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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0402400 | XP_013461367.1 | 92.982 | 57 | 4 | 0 | 3 | 59 | 8 | 64 | 1.91e-29 | 115 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0402400 | sp|Q9FX36|MYB54_ARATH | 78.431 | 51 | 11 | 0 | 9 | 59 | 4 | 54 | 2.51e-23 | 90.9 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0402400 | A0A072V0T7 | 92.982 | 57 | 4 | 0 | 3 | 59 | 8 | 64 | 9.11e-30 | 115 |
| Gene ID | Type | Classification |
|---|---|---|
| Msa0402400 | TF | MYB-related |
| Gene ID | Type | Classification |
|---|
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0402400 | MtrunA17_Chr3g0125801 | 92.982 | 57 | 4 | 0 | 3 | 59 | 8 | 64 | 1.75e-33 | 115 |
| Msa0402400 | MtrunA17_Chr7g0254261 | 70.370 | 54 | 16 | 0 | 6 | 59 | 84 | 137 | 8.91e-24 | 90.9 |
| Msa0402400 | MtrunA17_Chr4g0042501 | 74.074 | 54 | 14 | 0 | 6 | 59 | 100 | 153 | 3.29e-23 | 89.7 |
| Msa0402400 | MtrunA17_Chr6g0480581 | 74.510 | 51 | 13 | 0 | 9 | 59 | 2 | 52 | 5.27e-23 | 87.0 |
| Msa0402400 | MtrunA17_Chr5g0417621 | 72.222 | 54 | 15 | 0 | 6 | 59 | 129 | 182 | 7.50e-23 | 89.0 |
| Msa0402400 | MtrunA17_Chr6g0460671 | 61.818 | 55 | 21 | 0 | 5 | 59 | 93 | 147 | 1.00e-20 | 82.4 |
| Msa0402400 | MtrunA17_Chr6g0460661 | 66.667 | 48 | 16 | 0 | 12 | 59 | 17 | 64 | 2.09e-20 | 78.6 |
| Msa0402400 | MtrunA17_Chr4g0008551 | 60.417 | 48 | 19 | 0 | 12 | 59 | 39 | 86 | 1.54e-14 | 65.5 |
| Msa0402400 | MtrunA17_Chr5g0401731 | 56.250 | 48 | 21 | 0 | 12 | 59 | 16 | 63 | 3.96e-14 | 64.3 |
| Msa0402400 | MtrunA17_Chr4g0053431 | 56.250 | 48 | 21 | 0 | 12 | 59 | 6 | 53 | 1.06e-13 | 62.8 |
| Msa0402400 | MtrunA17_Chr3g0104501 | 58.333 | 48 | 20 | 0 | 12 | 59 | 134 | 181 | 1.25e-13 | 61.6 |
| Msa0402400 | MtrunA17_Chr5g0429661 | 58.333 | 48 | 20 | 0 | 12 | 59 | 123 | 170 | 1.72e-13 | 62.4 |
| Msa0402400 | MtrunA17_Chr5g0437321 | 54.167 | 48 | 22 | 0 | 12 | 59 | 20 | 67 | 3.35e-13 | 61.6 |
| Msa0402400 | MtrunA17_Chr3g0133601 | 56.250 | 48 | 21 | 0 | 12 | 59 | 38 | 85 | 1.08e-12 | 59.7 |
| Msa0402400 | MtrunA17_Chr6g0454921 | 54.167 | 48 | 22 | 0 | 12 | 59 | 16 | 63 | 1.17e-12 | 59.3 |
| Msa0402400 | MtrunA17_Chr4g0058991 | 56.250 | 48 | 21 | 0 | 12 | 59 | 210 | 257 | 8.67e-12 | 57.8 |
| Msa0402400 | MtrunA17_Chr7g0233161 | 52.083 | 48 | 23 | 0 | 12 | 59 | 300 | 347 | 3.66e-11 | 55.8 |
| Msa0402400 | MtrunA17_Chr3g0139671 | 50.000 | 48 | 24 | 0 | 12 | 59 | 86 | 133 | 5.37e-11 | 55.5 |
| Msa0402400 | MtrunA17_Chr3g0117511 | 52.083 | 48 | 23 | 0 | 12 | 59 | 184 | 231 | 6.01e-11 | 55.5 |
