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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0236460 | KEH41604.1 | 62.264 | 159 | 59 | 1 | 1 | 158 | 41 | 199 | 1.17e-66 | 217 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0236460 | A0A072VHU7 | 62.264 | 159 | 59 | 1 | 1 | 158 | 41 | 199 | 5.58e-67 | 217 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0236460 | Msa0309370 | 0.973862 | 3.749903e-137 | -8.615850e-47 |
| Msa0236460 | Msa0946430 | 0.950328 | 2.065588e-108 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0236460 | MtrunA17_Chr1g0206481 | 46.296 | 162 | 87 | 0 | 1 | 162 | 82 | 243 | 2.11e-53 | 171 |
| Msa0236460 | MtrunA17_Chr5g0423441 | 46.104 | 154 | 83 | 0 | 5 | 158 | 86 | 239 | 1.21e-46 | 153 |
| Msa0236460 | MtrunA17_Chr2g0280031 | 44.910 | 167 | 83 | 1 | 1 | 158 | 63 | 229 | 1.54e-46 | 153 |
| Msa0236460 | MtrunA17_Chr5g0411141 | 46.104 | 154 | 83 | 0 | 5 | 158 | 87 | 240 | 1.93e-46 | 154 |
| Msa0236460 | MtrunA17_Chr2g0278111 | 46.104 | 154 | 83 | 0 | 5 | 158 | 86 | 239 | 1.95e-46 | 154 |
| Msa0236460 | MtrunA17_Chr1g0158831 | 48.000 | 100 | 52 | 0 | 59 | 158 | 3 | 102 | 2.90e-33 | 116 |
| Msa0236460 | MtrunA17_Chr3g0096071 | 49.020 | 102 | 49 | 1 | 57 | 158 | 27 | 125 | 8.70e-32 | 114 |
| Msa0236460 | MtrunA17_Chr5g0421841 | 40.310 | 129 | 76 | 1 | 1 | 129 | 82 | 209 | 1.57e-27 | 102 |
| Msa0236460 | MtrunA17_Chr1g0167871 | 30.435 | 161 | 105 | 3 | 1 | 159 | 283 | 438 | 2.76e-16 | 75.9 |
| Msa0236460 | MtrunA17_Chr6g0462951 | 30.000 | 140 | 94 | 3 | 5 | 142 | 2 | 139 | 3.73e-14 | 66.2 |
| Msa0236460 | MtrunA17_Chr4g0044661 | 27.607 | 163 | 110 | 4 | 2 | 159 | 86 | 245 | 8.83e-14 | 68.6 |
| Msa0236460 | MtrunA17_Chr7g0231491 | 32.308 | 130 | 84 | 3 | 1 | 128 | 112 | 239 | 1.80e-12 | 63.5 |
| Msa0236460 | MtrunA17_Chr2g0304851 | 31.250 | 160 | 88 | 4 | 2 | 159 | 83 | 222 | 2.64e-12 | 63.9 |
| Msa0236460 | MtrunA17_Chr6g0469931 | 29.375 | 160 | 106 | 5 | 5 | 159 | 82 | 239 | 1.27e-11 | 62.4 |
| Msa0236460 | MtrunA17_Chr3g0112231 | 46.296 | 54 | 29 | 0 | 106 | 159 | 1 | 54 | 2.38e-11 | 60.1 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0236460 | AT1G52950.1 | 26.144 | 153 | 108 | 4 | 9 | 159 | 89 | 238 | 7.96e-16 | 74.7 |
Find 28 sgRNAs with CRISPR-Local
Find 88 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| TAAGTACAAGTTAAGCTTTA+TGG | 0.204177 | 2_2:+9459172 | Msa0236460:CDS |
| TGAGAAACTTCAGGAATATT+AGG | 0.210888 | 2_2:-9459883 | None:intergenic |
| ATTAGGATTCAACATCATTT+TGG | 0.212610 | 2_2:-9459866 | None:intergenic |
| ACAGAATTCATTGCACTCTT+TGG | 0.243423 | 2_2:+9459585 | Msa0236460:CDS |
| CTGTAATCATTCACACCTTT+TGG | 0.257336 | 2_2:+9459935 | Msa0236460:CDS |
