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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0390440 | XP_003620169.1 | 97.537 | 203 | 5 | 0 | 1 | 203 | 1 | 203 | 1.72e-143 | 408 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0390440 | sp|Q9LMU2|KTI5_ARATH | 48.309 | 207 | 88 | 8 | 3 | 203 | 2 | 195 | 2.41e-53 | 172 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0390440 | G7KKP1 | 97.537 | 203 | 5 | 0 | 1 | 203 | 1 | 203 | 8.23e-144 | 408 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0106620 | Msa0390440 | 0.807743 | 4.354208e-50 | -8.615850e-47 |
| Msa0187030 | Msa0390440 | 0.806935 | 6.460557e-50 | -8.615850e-47 |
| Msa0390440 | Msa0430750 | 0.819139 | 1.358309e-52 | -8.615850e-47 |
| Msa0390440 | Msa0592080 | 0.803777 | 2.965020e-49 | -8.615850e-47 |
| Msa0390440 | Msa0715420 | 0.827520 | 1.495155e-54 | -8.615850e-47 |
| Msa0390440 | Msa0798310 | 0.809964 | 1.458197e-50 | -8.615850e-47 |
| Msa0390440 | Msa1219000 | 0.802719 | 4.909873e-49 | -8.615850e-47 |
| Msa0390440 | Msa1321050 | 0.833768 | 4.410269e-56 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0390440 | MtrunA17_Chr6g0481911 | 97.537 | 203 | 5 | 0 | 1 | 203 | 1 | 203 | 1.58e-147 | 408 |
| Msa0390440 | MtrunA17_Chr6g0481941 | 82.039 | 206 | 33 | 2 | 1 | 203 | 1 | 205 | 1.31e-118 | 335 |
| Msa0390440 | MtrunA17_Chr6g0482041 | 44.444 | 207 | 98 | 8 | 5 | 201 | 11 | 210 | 2.47e-45 | 149 |
| Msa0390440 | MtrunA17_Chr7g0228581 | 41.935 | 186 | 94 | 7 | 23 | 203 | 26 | 202 | 4.99e-37 | 127 |
| Msa0390440 | MtrunA17_Chr6g0481951 | 40.933 | 193 | 99 | 7 | 21 | 203 | 26 | 213 | 2.36e-35 | 124 |
| Msa0390440 | MtrunA17_Chr6g0481961 | 40.415 | 193 | 100 | 7 | 21 | 203 | 26 | 213 | 5.26e-34 | 120 |
| Msa0390440 | MtrunA17_Chr6g0482031 | 36.923 | 195 | 104 | 7 | 21 | 203 | 25 | 212 | 1.63e-30 | 111 |
| Msa0390440 | MtrunA17_Chr6g0482011 | 40.000 | 175 | 93 | 7 | 24 | 191 | 25 | 194 | 7.81e-30 | 109 |
| Msa0390440 | MtrunA17_Chr3g0137411 | 36.508 | 189 | 99 | 7 | 21 | 202 | 24 | 198 | 3.64e-24 | 94.7 |
| Msa0390440 | MtrunA17_Chr6g0482021 | 32.961 | 179 | 109 | 6 | 26 | 203 | 31 | 199 | 1.27e-23 | 93.2 |
| Msa0390440 | MtrunA17_Chr3g0137421 | 33.014 | 209 | 113 | 9 | 5 | 203 | 6 | 197 | 7.90e-23 | 91.3 |
| Msa0390440 | MtrunA17_Chr3g0137441 | 32.057 | 209 | 117 | 10 | 5 | 203 | 6 | 199 | 7.34e-20 | 83.6 |
| Msa0390440 | MtrunA17_Chr2g0314431 | 31.188 | 202 | 127 | 6 | 3 | 203 | 9 | 199 | 1.08e-19 | 82.8 |
