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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0549040 | XP_013456236.1 | 95.238 | 84 | 2 | 1 | 1 | 84 | 1 | 82 | 2.23e-49 | 160 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0549040 | A0A072UKM6 | 95.238 | 84 | 2 | 1 | 1 | 84 | 1 | 82 | 1.07e-49 | 160 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0549040 | Msa0632830 | 0.851259 | 9.969317e-61 | -8.615850e-47 |
| Msa0549040 | Msa0684850 | 0.805052 | 1.608168e-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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0549040 | MtrunA17_Chr4g0033121 | 95.238 | 84 | 2 | 1 | 1 | 84 | 1 | 82 | 2.06e-53 | 160 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|
Find 16 sgRNAs with CRISPR-Local
Find 31 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| GAAAGTTAACACTTTGTTCT+TGG | 0.265427 | 4_1:-43802897 | Msa0549040:CDS |
| TCATGAAACCTAACAACTTA+AGG | 0.327541 | 4_1:+43802431 | None:intergenic |
| ATAAGATATATCATCATATA+TGG | 0.365739 | 4_1:+43802296 | None:intergenic |
| CTAACAACTTAAGGTTCAAA+AGG | 0.365834 | 4_1:+43802440 | None:intergenic |
| TTTGCAAGGTTTAAGAATGA+AGG | 0.443415 | 4_1:-43802539 | Msa0549040:CDS |
| TTGTTGTGATGAAGAGGGTC+AGG | 0.472110 | 4_1:+43802467 | None:intergenic |
| GATATTAGGTTGCATTTGCA+AGG | 0.488673 | 4_1:-43802553 | Msa0549040:intron |
| TAACAACTTAAGGTTCAAAA+GGG | 0.507728 | 4_1:+43802441 | None:intergenic |
| TCAGCAAGAGAAGTTCCAAC+TGG | 0.518114 | 4_1:-43802491 | Msa0549040:CDS |
| AAGAATGAAGGAGTAACTGT+TGG | 0.526498 | 4_1:-43802527 | Msa0549040:CDS |
| GGGTTATTGTTGTGATGAAG+AGG | 0.548786 | 4_1:+43802461 | None:intergenic |
| GGTTATTGTTGTGATGAAGA+GGG | 0.581176 | 4_1:+43802462 | None:intergenic |
| TGAAGAGGGTCAGGTCCAGT+TGG | 0.596354 | 4_1:+43802476 | None:intergenic |
| ATTTATCGTTCAAACATGGA+AGG | 0.596798 | 4_1:-43802723 | Msa0549040:CDS |
| TCGTATTTATCGTTCAAACA+TGG | 0.631736 | 4_1:-43802727 | Msa0549040:CDS |
| TATCGTTCAAACATGGAAGG+AGG | 0.633179 | 4_1:-43802720 | Msa0549040:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !! | ACAATAATGATATAAAAAAA+TGG | + | chr4_1:43802465-43802484 | None:intergenic | 10.0% |
| !!! | TTTTTTTTTCTTTTGATATT+AGG | - | chr4_1:43802648-43802667 | Msa0549040:intron | 10.0% |
| !! | ATAAGATATATCATCATATA+TGG | + | chr4_1:43802922-43802941 | None:intergenic | 15.0% |
| !!! | ATTAGTTTTTCTTGGTTTTT+GGG | - | chr4_1:43802419-43802438 | Msa0549040:three_prime_UTR | 20.0% |
| !!! | AAGATGAAAACTTTGTTTTT+TGG | - | chr4_1:43802568-43802587 | Msa0549040:intron | 20.0% |
| !! | TATTAACATAGACCAAAAAA+GGG | + | chr4_1:43802618-43802637 | None:intergenic | 20.0% |
| !! | TTATTAACATAGACCAAAAA+AGG | + | chr4_1:43802619-43802638 | None:intergenic | 20.0% |
| !! | TTGGTCTATGTTAATAAAAA+TGG | - | chr4_1:43802622-43802641 | Msa0549040:intron | 20.0% |
| !!! | CTTTTTTCTTCTCTTCTATT+TGG | - | chr4_1:43802259-43802278 | Msa0549040:three_prime_UTR | 25.0% |
| !! | TTCTTCATCTTCATTGTTTT+AGG | + | chr4_1:43802301-43802320 | None:intergenic | 25.0% |
| !!! | CATTAGTTTTTCTTGGTTTT+TGG | - | chr4_1:43802418-43802437 | Msa0549040:three_prime_UTR | 25.0% |