| Msa0402400 | MtrunA17_Chr5g0397841 | 52.174 | 46 | 22 | 0 | 14 | 59 | 113 | 158 | 8.73e-11 | 55.1 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0402400 | AT1G73410.2 | 78.431 | 51 | 11 | 0 | 9 | 59 | 4 | 54 | 1.36e-24 | 90.5 |
| Msa0402400 | AT1G73410.1 | 78.431 | 51 | 11 | 0 | 9 | 59 | 4 | 54 | 2.55e-24 | 90.9 |
| Msa0402400 | AT1G17950.1 | 76.471 | 51 | 12 | 0 | 9 | 59 | 3 | 53 | 6.12e-24 | 89.7 |
| Msa0402400 | AT1G69560.1 | 76.923 | 52 | 12 | 0 | 8 | 59 | 104 | 155 | 1.00e-22 | 88.2 |
| Msa0402400 | AT1G69560.2 | 76.923 | 52 | 12 | 0 | 8 | 59 | 120 | 171 | 1.22e-22 | 87.8 |
| Msa0402400 | AT1G26780.1 | 81.250 | 48 | 9 | 0 | 12 | 59 | 99 | 146 | 2.15e-22 | 86.3 |
| Msa0402400 | AT4G33450.1 | 71.154 | 52 | 15 | 0 | 8 | 59 | 16 | 67 | 4.60e-22 | 85.1 |
| Msa0402400 | AT1G26780.2 | 81.250 | 48 | 9 | 0 | 12 | 59 | 99 | 146 | 5.41e-22 | 86.3 |
| Msa0402400 | AT5G17800.1 | 67.273 | 55 | 18 | 0 | 5 | 59 | 87 | 141 | 9.33e-22 | 85.5 |
| Msa0402400 | AT3G29020.1 | 64.815 | 54 | 19 | 0 | 6 | 59 | 60 | 113 | 1.67e-21 | 83.2 |
| Msa0402400 | AT3G29020.2 | 64.815 | 54 | 19 | 0 | 6 | 59 | 62 | 115 | 5.37e-21 | 83.2 |
| Msa0402400 | AT5G67300.1 | 56.250 | 48 | 21 | 0 | 12 | 59 | 7 | 54 | 1.48e-13 | 62.8 |
| Msa0402400 | AT5G39700.1 | 50.000 | 58 | 29 | 0 | 2 | 59 | 47 | 104 | 1.92e-13 | 61.2 |
| Msa0402400 | AT3G50060.1 | 54.167 | 48 | 22 | 0 | 12 | 59 | 7 | 54 | 2.29e-13 | 62.4 |
| Msa0402400 | AT5G40360.1 | 54.167 | 48 | 22 | 0 | 12 | 59 | 159 | 206 | 1.32e-12 | 60.5 |
| Msa0402400 | AT3G27785.1 | 54.167 | 48 | 22 | 0 | 12 | 59 | 190 | 237 | 1.76e-12 | 60.1 |
| Msa0402400 | AT2G39880.1 | 54.717 | 53 | 24 | 0 | 7 | 59 | 46 | 98 | 3.92e-12 | 59.3 |
| Msa0402400 | AT5G58850.1 | 50.000 | 54 | 27 | 0 | 6 | 59 | 100 | 153 | 5.14e-12 | 58.9 |
| Msa0402400 | AT3G09230.1 | 54.167 | 48 | 22 | 0 | 12 | 59 | 56 | 103 | 5.45e-12 | 58.9 |
| Msa0402400 | AT5G11050.1 | 50.943 | 53 | 26 | 0 | 7 | 59 | 101 | 153 | 6.69e-12 | 58.5 |
| Msa0402400 | AT2G23290.1 | 52.083 | 48 | 23 | 0 | 12 | 59 | 14 | 61 | 6.76e-12 | 58.2 |
| Msa0402400 | AT4G37260.1 | 52.083 | 48 | 23 | 0 | 12 | 59 | 14 | 61 | 9.65e-12 | 57.8 |
| Msa0402400 | AT3G09370.1 | 54.167 | 48 | 22 | 0 | 12 | 59 | 131 | 178 | 1.27e-11 | 57.8 |
| Msa0402400 | AT3G09370.2 | 54.167 | 48 | 22 | 0 | 12 | 59 | 136 | 183 | 1.27e-11 | 57.8 |
| Msa0402400 | AT3G09370.3 | 54.167 | 48 | 22 | 0 | 12 | 59 | 144 | 191 | 1.29e-11 | 57.8 |
| Msa0402400 | AT5G11510.2 | 52.083 | 48 | 23 | 0 | 12 | 59 | 82 | 129 | 1.88e-11 | 57.4 |
| Msa0402400 | AT5G11510.3 | 52.083 | 48 | 23 | 0 | 12 | 59 | 82 | 129 | 1.94e-11 | 57.4 |
| Msa0402400 | AT5G11510.1 | 52.083 | 48 | 23 | 0 | 12 | 59 | 82 | 129 | 1.94e-11 | 57.4 |