| Msa0390440 | MtrunA17_Chr1g0173431 | 31.884 | 207 | 122 | 10 | 4 | 202 | 5 | 200 | 3.93e-19 | 81.3 |
| Msa0390440 | MtrunA17_Chr2g0314441 | 32.039 | 206 | 119 | 8 | 3 | 203 | 9 | 198 | 5.33e-19 | 80.9 |
| Msa0390440 | MtrunA17_Chr4g0022751 | 29.268 | 205 | 129 | 9 | 4 | 202 | 7 | 201 | 1.83e-17 | 77.0 |
| Msa0390440 | MtrunA17_Chr6g0476921 | 31.720 | 186 | 118 | 7 | 20 | 202 | 22 | 201 | 5.06e-17 | 75.9 |
| Msa0390440 | MtrunA17_Chr6g0476871 | 34.595 | 185 | 114 | 6 | 22 | 203 | 28 | 208 | 5.23e-17 | 76.3 |
| Msa0390440 | MtrunA17_Chr3g0104591 | 30.233 | 172 | 115 | 4 | 18 | 189 | 21 | 187 | 2.08e-16 | 74.3 |
| Msa0390440 | MtrunA17_Chr6g0476951 | 31.553 | 206 | 127 | 7 | 1 | 203 | 1 | 195 | 2.77e-16 | 73.9 |
| Msa0390440 | MtrunA17_Chr6g0476831 | 33.333 | 183 | 112 | 6 | 24 | 203 | 29 | 204 | 9.01e-16 | 73.2 |
| Msa0390440 | MtrunA17_Chr3g0082681 | 29.952 | 207 | 126 | 9 | 4 | 202 | 7 | 202 | 1.80e-15 | 71.6 |
| Msa0390440 | MtrunA17_Chr3g0082651 | 29.952 | 207 | 128 | 8 | 4 | 202 | 5 | 202 | 2.10e-15 | 71.6 |
| Msa0390440 | MtrunA17_Chr6g0476961 | 31.553 | 206 | 126 | 8 | 1 | 203 | 1 | 194 | 2.54e-15 | 71.2 |
| Msa0390440 | MtrunA17_Chr8g0359111 | 32.843 | 204 | 117 | 13 | 10 | 202 | 7 | 201 | 6.49e-15 | 70.1 |
| Msa0390440 | MtrunA17_Chr3g0082671 | 28.502 | 207 | 129 | 9 | 4 | 202 | 7 | 202 | 8.37e-15 | 69.7 |
| Msa0390440 | MtrunA17_Chr6g0452491 | 30.882 | 204 | 127 | 9 | 6 | 203 | 7 | 202 | 3.60e-12 | 62.8 |
| Msa0390440 | MtrunA17_Chr6g0477751 | 28.846 | 208 | 132 | 8 | 5 | 203 | 4 | 204 | 4.54e-12 | 62.8 |
| Msa0390440 | MtrunA17_Chr6g0452521 | 30.693 | 202 | 124 | 9 | 10 | 203 | 42 | 235 | 5.30e-12 | 62.8 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0390440 | AT1G17860.1 | 48.309 | 207 | 88 | 8 | 3 | 203 | 2 | 195 | 2.45e-54 | 172 |
| Msa0390440 | AT1G73260.1 | 37.017 | 181 | 106 | 5 | 26 | 203 | 30 | 205 | 3.02e-29 | 108 |
| Msa0390440 | AT1G73325.1 | 33.659 | 205 | 120 | 7 | 4 | 203 | 10 | 203 | 4.50e-23 | 92.8 |
Find 39 sgRNAs with CRISPR-Local
Find 50 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| CATTTAGGGTTGTGTTTAAA+AGG | 0.160681 | 3_2:+1281093 | Msa0390440:CDS |
| GTGATCAAATTCCATCATTT+AGG | 0.169249 | 3_2:+1281078 | Msa0390440:CDS |
| ACACCTTGTTTAGCATTATA+AGG | 0.259304 | 3_2:-1280765 | None:intergenic |
| GTATGGCAACTGTTGGTAAT+TGG | 0.271386 | 3_2:+1280925 | Msa0390440:CDS |
| GAACCAGTTCTTGACATTTC+AGG | 0.287884 | 3_2:+1280579 | Msa0390440:CDS |