| ! | TAACAACTTAAGGTTCAAAA+GGG | + | chr4_1:43802777-43802796 | None:intergenic | 25.0% |
| GAAAGTTAACACTTTGTTCT+TGG | - | chr4_1:43802318-43802337 | Msa0549040:three_prime_UTR | 30.0% | |
| TAATGAAGAGTGATTGAACA+TGG | + | chr4_1:43802403-43802422 | None:intergenic | 30.0% | |
| !!! | CACTCTTCATTAGTTTTTCT+TGG | - | chr4_1:43802411-43802430 | Msa0549040:three_prime_UTR | 30.0% |
| TCGTATTTATCGTTCAAACA+TGG | - | chr4_1:43802488-43802507 | Msa0549040:CDS | 30.0% | |
| ATTTATCGTTCAAACATGGA+AGG | - | chr4_1:43802492-43802511 | Msa0549040:CDS | 30.0% | |
| !! | AAACATAGCAAAAAGCATTG+AGG | - | chr4_1:43802524-43802543 | Msa0549040:CDS | 30.0% |
| !!! | GAACTTTCAAAACCCTTTTT+TGG | - | chr4_1:43802603-43802622 | Msa0549040:intron | 30.0% |
| TTTGCAAGGTTTAAGAATGA+AGG | - | chr4_1:43802676-43802695 | Msa0549040:intron | 30.0% | |
| CTAACAACTTAAGGTTCAAA+AGG | + | chr4_1:43802778-43802797 | None:intergenic | 30.0% | |
| !! | CTTTTGAACCTTAAGTTGTT+AGG | - | chr4_1:43802776-43802795 | Msa0549040:intron | 30.0% |
| TCATGAAACCTAACAACTTA+AGG | + | chr4_1:43802787-43802806 | None:intergenic | 30.0% | |
| ! | GATATTAGGTTGCATTTGCA+AGG | - | chr4_1:43802662-43802681 | Msa0549040:intron | 35.0% |
| AAGAATGAAGGAGTAACTGT+TGG | - | chr4_1:43802688-43802707 | Msa0549040:intron | 35.0% | |
| GGTTATTGTTGTGATGAAGA+GGG | + | chr4_1:43802756-43802775 | None:intergenic | 35.0% | |
| TATCGTTCAAACATGGAAGG+AGG | - | chr4_1:43802495-43802514 | Msa0549040:CDS | 40.0% | |
| GGGTTATTGTTGTGATGAAG+AGG | + | chr4_1:43802757-43802776 | None:intergenic | 40.0% | |
| TCAGCAAGAGAAGTTCCAAC+TGG | - | chr4_1:43802724-43802743 | Msa0549040:CDS | 45.0% | |
| TTGTTGTGATGAAGAGGGTC+AGG | + | chr4_1:43802751-43802770 | None:intergenic | 45.0% | |
| TGAAGAGGGTCAGGTCCAGT+TGG | + | chr4_1:43802742-43802761 | None:intergenic | 55.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr4_1 | gene | 43802259 | 43802978 | 43802259 | ID=Msa0549040;Name=Msa0549040 |
| chr4_1 | mRNA | 43802259 | 43802978 | 43802259 | ID=Msa0549040-mRNA-1;Parent=Msa0549040;Name=Msa0549040-mRNA-1;_AED=0.01;_eAED=0.01;_QI=48|1|1|1|1|1|3|189|84 |
| chr4_1 | exon | 43802259 | 43802567 | 43802259 | ID=Msa0549040-mRNA-1:exon:11316;Parent=Msa0549040-mRNA-1 |
| chr4_1 | exon | 43802692 | 43802750 | 43802692 | ID=Msa0549040-mRNA-1:exon:11315;Parent=Msa0549040-mRNA-1 |
| chr4_1 | exon | 43802855 | 43802978 | 43802855 | ID=Msa0549040-mRNA-1:exon:11314;Parent=Msa0549040-mRNA-1 |
| chr4_1 | five_prime_UTR | 43802931 | 43802978 | 43802931 | ID=Msa0549040-mRNA-1:five_prime_utr;Parent=Msa0549040-mRNA-1 |
| chr4_1 | CDS | 43802855 | 43802930 | 43802855 | ID=Msa0549040-mRNA-1:cds;Parent=Msa0549040-mRNA-1 |
| chr4_1 | CDS | 43802692 | 43802750 | 43802692 | ID=Msa0549040-mRNA-1:cds;Parent=Msa0549040-mRNA-1 |
| chr4_1 | CDS | 43802448 | 43802567 | 43802448 | ID=Msa0549040-mRNA-1:cds;Parent=Msa0549040-mRNA-1 |
| chr4_1 | three_prime_UTR | 43802259 | 43802447 | 43802259 | ID=Msa0549040-mRNA-1:three_prime_utr;Parent=Msa0549040-mRNA-1 |
| Gene Sequence |
| Protein sequence |
