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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0636080 | XP_024636235.1 | 94.650 | 243 | 13 | 0 | 1 | 243 | 1 | 243 | 1.49e-173 | 487 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0636080 | sp|Q9M202|ZAT9_ARATH | 30.400 | 250 | 136 | 7 | 9 | 229 | 6 | 246 | 6.06e-17 | 81.3 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0636080 | A0A396I2K7 | 66.531 | 245 | 76 | 1 | 1 | 239 | 1 | 245 | 9.53e-114 | 335 |
| Gene ID | Type | Classification |
|---|---|---|
| Msa0636080 | TF | C2H2 |
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0636080 | Msa0675400 | 0.974220 | 8.984716e-138 | -8.615850e-47 |
| Msa0636080 | Msa0688950 | 0.956195 | 5.224786e-114 | -8.615850e-47 |
| Msa0541370 | Msa0636080 | 0.987734 | 2.430868e-171 | -8.615850e-47 |
| Msa0541400 | Msa0636080 | 0.980489 | 2.446874e-150 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0636080 | MtrunA17_Chr4g0018761 | 66.531 | 245 | 76 | 1 | 1 | 239 | 1 | 245 | 1.84e-117 | 335 |
| Msa0636080 | MtrunA17_Chr4g0018741 | 77.885 | 104 | 23 | 0 | 78 | 181 | 1 | 104 | 7.46e-55 | 171 |
| Msa0636080 | MtrunA17_Chr3g0079131 | 26.165 | 279 | 138 | 7 | 7 | 232 | 6 | 269 | 3.47e-18 | 81.3 |
| Msa0636080 | MtrunA17_Chr3g0079061 | 26.415 | 265 | 157 | 7 | 3 | 229 | 2 | 266 | 3.87e-16 | 75.9 |
| Msa0636080 | MtrunA17_Chr3g0079091 | 38.532 | 109 | 62 | 2 | 3 | 107 | 2 | 109 | 9.24e-14 | 67.4 |
| Msa0636080 | MtrunA17_Chr4g0056091 | 59.322 | 59 | 22 | 1 | 173 | 229 | 210 | 268 | 2.06e-13 | 68.6 |
| Msa0636080 | MtrunA17_Chr7g0231181 | 40.741 | 81 | 38 | 1 | 170 | 240 | 239 | 319 | 6.98e-13 | 67.4 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0636080 | AT3G60580.1 | 30.400 | 250 | 136 | 7 | 9 | 229 | 6 | 246 | 6.16e-18 | 81.3 |
| Msa0636080 | AT1G02030.1 | 27.132 | 258 | 132 | 6 | 9 | 236 | 7 | 238 | 4.01e-13 | 67.4 |
| Msa0636080 | AT5G61470.1 | 41.096 | 73 | 31 | 2 | 168 | 229 | 225 | 296 | 3.91e-12 | 65.1 |
Find 68 sgRNAs with CRISPR-Local
Find 72 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| TTCTGTGTTTGTTGTATTTC+GGG | 0.187551 | 4_3:+25870522 | None:intergenic |
| ATTCTGTGTTTGTTGTATTT+CGG | 0.237824 | 4_3:+25870521 | None:intergenic |
| GCCGCAATTGGATCTCTTGC+GGG | 0.303465 | 4_3:+25870413 | None:intergenic |
| AATTGGATCTCTTGCGGGTT+GGG | 0.313326 | 4_3:+25870418 | None:intergenic |