| TGCAAGCTTAAGAAGTATTA+TGG | 0.272495 | 2_2:+9459686 | Msa0236460:CDS |
| ACAAAGCAGATAACTCTTTC+AGG | 0.297357 | 2_2:-9459233 | None:intergenic |
| AGGAAAGACTAGCAAGGTTT+TGG | 0.297514 | 2_2:+9459436 | Msa0236460:CDS |
| CAGAATTCATTGCACTCTTT+GGG | 0.309559 | 2_2:+9459586 | Msa0236460:CDS |
| GTATGATGTTGCAATTCTTC+TGG | 0.336370 | 2_2:+9459912 | Msa0236460:CDS |
| ATGTAATTTATAGATGTTAT+CGG | 0.353224 | 2_2:+9459371 | Msa0236460:intron |
| ACATGACTCATCCCTGCCTT+TGG | 0.403365 | 2_2:+9459646 | Msa0236460:CDS |
| TACCTATATTGAGAAACTTC+AGG | 0.419821 | 2_2:-9459892 | None:intergenic |
| TTCCTGAAGTTTCTCAATAT+AGG | 0.426742 | 2_2:+9459890 | Msa0236460:CDS |
| CACAATGAGGATCGTTTGCT+TGG | 0.465741 | 2_2:+9459281 | Msa0236460:CDS |
| CAAAGCAGATAACTCTTTCA+GGG | 0.513038 | 2_2:-9459232 | None:intergenic |
| GTTAAAGAGACTGTGAAAGA+AGG | 0.519632 | 2_2:+9459416 | Msa0236460:CDS |
| AGATGTTATCGGCCATGTTG+TGG | 0.530639 | 2_2:+9459382 | Msa0236460:intron |
| ACATCACCAAACAAACCAAA+AGG | 0.544013 | 2_2:-9459950 | None:intergenic |
| TATGAAGATGCAACAATGCT+TGG | 0.548233 | 2_2:+9459619 | Msa0236460:CDS |
| GAAAGATAACAACCAAAGGC+AGG | 0.548872 | 2_2:-9459658 | None:intergenic |
| TACAAGTTAAGCTTTATGGC+AGG | 0.552310 | 2_2:+9459176 | Msa0236460:CDS |
| TATCGGCCATGTTGTGGAGA+AGG | 0.582289 | 2_2:+9459388 | Msa0236460:CDS |
| AACTGAAAGATAACAACCAA+AGG | 0.618472 | 2_2:-9459662 | None:intergenic |
| AAAGATAACAACCAAAGGCA+GGG | 0.642200 | 2_2:-9459657 | None:intergenic |
| CATCGTCCTTCTCCACAACA+TGG | 0.644418 | 2_2:-9459394 | None:intergenic |
| AATTCTGTCTGCTCACAATG+AGG | 0.645022 | 2_2:+9459268 | Msa0236460:CDS |
| GAAAGAAGGAAAGACTAGCA+AGG | 0.648178 | 2_2:+9459430 | Msa0236460:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | TTCATTTTATTAATTTTTGT+AGG | + | chr2_2:9459811-9459830 | Msa0236460:intron | 10.0% |
| !!! | TTCATTTTATTAATTTTTGT+AGG | + | chr2_2:9459811-9459830 | Msa0236460:intron | 10.0% |
| !! | ATGTAATTTATAGATGTTAT+CGG | + | chr2_2:9459371-9459390 | Msa0236460:intron | 15.0% |
| !! | ATGTAATTTATAGATGTTAT+CGG | + | chr2_2:9459371-9459390 | Msa0236460:intron | 15.0% |
| !!! | GCTCTTTTTAATTCAAATTT+TGG | + | chr2_2:9459313-9459332 | Msa0236460:intron | 20.0% |
| !! | AATACTCTTATGTATATTGT+AGG | + | chr2_2:9459558-9459577 | Msa0236460:intron | 20.0% |
| !! | ATACTCTTATGTATATTGTA+GGG | + | chr2_2:9459559-9459578 | Msa0236460:intron | 20.0% |
| !!! | GCTCTTTTTAATTCAAATTT+TGG | + | chr2_2:9459313-9459332 | Msa0236460:intron | 20.0% |
| !! | AATACTCTTATGTATATTGT+AGG | + | chr2_2:9459558-9459577 | Msa0236460:intron | 20.0% |
| !! | ATACTCTTATGTATATTGTA+GGG | + | chr2_2:9459559-9459578 | Msa0236460:intron | 20.0% |
