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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1021970 | KEH32781.1 | 48.744 | 199 | 93 | 2 | 1 | 190 | 26 | 224 | 9.14e-53 | 186 |
| Msa1021970 | KEH32781.1 | 78.802 | 217 | 22 | 4 | 3 | 195 | 258 | 474 | 4.71e-106 | 323 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1021970 | sp|Q84R27|Y3896_ARATH | 40.909 | 88 | 52 | 0 | 1 | 88 | 43 | 130 | 2.35e-18 | 82.4 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1021970 | A0A072UTW5 | 48.744 | 199 | 93 | 2 | 1 | 190 | 26 | 224 | 4.37e-53 | 186 |
| Msa1021970 | A0A072UTW5 | 78.802 | 217 | 22 | 4 | 3 | 195 | 258 | 474 | 2.25e-106 | 323 |
| Gene ID | Type | Classification |
|---|---|---|
| Msa1021970 | TF | B3 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1021970 | MtrunA17_Chr3g0077461 | 78.802 | 217 | 22 | 4 | 3 | 195 | 252 | 468 | 4.80e-110 | 322 |
| Msa1021970 | MtrunA17_Chr3g0077461 | 49.749 | 199 | 91 | 2 | 1 | 190 | 20 | 218 | 4.02e-58 | 189 |
| Msa1021970 | MtrunA17_Chr5g0429931 | 51.082 | 231 | 74 | 4 | 1 | 192 | 8 | 238 | 1.49e-70 | 214 |
| Msa1021970 | MtrunA17_Chr3g0077451 | 51.818 | 220 | 76 | 4 | 3 | 192 | 11 | 230 | 1.20e-66 | 204 |
| Msa1021970 | MtrunA17_Chr3g0077411 | 48.523 | 237 | 75 | 6 | 3 | 192 | 277 | 513 | 3.88e-61 | 198 |
| Msa1021970 | MtrunA17_Chr3g0077411 | 47.549 | 204 | 91 | 3 | 3 | 190 | 40 | 243 | 4.64e-55 | 182 |
| Msa1021970 | MtrunA17_Chr4g0009491 | 47.396 | 192 | 84 | 3 | 1 | 175 | 10 | 201 | 1.32e-50 | 169 |
| Msa1021970 | MtrunA17_Chr4g0009491 | 47.826 | 184 | 59 | 3 | 3 | 149 | 240 | 423 | 5.99e-46 | 156 |
| Msa1021970 | MtrunA17_Chr3g0077431 | 49.215 | 191 | 67 | 4 | 32 | 192 | 1 | 191 | 1.51e-50 | 162 |
| Msa1021970 | MtrunA17_Chr3g0077361 | 48.058 | 206 | 89 | 5 | 3 | 190 | 55 | 260 | 2.35e-50 | 169 |
| Msa1021970 | MtrunA17_Chr3g0077361 | 45.876 | 194 | 101 | 3 | 3 | 192 | 304 | 497 | 1.85e-44 | 154 |
| Msa1021970 | MtrunA17_Chr3g0077421 | 46.875 | 192 | 71 | 4 | 32 | 192 | 1 | 192 | 1.98e-49 | 159 |
| Msa1021970 | MtrunA17_Chr3g0077441 | 46.875 | 192 | 71 | 4 | 32 | 192 | 1 | 192 | 1.98e-49 | 159 |
| Msa1021970 | MtrunA17_Chr3g0077381 | 44.231 | 208 | 81 | 3 | 1 | 193 | 33 | 220 | 1.12e-45 | 156 |
| Msa1021970 | MtrunA17_Chr3g0077381 | 46.893 | 177 | 64 | 2 | 3 | 149 | 262 | 438 | 4.21e-43 | 149 |
