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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0541400 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0541400 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0541400 | A0A396I2K7 | 66.531 | 245 | 76 | 1 | 1 | 239 | 1 | 245 | 9.53e-114 | 335 |
| Gene ID | Type | Classification |
|---|---|---|
| Msa0541400 | TF | C2H2 |
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0541370 | Msa0541400 | 0.972144 | 2.742086e-134 | -8.615850e-47 |
| Msa0541400 | Msa0636080 | 0.980489 | 2.446874e-150 | -8.615850e-47 |
| Msa0541400 | Msa0675400 | 0.989982 | 1.607311e-180 | -8.615850e-47 |
| Msa0541400 | Msa0688950 | 0.975344 | 8.834010e-140 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0541400 | MtrunA17_Chr4g0018761 | 66.531 | 245 | 76 | 1 | 1 | 239 | 1 | 245 | 1.84e-117 | 335 |
| Msa0541400 | MtrunA17_Chr4g0018741 | 77.885 | 104 | 23 | 0 | 78 | 181 | 1 | 104 | 7.46e-55 | 171 |
| Msa0541400 | MtrunA17_Chr3g0079131 | 26.165 | 279 | 138 | 7 | 7 | 232 | 6 | 269 | 3.47e-18 | 81.3 |
| Msa0541400 | MtrunA17_Chr3g0079061 | 26.415 | 265 | 157 | 7 | 3 | 229 | 2 | 266 | 3.87e-16 | 75.9 |
| Msa0541400 | MtrunA17_Chr3g0079091 | 38.532 | 109 | 62 | 2 | 3 | 107 | 2 | 109 | 9.24e-14 | 67.4 |
| Msa0541400 | MtrunA17_Chr4g0056091 | 59.322 | 59 | 22 | 1 | 173 | 229 | 210 | 268 | 2.06e-13 | 68.6 |
| Msa0541400 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0541400 | AT3G60580.1 | 30.400 | 250 | 136 | 7 | 9 | 229 | 6 | 246 | 6.16e-18 | 81.3 |
| Msa0541400 | AT1G02030.1 | 27.132 | 258 | 132 | 6 | 9 | 236 | 7 | 238 | 4.01e-13 | 67.4 |
| Msa0541400 | 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_1:-25280597 | None:intergenic |
| ATTCTGTGTTTGTTGTATTT+CGG | 0.237824 | 4_1:-25280598 | None:intergenic |
| GCCGCAATTGGATCTCTTGC+GGG | 0.303465 | 4_1:-25280706 | None:intergenic |
| AATTGGATCTCTTGCGGGTT+GGG | 0.313326 | 4_1:-25280701 | None:intergenic |
| ATCCAGGTGTTCTGATGTTA+TGG | 0.324938 | 4_1:+25280772 | Msa0541400:CDS |
| TGAGTATTAGTTTCAAGCTT+TGG | 0.337317 | 4_1:-25280507 | None:intergenic |
| CAGCCGCAGCATTAACTTCT+CGG | 0.371873 | 4_1:-25280728 | None:intergenic |
| CAATTGGATCTCTTGCGGGT+TGG | 0.402481 | 4_1:-25280702 | None:intergenic |
| ATTAACTTCTCGGCCGCAAT+TGG | 0.433182 | 4_1:-25280718 | None:intergenic |
| TACTCAAGCTGTAGACAATT+CGG | 0.436960 | 4_1:+25280524 | Msa0541400:CDS |
| ATTTGTGGGAAGTGGTTCTC+CGG | 0.453707 | 4_1:+25280429 | Msa0541400:CDS |
| GTTTCAAGCTTTGGAGCAAT+CGG | 0.454553 | 4_1:-25280498 | None:intergenic |
| TTCCGATCTTATCAGGCTCT+TGG | 0.457389 | 4_1:+25280936 | Msa0541400:CDS |
| TTTACAAAGATGCGCAGAAA+AGG | 0.459521 | 4_1:+25280799 | Msa0541400:CDS |
| TACAGAATCACAAATCAATA+CGG | 0.462697 | 4_1:-25281122 | None:intergenic |
