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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0360550 | RDX99926.1 | 54.795 | 73 | 31 | 1 | 24 | 94 | 96 | 168 | 2.25e-13 | 75.5 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0360550 | sp|Q9M2E8|HDG1_ARATH | 50.000 | 60 | 30 | 0 | 35 | 94 | 166 | 225 | 9.74e-13 | 65.5 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0360550 | A0A371HB02 | 54.795 | 73 | 31 | 1 | 24 | 94 | 96 | 168 | 1.07e-13 | 75.5 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0360550 | Msa1082500 | 0.800182 | 1.624632e-48 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0360550 | MtrunA17_Chr7g0246631 | 55.385 | 65 | 29 | 0 | 30 | 94 | 142 | 206 | 1.09e-15 | 70.5 |
| Msa0360550 | MtrunA17_Chr8g0350321 | 55.000 | 60 | 27 | 0 | 35 | 94 | 171 | 230 | 1.03e-14 | 67.8 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0360550 | AT3G61150.1 | 50.000 | 60 | 30 | 0 | 35 | 94 | 166 | 225 | 9.90e-14 | 65.5 |
| Msa0360550 | AT4G00730.1 | 48.333 | 60 | 31 | 0 | 35 | 94 | 190 | 249 | 1.32e-12 | 62.4 |
| Msa0360550 | AT4G00730.2 | 48.333 | 60 | 31 | 0 | 35 | 94 | 190 | 249 | 1.48e-12 | 62.0 |
Find 22 sgRNAs with CRISPR-Local
Find 64 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| TTCATCTTCTCTTAGCTAAT+TGG | 0.219778 | 3_1:+49978274 | Msa0360550:three_prime_UTR |
| CTTCTCTTAGCTAATTGGTT+AGG | 0.340972 | 3_1:+49978279 | Msa0360550:three_prime_UTR |
| AATGGTACACTAACACTCTT+AGG | 0.349146 | 3_1:-49977574 | None:intergenic |
| GCCATGCACTTATTTGTTGA+AGG | 0.417192 | 3_1:+49978212 | Msa0360550:three_prime_UTR |
| CTCACTAATAATAGTTGGAT+TGG | 0.440763 | 3_1:-49978124 | None:intergenic |
| GAAATCTCACTAATAATAGT+TGG | 0.456589 | 3_1:-49978129 | None:intergenic |
| TTCAATCCAGTCCTTGCCAT+TGG | 0.499157 | 3_1:-49977607 | None:intergenic |
| TTATTACCAATGGCAAGGAC+TGG | 0.510491 | 3_1:+49977601 | Msa0360550:CDS |
| ATCTTCAAATTGAAAATGCC+AGG | 0.525962 | 3_1:+49978166 | Msa0360550:CDS |
| CAAGGACTGGATTGAATCAA+AGG | 0.534230 | 3_1:+49977614 | Msa0360550:CDS |
| GCCTTCAACAAATAAGTGCA+TGG | 0.535771 | 3_1:-49978213 | None:intergenic |
| ACCATTGCTCTTATTACCAA+TGG | 0.538424 | 3_1:+49977591 | Msa0360550:CDS |
| TGCTCTTATTACCAATGGCA+AGG | 0.553333 | 3_1:+49977596 | Msa0360550:CDS |
| GTGCACAAAGTTTGTCTACC+TGG | 0.554950 | 3_1:-49978184 | None:intergenic |
| TATTAGTGAGATTTCACTAG+AGG | 0.569396 | 3_1:+49978137 | Msa0360550:CDS |
| TGGTCACAATTTGAACATGT+AGG | 0.570565 | 3_1:-49978104 | None:intergenic |
| GCCATTGGTAATAAGAGCAA+TGG | 0.577632 | 3_1:-49977592 | None:intergenic |
| TAATTGGTTAGGTGTGCTGC+AGG | 0.580065 | 3_1:+49978290 | Msa0360550:three_prime_UTR |
| ATTAGCTAAGAGAAGATGAA+AGG | 0.586853 | 3_1:-49978271 | None:intergenic |
| TTAATTGTGCCATATGAGAG+TGG | 0.663776 | 3_1:+49977534 | None:intergenic |
| GCCATATGAGAGTGGTACAA+TGG | 0.694055 | 3_1:+49977542 | None:intergenic |
| ATATGAGAGTGGTACAATGG+CGG | 0.703333 | 3_1:+49977545 | None:intergenic |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | TAATATGTTTCAGATTTTTT+TGG | + | chr3_1:49977735-49977754 | Msa0360550:intron | 15.0% |
| !!! | TAATATGTTTCAGATTTTTT+TGG | + | chr3_1:49977735-49977754 | Msa0360550:intron | 15.0% |
| ! | AATCTCAGAACATTGAAAAA+AGG | - | chr3_1:49977683-49977702 | None:intergenic | 25.0% |