| ATCCAGGTGTTCTGATGTTA+TGG | 0.324938 | 4_3:-25870347 | Msa0636080:CDS |
| TGAGTATTAGTTTCAAGCTT+TGG | 0.337317 | 4_3:+25870612 | None:intergenic |
| CAGCCGCAGCATTAACTTCT+CGG | 0.371873 | 4_3:+25870391 | None:intergenic |
| CAATTGGATCTCTTGCGGGT+TGG | 0.402481 | 4_3:+25870417 | None:intergenic |
| ATTAACTTCTCGGCCGCAAT+TGG | 0.433182 | 4_3:+25870401 | None:intergenic |
| TACTCAAGCTGTAGACAATT+CGG | 0.436960 | 4_3:-25870595 | Msa0636080:CDS |
| ATTTGTGGGAAGTGGTTCTC+CGG | 0.453707 | 4_3:-25870690 | Msa0636080:CDS |
| GTTTCAAGCTTTGGAGCAAT+CGG | 0.454553 | 4_3:+25870621 | None:intergenic |
| TTCCGATCTTATCAGGCTCT+TGG | 0.457389 | 4_3:-25870183 | Msa0636080:CDS |
| TTTACAAAGATGCGCAGAAA+AGG | 0.459521 | 4_3:-25870320 | Msa0636080:CDS |
| TACAGAATCACAAATCAATA+CGG | 0.462697 | 4_3:+25869997 | None:intergenic |
| TTCTCCGGTGGGAAAGCCCT+TGG | 0.463478 | 4_3:-25870675 | Msa0636080:CDS |
| GGAAAGCCTGTGGGATTTGT+GGG | 0.467351 | 4_3:-25870704 | Msa0636080:CDS |
| GGGAAAGCCTGTGGGATTTG+TGG | 0.468727 | 4_3:-25870705 | Msa0636080:CDS |
| CGATCTTATCAGGCTCTTGG+TGG | 0.468794 | 4_3:-25870180 | Msa0636080:CDS |
| TTGCAATTTGAGCAGTGAAA+AGG | 0.471865 | 4_3:+25870105 | None:intergenic |
| GCCTCCAAGGGCTTTCCCAC+CGG | 0.472807 | 4_3:+25870671 | None:intergenic |
| CCCCATAACATCAGAACACC+TGG | 0.474579 | 4_3:+25870345 | None:intergenic |
| AGATCTCATGTGGCCTCCAA+GGG | 0.485485 | 4_3:+25870659 | None:intergenic |
| GGCCGCAATTGGATCTCTTG+CGG | 0.489489 | 4_3:+25870412 | None:intergenic |
| TCCAGGTGTTCTGATGTTAT+GGG | 0.494593 | 4_3:-25870346 | Msa0636080:CDS |
| TCCGGTGGGAAAGCCCTTGG+AGG | 0.494800 | 4_3:-25870672 | Msa0636080:CDS |
| TTCTCTGTTTGAGCTTGCAG+AGG | 0.496954 | 4_3:+25870467 | None:intergenic |
| TCTGTTTGAGCTTGCAGAGG+AGG | 0.498454 | 4_3:+25870470 | None:intergenic |
| TTACAAAGATGCGCAGAAAA+GGG | 0.499625 | 4_3:-25870319 | Msa0636080:CDS |
| TTCAAGTCTGCTCAGGCACT+CGG | 0.500253 | 4_3:-25870075 | Msa0636080:CDS |
| AACGATGGCGAAAGCAGTAC+AGG | 0.507873 | 4_3:-25870267 | Msa0636080:CDS |
| AGCAAATTGATTTCGACGAT+GGG | 0.509489 | 4_3:+25870563 | None:intergenic |
| GCACCTCTCACAGTTGAACC+TGG | 0.509618 | 4_3:+25870215 | None:intergenic |
| ATTTCGACGATGGGTTGAAT+CGG | 0.510947 | 4_3:+25870572 | None:intergenic |
| GAGATCTCATGTGGCCTCCA+AGG | 0.514030 | 4_3:+25870658 | None:intergenic |
| GAAGATATGTCAAGAGATCC+AGG | 0.516117 | 4_3:-25870363 | Msa0636080:CDS |