| TTCTCCGGTGGGAAAGCCCT+TGG | 0.463478 | 4_1:+25280444 | Msa0541400:CDS |
| GGAAAGCCTGTGGGATTTGT+GGG | 0.467351 | 4_1:+25280415 | Msa0541400:CDS |
| GGGAAAGCCTGTGGGATTTG+TGG | 0.468727 | 4_1:+25280414 | Msa0541400:CDS |
| CGATCTTATCAGGCTCTTGG+TGG | 0.468794 | 4_1:+25280939 | Msa0541400:CDS |
| TTGCAATTTGAGCAGTGAAA+AGG | 0.471865 | 4_1:-25281014 | None:intergenic |
| GCCTCCAAGGGCTTTCCCAC+CGG | 0.472807 | 4_1:-25280448 | None:intergenic |
| CCCCATAACATCAGAACACC+TGG | 0.474579 | 4_1:-25280774 | None:intergenic |
| AGATCTCATGTGGCCTCCAA+GGG | 0.485485 | 4_1:-25280460 | None:intergenic |
| GGCCGCAATTGGATCTCTTG+CGG | 0.489489 | 4_1:-25280707 | None:intergenic |
| TCCAGGTGTTCTGATGTTAT+GGG | 0.494593 | 4_1:+25280773 | Msa0541400:CDS |
| TCCGGTGGGAAAGCCCTTGG+AGG | 0.494800 | 4_1:+25280447 | Msa0541400:CDS |
| TTCTCTGTTTGAGCTTGCAG+AGG | 0.496954 | 4_1:-25280652 | None:intergenic |
| TCTGTTTGAGCTTGCAGAGG+AGG | 0.498454 | 4_1:-25280649 | None:intergenic |
| TTACAAAGATGCGCAGAAAA+GGG | 0.499625 | 4_1:+25280800 | Msa0541400:CDS |
| TTCAAGTCTGCTCAGGCACT+CGG | 0.500253 | 4_1:+25281044 | Msa0541400:CDS |
| AACGATGGCGAAAGCAGTAC+AGG | 0.507873 | 4_1:+25280852 | Msa0541400:CDS |
| AGCAAATTGATTTCGACGAT+GGG | 0.509489 | 4_1:-25280556 | None:intergenic |
| GCACCTCTCACAGTTGAACC+TGG | 0.509618 | 4_1:-25280904 | None:intergenic |
| ATTTCGACGATGGGTTGAAT+CGG | 0.510947 | 4_1:-25280547 | None:intergenic |
| GAGATCTCATGTGGCCTCCA+AGG | 0.514030 | 4_1:-25280461 | None:intergenic |
| GAAGATATGTCAAGAGATCC+AGG | 0.516117 | 4_1:+25280756 | Msa0541400:CDS |
| TGTGGGAAGTGGTTCTCCGG+TGG | 0.517822 | 4_1:+25280432 | Msa0541400:CDS |
| ACTTTGAAATTCCTTAGCAC+TGG | 0.521740 | 4_1:-25281090 | None:intergenic |
| CAAAGTGTTCAAGTCTGCTC+AGG | 0.524975 | 4_1:+25281037 | Msa0541400:CDS |
| CACAAGCAGACTCTGAAGCC+AGG | 0.539423 | 4_1:+25280886 | Msa0541400:CDS |
| AAGCAAATTGATTTCGACGA+TGG | 0.551421 | 4_1:-25280557 | None:intergenic |
| GTGTTTGTTGTATTTCGGGA+AGG | 0.552910 | 4_1:-25280593 | None:intergenic |
| CCTGTGGGATTTGTGGGAAG+TGG | 0.558125 | 4_1:+25280421 | Msa0541400:CDS |
| GTGGGAAGTGGTTCTCCGGT+GGG | 0.561353 | 4_1:+25280433 | Msa0541400:CDS |
| GATCTTATCAGGCTCTTGGT+GGG | 0.571526 | 4_1:+25280940 | Msa0541400:CDS |
| GGTACACTCTTCCAGTGCTA+AGG | 0.575791 | 4_1:+25281079 | Msa0541400:CDS |
| GCAACTATGGAGAAGAGCGA+TGG | 0.579019 | 4_1:+25280393 | None:intergenic |
| AAAGATGCGCAGAAAAGGGA+AGG | 0.579501 | 4_1:+25280804 | Msa0541400:CDS |
| CACCAAGAGCCTGATAAGAT+CGG | 0.582662 | 4_1:-25280938 | None:intergenic |
| CCAGGTGTTCTGATGTTATG+GGG | 0.595199 | 4_1:+25280774 | Msa0541400:CDS |
| AAGAGCGATGGGAAAGCCTG+TGG | 0.598960 | 4_1:+25280405 | Msa0541400:CDS |
| AGGCACTCGGTGGACACAAG+AGG | 0.606213 | 4_1:+25281057 | Msa0541400:CDS |
