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 |
|---|
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0177880 | A0A1S2XYA7 | 61.712 | 222 | 68 | 4 | 1 | 218 | 1 | 209 | 4.16e-66 | 213 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0177880 | Msa0453040 | 0.801305 | 9.586080e-49 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0177880 | MtrunA17_Chr1g0200851 | 57.391 | 230 | 75 | 6 | 1 | 219 | 1 | 218 | 5.13e-64 | 198 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|
Find 64 sgRNAs with CRISPR-Local
Find 72 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| GTTGGATTCGAATTTAAAAT+TGG | 0.205515 | 1_4:-65202194 | Msa0177880:CDS |
| CCAAATGGTGCTGCGGCTTC+AGG | 0.237162 | 1_4:+65202385 | None:intergenic |
| TGTGCGACACTTCAGGAAAA+TGG | 0.242925 | 1_4:-65202237 | Msa0177880:CDS |
| GCCGTGGATTCGGTGAATTC+TGG | 0.250481 | 1_4:-65202079 | Msa0177880:CDS |
| GGAGGAGGAGGATGAGGAGG+AGG | 0.324707 | 1_4:-65202326 | Msa0177880:CDS |
| CTGATGGAGTCTGAGGAAAA+TGG | 0.328101 | 1_4:+65202278 | None:intergenic |
| TGCCGTTGCGGCGGCTGCTC+CGG | 0.390827 | 1_4:+65202444 | None:intergenic |
| GCCGCAACGGCAGCTGTAGC+CGG | 0.398815 | 1_4:-65202433 | Msa0177880:CDS |
| GCATCGTTGACTAAAATTAC+TGG | 0.407944 | 1_4:-65201992 | Msa0177880:CDS |
| TCGTGAAGAGGCCGTGGATT+CGG | 0.408768 | 1_4:-65202089 | Msa0177880:CDS |
| CCTGAAGCCGCAGCACCATT+TGG | 0.411875 | 1_4:-65202385 | Msa0177880:CDS |
| GGAGGAGGATGAGGAGGAGG+AGG | 0.418192 | 1_4:-65202323 | Msa0177880:CDS |
| TCATCTGGAGGAGGAGGAGG+AGG | 0.432895 | 1_4:-65202350 | Msa0177880:CDS |
| ATGCGGTTTCGCATTAAAGT+TGG | 0.442497 | 1_4:-65202212 | Msa0177880:CDS |
| AACTCATCTGGAGGAGGAGG+AGG | 0.449789 | 1_4:-65202353 | Msa0177880:CDS |
| TGAGTTTGCTTCACTCCAAA+TGG | 0.460894 | 1_4:+65202370 | None:intergenic |
| TGGAGTGAAGCAAACTCATC+TGG | 0.467242 | 1_4:-65202365 | Msa0177880:CDS |
| CAGACTCCATCAGCAGGTTG+TGG | 0.490578 | 1_4:-65202268 | Msa0177880:CDS |
| AGAAGAAGAAAGTGGAGGGT+GGG | 0.493806 | 1_4:-65202488 | Msa0177880:CDS |
| ATCTTCTTGATAGTCCTCAC+TGG | 0.495655 | 1_4:-65202018 | Msa0177880:CDS |
| AGCCGGAGCAGCCGCCGCAA+CGG | 0.496626 | 1_4:-65202446 | Msa0177880:CDS |
| TGATGGAGTCTGAGGAAAAT+GGG | 0.500732 | 1_4:+65202279 | None:intergenic |
| TTTCCTCAGACTCCATCAGC+AGG | 0.505618 | 1_4:-65202274 | Msa0177880:CDS |
| TTTGCGTTGGGTTAACAGAA+AGG | 0.509963 | 1_4:-65202140 | Msa0177880:CDS |
| AAGAAGAAGAAAGTGGAGGG+TGG | 0.510838 | 1_4:-65202489 | Msa0177880:CDS |
