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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1346710 | MCH99725.1 | 77.419 | 62 | 14 | 0 | 55 | 116 | 69 | 130 | 9.64e-23 | 101 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1346710 | A0A392NKV9 | 77.419 | 62 | 14 | 0 | 55 | 116 | 69 | 130 | 4.61e-23 | 101 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0227400 | Msa1346710 | 0.801489 | 8.788287e-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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa1346710 | MtrunA17_Chr3g0144121 | 61.667 | 60 | 23 | 0 | 57 | 116 | 81 | 140 | 2.16e-18 | 79.7 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|
Find 24 sgRNAs with CRISPR-Local
Find 97 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| CAGAATGTCCCAAGCTTCTT+TGG | 0.191741 | tig0009218:-3295 | None:intergenic |
| AAACCTTCATTTCTGCTAAA+TGG | 0.204206 | tig0009218:-2824 | None:intergenic |
| GCAATGGATATTGTTGAGTT+TGG | 0.219681 | tig0009218:+2183 | Msa1346710:intron |
| CAAAGAAGCTTGGGACATTC+TGG | 0.267364 | tig0009218:+3296 | Msa1346710:CDS |
| AGAAGTAATCACTTGCATTT+TGG | 0.275709 | tig0009218:-3407 | None:intergenic |
| CAATGGATATTGTTGAGTTT+GGG | 0.278094 | tig0009218:+2184 | Msa1346710:exon |
| TTCTTTGGATCTTGTTGCCT+TGG | 0.384287 | tig0009218:-3280 | None:intergenic |
| TTAAGTTGCAATCATATAGA+AGG | 0.409711 | tig0009218:+3355 | Msa1346710:CDS |
| TATTGTTGAGTTTGGGGAGC+TGG | 0.414476 | tig0009218:+2191 | Msa1346710:CDS |
| GTGAATCTAATGAAAAGTTA+TGG | 0.432310 | tig0009218:+3448 | Msa1346710:CDS |
| ATTCTGGAAAACTATCATAA+TGG | 0.442895 | tig0009218:+3312 | Msa1346710:CDS |
| AACAAGATCCAAAGAAGCTT+GGG | 0.457541 | tig0009218:+3287 | Msa1346710:CDS |
| AAGCCATTTAGCAGAAATGA+AGG | 0.462537 | tig0009218:+2821 | Msa1346710:CDS |
| ATATCATGTGGAGAAGTTGC+AGG | 0.469859 | tig0009218:-2798 | None:intergenic |
| CAACAAGATCCAAAGAAGCT+TGG | 0.497408 | tig0009218:+3286 | Msa1346710:CDS |
| GAAGTACGAGAGGATTCAAA+TGG | 0.527749 | tig0009218:+3377 | Msa1346710:CDS |
| AATGGATATTGTTGAGTTTG+GGG | 0.565838 | tig0009218:+2185 | Msa1346710:exon |
| TTTGAAATGGCAGAAATGGA+AGG | 0.567982 | tig0009218:+3091 | Msa1346710:CDS |
| GCTAAATGGCTTATATCATG+TGG | 0.583284 | tig0009218:-2810 | None:intergenic |
| TCAACTTTCGTATAATAATG+AGG | 0.589577 | tig0009218:+965 | Msa1346710:five_prime_UTR |
| GTACGAGAGGATTCAAATGG+AGG | 0.628089 | tig0009218:+3380 | Msa1346710:CDS |
| CTTAAGTTAGAGCTACTCAC+TGG | 0.628873 | tig0009218:+936 | Msa1346710:five_prime_UTR |