| ACAGAATCACAAATCAATAC+GGG | 0.613334 | 4_1:-25281121 | None:intergenic |
| CAACTATGGAGAAGAGCGAT+GGG | 0.616240 | 4_1:+25280394 | None:intergenic |
| TACTGCAAAAGAGACAATGA+TGG | 0.621835 | 4_1:+25280972 | Msa0541400:CDS |
| AAGCCAGGTTCAACTGTGAG+AGG | 0.622627 | 4_1:+25280901 | Msa0541400:CDS |
| ATCACAAATCAATACGGGTG+TGG | 0.631203 | 4_1:-25281116 | None:intergenic |
| GGCACTCGGTGGACACAAGA+GGG | 0.632635 | 4_1:+25281058 | Msa0541400:CDS |
| CCACTTCCCACAAATCCCAC+AGG | 0.647858 | 4_1:-25280421 | None:intergenic |
| CGGCCGAGAAGTTAATGCTG+CGG | 0.653910 | 4_1:+25280725 | Msa0541400:CDS |
| AGAGCGATGGGAAAGCCTGT+GGG | 0.654994 | 4_1:+25280406 | Msa0541400:CDS |
| AGGTTCAACTGTGAGAGGTG+CGG | 0.663022 | 4_1:+25280906 | Msa0541400:CDS |
| AAGATGCGCAGAAAAGGGAA+GGG | 0.667779 | 4_1:+25280805 | Msa0541400:CDS |
| TTCGGGAAGGCAAGTCTGTG+AGG | 0.669270 | 4_1:-25280580 | None:intergenic |
| AAGTCTGCTCAGGCACTCGG+TGG | 0.670340 | 4_1:+25281047 | Msa0541400:CDS |
| AGGCCACATGAGATCTCACA+TGG | 0.682156 | 4_1:+25280467 | Msa0541400:CDS |
| ACCCGCAAGAGATCCAATTG+CGG | 0.686880 | 4_1:+25280705 | Msa0541400:CDS |
| GAACCATGTGAGATCTCATG+TGG | 0.730676 | 4_1:-25280470 | None:intergenic |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | ATTCTGTGTTTGTTGTATTT+CGG | - | chr4_1:25280601-25280620 | None:intergenic | 25.0% |
| ! | GATCAAGAAACAAAAAATGA+GGG | + | chr4_1:25280827-25280846 | Msa0541400:CDS | 25.0% |
| ! | TGAGTATTAGTTTCAAGCTT+TGG | - | chr4_1:25280510-25280529 | None:intergenic | 30.0% |
| !! | TTCTGTGTTTGTTGTATTTC+GGG | - | chr4_1:25280600-25280619 | None:intergenic | 30.0% |
| !!! | TGAAGTTTTGTTTCAAGGAT+AGG | - | chr4_1:25280626-25280645 | None:intergenic | 30.0% |
| GGATCAAGAAACAAAAAATG+AGG | + | chr4_1:25280826-25280845 | Msa0541400:CDS | 30.0% | |
| AAAAATGTTCCGATCTTATC+AGG | + | chr4_1:25280929-25280948 | Msa0541400:CDS | 30.0% | |
| TACTCAAGCTGTAGACAATT+CGG | + | chr4_1:25280524-25280543 | Msa0541400:CDS | 35.0% | |
| ! | AGCAAATTGATTTCGACGAT+GGG | - | chr4_1:25280559-25280578 | None:intergenic | 35.0% |
| ! | AAGCAAATTGATTTCGACGA+TGG | - | chr4_1:25280560-25280579 | None:intergenic | 35.0% |
| TTTACAAAGATGCGCAGAAA+AGG | + | chr4_1:25280799-25280818 | Msa0541400:CDS | 35.0% | |
| TTACAAAGATGCGCAGAAAA+GGG | + | chr4_1:25280800-25280819 | Msa0541400:CDS | 35.0% | |
| CAAAAAATGAGGGAAAACGA+TGG | + | chr4_1:25280837-25280856 | Msa0541400:CDS | 35.0% | |
| TACTGCAAAAGAGACAATGA+TGG | + | chr4_1:25280972-25280991 | Msa0541400:CDS | 35.0% | |
| TTGCAATTTGAGCAGTGAAA+AGG | - | chr4_1:25281017-25281036 | None:intergenic | 35.0% | |
| !! | ACTTTGAAATTCCTTAGCAC+TGG | - | chr4_1:25281093-25281112 | None:intergenic | 35.0% |