| TTGCGTTGGGTTAACAGAAA+GGG | 0.513396 | 1_4:-65202139 | Msa0177880:CDS |
| GTCAGATCGTGAAGAGGCCG+TGG | 0.518270 | 1_4:-65202095 | Msa0177880:CDS |
| GCAAACTCATCTGGAGGAGG+AGG | 0.525246 | 1_4:-65202356 | Msa0177880:CDS |
| AAAGTAAAATGAGCGGAGGG+AGG | 0.537391 | 1_4:-65202537 | None:intergenic |
| TTCATTATTTAAGTAGCCTG+TGG | 0.537670 | 1_4:+65201864 | None:intergenic |
| ACTCCATCAGCAGGTTGTGG+TGG | 0.540055 | 1_4:-65202265 | Msa0177880:CDS |
| AGAAAGAAGAAGAAAGTGGA+GGG | 0.546249 | 1_4:-65202492 | Msa0177880:CDS |
| AAAATTGGATGAAATTGAGA+AGG | 0.548683 | 1_4:-65202179 | Msa0177880:CDS |
| AATTACTGGTGATGAAAATG+AGG | 0.552132 | 1_4:-65201978 | Msa0177880:CDS |
| TAAGTAGCCTGTGGAGTGGA+GGG | 0.552377 | 1_4:+65201873 | None:intergenic |
| TCCAGAATTCACCGAATCCA+CGG | 0.552778 | 1_4:+65202078 | None:intergenic |
| GGCTACAGCTGCCGTTGCGG+CGG | 0.563313 | 1_4:+65202435 | None:intergenic |
| GGCAAGAAAGAAGAAGAAAG+TGG | 0.564422 | 1_4:-65202496 | Msa0177880:CDS |
| ACCGGCTACAGCTGCCGTTG+CGG | 0.568622 | 1_4:+65202432 | None:intergenic |
| TCAACGTTCTTAAAAGTAGC+CGG | 0.571988 | 1_4:-65202463 | Msa0177880:CDS |
| AAACCACCACAACCTGCTGA+TGG | 0.572353 | 1_4:+65202262 | None:intergenic |
| ACTGTGTCCCTCCACTCCAC+AGG | 0.572758 | 1_4:-65201880 | Msa0177880:CDS |
| AGGAGAAACGATGAGAAGGA+CGG | 0.574633 | 1_4:-65202517 | Msa0177880:CDS |
| TTAAGTAGCCTGTGGAGTGG+AGG | 0.575647 | 1_4:+65201872 | None:intergenic |
| TAGGAGACTGTATAAACCAC+CGG | 0.584304 | 1_4:+65202414 | None:intergenic |
| AGGGAGGAGAAACGATGAGA+AGG | 0.597275 | 1_4:-65202521 | Msa0177880:CDS |
| GAAGCAAACTCATCTGGAGG+AGG | 0.604005 | 1_4:-65202359 | Msa0177880:CDS |
| CTTCACTCCAAATGGTGCTG+CGG | 0.606303 | 1_4:+65202378 | None:intergenic |
| TATTTAAGTAGCCTGTGGAG+TGG | 0.607998 | 1_4:+65201869 | None:intergenic |
| AAAGAAAGTAAAATGAGCGG+AGG | 0.609854 | 1_4:-65202541 | None:intergenic |
| CAACCTGCTGATGGAGTCTG+AGG | 0.612791 | 1_4:+65202271 | None:intergenic |
| GCAACGGCAGCTGTAGCCGG+TGG | 0.612807 | 1_4:-65202430 | Msa0177880:CDS |
| TCTTCTTGATAGTCCTCACT+GGG | 0.620051 | 1_4:-65202017 | Msa0177880:CDS |
| ATATACGATCATCATTAGAT+CGG | 0.624129 | 1_4:+65202053 | None:intergenic |
| AAGAAAGTAAAATGAGCGGA+GGG | 0.626757 | 1_4:-65202540 | None:intergenic |
| GTCAACGATGCTTCCCAGTG+AGG | 0.651855 | 1_4:+65202004 | None:intergenic |
| AAGAAAGAAGAAGAAAGTGG+AGG | 0.654039 | 1_4:-65202493 | Msa0177880:CDS |
| AAAGGGAAAGAAGAAAGTAA+CGG | 0.662431 | 1_4:-65202122 | Msa0177880:CDS |