| Msa1021970 | MtrunA17_Chr1g0162441 | 45.238 | 84 | 46 | 0 | 3 | 86 | 22 | 105 | 2.57e-20 | 87.4 |
| Msa1021970 | MtrunA17_Chr3g0131891 | 26.316 | 266 | 120 | 7 | 4 | 193 | 35 | 300 | 6.88e-19 | 82.8 |
| Msa1021970 | MtrunA17_Chr7g0233531 | 38.835 | 103 | 61 | 1 | 4 | 106 | 2 | 102 | 1.50e-17 | 78.6 |
| Msa1021970 | MtrunA17_Chr5g0419201 | 36.538 | 104 | 64 | 2 | 4 | 105 | 32 | 135 | 1.70e-17 | 76.6 |
| Msa1021970 | MtrunA17_Chr3g0103171 | 43.023 | 86 | 49 | 0 | 1 | 86 | 3 | 88 | 3.70e-17 | 77.0 |
| Msa1021970 | MtrunA17_Chr7g0233541 | 33.333 | 105 | 70 | 0 | 4 | 108 | 2 | 106 | 2.10e-16 | 75.5 |
| Msa1021970 | MtrunA17_Chr7g0233561 | 34.906 | 106 | 67 | 1 | 3 | 108 | 33 | 136 | 1.77e-15 | 73.2 |
| Msa1021970 | MtrunA17_Chr7g0233521 | 39.535 | 86 | 52 | 0 | 4 | 89 | 2 | 87 | 1.79e-15 | 72.8 |
| Msa1021970 | MtrunA17_Chr4g0033961 | 38.095 | 84 | 52 | 0 | 3 | 86 | 21 | 104 | 2.64e-15 | 73.2 |
| Msa1021970 | MtrunA17_Chr1g0162411 | 44.000 | 75 | 42 | 0 | 3 | 77 | 22 | 96 | 3.59e-15 | 72.8 |
| Msa1021970 | MtrunA17_Chr7g0233571 | 36.275 | 102 | 63 | 1 | 4 | 105 | 26 | 125 | 4.67e-15 | 70.9 |
| Msa1021970 | MtrunA17_Chr1g0163071 | 36.538 | 104 | 63 | 1 | 4 | 104 | 2 | 105 | 1.03e-14 | 70.9 |
| Msa1021970 | MtrunA17_Chr3g0103181 | 42.268 | 97 | 51 | 2 | 1 | 95 | 21 | 114 | 1.58e-14 | 70.1 |
| Msa1021970 | MtrunA17_Chr3g0103151 | 42.045 | 88 | 49 | 1 | 1 | 86 | 21 | 108 | 2.06e-14 | 67.8 |
| Msa1021970 | MtrunA17_Chr6g0476181 | 34.746 | 118 | 74 | 2 | 4 | 121 | 2 | 116 | 4.26e-14 | 67.0 |
| Msa1021970 | MtrunA17_Chr1g0208771 | 33.028 | 109 | 73 | 0 | 1 | 109 | 10 | 118 | 1.32e-13 | 68.6 |
| Msa1021970 | MtrunA17_Chr3g0103191 | 41.667 | 84 | 49 | 0 | 3 | 86 | 25 | 108 | 2.53e-13 | 66.6 |
| Msa1021970 | MtrunA17_Chr8g0390841 | 34.524 | 84 | 55 | 0 | 3 | 86 | 54 | 137 | 3.77e-13 | 67.0 |
| Msa1021970 | MtrunA17_Chr1g0154071 | 40.000 | 75 | 45 | 0 | 4 | 78 | 43 | 117 | 1.60e-12 | 65.1 |
| Msa1021970 | MtrunA17_Chr6g0467351 | 34.906 | 106 | 62 | 2 | 3 | 104 | 30 | 132 | 1.96e-12 | 63.5 |
| Msa1021970 | MtrunA17_Chr1g0154161 | 24.111 | 253 | 117 | 6 | 4 | 183 | 46 | 296 | 2.26e-12 | 64.3 |
| Msa1021970 | MtrunA17_Chr1g0162421 | 42.105 | 57 | 33 | 0 | 3 | 59 | 8 | 64 | 2.41e-12 | 59.7 |