| TGTGGGAAGTGGTTCTCCGG+TGG | 0.517822 | 4_3:-25870687 | Msa0636080:CDS |
| ACTTTGAAATTCCTTAGCAC+TGG | 0.521740 | 4_3:+25870029 | None:intergenic |
| CAAAGTGTTCAAGTCTGCTC+AGG | 0.524975 | 4_3:-25870082 | Msa0636080:CDS |
| CACAAGCAGACTCTGAAGCC+AGG | 0.539423 | 4_3:-25870233 | Msa0636080:CDS |
| AAGCAAATTGATTTCGACGA+TGG | 0.551421 | 4_3:+25870562 | None:intergenic |
| GTGTTTGTTGTATTTCGGGA+AGG | 0.552910 | 4_3:+25870526 | None:intergenic |
| CCTGTGGGATTTGTGGGAAG+TGG | 0.558125 | 4_3:-25870698 | Msa0636080:CDS |
| GTGGGAAGTGGTTCTCCGGT+GGG | 0.561353 | 4_3:-25870686 | Msa0636080:CDS |
| GATCTTATCAGGCTCTTGGT+GGG | 0.571526 | 4_3:-25870179 | Msa0636080:CDS |
| GGTACACTCTTCCAGTGCTA+AGG | 0.575791 | 4_3:-25870040 | Msa0636080:CDS |
| GCAACTATGGAGAAGAGCGA+TGG | 0.579019 | 4_3:-25870726 | None:intergenic |
| AAAGATGCGCAGAAAAGGGA+AGG | 0.579501 | 4_3:-25870315 | Msa0636080:CDS |
| CACCAAGAGCCTGATAAGAT+CGG | 0.582662 | 4_3:+25870181 | None:intergenic |
| CCAGGTGTTCTGATGTTATG+GGG | 0.595199 | 4_3:-25870345 | Msa0636080:CDS |
| AAGAGCGATGGGAAAGCCTG+TGG | 0.598960 | 4_3:-25870714 | Msa0636080:CDS |
| AGGCACTCGGTGGACACAAG+AGG | 0.606213 | 4_3:-25870062 | Msa0636080:CDS |
| ACAGAATCACAAATCAATAC+GGG | 0.613334 | 4_3:+25869998 | None:intergenic |
| CAACTATGGAGAAGAGCGAT+GGG | 0.616240 | 4_3:-25870725 | None:intergenic |
| TACTGCAAAAGAGACAATGA+TGG | 0.621835 | 4_3:-25870147 | Msa0636080:CDS |
| AAGCCAGGTTCAACTGTGAG+AGG | 0.622627 | 4_3:-25870218 | Msa0636080:CDS |
| ATCACAAATCAATACGGGTG+TGG | 0.631203 | 4_3:+25870003 | None:intergenic |
| GGCACTCGGTGGACACAAGA+GGG | 0.632635 | 4_3:-25870061 | Msa0636080:CDS |
| CCACTTCCCACAAATCCCAC+AGG | 0.647858 | 4_3:+25870698 | None:intergenic |
| CGGCCGAGAAGTTAATGCTG+CGG | 0.653910 | 4_3:-25870394 | Msa0636080:CDS |
| AGAGCGATGGGAAAGCCTGT+GGG | 0.654994 | 4_3:-25870713 | Msa0636080:CDS |
| AGGTTCAACTGTGAGAGGTG+CGG | 0.663022 | 4_3:-25870213 | Msa0636080:CDS |
| AAGATGCGCAGAAAAGGGAA+GGG | 0.667779 | 4_3:-25870314 | Msa0636080:CDS |
| TTCGGGAAGGCAAGTCTGTG+AGG | 0.669270 | 4_3:+25870539 | None:intergenic |
| AAGTCTGCTCAGGCACTCGG+TGG | 0.670340 | 4_3:-25870072 | Msa0636080:CDS |
| AGGCCACATGAGATCTCACA+TGG | 0.682156 | 4_3:-25870652 | Msa0636080:CDS |
| ACCCGCAAGAGATCCAATTG+CGG | 0.686880 | 4_3:-25870414 | Msa0636080:CDS |