| ACTTCAGGAAAATGGATATG+CGG | 0.670826 | 1_4:-65202229 | Msa0177880:CDS |
| CAGAAAGAAAGTAAAATGAG+CGG | 0.671882 | 1_4:-65202544 | None:intergenic |
| GGTGAAGTCAGATCGTGAAG+AGG | 0.672844 | 1_4:-65202101 | Msa0177880:CDS |
| AGTGAAGCAAACTCATCTGG+AGG | 0.683777 | 1_4:-65202362 | Msa0177880:CDS |
| GGAGGAGGTGATACTATACG+TGG | 0.714917 | 1_4:-65202308 | Msa0177880:CDS |
| GAGGTGATACTATACGTGGA+CGG | 0.729335 | 1_4:-65202304 | Msa0177880:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | GTTGGATTCGAATTTAAAAT+TGG | - | chr1_4:65202203-65202222 | Msa0177880:CDS | 25.0% |
| ! | AAAATTGGATGAAATTGAGA+AGG | - | chr1_4:65202218-65202237 | Msa0177880:CDS | 25.0% |
| ! | ATATACGATCATCATTAGAT+CGG | + | chr1_4:65202347-65202366 | None:intergenic | 25.0% |
| !! | AATTTTAAGTGGTTTGCGTT+GGG | - | chr1_4:65202245-65202264 | Msa0177880:CDS | 30.0% |
| AAAGGGAAAGAAGAAAGTAA+CGG | - | chr1_4:65202275-65202294 | Msa0177880:CDS | 30.0% | |
| ! | AATTACTGGTGATGAAAATG+AGG | - | chr1_4:65202419-65202438 | Msa0177880:CDS | 30.0% |
| AAGAAAGAAGAAGAAAGTGG+AGG | - | chr1_4:65201904-65201923 | Msa0177880:CDS | 35.0% | |
| AGAAAGAAGAAGAAAGTGGA+GGG | - | chr1_4:65201905-65201924 | Msa0177880:CDS | 35.0% | |
| TCAACGTTCTTAAAAGTAGC+CGG | - | chr1_4:65201934-65201953 | Msa0177880:CDS | 35.0% | |
| ACTTCAGGAAAATGGATATG+CGG | - | chr1_4:65202168-65202187 | Msa0177880:CDS | 35.0% | |
| ! | GAGAAGGAAGCAATTTTAAG+TGG | - | chr1_4:65202234-65202253 | Msa0177880:CDS | 35.0% |
| !! | CAATTTTAAGTGGTTTGCGT+TGG | - | chr1_4:65202244-65202263 | Msa0177880:CDS | 35.0% |
| ! | GCATCGTTGACTAAAATTAC+TGG | - | chr1_4:65202405-65202424 | Msa0177880:CDS | 35.0% |
| GGCAAGAAAGAAGAAGAAAG+TGG | - | chr1_4:65201901-65201920 | Msa0177880:CDS | 40.0% | |
| TAGGAGACTGTATAAACCAC+CGG | + | chr1_4:65201986-65202005 | None:intergenic | 40.0% | |
| ! | TGAGTTTGCTTCACTCCAAA+TGG | + | chr1_4:65202030-65202049 | None:intergenic | 40.0% |
| TGATGGAGTCTGAGGAAAAT+GGG | + | chr1_4:65202121-65202140 | None:intergenic | 40.0% | |
| ATGCGGTTTCGCATTAAAGT+TGG | - | chr1_4:65202185-65202204 | Msa0177880:CDS | 40.0% | |
| TTTGCGTTGGGTTAACAGAA+AGG | - | chr1_4:65202257-65202276 | Msa0177880:CDS | 40.0% | |
| TTGCGTTGGGTTAACAGAAA+GGG | - | chr1_4:65202258-65202277 | Msa0177880:CDS | 40.0% | |
| ! | ATCTTCTTGATAGTCCTCAC+TGG | - | chr1_4:65202379-65202398 | Msa0177880:CDS | 40.0% |
| ! | TCTTCTTGATAGTCCTCACT+GGG | - | chr1_4:65202380-65202399 | Msa0177880:CDS | 40.0% |
| TATTTAAGTAGCCTGTGGAG+TGG | + | chr1_4:65202531-65202550 | None:intergenic | 40.0% | |
