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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0432420 | XP_013461880.1 | 98.104 | 211 | 4 | 0 | 1 | 211 | 1 | 211 | 5.75e-150 | 425 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0432420 | sp|P32765|ASP_THECC | 35.238 | 210 | 109 | 11 | 6 | 198 | 11 | 210 | 5.82e-15 | 73.9 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0432420 | A0A072VCP7 | 98.104 | 211 | 4 | 0 | 1 | 211 | 1 | 211 | 2.75e-150 | 425 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0432420 | Msa0476840 | 0.919180 | 6.210776e-87 | -8.615850e-47 |
| Msa0432420 | Msa0521210 | 0.968098 | 3.391473e-128 | -8.615850e-47 |
| Msa0432420 | Msa0714640 | 0.840907 | 6.554643e-58 | -8.615850e-47 |
| Msa0432420 | Msa0829130 | 0.920316 | 1.493026e-87 | -8.615850e-47 |
| Msa0432420 | Msa0893860 | 0.864946 | 8.432317e-65 | -8.615850e-47 |
| Msa0432420 | Msa0920520 | 0.839860 | 1.230663e-57 | -8.615850e-47 |
| Msa0432420 | Msa1031410 | 0.815741 | 7.913418e-52 | -8.615850e-47 |
| Msa0432420 | Msa1367040 | 0.836813 | 7.508301e-57 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0432420 | MtrunA17_Chr3g0137421 | 98.104 | 211 | 4 | 0 | 1 | 211 | 1 | 211 | 5.29e-154 | 425 |
| Msa0432420 | MtrunA17_Chr3g0137441 | 81.221 | 213 | 38 | 1 | 1 | 211 | 1 | 213 | 7.90e-126 | 353 |
| Msa0432420 | MtrunA17_Chr3g0137411 | 66.667 | 207 | 67 | 2 | 1 | 205 | 1 | 207 | 2.93e-96 | 279 |
| Msa0432420 | MtrunA17_Chr6g0481911 | 34.555 | 191 | 100 | 8 | 24 | 197 | 21 | 203 | 2.10e-22 | 90.1 |
| Msa0432420 | MtrunA17_Chr6g0482041 | 33.333 | 216 | 109 | 10 | 9 | 198 | 7 | 213 | 1.67e-21 | 88.2 |
| Msa0432420 | MtrunA17_Chr6g0481941 | 34.197 | 193 | 100 | 8 | 24 | 197 | 21 | 205 | 2.06e-20 | 85.1 |
| Msa0432420 | MtrunA17_Chr6g0481961 | 31.579 | 209 | 104 | 10 | 17 | 197 | 16 | 213 | 1.90e-15 | 72.0 |
| Msa0432420 | MtrunA17_Chr6g0481951 | 31.579 | 209 | 104 | 10 | 17 | 197 | 16 | 213 | 1.98e-15 | 72.0 |
| Msa0432420 | MtrunA17_Chr7g0269461 | 30.000 | 180 | 112 | 8 | 27 | 196 | 25 | 200 | 2.14e-13 | 66.2 |
| Msa0432420 | MtrunA17_Chr6g0452521 | 31.953 | 169 | 99 | 7 | 4 | 162 | 39 | 201 | 1.32e-12 | 64.7 |
| Msa0432420 | MtrunA17_Chr6g0452491 | 31.325 | 166 | 95 | 7 | 6 | 162 | 13 | 168 | 4.27e-12 | 62.8 |
| Msa0432420 | MtrunA17_Chr6g0476921 | 29.570 | 186 | 109 | 8 | 27 | 198 | 26 | 203 | 4.50e-12 | 62.8 |
| Msa0432420 | MtrunA17_Chr6g0457121 | 33.333 | 87 | 56 | 1 | 12 | 96 | 38 | 124 | 3.33e-11 | 58.5 |