| Msa0402400 | AT5G11510.4 | 52.083 | 48 | 23 | 0 | 12 | 59 | 82 | 129 | 1.94e-11 | 57.4 |
| Msa0402400 | AT5G11510.5 | 52.083 | 48 | 23 | 0 | 12 | 59 | 82 | 129 | 1.97e-11 | 57.0 |
| Msa0402400 | AT3G55730.1 | 54.167 | 48 | 22 | 0 | 12 | 59 | 57 | 104 | 4.03e-11 | 56.2 |
| Msa0402400 | AT4G18770.1 | 54.167 | 48 | 22 | 0 | 12 | 59 | 218 | 265 | 5.33e-11 | 55.8 |
Find 33 sgRNAs with CRISPR-Local
Find 41 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| ATTCATTGAAATTTCTTATT+TGG | 0.138946 | 3_2:+30446276 | None:intergenic |
| ACAACATTATCAGTTCTTTC+AGG | 0.182418 | 3_2:+30446493 | None:intergenic |
| AACAATATGGTGCTCAAAAT+TGG | 0.232647 | 3_2:-30446915 | Msa0402400:CDS |
| TTCCCTTACACGACGAGAAT+TGG | 0.299194 | 3_2:-30446366 | Msa0402400:three_prime_UTR |
| CCTCAACTTGTTGAACAATA+TGG | 0.300197 | 3_2:-30446928 | Msa0402400:CDS |
| AAAGGTCTCTTGTTAATTCA+TGG | 0.340427 | 3_2:+30446595 | None:intergenic |
| ATGATAGTTCTCTTGCCTCT+TGG | 0.365489 | 3_2:-30446323 | Msa0402400:three_prime_UTR |
| ACTTCTCTTGCCACATAACT+TGG | 0.368979 | 3_2:+30446423 | None:intergenic |
| ATCGAATTCACATAAACAAA+TGG | 0.389392 | 3_2:-30446537 | Msa0402400:three_prime_UTR |
| GAATCATAGGCATGTTATAA+TGG | 0.391053 | 3_2:-30446467 | Msa0402400:three_prime_UTR |
| TATCCAATTCTCGTCGTGTA+AGG | 0.396192 | 3_2:+30446363 | None:intergenic |
| TCTTCTTCCTCTTCTGTGAA+AGG | 0.428456 | 3_2:+30446577 | None:intergenic |
| CAACATTATCAGTTCTTTCA+GGG | 0.435680 | 3_2:+30446494 | None:intergenic |
| ATAATGTTGTCAAGAATCAT+AGG | 0.447489 | 3_2:-30446480 | Msa0402400:three_prime_UTR |
| TAGGGAAACGTTGTAGGTTG+AGG | 0.463106 | 3_2:-30446636 | Msa0402400:CDS |
| AACTTGTAGGGAAACGTTGT+AGG | 0.477303 | 3_2:-30446642 | Msa0402400:intron |
| TCGAATTCACATAAACAAAT+GGG | 0.494256 | 3_2:-30446536 | Msa0402400:three_prime_UTR |
| CAAGAGACCTTTCACAGAAG+AGG | 0.503737 | 3_2:-30446584 | Msa0402400:three_prime_UTR |
| AGAGTTGTCCATGTGGTCAC+TGG | 0.512701 | 3_2:-30446975 | Msa0402400:CDS |
| ACGAGAATTGGATATGAGAA+TGG | 0.523637 | 3_2:-30446354 | Msa0402400:three_prime_UTR |
| TATAATGGCTACAAAACAAA+GGG | 0.531749 | 3_2:-30446452 | Msa0402400:three_prime_UTR |
| GTGACCACATGGACAACTCT+TGG | 0.543251 | 3_2:+30446978 | None:intergenic |
| GTGTAAGGGAAATTAAGTAT+AGG | 0.547906 | 3_2:+30446378 | None:intergenic |
| ATCCAATTCTCGTCGTGTAA+GGG | 0.553745 | 3_2:+30446364 | None:intergenic |
| CCATATTGTTCAACAAGTTG+AGG | 0.564383 | 3_2:+30446928 | None:intergenic |
| AGGGAACAATCCAAGTTATG+TGG | 0.586173 | 3_2:-30446433 | Msa0402400:three_prime_UTR |
| TTATAATGGCTACAAAACAA+AGG | 0.590289 | 3_2:-30446453 | Msa0402400:three_prime_UTR |
| GGAAACGTTGTAGGTTGAGG+TGG | 0.592608 | 3_2:-30446633 | Msa0402400:CDS |