| AGGAGAAACGATGAGAAGGA+CGG | - | chr1_4:65201880-65201899 | Msa0177880:CDS | 45.0% | |
| AAGAAGAAGAAAGTGGAGGG+TGG | - | chr1_4:65201908-65201927 | Msa0177880:CDS | 45.0% | |
| AGAAGAAGAAAGTGGAGGGT+GGG | - | chr1_4:65201909-65201928 | Msa0177880:CDS | 45.0% | |
| TGGAGTGAAGCAAACTCATC+TGG | - | chr1_4:65202032-65202051 | Msa0177880:CDS | 45.0% | |
| AGTGAAGCAAACTCATCTGG+AGG | - | chr1_4:65202035-65202054 | Msa0177880:CDS | 45.0% | |
| GAGGTGATACTATACGTGGA+CGG | - | chr1_4:65202093-65202112 | Msa0177880:CDS | 45.0% | |
| CTGATGGAGTCTGAGGAAAA+TGG | + | chr1_4:65202122-65202141 | None:intergenic | 45.0% | |
| TGTGCGACACTTCAGGAAAA+TGG | - | chr1_4:65202160-65202179 | Msa0177880:CDS | 45.0% | |
| TCCAGAATTCACCGAATCCA+CGG | + | chr1_4:65202322-65202341 | None:intergenic | 45.0% | |
| AGGGAGGAGAAACGATGAGA+AGG | - | chr1_4:65201876-65201895 | Msa0177880:CDS | 50.0% | |
| !!! | CTGCGGCTTCAGGTTGTTTT+AGG | + | chr1_4:65202005-65202024 | None:intergenic | 50.0% |
| ! | CTTCACTCCAAATGGTGCTG+CGG | + | chr1_4:65202022-65202041 | None:intergenic | 50.0% |
| GAAGCAAACTCATCTGGAGG+AGG | - | chr1_4:65202038-65202057 | Msa0177880:CDS | 50.0% | |
| GGAGGAGGTGATACTATACG+TGG | - | chr1_4:65202089-65202108 | Msa0177880:CDS | 50.0% | |
| TTTCCTCAGACTCCATCAGC+AGG | - | chr1_4:65202123-65202142 | Msa0177880:CDS | 50.0% | |
| AAACCACCACAACCTGCTGA+TGG | + | chr1_4:65202138-65202157 | None:intergenic | 50.0% | |
| ! | GGTTTTCTGTGCGACACTTC+AGG | - | chr1_4:65202153-65202172 | Msa0177880:CDS | 50.0% |
| GGTGAAGTCAGATCGTGAAG+AGG | - | chr1_4:65202296-65202315 | Msa0177880:CDS | 50.0% | |
| ! | AGTGGAGGGACACAGTTTTG+AGG | + | chr1_4:65202513-65202532 | None:intergenic | 50.0% |
| TAAGTAGCCTGTGGAGTGGA+GGG | + | chr1_4:65202527-65202546 | None:intergenic | 50.0% | |
| TTAAGTAGCCTGTGGAGTGG+AGG | + | chr1_4:65202528-65202547 | None:intergenic | 50.0% | |
| GCAAACTCATCTGGAGGAGG+AGG | - | chr1_4:65202041-65202060 | Msa0177880:CDS | 55.0% | |
| AACTCATCTGGAGGAGGAGG+AGG | - | chr1_4:65202044-65202063 | Msa0177880:CDS | 55.0% | |
| CAACCTGCTGATGGAGTCTG+AGG | + | chr1_4:65202129-65202148 | None:intergenic | 55.0% | |
| CAGACTCCATCAGCAGGTTG+TGG | - | chr1_4:65202129-65202148 | Msa0177880:CDS | 55.0% | |
| ACTCCATCAGCAGGTTGTGG+TGG | - | chr1_4:65202132-65202151 | Msa0177880:CDS | 55.0% | |
| TCGTGAAGAGGCCGTGGATT+CGG | - | chr1_4:65202308-65202327 | Msa0177880:CDS | 55.0% | |