| GAACCATGTGAGATCTCATG+TGG | 0.730676 | 4_3:+25870649 | None:intergenic |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | ATTCTGTGTTTGTTGTATTT+CGG | + | chr4_3:25870213-25870232 | None:intergenic | 25.0% |
| ! | GATCAAGAAACAAAAAATGA+GGG | - | chr4_3:25870439-25870458 | Msa0636080:CDS | 25.0% |
| ! | TGAGTATTAGTTTCAAGCTT+TGG | + | chr4_3:25870122-25870141 | None:intergenic | 30.0% |
| !! | TTCTGTGTTTGTTGTATTTC+GGG | + | chr4_3:25870212-25870231 | None:intergenic | 30.0% |
| !!! | TGAAGTTTTGTTTCAAGGAT+AGG | + | chr4_3:25870238-25870257 | None:intergenic | 30.0% |
| GGATCAAGAAACAAAAAATG+AGG | - | chr4_3:25870438-25870457 | Msa0636080:CDS | 30.0% | |
| AAAAATGTTCCGATCTTATC+AGG | - | chr4_3:25870541-25870560 | Msa0636080:CDS | 30.0% | |
| TACTCAAGCTGTAGACAATT+CGG | - | chr4_3:25870136-25870155 | Msa0636080:CDS | 35.0% | |
| ! | AGCAAATTGATTTCGACGAT+GGG | + | chr4_3:25870171-25870190 | None:intergenic | 35.0% |
| ! | AAGCAAATTGATTTCGACGA+TGG | + | chr4_3:25870172-25870191 | None:intergenic | 35.0% |
| TTTACAAAGATGCGCAGAAA+AGG | - | chr4_3:25870411-25870430 | Msa0636080:CDS | 35.0% | |
| TTACAAAGATGCGCAGAAAA+GGG | - | chr4_3:25870412-25870431 | Msa0636080:CDS | 35.0% | |
| CAAAAAATGAGGGAAAACGA+TGG | - | chr4_3:25870449-25870468 | Msa0636080:CDS | 35.0% | |
| TACTGCAAAAGAGACAATGA+TGG | - | chr4_3:25870584-25870603 | Msa0636080:CDS | 35.0% | |
| TTGCAATTTGAGCAGTGAAA+AGG | + | chr4_3:25870629-25870648 | None:intergenic | 35.0% | |
| !! | ACTTTGAAATTCCTTAGCAC+TGG | + | chr4_3:25870705-25870724 | None:intergenic | 35.0% |
| !! | GTTTCAAGCTTTGGAGCAAT+CGG | + | chr4_3:25870113-25870132 | None:intergenic | 40.0% |
| !! | ATTTCGACGATGGGTTGAAT+CGG | + | chr4_3:25870162-25870181 | None:intergenic | 40.0% |
| !! | GTGTTTGTTGTATTTCGGGA+AGG | + | chr4_3:25870208-25870227 | None:intergenic | 40.0% |
| !!! | GGCAGTGAAGTTTTGTTTCA+AGG | + | chr4_3:25870243-25870262 | None:intergenic | 40.0% |
| GAAGATATGTCAAGAGATCC+AGG | - | chr4_3:25870368-25870387 | Msa0636080:CDS | 40.0% | |
| ATCCAGGTGTTCTGATGTTA+TGG | - | chr4_3:25870384-25870403 | Msa0636080:CDS | 40.0% | |
| TCCAGGTGTTCTGATGTTAT+GGG | - | chr4_3:25870385-25870404 | Msa0636080:CDS | 40.0% | |
| ATTTGTGGGAAGTGGTTCTC+CGG | - | chr4_3:25870041-25870060 | Msa0636080:CDS | 45.0% | |
| GAACCATGTGAGATCTCATG+TGG | + | chr4_3:25870085-25870104 | None:intergenic | 45.0% | |