| CATATAGAAGGAAGTACGAG+AGG | 0.643965 | tig0009218:+3367 | Msa1346710:CDS |
| GAAGAAGCAATAGTTCAGCA+AGG | 0.666882 | tig0009218:+2213 | Msa1346710:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | TTTTATTGTTTCTTTAATAA+AGG | + | tig0009218:1016-1035 | Msa1346710:intron | 10.0% |
| !!! | CTTTTAAATTTTAACTATAA+AGG | - | tig0009218:1521-1540 | None:intergenic | 10.0% |
| !! | TATAGTTAAAATTTAAAAGT+AGG | + | tig0009218:1522-1541 | Msa1346710:intron | 10.0% |
| !!! | TAATATTCAATAATATGTTT+TGG | + | tig0009218:2137-2156 | Msa1346710:intron | 10.0% |
| !!! | AAAGTTAAAAGTTTCAATTT+TGG | + | tig0009218:1074-1093 | Msa1346710:intron | 15.0% |
| !! | AAAACAATACTTACTAATTA+AGG | - | tig0009218:2078-2097 | None:intergenic | 15.0% |
| !! | CAAAATATAACAATTAAAAG+AGG | - | tig0009218:2343-2362 | None:intergenic | 15.0% |
| !! | GAGACAATATTCTTTAATAA+AGG | + | tig0009218:993-1012 | Msa1346710:intron | 20.0% |
| !!! | AGGTTTTATTGTATCTTTAT+TGG | + | tig0009218:1036-1055 | Msa1346710:intron | 20.0% |
| !! | TTGAGTTCAAAATAGAAATT+GGG | - | tig0009218:1174-1193 | None:intergenic | 20.0% |
| !!! | TTTGAGTTCAAAATAGAAAT+TGG | - | tig0009218:1175-1194 | None:intergenic | 20.0% |
| !!! | AATTTTAAATTCCTCAGTTT+AGG | + | tig0009218:1255-1274 | Msa1346710:intron | 20.0% |
| !! | TTTAACAGTAAAAATGAGTT+TGG | - | tig0009218:1316-1335 | None:intergenic | 20.0% |
| !!! | CTTTTTTCATAGAAGATATT+CGG | + | tig0009218:1809-1828 | Msa1346710:intron | 20.0% |
| !! | AGTAGTAAGAATAATGTAAT+TGG | + | tig0009218:1944-1963 | Msa1346710:intron | 20.0% |
| !! | GTAGTAAGAATAATGTAATT+GGG | + | tig0009218:1945-1964 | Msa1346710:intron | 20.0% |
| !!! | CTTTATTTTATTGTTGTTGA+AGG | - | tig0009218:1983-2002 | None:intergenic | 20.0% |
| !!! | ATGCTTGTTTAAATTCATTT+TGG | + | tig0009218:2106-2125 | Msa1346710:intron | 20.0% |
| !! | ATAGAAAAAGATAACTTACA+TGG | - | tig0009218:2267-2286 | None:intergenic | 20.0% |
| !!! | TTATTTTACAACAGAAAAAG+TGG | - | tig0009218:2296-2315 | None:intergenic | 20.0% |
| !! | TATTCAATAAATCATACACA+AGG | - | tig0009218:2618-2637 | None:intergenic | 20.0% |
| !! | TATAGTAAGAAGTTCAATTT+GGG | + | tig0009218:3129-3148 | Msa1346710:intron | 20.0% |
| !!! | TTTTACATTCAAACATAATG+TGG | + | tig0009218:3233-3252 | Msa1346710:intron | 20.0% |
| ! | TCAACTTTCGTATAATAATG+AGG | + | tig0009218:965-984 | Msa1346710:five_prime_UTR | 25.0% |
| ! | TTCGTATAATAATGAGGTAA+TGG | + | tig0009218:971-990 | Msa1346710:intron | 25.0% |
| ! | TGAGTTCAAAATAGAAATTG+GGG | - | tig0009218:1173-1192 | None:intergenic | 25.0% |