| Msa0432420 | MtrunA17_Chr6g0482031 | 28.571 | 203 | 114 | 10 | 19 | 197 | 17 | 212 | 7.39e-11 | 59.3 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0432420 | AT1G73260.1 | 33.871 | 186 | 100 | 11 | 28 | 198 | 29 | 206 | 3.23e-15 | 71.6 |
| Msa0432420 | AT1G17860.1 | 32.857 | 210 | 104 | 14 | 6 | 197 | 5 | 195 | 4.16e-15 | 71.2 |
| Msa0432420 | AT1G73330.1 | 31.694 | 183 | 108 | 10 | 24 | 199 | 22 | 194 | 2.09e-14 | 69.3 |
| Msa0432420 | AT1G73325.1 | 28.426 | 197 | 123 | 7 | 12 | 197 | 14 | 203 | 4.18e-12 | 63.5 |
Find 49 sgRNAs with CRISPR-Local
Find 57 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| CACCATTGAGATTCCAATTC+TGG | 0.176056 | 3_2:-84564084 | Msa0432420:CDS |
| AAGTTCTGTCCTTCTGTTCC+TGG | 0.220195 | 3_2:-84563909 | Msa0432420:CDS |
| TAAAGGTTGGATCTGGGTTT+TGG | 0.257005 | 3_2:-84564025 | Msa0432420:CDS |
| TTTAAAAGTCTCCACACTTT+TGG | 0.285295 | 3_2:+84564044 | None:intergenic |
| GTGAGCACTGGTGGTGCAGC+TGG | 0.296941 | 3_2:-84563999 | Msa0432420:CDS |
| TTCAAGATTGAGAGGCTTGC+AGG | 0.297937 | 3_2:-84563960 | Msa0432420:CDS |
| TTATTATGTATTTCCACTTT+GGG | 0.342016 | 3_2:-84564246 | Msa0432420:CDS |
| TTGCAAGGACTGCCCAGAAT+TGG | 0.350605 | 3_2:+84564071 | None:intergenic |
| CCAGTTTATTTCTCTGCATC+AGG | 0.372005 | 3_2:-84564137 | Msa0432420:CDS |
| GTTATTATGTATTTCCACTT+TGG | 0.390718 | 3_2:-84564247 | Msa0432420:CDS |
| ACTGGTGTGCCAATTGCATC+AGG | 0.400173 | 3_2:+84564155 | None:intergenic |
| TAATGTTATGCCTCCATTGT+CGG | 0.403372 | 3_2:+84564223 | None:intergenic |
| TGCCAATTGCATCAGGGTTA+CGG | 0.410323 | 3_2:+84564162 | None:intergenic |
| ACCATTGAGATTCCAATTCT+GGG | 0.428272 | 3_2:-84564083 | Msa0432420:CDS |
| CCTGATGCAGAGAAATAAAC+TGG | 0.432071 | 3_2:+84564137 | None:intergenic |
| TTCTGAAATCTAACATAGTA+AGG | 0.445442 | 3_2:+84563807 | None:intergenic |
| TGTTTGTCTACTACTGCCTC+TGG | 0.457272 | 3_2:+84564296 | None:intergenic |
| ATCCGTAACCCTGATGCAAT+TGG | 0.467790 | 3_2:-84564164 | Msa0432420:CDS |
| ATTATTGCTCTGAGCAAAAG+TGG | 0.480580 | 3_2:+84563779 | None:intergenic |
| TGAGCACTGGTGGTGCAGCT+GGG | 0.484946 | 3_2:-84563998 | Msa0432420:CDS |
| CAAAGAACACCAGGAACAGA+AGG | 0.492794 | 3_2:+84563900 | None:intergenic |
| GACAATGGAGGCATAACATT+AGG | 0.494830 | 3_2:-84564221 | Msa0432420:CDS |
| TACTGATGGAACTAAAGTTA+TGG | 0.520354 | 3_2:-84563853 | Msa0432420:CDS |
| GGTGTTCTTTGTGCTCCTGT+AGG | 0.523697 | 3_2:-84563888 | Msa0432420:CDS |
| TCTGGTTCAGCTCCTTGTAG+TGG | 0.532299 | 3_2:+84564314 | None:intergenic |
