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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0329890 | XP_027929706.1 | 71.250 | 80 | 18 | 2 | 1 | 75 | 1 | 80 | 5.39e-32 | 116 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0329890 | sp|Q9SKY1|CSTM4_ARATH | 53.333 | 75 | 31 | 2 | 1 | 75 | 1 | 71 | 6.21e-19 | 75.9 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0329890 | A0A4D6NCS9 | 71.250 | 80 | 18 | 2 | 1 | 75 | 1 | 80 | 2.57e-32 | 116 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0029020 | Msa0329890 | 0.812457 | 4.199967e-51 | -8.615850e-47 |
| Msa0076650 | Msa0329890 | 0.810310 | 1.228315e-50 | -8.615850e-47 |
| Msa0253120 | Msa0329890 | 0.801472 | 8.862352e-49 | -8.615850e-47 |
| Msa0329880 | Msa0329890 | 0.830614 | 2.659815e-55 | -8.615850e-47 |
| Msa0329890 | Msa0494560 | 0.801839 | 7.450967e-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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0329890 | MtrunA17_Chr2g0312051 | 81.579 | 76 | 13 | 1 | 1 | 75 | 1 | 76 | 7.05e-34 | 110 |
| Msa0329890 | MtrunA17_Chr1g0166081 | 77.215 | 79 | 14 | 2 | 1 | 75 | 1 | 79 | 4.50e-32 | 106 |
| Msa0329890 | MtrunA17_Chr5g0417951 | 75.949 | 79 | 15 | 2 | 1 | 75 | 1 | 79 | 1.38e-31 | 105 |
| Msa0329890 | MtrunA17_Chr4g0048281 | 80.000 | 80 | 11 | 3 | 1 | 75 | 1 | 80 | 6.38e-29 | 98.2 |
| Msa0329890 | MtrunA17_Chr2g0312011 | 59.375 | 64 | 21 | 2 | 1 | 63 | 1 | 60 | 6.68e-13 | 57.8 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0329890 | AT2G32190.1 | 53.333 | 75 | 31 | 2 | 1 | 75 | 1 | 71 | 6.32e-20 | 75.9 |
| Msa0329890 | AT2G32210.1 | 53.333 | 75 | 31 | 2 | 1 | 75 | 1 | 71 | 1.08e-19 | 75.1 |
| Msa0329890 | AT2G32200.2 | 50.000 | 78 | 32 | 3 | 1 | 75 | 35 | 108 | 4.66e-16 | 67.0 |
| Msa0329890 | AT2G32200.1 | 50.000 | 78 | 32 | 3 | 1 | 75 | 1 | 74 | 7.29e-16 | 65.5 |
| Msa0329890 | AT3G22240.1 | 52.055 | 73 | 33 | 2 | 3 | 75 | 2 | 72 | 5.13e-11 | 53.1 |
| Msa0329890 | AT1G56060.2 | 51.667 | 60 | 25 | 3 | 18 | 75 | 14 | 71 | 6.87e-11 | 52.8 |
Find 32 sgRNAs with CRISPR-Local
Find 30 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| CATCCAAGGGTGATGGTTTC+TGG | 0.136023 | 2_4:+43841421 | Msa0329890:CDS |
| GTGCCCTTCAGTGCCATCTT+TGG | 0.313951 | 2_4:-43841370 | None:intergenic |
| GAACTTAAAAGCAGATATCT+AGG | 0.339148 | 2_4:-43841479 | None:intergenic |
| ACTGGTGGTGGATATGATAC+TGG | 0.355057 | 2_4:-43841300 | None:intergenic |
| CATCACCCTTGGATGTAGTT+TGG | 0.380276 | 2_4:-43841413 | None:intergenic |
| CCCTTGGATGTAGTTTGGTC+TGG | 0.389865 | 2_4:-43841408 | None:intergenic |