| !! | GTTTCAAGCTTTGGAGCAAT+CGG | - | chr4_1:25280501-25280520 | None:intergenic | 40.0% |
| !! | ATTTCGACGATGGGTTGAAT+CGG | - | chr4_1:25280550-25280569 | None:intergenic | 40.0% |
| !! | GTGTTTGTTGTATTTCGGGA+AGG | - | chr4_1:25280596-25280615 | None:intergenic | 40.0% |
| !!! | GGCAGTGAAGTTTTGTTTCA+AGG | - | chr4_1:25280631-25280650 | None:intergenic | 40.0% |
| GAAGATATGTCAAGAGATCC+AGG | + | chr4_1:25280756-25280775 | Msa0541400:CDS | 40.0% | |
| ATCCAGGTGTTCTGATGTTA+TGG | + | chr4_1:25280772-25280791 | Msa0541400:CDS | 40.0% | |
| TCCAGGTGTTCTGATGTTAT+GGG | + | chr4_1:25280773-25280792 | Msa0541400:CDS | 40.0% | |
| ATTTGTGGGAAGTGGTTCTC+CGG | + | chr4_1:25280429-25280448 | Msa0541400:CDS | 45.0% | |
| GAACCATGTGAGATCTCATG+TGG | - | chr4_1:25280473-25280492 | None:intergenic | 45.0% | |
| TTCTCTGTTTGAGCTTGCAG+AGG | - | chr4_1:25280655-25280674 | None:intergenic | 45.0% | |
| AATTGGATCTCTTGCGGGTT+GGG | - | chr4_1:25280704-25280723 | None:intergenic | 45.0% | |
| ATTAACTTCTCGGCCGCAAT+TGG | - | chr4_1:25280721-25280740 | None:intergenic | 45.0% | |
| CCAGGTGTTCTGATGTTATG+GGG | + | chr4_1:25280774-25280793 | Msa0541400:CDS | 45.0% | |
| AAAGATGCGCAGAAAAGGGA+AGG | + | chr4_1:25280804-25280823 | Msa0541400:CDS | 45.0% | |
| AAGATGCGCAGAAAAGGGAA+GGG | + | chr4_1:25280805-25280824 | Msa0541400:CDS | 45.0% | |
| TTCCGATCTTATCAGGCTCT+TGG | + | chr4_1:25280936-25280955 | Msa0541400:CDS | 45.0% | |
| CACCAAGAGCCTGATAAGAT+CGG | - | chr4_1:25280941-25280960 | None:intergenic | 45.0% | |
| GATCTTATCAGGCTCTTGGT+GGG | + | chr4_1:25280940-25280959 | Msa0541400:CDS | 45.0% | |
| ! | CAAAGTGTTCAAGTCTGCTC+AGG | + | chr4_1:25281037-25281056 | Msa0541400:CDS | 45.0% |
| GGAAAGCCTGTGGGATTTGT+GGG | + | chr4_1:25280415-25280434 | Msa0541400:CDS | 50.0% | |
| AGATCTCATGTGGCCTCCAA+GGG | - | chr4_1:25280463-25280482 | None:intergenic | 50.0% | |
| AGGCCACATGAGATCTCACA+TGG | + | chr4_1:25280467-25280486 | Msa0541400:CDS | 50.0% | |
| TCTGTTTGAGCTTGCAGAGG+AGG | - | chr4_1:25280652-25280671 | None:intergenic | 50.0% | |
| !!! | TCTTGCGGGTTGGGTTTTTC+GGG | - | chr4_1:25280695-25280714 | None:intergenic | 50.0% |
| !!! | CTCTTGCGGGTTGGGTTTTT+CGG | - | chr4_1:25280696-25280715 | None:intergenic | 50.0% |
| CAATTGGATCTCTTGCGGGT+TGG | - | chr4_1:25280705-25280724 | None:intergenic | 50.0% | |
| ACCCGCAAGAGATCCAATTG+CGG | + | chr4_1:25280705-25280724 | Msa0541400:CDS | 50.0% | |
| CAGCCGCAGCATTAACTTCT+CGG | - | chr4_1:25280731-25280750 | None:intergenic | 50.0% | |
| CCCCATAACATCAGAACACC+TGG | - | chr4_1:25280777-25280796 | None:intergenic | 50.0% | |
| AACGATGGCGAAAGCAGTAC+AGG | + | chr4_1:25280852-25280871 | Msa0541400:CDS | 50.0% | |
| AAGCCAGGTTCAACTGTGAG+AGG | + | chr4_1:25280901-25280920 | Msa0541400:CDS | 50.0% | |
