTGAAAAACC+AGG | + | chr3.3:85854097-85854116 | MS.gene012816:intron | 50.0% | |
| GGACTTGAGAAGCTTGGGAA+GGG | + | chr3.3:85853834-85853853 | MS.gene012816:CDS | 50.0% | |
| TGAGGATGAGAAAGCCACTG+AGG | - | chr3.3:85854187-85854206 | None:intergenic | 50.0% | |
| CTTGGGAAGGGTAACTGGAG+AGG | + | chr3.3:85853846-85853865 | MS.gene012816:CDS | 55.0% | |
| ! | GCATGACTAGCTACCTGGGT+TGG | - | chr3.3:85853903-85853922 | None:intergenic | 55.0% |
| ATGTGCTCCTCCTCGGTCCA+CGG | - | chr3.3:85853801-85853820 | None:intergenic | 60.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3.3 | gene | 85853795 | 85854336 | 85853795 | ID=MS.gene012816 |
| chr3.3 | mRNA | 85853795 | 85854336 | 85853795 | ID=MS.gene012816.t1;Parent=MS.gene012816 |
| chr3.3 | exon | 85853795 | 85853995 | 85853795 | ID=MS.gene012816.t1.exon1;Parent=MS.gene012816.t1 |
| chr3.3 | CDS | 85853795 | 85853995 | 85853795 | ID=cds.MS.gene012816.t1;Parent=MS.gene012816.t1 |
| chr3.3 | exon | 85854100 | 85854336 | 85854100 | ID=MS.gene012816.t1.exon2;Parent=MS.gene012816.t1 |
| chr3.3 | CDS | 85854100 | 85854336 | 85854100 | ID=cds.MS.gene012816.t1;Parent=MS.gene012816.t1 |
| Gene Sequence |
| Protein sequence |