| TGTAACTGCACCACCACCTA+TGG | 0.404681 | 2_4:+43841338 | Msa0329890:CDS |
| ACATATGGAGCTGTAGATAC+TGG | 0.438751 | 2_4:-43841318 | None:intergenic |
| GGTCTGGAATCCTTTGTTGA+GGG | 0.445983 | 2_4:-43841392 | None:intergenic |
| TAACTTCAACAATAAGCAAC+AGG | 0.473699 | 2_4:+43841275 | Msa0329890:CDS |
| CTGGTGGTGGATATGATACT+GGG | 0.477844 | 2_4:-43841299 | None:intergenic |
| GGTGGTGGTGCAGTTACATA+TGG | 0.482974 | 2_4:-43841333 | None:intergenic |
| CCTTCCAAAGATGGCACTGA+AGG | 0.487973 | 2_4:+43841366 | Msa0329890:CDS |
| CTTCCAGAAACCATCACCCT+TGG | 0.519384 | 2_4:-43841424 | None:intergenic |
| ATGGGTTATCCTTCCAAAGA+TGG | 0.529377 | 2_4:+43841357 | Msa0329890:CDS |
| CCTTCAGTGCCATCTTTGGA+AGG | 0.555857 | 2_4:-43841366 | None:intergenic |
| TCCAGACCAAACTACATCCA+AGG | 0.577183 | 2_4:+43841407 | Msa0329890:CDS |
| TGGTCTGGAATCCTTTGTTG+AGG | 0.581792 | 2_4:-43841393 | None:intergenic |
| CAAGGGTGATGGTTTCTGGA+AGG | 0.584891 | 2_4:+43841425 | Msa0329890:CDS |
| AAGGGTGATGGTTTCTGGAA+GGG | 0.585272 | 2_4:+43841426 | Msa0329890:CDS |
| GAAGGATAACCCATAGGTGG+TGG | 0.596519 | 2_4:-43841348 | None:intergenic |
| GTAACTGCACCACCACCTAT+GGG | 0.597034 | 2_4:+43841339 | Msa0329890:CDS |
| CTTCCAAAGATGGCACTGAA+GGG | 0.598808 | 2_4:+43841367 | Msa0329890:CDS |
| AACTTAAAAGCAGATATCTA+GGG | 0.606743 | 2_4:-43841478 | None:intergenic |
| GGAGCTGTAGATACTGGTGG+TGG | 0.617769 | 2_4:-43841312 | None:intergenic |
| CTGAAGGGCACCCTCAACAA+AGG | 0.624674 | 2_4:+43841382 | Msa0329890:CDS |
| CAAACTACATCCAAGGGTGA+TGG | 0.635551 | 2_4:+43841414 | Msa0329890:CDS |
| CCAGACCAAACTACATCCAA+GGG | 0.646562 | 2_4:+43841408 | Msa0329890:CDS |
| TCTTTGGAAGGATAACCCAT+AGG | 0.652777 | 2_4:-43841354 | None:intergenic |
| TTGGAAGGATAACCCATAGG+TGG | 0.675232 | 2_4:-43841351 | None:intergenic |
| TGGTGGTGGATATGATACTG+GGG | 0.717786 | 2_4:-43841298 | None:intergenic |
| TATGGAGCTGTAGATACTGG+TGG | 0.763094 | 2_4:-43841315 | None:intergenic |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| TAACTTCAACAATAAGCAAC+AGG | + | chr2_4:43841275-43841294 | Msa0329890:CDS | 30.0% | |
| ACATATGGAGCTGTAGATAC+TGG | - | chr2_4:43841321-43841340 | None:intergenic | 40.0% | |
| ! | TCTTTGGAAGGATAACCCAT+AGG | - | chr2_4:43841357-43841376 | None:intergenic | 40.0% |
| ! | ATGGGTTATCCTTCCAAAGA+TGG | + | chr2_4:43841357-43841376 | Msa0329890:CDS | 40.0% |
| !! | TGGTGGTGGATATGATACTG+GGG | - | chr2_4:43841301-43841320 | None:intergenic | 45.0% |
| !! | CTGGTGGTGGATATGATACT+GGG | - | chr2_4:43841302-43841321 | None:intergenic | 45.0% |
| !! | ACTGGTGGTGGATATGATAC+TGG | - | chr2_4:43841303-43841322 | None:intergenic | 45.0% |
