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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0541860 | XP_013446710.1 | 100.000 | 64 | 0 | 0 | 1 | 64 | 1 | 64 | 4.86e-38 | 130 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0541860 | A0A072TTH9 | 100.000 | 64 | 0 | 0 | 1 | 64 | 1 | 64 | 2.32e-38 | 130 |
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0001450 | Msa0541860 | 0.801573 | 8.448806e-49 | -8.615850e-47 |
| Msa0002490 | Msa0541860 | 0.864582 | 1.096066e-64 | -8.615850e-47 |
| Msa0002540 | Msa0541860 | 0.823345 | 1.456072e-53 | -8.615850e-47 |
| Msa0003700 | Msa0541860 | 0.816327 | 5.854063e-52 | -8.615850e-47 |
| Msa0004860 | Msa0541860 | 0.810380 | 1.186544e-50 | -8.615850e-47 |
| Msa0004920 | Msa0541860 | 0.805570 | 1.252663e-49 | -8.615850e-47 |
| Msa0004980 | Msa0541860 | 0.825714 | 4.032035e-54 | -8.615850e-47 |
| Msa0008090 | Msa0541860 | 0.827741 | 1.322884e-54 | -8.615850e-47 |
| Msa0008410 | Msa0541860 | 0.851187 | 1.045219e-60 | -8.615850e-47 |
| Msa0009760 | Msa0541860 | 0.806741 | 7.098429e-50 | -8.615850e-47 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0541860 | MtrunA17_Chr8g0381271 | 100.000 | 64 | 0 | 0 | 1 | 64 | 1 | 64 | 4.47e-42 | 130 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0541860 | AT1G67785.1 | 77.419 | 62 | 13 | 1 | 1 | 62 | 1 | 61 | 2.32e-30 | 101 |
Find 62 sgRNAs with CRISPR-Local
Find 158 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| AAACTGAATCGAAGCAAAGA+AGG | 0.560808 | 4_1:-25872122 | Msa0541860:five_prime_UTR |
| AACGTACTTTGGAATGTCCT+TGG | 0.500806 | 4_1:-25872063 | Msa0541860:CDS |
| AATATCATGTATAACATCAA+AGG | 0.580442 | 4_1:+25871416 | None:intergenic |
| ACACATGATCCCTACTAAGT+CGG | 0.610810 | 4_1:+25871222 | None:intergenic |
| ACATTTGTGGGCTATTGATC+TGG | 0.411130 | 4_1:-25871176 | Msa0541860:three_prime_UTR |
| ACGATAAAGAGATTGAAGAA+GGG | 0.597047 | 4_1:+25871009 | None:intergenic |
| ACTTCTTCGTTGAGATGAGA+TGG | 0.481225 | 4_1:+25872170 | None:intergenic |
| AGAAGGAAGCGGAGATCAGA+AGG | 0.504547 | 4_1:-25871629 | Msa0541860:CDS |
| AGAGAGGTTGGAGAAGGAAG+CGG | 0.542879 | 4_1:-25871640 | Msa0541860:CDS |
| AGATACATTTGCCTGCTTGT+TGG | 0.455588 | 4_1:-25871072 | Msa0541860:three_prime_UTR |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| TGAAGAATTCGAAGAAGTAA+GGG | + | chr4_1:25871246-25871265 | None:intergenic | 30.0% | |
| ATGAAGAATTCGAAGAAGTA+AGG | + | chr4_1:25871247-25871266 | None:intergenic | 30.0% | |
| AGCATTGTTCCAACAATTAT+TGG | + | chr4_1:25871837-25871856 | None:intergenic | 30.0% | |
| CCAAAAATAAGCAATGCAAA+CGG | + | chr4_1:25871920-25871939 | None:intergenic | 30.0% | |
| GGAATTTAAGTCTACATTTG+TGG | - | chr4_1:25872018-25872037 | Msa0541860:CDS | 30.0% | |
| GAAAGCAAACATATACTCAA+AGG | + | chr4_1:25872090-25872109 | None:intergenic | 30.0% | |
| ACGATAAAGAGATTGAAGAA+GGG | + | chr4_1:25872201-25872220 | None:intergenic | 30.0% | |
| TGAAGAATTCGAAGAAGTAA+GGG | + | chr4_1:25871246-25871265 | None:intergenic | 30.0% | |
| ATGAAGAATTCGAAGAAGTA+AGG | + | chr4_1:25871247-25871266 | None:intergenic | 30.0% | |
| AGCATTGTTCCAACAATTAT+TGG | + | chr4_1:25871837-25871856 | None:intergenic | 30.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr4_1 | gene | 25870974 | 25872255 | 25870974 | ID=Msa0541860;Name=Msa0541860 |
| chr4_1 | mRNA | 25870974 | 25872255 | 25870974 | ID=Msa0541860-mRNA-1;Parent=Msa0541860;Name=Msa0541860-mRNA-1;_AED=0.00;_eAED=0.00;_QI=156|1|1|1|1|0.5|2|601|64 |
| chr4_1 | exon | 25870974 | 25871664 | 25870974 | ID=Msa0541860-mRNA-1:exon:7006;Parent=Msa0541860-mRNA-1 |
| chr4_1 | exon | 25871995 | 25872255 | 25871995 | ID=Msa0541860-mRNA-1:exon:7005;Parent=Msa0541860-mRNA-1 |
| chr4_1 | five_prime_UTR | 25872100 | 25872255 | 25872100 | ID=Msa0541860-mRNA-1:five_prime_utr;Parent=Msa0541860-mRNA-1 |
| chr4_1 | CDS | 25871995 | 25872099 | 25871995 | ID=Msa0541860-mRNA-1:cds;Parent=Msa0541860-mRNA-1 |
| chr4_1 | CDS | 25871575 | 25871664 | 25871575 | ID=Msa0541860-mRNA-1:cds;Parent=Msa0541860-mRNA-1 |
| chr4_1 | three_prime_UTR | 25870974 | 25871574 | 25870974 | ID=Msa0541860-mRNA-1:three_prime_utr;Parent=Msa0541860-mRNA-1 |
| Gene Sequence |
>Msa0541860 ATGGTGAAGGTTGCAACGTACTTTGGAATGTCCTTGGCAGCATTCGTTTTCTGGCAATCCATGGACAAAGTCCATGTCTGGATCGCTCTTCATCAGGACGAAAAGCAAGAGAGGTTGGAGAAGGAAGCGGAGATCAGAAGGGTCAGAGAACAATTAATTCGGGAGCAAGCCAGTCAGAAGGATTCTTCATATTGA |
| Protein sequence |
>Msa0541860 MVKVATYFGMSLAAFVFWQSMDKVHVWIALHQDEKQERLEKEAEIRRVREQLIREQASQKDSSY* |