| Msa1021970 | MtrunA17_Chr1g0162161 | 37.374 | 99 | 57 | 3 | 1 | 99 | 1 | 94 | 6.68e-12 | 60.8 |
| Msa1021970 | MtrunA17_Chr1g0163081 | 40.698 | 86 | 48 | 2 | 1 | 86 | 3 | 85 | 9.32e-12 | 60.5 |
| Msa1021970 | MtrunA17_Chr1g0163131 | 42.169 | 83 | 45 | 2 | 4 | 86 | 34 | 113 | 9.98e-12 | 62.4 |
| Msa1021970 | MtrunA17_Chr1g0163141 | 39.759 | 83 | 47 | 2 | 4 | 86 | 11 | 90 | 1.17e-11 | 60.8 |
| Msa1021970 | MtrunA17_Chr1g0163221 | 38.824 | 85 | 51 | 1 | 4 | 87 | 27 | 111 | 2.56e-11 | 61.6 |
| Msa1021970 | MtrunA17_Chr1g0154101 | 38.667 | 75 | 46 | 0 | 4 | 78 | 198 | 272 | 6.05e-11 | 60.8 |
| Msa1021970 | MtrunA17_Chr1g0163101 | 39.759 | 83 | 47 | 2 | 4 | 86 | 33 | 112 | 9.98e-11 | 58.2 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1021970 | AT3G18960.3 | 42.529 | 87 | 50 | 0 | 2 | 88 | 7 | 93 | 6.63e-20 | 82.8 |
| Msa1021970 | AT3G18960.2 | 40.909 | 88 | 52 | 0 | 1 | 88 | 43 | 130 | 1.74e-19 | 82.4 |
| Msa1021970 | AT3G18960.1 | 40.909 | 88 | 52 | 0 | 1 | 88 | 43 | 130 | 2.39e-19 | 82.4 |
| Msa1021970 | AT4G01580.1 | 40.909 | 88 | 52 | 0 | 1 | 88 | 43 | 130 | 4.65e-19 | 81.3 |
| Msa1021970 | AT1G49475.1 | 37.255 | 102 | 63 | 1 | 1 | 102 | 47 | 147 | 1.25e-18 | 80.1 |
| Msa1021970 | AT3G18990.1 | 40.476 | 84 | 50 | 0 | 3 | 86 | 21 | 104 | 1.70e-17 | 79.3 |
| Msa1021970 | AT3G18990.2 | 40.476 | 84 | 50 | 0 | 3 | 86 | 21 | 104 | 2.07e-17 | 79.3 |
| Msa1021970 | AT4G31690.1 | 26.147 | 218 | 129 | 7 | 3 | 192 | 27 | 240 | 7.86e-11 | 60.1 |
Find 35 sgRNAs with CRISPR-Local
Find 47 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| ATTGCTTTCCATTGCAATTT+TGG | 0.107151 | 7_1:+47189701 | None:intergenic |
| TGATGGTCTTACTTGGAAAT+TGG | 0.227158 | 7_1:-47190191 | Msa1021970:CDS |
| ACTTTGAATTCCCTTCATAT+TGG | 0.318436 | 7_1:+47190074 | None:intergenic |
| TGTTGTCCGCTGCAAATCTA+AGG | 0.346545 | 7_1:+47189623 | None:intergenic |
| TTGAAAACTCCAAGTACTAA+TGG | 0.358408 | 7_1:-47190004 | Msa1021970:CDS |
| GGTTGTTCAGGACTGCAATT+GGG | 0.400182 | 7_1:-47189655 | Msa1021970:CDS |
| CTGTACCTGATGGTCTTACT+TGG | 0.408265 | 7_1:-47190198 | Msa1021970:CDS |
| TGTACACGTATAGGTTGTTC+AGG | 0.408787 | 7_1:-47189667 | Msa1021970:CDS |
| TCCCTTCATATTGGAAAGAC+AGG | 0.414535 | 7_1:+47190083 | None:intergenic |
| TATTATATTTGATGTAACTT+TGG | 0.444169 | 7_1:-47190044 | Msa1021970:CDS |