| ! | TAAGTACAAGTTAAGCTTTA+TGG | + | chr2_2:9459172-9459191 | Msa0236460:CDS | 25.0% |
| ! | TACTCTTATGTATATTGTAG+GGG | + | chr2_2:9459560-9459579 | Msa0236460:intron | 25.0% |
| !!! | AGAATCTTCAATGCTTTTTA+TGG | + | chr2_2:9459841-9459860 | Msa0236460:CDS | 25.0% |
| !! | ATTAGGATTCAACATCATTT+TGG | - | chr2_2:9459869-9459888 | None:intergenic | 25.0% |
| ! | TAAGTACAAGTTAAGCTTTA+TGG | + | chr2_2:9459172-9459191 | Msa0236460:CDS | 25.0% |
| ! | TACTCTTATGTATATTGTAG+GGG | + | chr2_2:9459560-9459579 | Msa0236460:intron | 25.0% |
| !!! | AGAATCTTCAATGCTTTTTA+TGG | + | chr2_2:9459841-9459860 | Msa0236460:CDS | 25.0% |
| !! | ATTAGGATTCAACATCATTT+TGG | - | chr2_2:9459869-9459888 | None:intergenic | 25.0% |
| !! | TTTGAAAGTAGGGTCATTTT+GGG | - | chr2_2:9459141-9459160 | None:intergenic | 30.0% |
| !! | TTTTGAAAGTAGGGTCATTT+TGG | - | chr2_2:9459142-9459161 | None:intergenic | 30.0% |
| !!! | GATCAGTAGTTTTGAAAGTA+GGG | - | chr2_2:9459151-9459170 | None:intergenic | 30.0% |
| !!! | TGATCAGTAGTTTTGAAAGT+AGG | - | chr2_2:9459152-9459171 | None:intergenic | 30.0% |
| ! | TGTGTATTAGATAGCTTTTG+AGG | + | chr2_2:9459510-9459529 | Msa0236460:intron | 30.0% |
| AACTGAAAGATAACAACCAA+AGG | - | chr2_2:9459665-9459684 | None:intergenic | 30.0% | |
| !! | TGCAAGCTTAAGAAGTATTA+TGG | + | chr2_2:9459686-9459705 | Msa0236460:CDS | 30.0% |
| !!! | TTAAACTGCATGAGCTTTTT+TGG | + | chr2_2:9459775-9459794 | Msa0236460:intron | 30.0% |
| TGAGAAACTTCAGGAATATT+AGG | - | chr2_2:9459886-9459905 | None:intergenic | 30.0% | |
| TTCCTGAAGTTTCTCAATAT+AGG | + | chr2_2:9459890-9459909 | Msa0236460:CDS | 30.0% | |
| TACCTATATTGAGAAACTTC+AGG | - | chr2_2:9459895-9459914 | None:intergenic | 30.0% | |
| !! | TTTGAAAGTAGGGTCATTTT+GGG | - | chr2_2:9459141-9459160 | None:intergenic | 30.0% |
| !! | TTTTGAAAGTAGGGTCATTT+TGG | - | chr2_2:9459142-9459161 | None:intergenic | 30.0% |
| !!! | GATCAGTAGTTTTGAAAGTA+GGG | - | chr2_2:9459151-9459170 | None:intergenic | 30.0% |
| !!! | TGATCAGTAGTTTTGAAAGT+AGG | - | chr2_2:9459152-9459171 | None:intergenic | 30.0% |
| ! | TGTGTATTAGATAGCTTTTG+AGG | + | chr2_2:9459510-9459529 | Msa0236460:intron | 30.0% |
| AACTGAAAGATAACAACCAA+AGG | - | chr2_2:9459665-9459684 | None:intergenic | 30.0% | |
| !! | TGCAAGCTTAAGAAGTATTA+TGG | + | chr2_2:9459686-9459705 | Msa0236460:CDS | 30.0% |
| !!! | TTAAACTGCATGAGCTTTTT+TGG | + | chr2_2:9459775-9459794 | Msa0236460:intron | 30.0% |
| TGAGAAACTTCAGGAATATT+AGG | - | chr2_2:9459886-9459905 | None:intergenic | 30.0% | |
| TTCCTGAAGTTTCTCAATAT+AGG | + | chr2_2:9459890-9459909 | Msa0236460:CDS | 30.0% | |
| TACCTATATTGAGAAACTTC+AGG | - | chr2_2:9459895-9459914 | None:intergenic | 30.0% | |