| TTACTATGTTAGATTTCAGA+AGG | 0.535320 | 3_2:-84563805 | Msa0432420:CDS |
| GTATCTACAAAAGTTCCTAC+AGG | 0.540405 | 3_2:+84563873 | None:intergenic |
| GAGCACTGGTGGTGCAGCTG+GGG | 0.547443 | 3_2:-84563997 | Msa0432420:CDS |
| TGAACAACGCTAAGAGAGAA+AGG | 0.548980 | 3_2:+84564345 | None:intergenic |
| CCACTTTGGGCCGACAATGG+AGG | 0.549557 | 3_2:-84564233 | Msa0432420:CDS |
| AACCTTCACCTGGTTGAAGA+GGG | 0.550922 | 3_2:+84564267 | None:intergenic |
| ATGGTGAGATCAGTGAGAGT+TGG | 0.553098 | 3_2:+84564101 | None:intergenic |
| TAACCTTCACCTGGTTGAAG+AGG | 0.554679 | 3_2:+84564266 | None:intergenic |
| TTTCCACTTTGGGCCGACAA+TGG | 0.555677 | 3_2:-84564236 | Msa0432420:CDS |
| GCCCAGAATTGGAATCTCAA+TGG | 0.560561 | 3_2:+84564082 | None:intergenic |
| AAAGTTATGGCTGTTGGCGA+TGG | 0.567290 | 3_2:-84563840 | Msa0432420:CDS |
| TTAGCAAGTTCAAGATTGAG+AGG | 0.571309 | 3_2:-84563968 | Msa0432420:CDS |
| TTCAACACAAAGCCACTACA+AGG | 0.573110 | 3_2:-84564326 | Msa0432420:CDS |
| CCTCCATTGTCGGCCCAAAG+TGG | 0.575834 | 3_2:+84564233 | None:intergenic |
| AACCCTCTTCAACCAGGTGA+AGG | 0.586328 | 3_2:-84564269 | Msa0432420:CDS |
| CAAGGTAACCCTCTTCAACC+AGG | 0.592964 | 3_2:-84564275 | Msa0432420:CDS |
| GGAACTAAAGTTATGGCTGT+TGG | 0.595929 | 3_2:-84563846 | Msa0432420:CDS |
| ACAGGAGCACAAAGAACACC+AGG | 0.637032 | 3_2:+84563891 | None:intergenic |
| CTGGTGTGCCAATTGCATCA+GGG | 0.645208 | 3_2:+84564156 | None:intergenic |
| CTTGCAATGAACCAAAAGTG+TGG | 0.645641 | 3_2:-84564055 | Msa0432420:CDS |
| ACTACAAGGAGCTGAACCAG+AGG | 0.651073 | 3_2:-84564312 | Msa0432420:CDS |
| GGGTTACGGATTACGTCAAG+AGG | 0.654762 | 3_2:+84564176 | None:intergenic |
| AATACATAATAACCTTCACC+TGG | 0.663956 | 3_2:+84564257 | None:intergenic |
| GAGGCAGTAGTAGACAAACA+AGG | 0.729599 | 3_2:-84564293 | Msa0432420:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | TTATTATGTATTTCCACTTT+GGG | - | chr3_2:84563883-84563902 | Msa0432420:CDS | 20.0% |
| ! | GTTATTATGTATTTCCACTT+TGG | - | chr3_2:84563882-84563901 | Msa0432420:CDS | 25.0% |
| !!! | TTCTGAAATCTAACATAGTA+AGG | + | chr3_2:84564325-84564344 | None:intergenic | 25.0% |
| ! | TTACTATGTTAGATTTCAGA+AGG | - | chr3_2:84564324-84564343 | Msa0432420:CDS | 25.0% |
| AATACATAATAACCTTCACC+TGG | + | chr3_2:84563875-84563894 | None:intergenic | 30.0% | |
| ! | TTTAAAAGTCTCCACACTTT+TGG | + | chr3_2:84564088-84564107 | None:intergenic | 30.0% |
| !! | AAAAGTGTGGAGACTTTTAA+AGG | - | chr3_2:84564087-84564106 | Msa0432420:CDS | 30.0% |