| TTCTCTGTTTGAGCTTGCAG+AGG | + | chr4_3:25870267-25870286 | None:intergenic | 45.0% | |
| AATTGGATCTCTTGCGGGTT+GGG | + | chr4_3:25870316-25870335 | None:intergenic | 45.0% | |
| ATTAACTTCTCGGCCGCAAT+TGG | + | chr4_3:25870333-25870352 | None:intergenic | 45.0% | |
| CCAGGTGTTCTGATGTTATG+GGG | - | chr4_3:25870386-25870405 | Msa0636080:CDS | 45.0% | |
| AAAGATGCGCAGAAAAGGGA+AGG | - | chr4_3:25870416-25870435 | Msa0636080:CDS | 45.0% | |
| AAGATGCGCAGAAAAGGGAA+GGG | - | chr4_3:25870417-25870436 | Msa0636080:CDS | 45.0% | |
| TTCCGATCTTATCAGGCTCT+TGG | - | chr4_3:25870548-25870567 | Msa0636080:CDS | 45.0% | |
| CACCAAGAGCCTGATAAGAT+CGG | + | chr4_3:25870553-25870572 | None:intergenic | 45.0% | |
| GATCTTATCAGGCTCTTGGT+GGG | - | chr4_3:25870552-25870571 | Msa0636080:CDS | 45.0% | |
| ! | CAAAGTGTTCAAGTCTGCTC+AGG | - | chr4_3:25870649-25870668 | Msa0636080:CDS | 45.0% |
| GGAAAGCCTGTGGGATTTGT+GGG | - | chr4_3:25870027-25870046 | Msa0636080:CDS | 50.0% | |
| AGATCTCATGTGGCCTCCAA+GGG | + | chr4_3:25870075-25870094 | None:intergenic | 50.0% | |
| AGGCCACATGAGATCTCACA+TGG | - | chr4_3:25870079-25870098 | Msa0636080:CDS | 50.0% | |
| TCTGTTTGAGCTTGCAGAGG+AGG | + | chr4_3:25870264-25870283 | None:intergenic | 50.0% | |
| !!! | TCTTGCGGGTTGGGTTTTTC+GGG | + | chr4_3:25870307-25870326 | None:intergenic | 50.0% |
| !!! | CTCTTGCGGGTTGGGTTTTT+CGG | + | chr4_3:25870308-25870327 | None:intergenic | 50.0% |
| CAATTGGATCTCTTGCGGGT+TGG | + | chr4_3:25870317-25870336 | None:intergenic | 50.0% | |
| ACCCGCAAGAGATCCAATTG+CGG | - | chr4_3:25870317-25870336 | Msa0636080:CDS | 50.0% | |
| CAGCCGCAGCATTAACTTCT+CGG | + | chr4_3:25870343-25870362 | None:intergenic | 50.0% | |
| CCCCATAACATCAGAACACC+TGG | + | chr4_3:25870389-25870408 | None:intergenic | 50.0% | |
| AACGATGGCGAAAGCAGTAC+AGG | - | chr4_3:25870464-25870483 | Msa0636080:CDS | 50.0% | |
| AAGCCAGGTTCAACTGTGAG+AGG | - | chr4_3:25870513-25870532 | Msa0636080:CDS | 50.0% | |
| AGGTTCAACTGTGAGAGGTG+CGG | - | chr4_3:25870518-25870537 | Msa0636080:CDS | 50.0% | |
| CGATCTTATCAGGCTCTTGG+TGG | - | chr4_3:25870551-25870570 | Msa0636080:CDS | 50.0% | |
| TTCAAGTCTGCTCAGGCACT+CGG | - | chr4_3:25870656-25870675 | Msa0636080:CDS | 50.0% | |
| GGTACACTCTTCCAGTGCTA+AGG | - | chr4_3:25870691-25870710 | Msa0636080:CDS | 50.0% | |
| AAGAGCGATGGGAAAGCCTG+TGG | - | chr4_3:25870017-25870036 | Msa0636080:CDS | 55.0% | |