| GCTTCTCTTGAACAACATAA+AGG | 0.342977 | 3_2:-1280707 | None:intergenic |
| TGATCAAATTCCATCATTTA+GGG | 0.346172 | 3_2:+1281079 | Msa0390440:CDS |
| CAAACTTTGTGTAGGGAACT+AGG | 0.366708 | 3_2:+1281014 | Msa0390440:CDS |
| CTTCTCTTGAACAACATAAA+GGG | 0.369437 | 3_2:-1280706 | None:intergenic |
| AGGGTTGTTTGTTGATGATA+AGG | 0.370874 | 3_2:+1281034 | Msa0390440:CDS |
| AATGTCCTCAAACACAAGTT+TGG | 0.377880 | 3_2:+1280838 | Msa0390440:CDS |
| TTACCAACAGTTGCCATACT+TGG | 0.386300 | 3_2:-1280921 | None:intergenic |
| CAACATAAAGGGGACATGTT+TGG | 0.398228 | 3_2:-1280695 | None:intergenic |
| AGCTTCCAAACTTGTGTTTG+AGG | 0.408512 | 3_2:-1280843 | None:intergenic |
| GGGTTGTTTGTTGATGATAA+GGG | 0.441383 | 3_2:+1281035 | Msa0390440:CDS |
| TTAAACACAACCCTAAATGA+TGG | 0.447080 | 3_2:-1281089 | None:intergenic |
| TGTAGAAGGTAATCCAAGTA+TGG | 0.452203 | 3_2:+1280908 | Msa0390440:CDS |
| ATTTAGGGTTGTGTTTAAAA+GGG | 0.479397 | 3_2:+1281094 | Msa0390440:CDS |
| GAAATGTCAAGAACTGGTTC+AGG | 0.479615 | 3_2:-1280576 | None:intergenic |
| TGACATTTGCAAGCTTCAGC+AGG | 0.493041 | 3_2:-1280993 | None:intergenic |
| AAGCTTCTTAAAGAGTTGAC+AGG | 0.493248 | 3_2:+1280861 | Msa0390440:CDS |
| GCAAATGTCAAACTTTGTGT+AGG | 0.501531 | 3_2:+1281006 | Msa0390440:CDS |
| TCAGGCAAACAAGTGACAAC+TGG | 0.504943 | 3_2:+1280597 | Msa0390440:CDS |
| TTGCCTGAAATGTCAAGAAC+TGG | 0.505604 | 3_2:-1280582 | None:intergenic |
| CAAATGTCAAACTTTGTGTA+GGG | 0.511038 | 3_2:+1281007 | Msa0390440:CDS |
| TTACCAGTCATAAGAGGTAA+AGG | 0.515215 | 3_2:+1280636 | Msa0390440:CDS |
| TTAAAGAGTTGACAGGGGTG+TGG | 0.531517 | 3_2:+1280868 | Msa0390440:CDS |
| GAGAAGCTTGAAGTAAAGAA+TGG | 0.531990 | 3_2:+1280723 | Msa0390440:CDS |
| AAACTTTGTGTAGGGAACTA+GGG | 0.532296 | 3_2:+1281015 | Msa0390440:CDS |
| GTCATAAGAGGTAAAGGTGG+TGG | 0.556783 | 3_2:+1280642 | Msa0390440:CDS |
| CCACCTTTACCTCTTATGAC+TGG | 0.557512 | 3_2:-1280639 | None:intergenic |
| AGCTTCTTAAAGAGTTGACA+GGG | 0.566536 | 3_2:+1280862 | Msa0390440:CDS |
| TTCTCTTGAACAACATAAAG+GGG | 0.573118 | 3_2:-1280705 | None:intergenic |
| AATCCAAGTATGGCAACTGT+TGG | 0.585675 | 3_2:+1280918 | Msa0390440:CDS |
| GGTGGAAAATGCTAAGAGTG+AGG | 0.614319 | 3_2:-1280517 | None:intergenic |
| ACACCTTATAATGCTAAACA+AGG | 0.651507 | 3_2:+1280762 | Msa0390440:CDS |
| CCAGTCATAAGAGGTAAAGG+TGG | 0.660270 | 3_2:+1280639 | Msa0390440:CDS |
| GGTTTAACAGTTGCAAACCA+TGG | 0.676406 | 3_2:+1280663 | Msa0390440:CDS |