| TACTGATGGAACTAAAGTTA+TGG | - | chr3_2:84564276-84564295 | Msa0432420:CDS | 30.0% | |
| TAATGTTATGCCTCCATTGT+CGG | + | chr3_2:84563909-84563928 | None:intergenic | 35.0% | |
| ACCATTGAGATTCCAATTCT+GGG | - | chr3_2:84564046-84564065 | Msa0432420:CDS | 35.0% | |
| !! | AGACTTTTAAAGGTTGGATC+TGG | - | chr3_2:84564097-84564116 | Msa0432420:CDS | 35.0% |
| !! | GACTTTTAAAGGTTGGATCT+GGG | - | chr3_2:84564098-84564117 | Msa0432420:CDS | 35.0% |
| TTAGCAAGTTCAAGATTGAG+AGG | - | chr3_2:84564161-84564180 | Msa0432420:CDS | 35.0% | |
| GTATCTACAAAAGTTCCTAC+AGG | + | chr3_2:84564259-84564278 | None:intergenic | 35.0% | |
| ! | GGAACTTTTGTAGATACTGA+TGG | - | chr3_2:84564262-84564281 | Msa0432420:CDS | 35.0% |
| ! | ATTATTGCTCTGAGCAAAAG+TGG | + | chr3_2:84564353-84564372 | None:intergenic | 35.0% |
| TGAACAACGCTAAGAGAGAA+AGG | + | chr3_2:84563787-84563806 | None:intergenic | 40.0% | |
| TTCAACACAAAGCCACTACA+AGG | - | chr3_2:84563803-84563822 | Msa0432420:CDS | 40.0% | |
| ! | GACAATGGAGGCATAACATT+AGG | - | chr3_2:84563908-84563927 | Msa0432420:CDS | 40.0% |
| CCTGATGCAGAGAAATAAAC+TGG | + | chr3_2:84563995-84564014 | None:intergenic | 40.0% | |
| ! | CCAGTTTATTTCTCTGCATC+AGG | - | chr3_2:84563992-84564011 | Msa0432420:CDS | 40.0% |
| CACCATTGAGATTCCAATTC+TGG | - | chr3_2:84564045-84564064 | Msa0432420:CDS | 40.0% | |
| !!! | CACACTTTTGGTTCATTGCA+AGG | + | chr3_2:84564076-84564095 | None:intergenic | 40.0% |
| CTTGCAATGAACCAAAAGTG+TGG | - | chr3_2:84564074-84564093 | Msa0432420:CDS | 40.0% | |
| !! | GTGTGGAGACTTTTAAAGGT+TGG | - | chr3_2:84564091-84564110 | Msa0432420:CDS | 40.0% |
| ! | TAAAGGTTGGATCTGGGTTT+TGG | - | chr3_2:84564104-84564123 | Msa0432420:CDS | 40.0% |
| GGAACTAAAGTTATGGCTGT+TGG | - | chr3_2:84564283-84564302 | Msa0432420:CDS | 40.0% | |
| TGTTTGTCTACTACTGCCTC+TGG | + | chr3_2:84563836-84563855 | None:intergenic | 45.0% | |
| GAGGCAGTAGTAGACAAACA+AGG | - | chr3_2:84563836-84563855 | Msa0432420:CDS | 45.0% | |
| AACCTTCACCTGGTTGAAGA+GGG | + | chr3_2:84563865-84563884 | None:intergenic | 45.0% | |
| TAACCTTCACCTGGTTGAAG+AGG | + | chr3_2:84563866-84563885 | None:intergenic | 45.0% | |
| ATCCGTAACCCTGATGCAAT+TGG | - | chr3_2:84563965-84563984 | Msa0432420:CDS | 45.0% | |
| TGCCAATTGCATCAGGGTTA+CGG | + | chr3_2:84563970-84563989 | None:intergenic | 45.0% | |
| ATGGTGAGATCAGTGAGAGT+TGG | + | chr3_2:84564031-84564050 | None:intergenic | 45.0% | |
| GCCCAGAATTGGAATCTCAA+TGG | + | chr3_2:84564050-84564069 | None:intergenic | 45.0% | |