| !! | GCCGTGGATTCGGTGAATTC+TGG | - | chr1_4:65202318-65202337 | Msa0177880:CDS | 55.0% |
| GTCAACGATGCTTCCCAGTG+AGG | + | chr1_4:65202396-65202415 | None:intergenic | 55.0% | |
| !!! | GGAGGGACACAGTTTTGAGG+AGG | + | chr1_4:65202510-65202529 | None:intergenic | 55.0% |
| !! | CCAAATGGTGCTGCGGCTTC+AGG | + | chr1_4:65202015-65202034 | None:intergenic | 60.0% |
| CCTGAAGCCGCAGCACCATT+TGG | - | chr1_4:65202012-65202031 | Msa0177880:CDS | 60.0% | |
| TCATCTGGAGGAGGAGGAGG+AGG | - | chr1_4:65202047-65202066 | Msa0177880:CDS | 60.0% | |
| GTCAGATCGTGAAGAGGCCG+TGG | - | chr1_4:65202302-65202321 | Msa0177880:CDS | 60.0% | |
| ACTGTGTCCCTCCACTCCAC+AGG | - | chr1_4:65202517-65202536 | Msa0177880:CDS | 60.0% | |
| ACCGGCTACAGCTGCCGTTG+CGG | + | chr1_4:65201968-65201987 | None:intergenic | 65.0% | |
| TCTGGAGGAGGAGGAGGAGG+AGG | - | chr1_4:65202050-65202069 | Msa0177880:CDS | 65.0% | |
| GGAGGAGGAGGAGGAGGATG+AGG | - | chr1_4:65202065-65202084 | Msa0177880:CDS | 65.0% | |
| GGAGGAGGAGGAGGATGAGG+AGG | - | chr1_4:65202068-65202087 | Msa0177880:CDS | 65.0% | |
| GGAGGAGGAGGATGAGGAGG+AGG | - | chr1_4:65202071-65202090 | Msa0177880:CDS | 65.0% | |
| GGAGGAGGATGAGGAGGAGG+AGG | - | chr1_4:65202074-65202093 | Msa0177880:CDS | 65.0% | |
| GGCTACAGCTGCCGTTGCGG+CGG | + | chr1_4:65201965-65201984 | None:intergenic | 70.0% | |
| GCCGCAACGGCAGCTGTAGC+CGG | - | chr1_4:65201964-65201983 | Msa0177880:CDS | 70.0% | |
| GCAACGGCAGCTGTAGCCGG+TGG | - | chr1_4:65201967-65201986 | Msa0177880:CDS | 70.0% | |
| GGAGGAGGAGGAGGAGGAGG+AGG | - | chr1_4:65202053-65202072 | Msa0177880:CDS | 70.0% | |
| GGAGGAGGAGGAGGAGGAGG+AGG | - | chr1_4:65202053-65202072 | Msa0177880:CDS | 70.0% | |
| GGAGGAGGAGGAGGAGGAGG+AGG | - | chr1_4:65202053-65202072 | Msa0177880:CDS | 70.0% | |
| AGCCGGAGCAGCCGCCGCAA+CGG | - | chr1_4:65201951-65201970 | Msa0177880:CDS | 75.0% | |
| TGCCGTTGCGGCGGCTGCTC+CGG | + | chr1_4:65201956-65201975 | None:intergenic | 75.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr1_4 | gene | 65201868 | 65202551 | 65201868 | ID=Msa0177880;Name=Msa0177880 |
| chr1_4 | mRNA | 65201868 | 65202551 | 65201868 | ID=Msa0177880-mRNA-1;Parent=Msa0177880;Name=Msa0177880-mRNA-1;_AED=0.58;_eAED=0.58;_QI=0|-1|0|1|-1|1|1|0|227 |
| chr1_4 | exon | 65201868 | 65202551 | 65201868 | ID=Msa0177880-mRNA-1:exon:21208;Parent=Msa0177880-mRNA-1 |
| chr1_4 | CDS | 65201868 | 65202551 | 65201868 | ID=Msa0177880-mRNA-1:cds;Parent=Msa0177880-mRNA-1 |
| Gene Sequence |
| Protein sequence |