| ! | TACAAGTTAAGCTTTATGGC+AGG | + | chr2_2:9459176-9459195 | Msa0236460:CDS | 35.0% |
| CAAAGCAGATAACTCTTTCA+GGG | - | chr2_2:9459235-9459254 | None:intergenic | 35.0% | |
| ACAAAGCAGATAACTCTTTC+AGG | - | chr2_2:9459236-9459255 | None:intergenic | 35.0% | |
| GTTAAAGAGACTGTGAAAGA+AGG | + | chr2_2:9459416-9459435 | Msa0236460:CDS | 35.0% | |
| AGTATTTAGTTATCCTGCTG+AGG | - | chr2_2:9459544-9459563 | None:intergenic | 35.0% | |
| ACAGAATTCATTGCACTCTT+TGG | + | chr2_2:9459585-9459604 | Msa0236460:CDS | 35.0% | |
| CAGAATTCATTGCACTCTTT+GGG | + | chr2_2:9459586-9459605 | Msa0236460:CDS | 35.0% | |
| TATGAAGATGCAACAATGCT+TGG | + | chr2_2:9459619-9459638 | Msa0236460:CDS | 35.0% | |
| AAAGATAACAACCAAAGGCA+GGG | - | chr2_2:9459660-9459679 | None:intergenic | 35.0% | |
| AAAGCTCATGCAGTTTAATG+CGG | - | chr2_2:9459773-9459792 | None:intergenic | 35.0% | |
| GTATGATGTTGCAATTCTTC+TGG | + | chr2_2:9459912-9459931 | Msa0236460:CDS | 35.0% | |
| ! | CTGTAATCATTCACACCTTT+TGG | + | chr2_2:9459935-9459954 | Msa0236460:CDS | 35.0% |
| !!! | TTCACACCTTTTGGTTTGTT+TGG | + | chr2_2:9459944-9459963 | Msa0236460:CDS | 35.0% |
| ! | TACAAGTTAAGCTTTATGGC+AGG | + | chr2_2:9459176-9459195 | Msa0236460:CDS | 35.0% |
| CAAAGCAGATAACTCTTTCA+GGG | - | chr2_2:9459235-9459254 | None:intergenic | 35.0% | |
| ACAAAGCAGATAACTCTTTC+AGG | - | chr2_2:9459236-9459255 | None:intergenic | 35.0% | |
| GTTAAAGAGACTGTGAAAGA+AGG | + | chr2_2:9459416-9459435 | Msa0236460:CDS | 35.0% | |
| AGTATTTAGTTATCCTGCTG+AGG | - | chr2_2:9459544-9459563 | None:intergenic | 35.0% | |
| ACAGAATTCATTGCACTCTT+TGG | + | chr2_2:9459585-9459604 | Msa0236460:CDS | 35.0% | |
| CAGAATTCATTGCACTCTTT+GGG | + | chr2_2:9459586-9459605 | Msa0236460:CDS | 35.0% | |
| TATGAAGATGCAACAATGCT+TGG | + | chr2_2:9459619-9459638 | Msa0236460:CDS | 35.0% | |
| AAAGATAACAACCAAAGGCA+GGG | - | chr2_2:9459660-9459679 | None:intergenic | 35.0% | |
| AAAGCTCATGCAGTTTAATG+CGG | - | chr2_2:9459773-9459792 | None:intergenic | 35.0% | |
| GTATGATGTTGCAATTCTTC+TGG | + | chr2_2:9459912-9459931 | Msa0236460:CDS | 35.0% | |
| ! | CTGTAATCATTCACACCTTT+TGG | + | chr2_2:9459935-9459954 | Msa0236460:CDS | 35.0% |
| !!! | TTCACACCTTTTGGTTTGTT+TGG | + | chr2_2:9459944-9459963 | Msa0236460:CDS | 35.0% |
| AATTCTGTCTGCTCACAATG+AGG | + | chr2_2:9459268-9459287 | Msa0236460:CDS | 40.0% | |
| GAAAGAAGGAAAGACTAGCA+AGG | + | chr2_2:9459430-9459449 | Msa0236460:CDS | 40.0% | |
| ! | AGGAAAGACTAGCAAGGTTT+TGG | + | chr2_2:9459436-9459455 | Msa0236460:CDS | 40.0% |
| !!! | CAAGGTTTTGGATGCTACTT+TGG | + | chr2_2:9459448-9459467 | Msa0236460:CDS | 40.0% |
| GAAAGATAACAACCAAAGGC+AGG | - | chr2_2:9459661-9459680 | None:intergenic | 40.0% | |