| TTCCTGTCTTTCCAATATGA+AGG | 0.445348 | 7_1:-47190085 | Msa1021970:CDS |
| AGGTTGTTCAGGACTGCAAT+TGG | 0.452996 | 7_1:-47189656 | Msa1021970:CDS |
| ATTGTTTCTCCATTAGTACT+TGG | 0.459649 | 7_1:+47189995 | None:intergenic |
| AATTTCCAAGTAAGACCATC+AGG | 0.471155 | 7_1:+47190193 | None:intergenic |
| TATAGGTAGAAGTAAAAGAA+GGG | 0.471983 | 7_1:+47189948 | None:intergenic |
| CGACGAAGTTGTAACACAAC+TGG | 0.478088 | 7_1:+47189553 | None:intergenic |
| TGCAGCGGACAACAATTTGT+CGG | 0.480786 | 7_1:-47189614 | Msa1021970:CDS |
| GATGTTACTTGTACACGTAT+AGG | 0.490112 | 7_1:-47189676 | Msa1021970:CDS |
| TTATAGGTAGAAGTAAAAGA+AGG | 0.493463 | 7_1:+47189947 | None:intergenic |
| GAATACTATTCTTTAAGATA+CGG | 0.502713 | 7_1:-47190112 | Msa1021970:CDS |
| AAATTGCAATGGAAAGCAAT+GGG | 0.520291 | 7_1:-47189698 | Msa1021970:CDS |
| AAAATTGCAATGGAAAGCAA+TGG | 0.527431 | 7_1:-47189699 | Msa1021970:CDS |
| TACCTATAAGTATAAAACTC+TGG | 0.535942 | 7_1:-47189933 | Msa1021970:intron |
| TCCTGTCTTTCCAATATGAA+GGG | 0.540870 | 7_1:-47190084 | Msa1021970:CDS |
| TCAGGACTGCAATTGGGGAA+AGG | 0.545358 | 7_1:-47189649 | Msa1021970:CDS |
| GAAACAATTAGTGAGGATGA+AGG | 0.546377 | 7_1:-47189980 | Msa1021970:CDS |
| GTCGGACGGTGATAAATGCA+AGG | 0.596936 | 7_1:-47189596 | Msa1021970:CDS |
| AAATTGGAATTGAAGAAACG+TGG | 0.603079 | 7_1:-47190175 | Msa1021970:CDS |
| GTTGTTCAGGACTGCAATTG+GGG | 0.606112 | 7_1:-47189654 | Msa1021970:CDS |
| AGGATTCCTTAGATTTGCAG+CGG | 0.644386 | 7_1:-47189629 | Msa1021970:CDS |
| GTGAAGCTCCAAAATTGCAA+TGG | 0.646086 | 7_1:-47189709 | Msa1021970:CDS |
| GCGGACAACAATTTGTCGGA+CGG | 0.655494 | 7_1:-47189610 | Msa1021970:CDS |
| TAATGGAGAAACAATTAGTG+AGG | 0.660327 | 7_1:-47189987 | Msa1021970:CDS |
| GCTACAATTACTGTACCTGA+TGG | 0.671121 | 7_1:-47190208 | Msa1021970:CDS |
| GGAATTGAAGAAACGTGGAG+AGG | 0.678214 | 7_1:-47190170 | Msa1021970:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | TATATTGTTATAAAATTTTC+TGG | + | chr7_1:47189561-47189580 | None:intergenic | 10.0% |
| !!! | GAAAATTTTATAACAATATA+TGG | - | chr7_1:47189561-47189580 | Msa1021970:CDS | 10.0% |
| !! | TATTATATTTGATGTAACTT+TGG | - | chr7_1:47189767-47189786 | Msa1021970:intron | 15.0% |
| !!! | GAATACTATTCTTTAAGATA+CGG | - | chr7_1:47189699-47189718 | Msa1021970:CDS | 20.0% |