| ! | AACACTAAAAGTTACAATCT+AGG | - | tig0009218:1359-1378 | None:intergenic | 25.0% |
| !!! | TAGTGTTGTTTAATCTCATT+TGG | + | tig0009218:1372-1391 | Msa1346710:intron | 25.0% |
| !!! | AGTGTTGTTTAATCTCATTT+GGG | + | tig0009218:1373-1392 | Msa1346710:intron | 25.0% |
| ! | ATCTGCCACAAAAAAAAAAA+AGG | - | tig0009218:1421-1440 | None:intergenic | 25.0% |
| ! | AATCTTATCTTTCTCAGTTT+AGG | + | tig0009218:1461-1480 | Msa1346710:intron | 25.0% |
| ! | TAAAAGTAGGTAAACATCAA+TGG | + | tig0009218:1535-1554 | Msa1346710:intron | 25.0% |
| ! | TGAAATCAATTGCTATATGA+TGG | - | tig0009218:1702-1721 | None:intergenic | 25.0% |
| !! | ATAGCAATTGATTTCATGTA+TGG | + | tig0009218:1706-1725 | Msa1346710:intron | 25.0% |
| !!! | AGAGGTATTATTTAACATGT+TGG | - | tig0009218:2325-2344 | None:intergenic | 25.0% |
| ! | AGATATTATCATGCAAAGTT+GGG | - | tig0009218:2396-2415 | None:intergenic | 25.0% |
| ! | AAGATATTATCATGCAAAGT+TGG | - | tig0009218:2397-2416 | None:intergenic | 25.0% |
| ! | TCAAACTCAAGAAATTATCA+TGG | - | tig0009218:2467-2486 | None:intergenic | 25.0% |
| !! | GTAACTTTTGTATGATTTAG+TGG | + | tig0009218:2498-2517 | Msa1346710:intron | 25.0% |
| !!! | AGCTTTAAACTTTAGTTTCT+TGG | + | tig0009218:2542-2561 | Msa1346710:intron | 25.0% |
| !! | GCTTTAAACTTTAGTTTCTT+GGG | + | tig0009218:2543-2562 | Msa1346710:intron | 25.0% |
| !!! | CAGAATTTTGATTAATACCT+TGG | + | tig0009218:2656-2675 | Msa1346710:intron | 25.0% |
| !!! | TTTTTTTTTCACATATGCCA+AGG | - | tig0009218:2676-2695 | None:intergenic | 25.0% |
| ! | TTTCAAAAGCAAAGCAAATA+AGG | - | tig0009218:2876-2895 | None:intergenic | 25.0% |
| !!! | TATTTGCTTTGCTTTTGAAA+AGG | + | tig0009218:2876-2895 | Msa1346710:intron | 25.0% |
| ! | CAAATACCACTAGTTATTTA+TGG | + | tig0009218:3043-3062 | Msa1346710:intron | 25.0% |
| ! | TTGAAACCATAAATAACTAG+TGG | - | tig0009218:3052-3071 | None:intergenic | 25.0% |
| !!! | CTTTGCAGAATATTTTGAAA+TGG | + | tig0009218:3078-3097 | Msa1346710:intron | 25.0% |
| !!! | ATATTTTGAAATGGCAGAAA+TGG | + | tig0009218:3087-3106 | Msa1346710:CDS | 25.0% |
| ! | GTATAGTAAGAAGTTCAATT+TGG | + | tig0009218:3128-3147 | Msa1346710:intron | 25.0% |
| ! | AGGATATAGTATACAGTATT+CGG | + | tig0009218:3158-3177 | Msa1346710:intron | 25.0% |
| !! | ATTCTGGAAAACTATCATAA+TGG | + | tig0009218:3312-3331 | Msa1346710:CDS | 25.0% |
| !! | TTAAGTTGCAATCATATAGA+AGG | + | tig0009218:3355-3374 | Msa1346710:CDS | 25.0% |
| ! | GTGAATCTAATGAAAAGTTA+TGG | + | tig0009218:3448-3467 | Msa1346710:CDS | 25.0% |
| TTTCAGATTTGAATAGTGAG+AGG | - | tig0009218:1201-1220 | None:intergenic | 30.0% | |