| AGAGCGATGGGAAAGCCTGT+GGG | - | chr4_3:25870018-25870037 | Msa0636080:CDS | 55.0% | |
| GGGAAAGCCTGTGGGATTTG+TGG | - | chr4_3:25870026-25870045 | Msa0636080:CDS | 55.0% | |
| CCACTTCCCACAAATCCCAC+AGG | + | chr4_3:25870036-25870055 | None:intergenic | 55.0% | |
| CCTGTGGGATTTGTGGGAAG+TGG | - | chr4_3:25870033-25870052 | Msa0636080:CDS | 55.0% | |
| GAGATCTCATGTGGCCTCCA+AGG | + | chr4_3:25870076-25870095 | None:intergenic | 55.0% | |
| TTCGGGAAGGCAAGTCTGTG+AGG | + | chr4_3:25870195-25870214 | None:intergenic | 55.0% | |
| GCCGCAATTGGATCTCTTGC+GGG | + | chr4_3:25870321-25870340 | None:intergenic | 55.0% | |
| GGCCGCAATTGGATCTCTTG+CGG | + | chr4_3:25870322-25870341 | None:intergenic | 55.0% | |
| CGGCCGAGAAGTTAATGCTG+CGG | - | chr4_3:25870337-25870356 | Msa0636080:CDS | 55.0% | |
| !! | CACAAGCAGACTCTGAAGCC+AGG | - | chr4_3:25870498-25870517 | Msa0636080:CDS | 55.0% |
| GCACCTCTCACAGTTGAACC+TGG | + | chr4_3:25870519-25870538 | None:intergenic | 55.0% | |
| TGTGGGAAGTGGTTCTCCGG+TGG | - | chr4_3:25870044-25870063 | Msa0636080:CDS | 60.0% | |
| GTGGGAAGTGGTTCTCCGGT+GGG | - | chr4_3:25870045-25870064 | Msa0636080:CDS | 60.0% | |
| TTCTCCGGTGGGAAAGCCCT+TGG | - | chr4_3:25870056-25870075 | Msa0636080:CDS | 60.0% | |
| !!! | GCGGGTTGGGTTTTTCGGGT+TGG | + | chr4_3:25870303-25870322 | None:intergenic | 60.0% |
| AAGTCTGCTCAGGCACTCGG+TGG | - | chr4_3:25870659-25870678 | Msa0636080:CDS | 60.0% | |
| ! | AGGCACTCGGTGGACACAAG+AGG | - | chr4_3:25870669-25870688 | Msa0636080:CDS | 60.0% |
| ! | GGCACTCGGTGGACACAAGA+GGG | - | chr4_3:25870670-25870689 | Msa0636080:CDS | 60.0% |
| TCCGGTGGGAAAGCCCTTGG+AGG | - | chr4_3:25870059-25870078 | Msa0636080:CDS | 65.0% | |
| GCCTCCAAGGGCTTTCCCAC+CGG | + | chr4_3:25870063-25870082 | None:intergenic | 65.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr4_3 | gene | 25870011 | 25870742 | 25870011 | ID=Msa0636080;Name=Msa0636080 |
| chr4_3 | mRNA | 25870011 | 25870742 | 25870011 | ID=Msa0636080-mRNA-1;Parent=Msa0636080;Name=Msa0636080-mRNA-1;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|1|1|0|243 |
| chr4_3 | exon | 25870011 | 25870742 | 25870011 | ID=Msa0636080-mRNA-1:exon:6495;Parent=Msa0636080-mRNA-1 |
| chr4_3 | CDS | 25870011 | 25870742 | 25870011 | ID=Msa0636080-mRNA-1:cds;Parent=Msa0636080-mRNA-1 |
| Gene Sequence |
| Protein sequence |