| !!! | ATGTTTACTTTTGCAACAAA+TGG | - | chr7_1:47189664-47189683 | Msa1021970:CDS | 25.0% |
| ! | TATAGGTAGAAGTAAAAGAA+GGG | + | chr7_1:47189866-47189885 | None:intergenic | 25.0% |
| ! | TTATAGGTAGAAGTAAAAGA+AGG | + | chr7_1:47189867-47189886 | None:intergenic | 25.0% |
| ! | TACCTATAAGTATAAAACTC+TGG | - | chr7_1:47189878-47189897 | Msa1021970:intron | 25.0% |
| AAATTGGAATTGAAGAAACG+TGG | - | chr7_1:47189636-47189655 | Msa1021970:CDS | 30.0% | |
| ACTTTGAATTCCCTTCATAT+TGG | + | chr7_1:47189740-47189759 | None:intergenic | 30.0% | |
| ! | TTAGTACTTGGAGTTTTCAA+TGG | + | chr7_1:47189807-47189826 | None:intergenic | 30.0% |
| TTGAAAACTCCAAGTACTAA+TGG | - | chr7_1:47189807-47189826 | Msa1021970:intron | 30.0% | |
| ! | ATTGTTTCTCCATTAGTACT+TGG | + | chr7_1:47189819-47189838 | None:intergenic | 30.0% |
| TAATGGAGAAACAATTAGTG+AGG | - | chr7_1:47189824-47189843 | Msa1021970:intron | 30.0% | |
| !! | CACCAGAGTTTTATACTTAT+AGG | + | chr7_1:47189883-47189902 | None:intergenic | 30.0% |
| ! | ATTGCTTTCCATTGCAATTT+TGG | + | chr7_1:47190113-47190132 | None:intergenic | 30.0% |
| AAAATTGCAATGGAAAGCAA+TGG | - | chr7_1:47190112-47190131 | Msa1021970:CDS | 30.0% | |
| AAATTGCAATGGAAAGCAAT+GGG | - | chr7_1:47190113-47190132 | Msa1021970:CDS | 30.0% | |
| AATTTCCAAGTAAGACCATC+AGG | + | chr7_1:47189621-47189640 | None:intergenic | 35.0% | |
| ! | TGATGGTCTTACTTGGAAAT+TGG | - | chr7_1:47189620-47189639 | Msa1021970:CDS | 35.0% |
| TTCCTGTCTTTCCAATATGA+AGG | - | chr7_1:47189726-47189745 | Msa1021970:CDS | 35.0% | |
| TCCTGTCTTTCCAATATGAA+GGG | - | chr7_1:47189727-47189746 | Msa1021970:CDS | 35.0% | |
| GAAACAATTAGTGAGGATGA+AGG | - | chr7_1:47189831-47189850 | Msa1021970:intron | 35.0% | |
| AGCGAGGACACATTAATTTA+AGG | + | chr7_1:47190023-47190042 | None:intergenic | 35.0% | |
| AGCATTAATATACTGCACAG+GGG | + | chr7_1:47190046-47190065 | None:intergenic | 35.0% | |
| CAGCATTAATATACTGCACA+GGG | + | chr7_1:47190047-47190066 | None:intergenic | 35.0% | |
| TCAGCATTAATATACTGCAC+AGG | + | chr7_1:47190048-47190067 | None:intergenic | 35.0% | |
| ! | GATGTTACTTGTACACGTAT+AGG | - | chr7_1:47190135-47190154 | Msa1021970:CDS | 35.0% |
| GCTACAATTACTGTACCTGA+TGG | - | chr7_1:47189603-47189622 | Msa1021970:CDS | 40.0% | |
| TCCCTTCATATTGGAAAGAC+AGG | + | chr7_1:47189731-47189750 | None:intergenic | 40.0% | |