| GCAGGTCGCCAGTGACCACA+TGG | 0.618887 | 3_2:+30446967 | None:intergenic |
| ACTTCCATAATCCATATGGA+GGG | 0.628080 | 3_2:-30447024 | None:intergenic |
| CACAAAAGTAGAATTCCAAG+AGG | 0.669761 | 3_2:+30446308 | None:intergenic |
| GGAAGAAGAGAGACTACTTG+CGG | 0.685866 | 3_2:-30446563 | Msa0402400:three_prime_UTR |
| GATACCAAGAGTTGTCCATG+TGG | 0.733953 | 3_2:-30446982 | Msa0402400:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | ATGAATTTGAAAATTAAATA+AGG | + | chr3_2:30446495-30446514 | None:intergenic | 10.0% |
| !! | AATTTGAAAATTAAATAAGG+AGG | + | chr3_2:30446492-30446511 | None:intergenic | 15.0% |
| !! | AATATTACATAATACATACC+TGG | + | chr3_2:30446437-30446456 | None:intergenic | 20.0% |
| !!! | ATTTTTTCCTTTTAACTTGT+AGG | - | chr3_2:30446641-30446660 | Msa0402400:intron | 20.0% |
| !!! | TTTTTTCCTTTTAACTTGTA+GGG | - | chr3_2:30446642-30446661 | Msa0402400:intron | 20.0% |
| ! | ATCGAATTCACATAAACAAA+TGG | - | chr3_2:30446759-30446778 | Msa0402400:intron | 25.0% |
| ! | TCGAATTCACATAAACAAAT+GGG | - | chr3_2:30446760-30446779 | Msa0402400:intron | 25.0% |
| ! | ATAATGTTGTCAAGAATCAT+AGG | - | chr3_2:30446816-30446835 | Msa0402400:intron | 25.0% |
| ! | TTATAATGGCTACAAAACAA+AGG | - | chr3_2:30446843-30446862 | Msa0402400:intron | 25.0% |
| ! | TATAATGGCTACAAAACAAA+GGG | - | chr3_2:30446844-30446863 | Msa0402400:intron | 25.0% |
| AACAATATGGTGCTCAAAAT+TGG | - | chr3_2:30446381-30446400 | Msa0402400:three_prime_UTR | 30.0% | |
| TCAATTGCTGAAAAACTTCA+AGG | - | chr3_2:30446407-30446426 | Msa0402400:three_prime_UTR | 30.0% | |
| AAAGGTCTCTTGTTAATTCA+TGG | + | chr3_2:30446704-30446723 | None:intergenic | 30.0% | |
| CAACATTATCAGTTCTTTCA+GGG | + | chr3_2:30446805-30446824 | None:intergenic | 30.0% | |
| ACAACATTATCAGTTCTTTC+AGG | + | chr3_2:30446806-30446825 | None:intergenic | 30.0% | |
| GAATCATAGGCATGTTATAA+TGG | - | chr3_2:30446829-30446848 | Msa0402400:intron | 30.0% | |
| GTGTAAGGGAAATTAAGTAT+AGG | + | chr3_2:30446921-30446940 | None:intergenic | 30.0% | |
| CCATATTGTTCAACAAGTTG+AGG | + | chr3_2:30446371-30446390 | None:intergenic | 35.0% | |
| !! | CCTCAACTTGTTGAACAATA+TGG | - | chr3_2:30446368-30446387 | Msa0402400:three_prime_UTR | 35.0% |
| ACGTTTCCCTACAAGTTAAA+AGG | + | chr3_2:30446651-30446670 | None:intergenic | 35.0% | |
| ACGAGAATTGGATATGAGAA+TGG | - | chr3_2:30446942-30446961 | Msa0402400:CDS | 35.0% | |
| CACAAAAGTAGAATTCCAAG+AGG | + | chr3_2:30446991-30447010 | None:intergenic | 35.0% | |
| ! | GGAAGTTTTTCATCTTCAGC+AGG | + | chr3_2:30446350-30446369 | None:intergenic | 40.0% |
| GAAAAACTTCAAGGAAGACC+AGG | - | chr3_2:30446416-30446435 | Msa0402400:three_prime_UTR | 40.0% | |