| !!! | GGTTGCCTTTTTTTTTTTTG+TGG | + | tig0009218:1413-1432 | Msa1346710:intron | 30.0% |
| ! | CAATTGATTTCATGTATGGA+TGG | + | tig0009218:1710-1729 | Msa1346710:intron | 30.0% |
| CATCTATTAGAATCTGCTAA+AGG | - | tig0009218:1757-1776 | None:intergenic | 30.0% | |
| CTTTAGCAGATTCTAATAGA+TGG | + | tig0009218:1755-1774 | Msa1346710:intron | 30.0% | |
| CACATCTATTAGAATTGCTT+AGG | - | tig0009218:1900-1919 | None:intergenic | 30.0% | |
| ! | GTTACTTTGTTTGTAAGCAA+TGG | + | tig0009218:2167-2186 | Msa1346710:intron | 30.0% |
| CAATGGATATTGTTGAGTTT+GGG | + | tig0009218:2184-2203 | Msa1346710:exon | 30.0% | |
| AATGGATATTGTTGAGTTTG+GGG | + | tig0009218:2185-2204 | Msa1346710:exon | 30.0% | |
| AAAGAATAAAGACACACACA+AGG | + | tig0009218:2699-2718 | Msa1346710:intron | 30.0% | |
| AAGAATAAAGACACACACAA+GGG | + | tig0009218:2700-2719 | Msa1346710:intron | 30.0% | |
| AAACCTTCATTTCTGCTAAA+TGG | - | tig0009218:2827-2846 | None:intergenic | 30.0% | |
| ATTCGGATAAATTGACATTC+TGG | + | tig0009218:3175-3194 | Msa1346710:intron | 30.0% | |
| ! | AGAAGTAATCACTTGCATTT+TGG | - | tig0009218:3410-3429 | None:intergenic | 30.0% |
| TAATGTTGAGACCTAAACTG+AGG | - | tig0009218:1269-1288 | None:intergenic | 35.0% | |
| !! | TGGGAAATATTCTAAGACAG+TGG | + | tig0009218:1392-1411 | Msa1346710:intron | 35.0% |
| GCAATGGATATTGTTGAGTT+TGG | + | tig0009218:2183-2202 | Msa1346710:intron | 35.0% | |
| CAATAAATCATACACAAGGC+TGG | - | tig0009218:2614-2633 | None:intergenic | 35.0% | |
| GTTGCAGGAATATTAAGATC+TGG | - | tig0009218:2786-2805 | None:intergenic | 35.0% | |
| GCTAAATGGCTTATATCATG+TGG | - | tig0009218:2813-2832 | None:intergenic | 35.0% | |
| AAGCCATTTAGCAGAAATGA+AGG | + | tig0009218:2821-2840 | Msa1346710:CDS | 35.0% | |
| ATCCAGTCTAAAAGAAGAAC+AGG | - | tig0009218:2958-2977 | None:intergenic | 35.0% | |
| ! | TTTGAAATGGCAGAAATGGA+AGG | + | tig0009218:3091-3110 | Msa1346710:CDS | 35.0% |
| AAGTTCAATTTGGGAAGTGA+AGG | + | tig0009218:3138-3157 | Msa1346710:intron | 35.0% | |
| !!! | GCGTTTTGAAAAGATTTCCA+AGG | + | tig0009218:3263-3282 | Msa1346710:intron | 35.0% |
| AACAAGATCCAAAGAAGCTT+GGG | + | tig0009218:3287-3306 | Msa1346710:CDS | 35.0% | |
| CTTAAGTTAGAGCTACTCAC+TGG | + | tig0009218:936-955 | Msa1346710:five_prime_UTR | 40.0% | |
| GAAGAAGCAATAGTTCAGCA+AGG | + | tig0009218:2213-2232 | Msa1346710:CDS | 40.0% | |
| !!! | CACAAGGGTCTTGTTCTTTT+TGG | + | tig0009218:2715-2734 | Msa1346710:intron | 40.0% |
| ATATCATGTGGAGAAGTTGC+AGG | - | tig0009218:2801-2820 | None:intergenic | 40.0% | |