| GCTTCTTAAAGAGTTGACAG+GGG | 0.746376 | 3_2:+1280863 | Msa0390440:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | ACATTTAGTTTTTGTTACAA+AGG | - | chr3_2:1280823-1280842 | None:intergenic | 20.0% |
| !! | TATATTTTACCAGTCATAAG+AGG | + | chr3_2:1280630-1280649 | Msa0390440:CDS | 25.0% |
| ! | TGATCAAATTCCATCATTTA+GGG | + | chr3_2:1281079-1281098 | Msa0390440:CDS | 25.0% |
| !! | ATTTAGGGTTGTGTTTAAAA+GGG | + | chr3_2:1281094-1281113 | Msa0390440:CDS | 25.0% |
| !! | TGCAATAGTTTTGCAAATGA+AGG | - | chr3_2:1280553-1280572 | None:intergenic | 30.0% |
| TTCTCTTGAACAACATAAAG+GGG | - | chr3_2:1280708-1280727 | None:intergenic | 30.0% | |
| CTTCTCTTGAACAACATAAA+GGG | - | chr3_2:1280709-1280728 | None:intergenic | 30.0% | |
| ACACCTTATAATGCTAAACA+AGG | + | chr3_2:1280762-1280781 | Msa0390440:CDS | 30.0% | |
| ! | ACACCTTGTTTAGCATTATA+AGG | - | chr3_2:1280768-1280787 | None:intergenic | 30.0% |
| CAAATGTCAAACTTTGTGTA+GGG | + | chr3_2:1281007-1281026 | Msa0390440:CDS | 30.0% | |
| GTGATCAAATTCCATCATTT+AGG | + | chr3_2:1281078-1281097 | Msa0390440:CDS | 30.0% | |
| TTAAACACAACCCTAAATGA+TGG | - | chr3_2:1281092-1281111 | None:intergenic | 30.0% | |
| ! | CATTTAGGGTTGTGTTTAAA+AGG | + | chr3_2:1281093-1281112 | Msa0390440:CDS | 30.0% |
| AATGAAGGCTAAAAAGATGG+TGG | - | chr3_2:1280538-1280557 | None:intergenic | 35.0% | |
| GCAAATGAAGGCTAAAAAGA+TGG | - | chr3_2:1280541-1280560 | None:intergenic | 35.0% | |
| TTACCAGTCATAAGAGGTAA+AGG | + | chr3_2:1280636-1280655 | Msa0390440:CDS | 35.0% | |
| !! | ATGTTTGGTTGTTTTCACCA+TGG | - | chr3_2:1280683-1280702 | None:intergenic | 35.0% |
| GCTTCTCTTGAACAACATAA+AGG | - | chr3_2:1280710-1280729 | None:intergenic | 35.0% | |
| GAGAAGCTTGAAGTAAAGAA+TGG | + | chr3_2:1280723-1280742 | Msa0390440:CDS | 35.0% | |
| AATGTCCTCAAACACAAGTT+TGG | + | chr3_2:1280838-1280857 | Msa0390440:CDS | 35.0% | |
| AAGCTTCTTAAAGAGTTGAC+AGG | + | chr3_2:1280861-1280880 | Msa0390440:CDS | 35.0% | |
| AGCTTCTTAAAGAGTTGACA+GGG | + | chr3_2:1280862-1280881 | Msa0390440:CDS | 35.0% | |
| TGTAGAAGGTAATCCAAGTA+TGG | + | chr3_2:1280908-1280927 | Msa0390440:CDS | 35.0% | |
| GCAAATGTCAAACTTTGTGT+AGG | + | chr3_2:1281006-1281025 | Msa0390440:CDS | 35.0% | |
| AAACTTTGTGTAGGGAACTA+GGG | + | chr3_2:1281015-1281034 | Msa0390440:CDS | 35.0% | |
| !! | AGGGTTGTTTGTTGATGATA+AGG | + | chr3_2:1281034-1281053 | Msa0390440:CDS | 35.0% |
| !! | GGGTTGTTTGTTGATGATAA+GGG | + | chr3_2:1281035-1281054 | Msa0390440:CDS | 35.0% |
| ! | GAAATGTCAAGAACTGGTTC+AGG | - | chr3_2:1280579-1280598 | None:intergenic | 40.0% |