| !!! | TTTTGGTTTGTGAGCACTGG+TGG | - | chr3_2:84564121-84564140 | Msa0432420:CDS | 45.0% |
| TTCAAGATTGAGAGGCTTGC+AGG | - | chr3_2:84564169-84564188 | Msa0432420:CDS | 45.0% | |
| AAGTTCTGTCCTTCTGTTCC+TGG | - | chr3_2:84564220-84564239 | Msa0432420:CDS | 45.0% | |
| CAAAGAACACCAGGAACAGA+AGG | + | chr3_2:84564232-84564251 | None:intergenic | 45.0% | |
| AAAGTTATGGCTGTTGGCGA+TGG | - | chr3_2:84564289-84564308 | Msa0432420:CDS | 45.0% | |
| ! | TCTGGTTCAGCTCCTTGTAG+TGG | + | chr3_2:84563818-84563837 | None:intergenic | 50.0% |
| ACTACAAGGAGCTGAACCAG+AGG | - | chr3_2:84563817-84563836 | Msa0432420:CDS | 50.0% | |
| CAAGGTAACCCTCTTCAACC+AGG | - | chr3_2:84563854-84563873 | Msa0432420:CDS | 50.0% | |
| AACCCTCTTCAACCAGGTGA+AGG | - | chr3_2:84563860-84563879 | Msa0432420:CDS | 50.0% | |
| TTTCCACTTTGGGCCGACAA+TGG | - | chr3_2:84563893-84563912 | Msa0432420:CDS | 50.0% | |
| ! | GGGTTACGGATTACGTCAAG+AGG | + | chr3_2:84563956-84563975 | None:intergenic | 50.0% |
| CTGGTGTGCCAATTGCATCA+GGG | + | chr3_2:84563976-84563995 | None:intergenic | 50.0% | |
| ACTGGTGTGCCAATTGCATC+AGG | + | chr3_2:84563977-84563996 | None:intergenic | 50.0% | |
| TTGCAAGGACTGCCCAGAAT+TGG | + | chr3_2:84564061-84564080 | None:intergenic | 50.0% | |
| !!! | GGGTTTTGGTTTGTGAGCAC+TGG | - | chr3_2:84564118-84564137 | Msa0432420:CDS | 50.0% |
| ! | ACAGGAGCACAAAGAACACC+AGG | + | chr3_2:84564241-84564260 | None:intergenic | 50.0% |
| GGTGTTCTTTGTGCTCCTGT+AGG | - | chr3_2:84564241-84564260 | Msa0432420:CDS | 50.0% | |
| CCTCCATTGTCGGCCCAAAG+TGG | + | chr3_2:84563899-84563918 | None:intergenic | 60.0% | |
| CCACTTTGGGCCGACAATGG+AGG | - | chr3_2:84563896-84563915 | Msa0432420:CDS | 60.0% | |
| !! | TGAGCACTGGTGGTGCAGCT+GGG | - | chr3_2:84564131-84564150 | Msa0432420:CDS | 60.0% |
| !! | GTGAGCACTGGTGGTGCAGC+TGG | - | chr3_2:84564130-84564149 | Msa0432420:CDS | 65.0% |
| !! | GAGCACTGGTGGTGCAGCTG+GGG | - | chr3_2:84564132-84564151 | Msa0432420:CDS | 65.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3_2 | gene | 84563758 | 84564393 | 84563758 | ID=Msa0432420;Name=Msa0432420 |
| chr3_2 | mRNA | 84563758 | 84564393 | 84563758 | ID=Msa0432420-mRNA-1;Parent=Msa0432420;Name=Msa0432420-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|211 |
| chr3_2 | exon | 84563758 | 84564393 | 84563758 | ID=Msa0432420-mRNA-1:exon:23943;Parent=Msa0432420-mRNA-1 |
| chr3_2 | CDS | 84563758 | 84564393 | 84563758 | ID=Msa0432420-mRNA-1:cds;Parent=Msa0432420-mRNA-1 |
| Gene Sequence |
| Protein sequence |