| GCAAAGCAAATAAGGTAGAG+TGG | - | tig0009218:2868-2887 | None:intergenic | 40.0% | |
| ! | TGCCTGTTCTTCTTTTAGAC+TGG | + | tig0009218:2953-2972 | Msa1346710:intron | 40.0% |
| AATGGAAGGTGAAGAAGTGA+AGG | + | tig0009218:3105-3124 | Msa1346710:intron | 40.0% | |
| ATGGAAGGTGAAGAAGTGAA+GGG | + | tig0009218:3106-3125 | Msa1346710:intron | 40.0% | |
| ! | CTGGATAATCAGCGTTTTGA+AGG | + | tig0009218:3194-3213 | Msa1346710:intron | 40.0% |
| TTCTTTGGATCTTGTTGCCT+TGG | - | tig0009218:3283-3302 | None:intergenic | 40.0% | |
| CAACAAGATCCAAAGAAGCT+TGG | + | tig0009218:3286-3305 | Msa1346710:CDS | 40.0% | |
| ! | CATATAGAAGGAAGTACGAG+AGG | + | tig0009218:3367-3386 | Msa1346710:CDS | 40.0% |
| GAAGTACGAGAGGATTCAAA+TGG | + | tig0009218:3377-3396 | Msa1346710:CDS | 40.0% | |
| TATTGTTGAGTTTGGGGAGC+TGG | + | tig0009218:2191-2210 | Msa1346710:CDS | 45.0% | |
| CAGAATGTCCCAAGCTTCTT+TGG | - | tig0009218:3298-3317 | None:intergenic | 45.0% | |
| CAAAGAAGCTTGGGACATTC+TGG | + | tig0009218:3296-3315 | Msa1346710:CDS | 45.0% | |
| GTACGAGAGGATTCAAATGG+AGG | + | tig0009218:3380-3399 | Msa1346710:CDS | 45.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| tig0009218 | gene | 897 | 3473 | 897 | ID=Msa1346710;Name=Msa1346710 |
| tig0009218 | mRNA | 897 | 3473 | 897 | ID=Msa1346710-mRNA-1;Parent=Msa1346710;Name=Msa1346710-mRNA-1;_AED=0.24;_eAED=0.24;_QI=92|0.75|0.6|1|0.75|0.6|5|0|124 |
| tig0009218 | exon | 897 | 986 | 897 | ID=Msa1346710-mRNA-1:exon:5618;Parent=Msa1346710-mRNA-1 |
| tig0009218 | exon | 2184 | 2267 | 2184 | ID=Msa1346710-mRNA-1:exon:5619;Parent=Msa1346710-mRNA-1 |
| tig0009218 | exon | 2787 | 2842 | 2787 | ID=Msa1346710-mRNA-1:exon:5620;Parent=Msa1346710-mRNA-1 |
| tig0009218 | exon | 3086 | 3112 | 3086 | ID=Msa1346710-mRNA-1:exon:5621;Parent=Msa1346710-mRNA-1 |
| tig0009218 | exon | 3264 | 3473 | 3264 | ID=Msa1346710-mRNA-1:exon:5622;Parent=Msa1346710-mRNA-1 |
| tig0009218 | five_prime_UTR | 897 | 986 | 897 | ID=Msa1346710-mRNA-1:five_prime_utr;Parent=Msa1346710-mRNA-1 |
| tig0009218 | five_prime_UTR | 2184 | 2185 | 2184 | ID=Msa1346710-mRNA-1:five_prime_utr;Parent=Msa1346710-mRNA-1 |
| tig0009218 | CDS | 2186 | 2267 | 2186 | ID=Msa1346710-mRNA-1:cds;Parent=Msa1346710-mRNA-1 |
| tig0009218 | CDS | 2787 | 2842 | 2787 | ID=Msa1346710-mRNA-1:cds;Parent=Msa1346710-mRNA-1 |
| tig0009218 | CDS | 3086 | 3112 | 3086 | ID=Msa1346710-mRNA-1:cds;Parent=Msa1346710-mRNA-1 |
| tig0009218 | CDS | 3264 | 3473 | 3264 | ID=Msa1346710-mRNA-1:cds;Parent=Msa1346710-mRNA-1 |
| Gene Sequence |
| Protein sequence |