| AACTTGTAGGGAAACGTTGT+AGG | - | chr3_2:30446654-30446673 | Msa0402400:intron | 40.0% | |
| TCTTCTTCCTCTTCTGTGAA+AGG | + | chr3_2:30446722-30446741 | None:intergenic | 40.0% | |
| AGGGAACAATCCAAGTTATG+TGG | - | chr3_2:30446863-30446882 | Msa0402400:intron | 40.0% | |
| ACTTCTCTTGCCACATAACT+TGG | + | chr3_2:30446876-30446895 | None:intergenic | 40.0% | |
| ATCCAATTCTCGTCGTGTAA+GGG | + | chr3_2:30446935-30446954 | None:intergenic | 40.0% | |
| TATCCAATTCTCGTCGTGTA+AGG | + | chr3_2:30446936-30446955 | None:intergenic | 40.0% | |
| ATGATAGTTCTCTTGCCTCT+TGG | - | chr3_2:30446973-30446992 | Msa0402400:CDS | 40.0% | |
| GATACCAAGAGTTGTCCATG+TGG | - | chr3_2:30446314-30446333 | Msa0402400:three_prime_UTR | 45.0% | |
| TAGGGAAACGTTGTAGGTTG+AGG | - | chr3_2:30446660-30446679 | Msa0402400:intron | 45.0% | |
| CAAGAGACCTTTCACAGAAG+AGG | - | chr3_2:30446712-30446731 | Msa0402400:intron | 45.0% | |
| GGAAGAAGAGAGACTACTTG+CGG | - | chr3_2:30446733-30446752 | Msa0402400:intron | 45.0% | |
| TTCCCTTACACGACGAGAAT+TGG | - | chr3_2:30446930-30446949 | Msa0402400:CDS | 45.0% | |
| !! | TATTATGTAATATTAATTAA+AGG | - | chr3_2:30446443-30446462 | Msa0402400:three_prime_UTR | 5.0% |
| GTGACCACATGGACAACTCT+TGG | + | chr3_2:30446321-30446340 | None:intergenic | 50.0% | |
| AGAGTTGTCCATGTGGTCAC+TGG | - | chr3_2:30446321-30446340 | Msa0402400:three_prime_UTR | 50.0% | |
| ! | GGAAACGTTGTAGGTTGAGG+TGG | - | chr3_2:30446663-30446682 | Msa0402400:intron | 50.0% |
| GCAGGTCGCCAGTGACCACA+TGG | + | chr3_2:30446332-30446351 | None:intergenic | 65.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3_2 | gene | 30446287 | 30447031 | 30446287 | ID=Msa0402400;Name=Msa0402400 |
| chr3_2 | mRNA | 30446287 | 30447031 | 30446287 | ID=Msa0402400-mRNA-1;Parent=Msa0402400;Name=Msa0402400-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0.5|0.33|1|1|1|3|325|59 |
| chr3_2 | exon | 30446287 | 30446655 | 30446287 | ID=Msa0402400-mRNA-1:exon:6112;Parent=Msa0402400-mRNA-1 |
| chr3_2 | exon | 30446881 | 30447009 | 30446881 | ID=Msa0402400-mRNA-1:exon:6111;Parent=Msa0402400-mRNA-1 |
| chr3_2 | exon | 30447025 | 30447031 | 30447025 | ID=Msa0402400-mRNA-1:exon:6110;Parent=Msa0402400-mRNA-1 |
| chr3_2 | CDS | 30447025 | 30447031 | 30447025 | ID=Msa0402400-mRNA-1:cds;Parent=Msa0402400-mRNA-1 |
| chr3_2 | CDS | 30446881 | 30447009 | 30446881 | ID=Msa0402400-mRNA-1:cds;Parent=Msa0402400-mRNA-1 |
| chr3_2 | CDS | 30446612 | 30446655 | 30446612 | ID=Msa0402400-mRNA-1:cds;Parent=Msa0402400-mRNA-1 |
| chr3_2 | three_prime_UTR | 30446287 | 30446611 | 30446287 | ID=Msa0402400-mRNA-1:three_prime_utr;Parent=Msa0402400-mRNA-1 |
| Gene Sequence |
| Protein sequence |