| AGGTTCAACTGTGAGAGGTG+CGG | + | chr4_1:25280906-25280925 | Msa0541400:CDS | 50.0% | |
| CGATCTTATCAGGCTCTTGG+TGG | + | chr4_1:25280939-25280958 | Msa0541400:CDS | 50.0% | |
| TTCAAGTCTGCTCAGGCACT+CGG | + | chr4_1:25281044-25281063 | Msa0541400:CDS | 50.0% | |
| GGTACACTCTTCCAGTGCTA+AGG | + | chr4_1:25281079-25281098 | Msa0541400:CDS | 50.0% | |
| AAGAGCGATGGGAAAGCCTG+TGG | + | chr4_1:25280405-25280424 | Msa0541400:CDS | 55.0% | |
| AGAGCGATGGGAAAGCCTGT+GGG | + | chr4_1:25280406-25280425 | Msa0541400:CDS | 55.0% | |
| GGGAAAGCCTGTGGGATTTG+TGG | + | chr4_1:25280414-25280433 | Msa0541400:CDS | 55.0% | |
| CCACTTCCCACAAATCCCAC+AGG | - | chr4_1:25280424-25280443 | None:intergenic | 55.0% | |
| CCTGTGGGATTTGTGGGAAG+TGG | + | chr4_1:25280421-25280440 | Msa0541400:CDS | 55.0% | |
| GAGATCTCATGTGGCCTCCA+AGG | - | chr4_1:25280464-25280483 | None:intergenic | 55.0% | |
| TTCGGGAAGGCAAGTCTGTG+AGG | - | chr4_1:25280583-25280602 | None:intergenic | 55.0% | |
| GCCGCAATTGGATCTCTTGC+GGG | - | chr4_1:25280709-25280728 | None:intergenic | 55.0% | |
| GGCCGCAATTGGATCTCTTG+CGG | - | chr4_1:25280710-25280729 | None:intergenic | 55.0% | |
| CGGCCGAGAAGTTAATGCTG+CGG | + | chr4_1:25280725-25280744 | Msa0541400:CDS | 55.0% | |
| !! | CACAAGCAGACTCTGAAGCC+AGG | + | chr4_1:25280886-25280905 | Msa0541400:CDS | 55.0% |
| GCACCTCTCACAGTTGAACC+TGG | - | chr4_1:25280907-25280926 | None:intergenic | 55.0% | |
| TGTGGGAAGTGGTTCTCCGG+TGG | + | chr4_1:25280432-25280451 | Msa0541400:CDS | 60.0% | |
| GTGGGAAGTGGTTCTCCGGT+GGG | + | chr4_1:25280433-25280452 | Msa0541400:CDS | 60.0% | |
| TTCTCCGGTGGGAAAGCCCT+TGG | + | chr4_1:25280444-25280463 | Msa0541400:CDS | 60.0% | |
| !!! | GCGGGTTGGGTTTTTCGGGT+TGG | - | chr4_1:25280691-25280710 | None:intergenic | 60.0% |
| AAGTCTGCTCAGGCACTCGG+TGG | + | chr4_1:25281047-25281066 | Msa0541400:CDS | 60.0% | |
| ! | AGGCACTCGGTGGACACAAG+AGG | + | chr4_1:25281057-25281076 | Msa0541400:CDS | 60.0% |
| ! | GGCACTCGGTGGACACAAGA+GGG | + | chr4_1:25281058-25281077 | Msa0541400:CDS | 60.0% |
| TCCGGTGGGAAAGCCCTTGG+AGG | + | chr4_1:25280447-25280466 | Msa0541400:CDS | 65.0% | |
| GCCTCCAAGGGCTTTCCCAC+CGG | - | chr4_1:25280451-25280470 | None:intergenic | 65.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr4_1 | gene | 25280399 | 25281130 | 25280399 | ID=Msa0541400;Name=Msa0541400 |
| chr4_1 | mRNA | 25280399 | 25281130 | 25280399 | ID=Msa0541400-mRNA-1;Parent=Msa0541400;Name=Msa0541400-mRNA-1;_AED=0.43;_eAED=0.43;_QI=0|-1|0|1|-1|1|1|0|243 |
| chr4_1 | exon | 25280399 | 25281130 | 25280399 | ID=Msa0541400-mRNA-1:exon:6789;Parent=Msa0541400-mRNA-1 |
| chr4_1 | CDS | 25280399 | 25281130 | 25280399 | ID=Msa0541400-mRNA-1:cds;Parent=Msa0541400-mRNA-1 |
| Gene Sequence |
| Protein sequence |