| GAACCAGTTCTTGACATTTC+AGG | + | chr3_2:1280579-1280598 | Msa0390440:CDS | 40.0% | |
| TTGCCTGAAATGTCAAGAAC+TGG | - | chr3_2:1280585-1280604 | None:intergenic | 40.0% | |
| GGTTTAACAGTTGCAAACCA+TGG | + | chr3_2:1280663-1280682 | Msa0390440:CDS | 40.0% | |
| CAACATAAAGGGGACATGTT+TGG | - | chr3_2:1280698-1280717 | None:intergenic | 40.0% | |
| AGCTTCCAAACTTGTGTTTG+AGG | - | chr3_2:1280846-1280865 | None:intergenic | 40.0% | |
| GCTTCTTAAAGAGTTGACAG+GGG | + | chr3_2:1280863-1280882 | Msa0390440:CDS | 40.0% | |
| AATCCAAGTATGGCAACTGT+TGG | + | chr3_2:1280918-1280937 | Msa0390440:CDS | 40.0% | |
| TTACCAACAGTTGCCATACT+TGG | - | chr3_2:1280924-1280943 | None:intergenic | 40.0% | |
| !! | GTATGGCAACTGTTGGTAAT+TGG | + | chr3_2:1280925-1280944 | Msa0390440:CDS | 40.0% |
| CAAACTTTGTGTAGGGAACT+AGG | + | chr3_2:1281014-1281033 | Msa0390440:CDS | 40.0% | |
| GGTGGAAAATGCTAAGAGTG+AGG | - | chr3_2:1280520-1280539 | None:intergenic | 45.0% | |
| TCAGGCAAACAAGTGACAAC+TGG | + | chr3_2:1280597-1280616 | Msa0390440:CDS | 45.0% | |
| CCACCTTTACCTCTTATGAC+TGG | - | chr3_2:1280642-1280661 | None:intergenic | 45.0% | |
| CCAGTCATAAGAGGTAAAGG+TGG | + | chr3_2:1280639-1280658 | Msa0390440:CDS | 45.0% | |
| GTCATAAGAGGTAAAGGTGG+TGG | + | chr3_2:1280642-1280661 | Msa0390440:CDS | 45.0% | |
| TTAAAGAGTTGACAGGGGTG+TGG | + | chr3_2:1280868-1280887 | Msa0390440:CDS | 45.0% | |
| !!! | GGGTGTGGTTTTTAGCTACA+GGG | + | chr3_2:1280883-1280902 | Msa0390440:CDS | 45.0% |
| !!! | GGTGTGGTTTTTAGCTACAG+GGG | + | chr3_2:1280884-1280903 | Msa0390440:CDS | 45.0% |
| !!! | GTGTGGTTTTTAGCTACAGG+GGG | + | chr3_2:1280885-1280904 | Msa0390440:CDS | 45.0% |
| TGACATTTGCAAGCTTCAGC+AGG | - | chr3_2:1280996-1281015 | None:intergenic | 45.0% | |
| !!! | GGGGTGTGGTTTTTAGCTAC+AGG | + | chr3_2:1280882-1280901 | Msa0390440:CDS | 50.0% |
| ! | TTAGCTACAGGGGGTGTAGA+AGG | + | chr3_2:1280894-1280913 | Msa0390440:CDS | 50.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3_2 | gene | 1280510 | 1281121 | 1280510 | ID=Msa0390440;Name=Msa0390440 |
| chr3_2 | mRNA | 1280510 | 1281121 | 1280510 | ID=Msa0390440-mRNA-1;Parent=Msa0390440;Name=Msa0390440-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|-1|0|1|-1|1|1|0|203 |
| chr3_2 | exon | 1280510 | 1281121 | 1280510 | ID=Msa0390440-mRNA-1:exon:382;Parent=Msa0390440-mRNA-1 |
| chr3_2 | CDS | 1280510 | 1281121 | 1280510 | ID=Msa0390440-mRNA-1:cds;Parent=Msa0390440-mRNA-1 |
| Gene Sequence |
| Protein sequence |