| !!! | CAATGTTCTGAGATTTTTTT+TGG | + | chr3_1:49977688-49977707 | Msa0360550:intron | 25.0% |
| ! | CATACTTCATTGATATCATT+TGG | + | chr3_1:49977901-49977920 | Msa0360550:intron | 25.0% |
| !!! | TGATGAAAGTCATTTTTACA+TGG | + | chr3_1:49977960-49977979 | Msa0360550:intron | 25.0% |
| !!! | TTTACATGGTTTTATCTTTC+AGG | + | chr3_1:49977974-49977993 | Msa0360550:intron | 25.0% |
| ! | GAAATCTCACTAATAATAGT+TGG | - | chr3_1:49978132-49978151 | None:intergenic | 25.0% |
| ! | AATCTCAGAACATTGAAAAA+AGG | - | chr3_1:49977683-49977702 | None:intergenic | 25.0% |
| !!! | CAATGTTCTGAGATTTTTTT+TGG | + | chr3_1:49977688-49977707 | Msa0360550:intron | 25.0% |
| ! | CATACTTCATTGATATCATT+TGG | + | chr3_1:49977901-49977920 | Msa0360550:intron | 25.0% |
| !!! | TGATGAAAGTCATTTTTACA+TGG | + | chr3_1:49977960-49977979 | Msa0360550:intron | 25.0% |
| !!! | TTTACATGGTTTTATCTTTC+AGG | + | chr3_1:49977974-49977993 | Msa0360550:intron | 25.0% |
| ! | GAAATCTCACTAATAATAGT+TGG | - | chr3_1:49978132-49978151 | None:intergenic | 25.0% |
| AACTTTCATCAGTGTTATCA+TGG | - | chr3_1:49977866-49977885 | None:intergenic | 30.0% | |
| CTCACTAATAATAGTTGGAT+TGG | - | chr3_1:49978127-49978146 | None:intergenic | 30.0% | |
| TATTAGTGAGATTTCACTAG+AGG | + | chr3_1:49978137-49978156 | Msa0360550:CDS | 30.0% | |
| ATCTTCAAATTGAAAATGCC+AGG | + | chr3_1:49978166-49978185 | Msa0360550:CDS | 30.0% | |
| ATTAGCTAAGAGAAGATGAA+AGG | - | chr3_1:49978274-49978293 | None:intergenic | 30.0% | |
| TTCATCTTCTCTTAGCTAAT+TGG | + | chr3_1:49978274-49978293 | Msa0360550:three_prime_UTR | 30.0% | |
| AACTTTCATCAGTGTTATCA+TGG | - | chr3_1:49977866-49977885 | None:intergenic | 30.0% | |
| CTCACTAATAATAGTTGGAT+TGG | - | chr3_1:49978127-49978146 | None:intergenic | 30.0% | |
| TATTAGTGAGATTTCACTAG+AGG | + | chr3_1:49978137-49978156 | Msa0360550:CDS | 30.0% | |
| ATCTTCAAATTGAAAATGCC+AGG | + | chr3_1:49978166-49978185 | Msa0360550:CDS | 30.0% | |
| ATTAGCTAAGAGAAGATGAA+AGG | - | chr3_1:49978274-49978293 | None:intergenic | 30.0% | |
| TTCATCTTCTCTTAGCTAAT+TGG | + | chr3_1:49978274-49978293 | Msa0360550:three_prime_UTR | 30.0% | |
| AATGGTACACTAACACTCTT+AGG | - | chr3_1:49977577-49977596 | None:intergenic | 35.0% | |
| ACCATTGCTCTTATTACCAA+TGG | + | chr3_1:49977591-49977610 | Msa0360550:CDS | 35.0% | |
| TTGAATCAAAGGTGAATGAG+TGG | + | chr3_1:49977625-49977644 | Msa0360550:intron | 35.0% | |
| CAATTTCTCCTTAACTCTGA+AGG | - | chr3_1:49977787-49977806 | None:intergenic | 35.0% | |
| TGGTCACAATTTGAACATGT+AGG | - | chr3_1:49978107-49978126 | None:intergenic | 35.0% | |
| CTTCTCTTAGCTAATTGGTT+AGG | + | chr3_1:49978279-49978298 | Msa0360550:three_prime_UTR | 35.0% | |
| AATGGTACACTAACACTCTT+AGG | - | chr3_1:49977577-49977596 | None:intergenic | 35.0% | |
| ACCATTGCTCTTATTACCAA+TGG | + | chr3_1:49977591-49977610 | Msa0360550:CDS | 35.0% | |
| TTGAATCAAAGGTGAATGAG+TGG | + | chr3_1:49977625-49977644 | Msa0360550:intron | 35.0% | |
| CAATTTCTCCTTAACTCTGA+AGG | - | chr3_1:49977787-49977806 | None:intergenic | 35.0% | |
| TGGTCACAATTTGAACATGT+AGG | - | chr3_1:49978107-49978126 | None:intergenic | 35.0% | |
| CTTCTCTTAGCTAATTGGTT+AGG | + | chr3_1:49978279-49978298 | Msa0360550:three_prime_UTR | 35.0% | |