| GTATAAAACTCTGGTGAGTG+AGG | - | chr7_1:47189887-47189906 | Msa1021970:intron | 40.0% | |
| GTGAAGCTCCAAAATTGCAA+TGG | - | chr7_1:47190102-47190121 | Msa1021970:CDS | 40.0% | |
| TGTACACGTATAGGTTGTTC+AGG | - | chr7_1:47190144-47190163 | Msa1021970:CDS | 40.0% | |
| AGGATTCCTTAGATTTGCAG+CGG | - | chr7_1:47190182-47190201 | Msa1021970:CDS | 40.0% | |
| ! | CTGTACCTGATGGTCTTACT+TGG | - | chr7_1:47189613-47189632 | Msa1021970:CDS | 45.0% |
| GGAATTGAAGAAACGTGGAG+AGG | - | chr7_1:47189641-47189660 | Msa1021970:CDS | 45.0% | |
| AGGTTGTTCAGGACTGCAAT+TGG | - | chr7_1:47190155-47190174 | Msa1021970:CDS | 45.0% | |
| GGTTGTTCAGGACTGCAATT+GGG | - | chr7_1:47190156-47190175 | Msa1021970:CDS | 45.0% | |
| GTTGTTCAGGACTGCAATTG+GGG | - | chr7_1:47190157-47190176 | Msa1021970:CDS | 45.0% | |
| TGTTGTCCGCTGCAAATCTA+AGG | + | chr7_1:47190191-47190210 | None:intergenic | 45.0% | |
| TGCAGCGGACAACAATTTGT+CGG | - | chr7_1:47190197-47190216 | Msa1021970:CDS | 45.0% | |
| CGACGAAGTTGTAACACAAC+TGG | + | chr7_1:47190261-47190280 | None:intergenic | 45.0% | |
| !!! | AAAATTTTATAACAATATAT+GGG | - | chr7_1:47189562-47189581 | Msa1021970:CDS | 5.0% |
| TCAGGACTGCAATTGGGGAA+AGG | - | chr7_1:47190162-47190181 | Msa1021970:CDS | 50.0% | |
| GCGGACAACAATTTGTCGGA+CGG | - | chr7_1:47190201-47190220 | Msa1021970:CDS | 50.0% | |
| GTCGGACGGTGATAAATGCA+AGG | - | chr7_1:47190215-47190234 | Msa1021970:CDS | 50.0% | |
| ATATACTGCACAGGGGAGCG+AGG | + | chr7_1:47190039-47190058 | None:intergenic | 55.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr7_1 | gene | 47189546 | 47190287 | 47189546 | ID=Msa1021970;Name=Msa1021970 |
| chr7_1 | mRNA | 47189546 | 47190287 | 47189546 | ID=Msa1021970-mRNA-1;Parent=Msa1021970;Name=Msa1021970-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0|0|1|1|1|2|0|195 |
| chr7_1 | exon | 47189934 | 47190287 | 47189934 | ID=Msa1021970-mRNA-1:exon:9318;Parent=Msa1021970-mRNA-1 |
| chr7_1 | exon | 47189546 | 47189779 | 47189546 | ID=Msa1021970-mRNA-1:exon:9317;Parent=Msa1021970-mRNA-1 |
| chr7_1 | CDS | 47189934 | 47190287 | 47189934 | ID=Msa1021970-mRNA-1:cds;Parent=Msa1021970-mRNA-1 |
| chr7_1 | CDS | 47189546 | 47189779 | 47189546 | ID=Msa1021970-mRNA-1:cds;Parent=Msa1021970-mRNA-1 |
| Gene Sequence |
| Protein sequence |