| TATGGAGCTGTAGATACTGG+TGG | - | chr2_4:43841318-43841337 | None:intergenic | 45.0% | |
| TTGGAAGGATAACCCATAGG+TGG | - | chr2_4:43841354-43841373 | None:intergenic | 45.0% | |
| ! | CTTCCAAAGATGGCACTGAA+GGG | + | chr2_4:43841367-43841386 | Msa0329890:CDS | 45.0% |
| ! | GGTCTGGAATCCTTTGTTGA+GGG | - | chr2_4:43841395-43841414 | None:intergenic | 45.0% |
| ! | TGGTCTGGAATCCTTTGTTG+AGG | - | chr2_4:43841396-43841415 | None:intergenic | 45.0% |
| TCCAGACCAAACTACATCCA+AGG | + | chr2_4:43841407-43841426 | Msa0329890:CDS | 45.0% | |
| CCAGACCAAACTACATCCAA+GGG | + | chr2_4:43841408-43841427 | Msa0329890:CDS | 45.0% | |
| CATCACCCTTGGATGTAGTT+TGG | - | chr2_4:43841416-43841435 | None:intergenic | 45.0% | |
| CAAACTACATCCAAGGGTGA+TGG | + | chr2_4:43841414-43841433 | Msa0329890:CDS | 45.0% | |
| ! | AAGGGTGATGGTTTCTGGAA+GGG | + | chr2_4:43841426-43841445 | Msa0329890:CDS | 45.0% |
| ! | GGTGGTGGTGCAGTTACATA+TGG | - | chr2_4:43841336-43841355 | None:intergenic | 50.0% |
| TGTAACTGCACCACCACCTA+TGG | + | chr2_4:43841338-43841357 | Msa0329890:CDS | 50.0% | |
| GTAACTGCACCACCACCTAT+GGG | + | chr2_4:43841339-43841358 | Msa0329890:CDS | 50.0% | |
| GAAGGATAACCCATAGGTGG+TGG | - | chr2_4:43841351-43841370 | None:intergenic | 50.0% | |
| CCTTCAGTGCCATCTTTGGA+AGG | - | chr2_4:43841369-43841388 | None:intergenic | 50.0% | |
| ! | CCTTCCAAAGATGGCACTGA+AGG | + | chr2_4:43841366-43841385 | Msa0329890:CDS | 50.0% |
| CCCTTGGATGTAGTTTGGTC+TGG | - | chr2_4:43841411-43841430 | None:intergenic | 50.0% | |
| ! | CATCCAAGGGTGATGGTTTC+TGG | + | chr2_4:43841421-43841440 | Msa0329890:CDS | 50.0% |
| CTTCCAGAAACCATCACCCT+TGG | - | chr2_4:43841427-43841446 | None:intergenic | 50.0% | |
| ! | CAAGGGTGATGGTTTCTGGA+AGG | + | chr2_4:43841425-43841444 | Msa0329890:CDS | 50.0% |
| GGAGCTGTAGATACTGGTGG+TGG | - | chr2_4:43841315-43841334 | None:intergenic | 55.0% | |
| GTGCCCTTCAGTGCCATCTT+TGG | - | chr2_4:43841373-43841392 | None:intergenic | 55.0% | |
| !! | CTGAAGGGCACCCTCAACAA+AGG | + | chr2_4:43841382-43841401 | Msa0329890:CDS | 55.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr2_4 | gene | 43841270 | 43841497 | 43841270 | ID=Msa0329890;Name=Msa0329890 |
| chr2_4 | mRNA | 43841270 | 43841497 | 43841270 | ID=Msa0329890-mRNA-1;Parent=Msa0329890;Name=Msa0329890-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|75 |
| chr2_4 | exon | 43841270 | 43841497 | 43841270 | ID=Msa0329890-mRNA-1:exon:13362;Parent=Msa0329890-mRNA-1 |
| chr2_4 | CDS | 43841270 | 43841497 | 43841270 | ID=Msa0329890-mRNA-1:cds;Parent=Msa0329890-mRNA-1 |
| Gene Sequence |
| Protein sequence |