| ! | GCCATTGGTAATAAGAGCAA+TGG | - | chr3_1:49977595-49977614 | None:intergenic | 40.0% |
| TGCTCTTATTACCAATGGCA+AGG | + | chr3_1:49977596-49977615 | Msa0360550:CDS | 40.0% | |
| TTATTACCAATGGCAAGGAC+TGG | + | chr3_1:49977601-49977620 | Msa0360550:CDS | 40.0% | |
| CAAGGACTGGATTGAATCAA+AGG | + | chr3_1:49977614-49977633 | Msa0360550:CDS | 40.0% | |
| ! | TTTCTCCTTAACTCTGAAGG+CGG | - | chr3_1:49977784-49977803 | None:intergenic | 40.0% |
| ATCACACACATCTGATTCTG+AGG | - | chr3_1:49977944-49977963 | None:intergenic | 40.0% | |
| ! | GCCATGCACTTATTTGTTGA+AGG | + | chr3_1:49978212-49978231 | Msa0360550:three_prime_UTR | 40.0% |
| GCCTTCAACAAATAAGTGCA+TGG | - | chr3_1:49978216-49978235 | None:intergenic | 40.0% | |
| ! | GCCATTGGTAATAAGAGCAA+TGG | - | chr3_1:49977595-49977614 | None:intergenic | 40.0% |
| TGCTCTTATTACCAATGGCA+AGG | + | chr3_1:49977596-49977615 | Msa0360550:CDS | 40.0% | |
| TTATTACCAATGGCAAGGAC+TGG | + | chr3_1:49977601-49977620 | Msa0360550:CDS | 40.0% | |
| CAAGGACTGGATTGAATCAA+AGG | + | chr3_1:49977614-49977633 | Msa0360550:CDS | 40.0% | |
| ! | TTTCTCCTTAACTCTGAAGG+CGG | - | chr3_1:49977784-49977803 | None:intergenic | 40.0% |
| ATCACACACATCTGATTCTG+AGG | - | chr3_1:49977944-49977963 | None:intergenic | 40.0% | |
| ! | GCCATGCACTTATTTGTTGA+AGG | + | chr3_1:49978212-49978231 | Msa0360550:three_prime_UTR | 40.0% |
| GCCTTCAACAAATAAGTGCA+TGG | - | chr3_1:49978216-49978235 | None:intergenic | 40.0% | |
| TTCAATCCAGTCCTTGCCAT+TGG | - | chr3_1:49977610-49977629 | None:intergenic | 45.0% | |
| ! | TTCTCCTTAACTCTGAAGGC+GGG | - | chr3_1:49977783-49977802 | None:intergenic | 45.0% |
| GTGCACAAAGTTTGTCTACC+TGG | - | chr3_1:49978187-49978206 | None:intergenic | 45.0% | |
| TAATTGGTTAGGTGTGCTGC+AGG | + | chr3_1:49978290-49978309 | Msa0360550:three_prime_UTR | 45.0% | |
| TTCAATCCAGTCCTTGCCAT+TGG | - | chr3_1:49977610-49977629 | None:intergenic | 45.0% | |
| ! | TTCTCCTTAACTCTGAAGGC+GGG | - | chr3_1:49977783-49977802 | None:intergenic | 45.0% |
| GTGCACAAAGTTTGTCTACC+TGG | - | chr3_1:49978187-49978206 | None:intergenic | 45.0% | |
| TAATTGGTTAGGTGTGCTGC+AGG | + | chr3_1:49978290-49978309 | Msa0360550:three_prime_UTR | 45.0% | |
| TAAGCCCGCCTTCAGAGTTA+AGG | + | chr3_1:49977776-49977795 | Msa0360550:intron | 50.0% | |
| TAAGCCCGCCTTCAGAGTTA+AGG | + | chr3_1:49977776-49977795 | Msa0360550:intron | 50.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr3_1 | gene | 49977547 | 49978335 | 49977547 | ID=Msa0360550;Name=Msa0360550 |
| chr3_1 | mRNA | 49977547 | 49978335 | 49977547 | ID=Msa0360550-mRNA-1;Parent=Msa0360550;Name=Msa0360550-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|0|0.5|0.5|0|0.5|2|144|94 |
| chr3_1 | exon | 49977547 | 49977635 | 49977547 | ID=Msa0360550-mRNA-1:exon:8798;Parent=Msa0360550-mRNA-1 |
| chr3_1 | exon | 49977996 | 49978335 | 49977996 | ID=Msa0360550-mRNA-1:exon:8799;Parent=Msa0360550-mRNA-1 |
| chr3_1 | CDS | 49977547 | 49977635 | 49977547 | ID=Msa0360550-mRNA-1:cds;Parent=Msa0360550-mRNA-1 |
| chr3_1 | CDS | 49977996 | 49978191 | 49977996 | ID=Msa0360550-mRNA-1:cds;Parent=Msa0360550-mRNA-1 |
| chr3_1 | three_prime_UTR | 49978192 | 49978335 | 49978192 | ID=Msa0360550-mRNA-1:three_prime_utr;Parent=Msa0360550-mRNA-1 |
| Gene Sequence |
| Protein sequence |