| AATTCTGTCTGCTCACAATG+AGG | + | chr2_2:9459268-9459287 | Msa0236460:CDS | 40.0% | |
| GAAAGAAGGAAAGACTAGCA+AGG | + | chr2_2:9459430-9459449 | Msa0236460:CDS | 40.0% | |
| ! | AGGAAAGACTAGCAAGGTTT+TGG | + | chr2_2:9459436-9459455 | Msa0236460:CDS | 40.0% |
| !!! | CAAGGTTTTGGATGCTACTT+TGG | + | chr2_2:9459448-9459467 | Msa0236460:CDS | 40.0% |
| GAAAGATAACAACCAAAGGC+AGG | - | chr2_2:9459661-9459680 | None:intergenic | 40.0% | |
| CACAATGAGGATCGTTTGCT+TGG | + | chr2_2:9459281-9459300 | Msa0236460:CDS | 45.0% | |
| AGATGTTATCGGCCATGTTG+TGG | + | chr2_2:9459382-9459401 | Msa0236460:intron | 45.0% | |
| TGAGGAAAATGTACCTCAGC+AGG | + | chr2_2:9459528-9459547 | Msa0236460:intron | 45.0% | |
| CACAATGAGGATCGTTTGCT+TGG | + | chr2_2:9459281-9459300 | Msa0236460:CDS | 45.0% | |
| AGATGTTATCGGCCATGTTG+TGG | + | chr2_2:9459382-9459401 | Msa0236460:intron | 45.0% | |
| TGAGGAAAATGTACCTCAGC+AGG | + | chr2_2:9459528-9459547 | Msa0236460:intron | 45.0% | |
| TATCGGCCATGTTGTGGAGA+AGG | + | chr2_2:9459388-9459407 | Msa0236460:CDS | 50.0% | |
| CATCGTCCTTCTCCACAACA+TGG | - | chr2_2:9459397-9459416 | None:intergenic | 50.0% | |
| ACATGACTCATCCCTGCCTT+TGG | + | chr2_2:9459646-9459665 | Msa0236460:CDS | 50.0% | |
| TATCGGCCATGTTGTGGAGA+AGG | + | chr2_2:9459388-9459407 | Msa0236460:CDS | 50.0% | |
| CATCGTCCTTCTCCACAACA+TGG | - | chr2_2:9459397-9459416 | None:intergenic | 50.0% | |
| ACATGACTCATCCCTGCCTT+TGG | + | chr2_2:9459646-9459665 | Msa0236460:CDS | 50.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr2_2 | gene | 9459131 | 9459969 | 9459131 | ID=Msa0236460;Name=Msa0236460 |
| chr2_2 | mRNA | 9459131 | 9459969 | 9459131 | ID=Msa0236460-mRNA-1;Parent=Msa0236460;Name=Msa0236460-mRNA-1;_AED=0.16;_eAED=0.17;_QI=0|0|0|1|1|1|4|0|177 |
| chr2_2 | exon | 9459131 | 9459302 | 9459131 | ID=Msa0236460-mRNA-1:exon:4094;Parent=Msa0236460-mRNA-1 |
| chr2_2 | exon | 9459384 | 9459480 | 9459384 | ID=Msa0236460-mRNA-1:exon:4095;Parent=Msa0236460-mRNA-1 |
| chr2_2 | exon | 9459580 | 9459707 | 9459580 | ID=Msa0236460-mRNA-1:exon:4096;Parent=Msa0236460-mRNA-1 |
| chr2_2 | exon | 9459833 | 9459969 | 9459833 | ID=Msa0236460-mRNA-1:exon:4097;Parent=Msa0236460-mRNA-1 |
| chr2_2 | CDS | 9459131 | 9459302 | 9459131 | ID=Msa0236460-mRNA-1:cds;Parent=Msa0236460-mRNA-1 |
| chr2_2 | CDS | 9459384 | 9459480 | 9459384 | ID=Msa0236460-mRNA-1:cds;Parent=Msa0236460-mRNA-1 |
| chr2_2 | CDS | 9459580 | 9459707 | 9459580 | ID=Msa0236460-mRNA-1:cds;Parent=Msa0236460-mRNA-1 |
| chr2_2 | CDS | 9459833 | 9459969 | 9459833 | ID=Msa0236460-mRNA-1:cds;Parent=Msa0236460-mRNA-1 |
| Gene Sequence |
| Protein sequence |
