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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0613870 | XP_003608382.2 | 95.588 | 68 | 3 | 0 | 1 | 68 | 1 | 68 | 5.72e-39 | 144 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0613870 | sp|Q9S7V4|HA22A_ARATH | 48.387 | 62 | 32 | 0 | 6 | 67 | 8 | 69 | 3.40e-11 | 58.2 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0613870 | G7JV31 | 95.588 | 68 | 3 | 0 | 1 | 68 | 1 | 68 | 2.73e-39 | 144 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0613810 | Msa0613870 | 0.832262 | 1.044828e-55 | -8.615850e-47 |
| Msa0613820 | Msa0613870 | 0.898017 | 8.003999e-77 | -8.615850e-47 |
| Msa0613860 | Msa0613870 | 0.805520 | 1.283284e-49 | -8.615850e-47 |
| Msa0613870 | Msa0638440 | 0.803424 | 3.509854e-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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0613870 | MtrunA17_Chr4g0049651 | 95.588 | 68 | 3 | 0 | 1 | 68 | 1 | 68 | 5.26e-43 | 144 |
| Msa0613870 | MtrunA17_Chr4g0049671 | 70.588 | 68 | 11 | 1 | 1 | 68 | 1 | 59 | 1.78e-25 | 97.1 |
| Msa0613870 | MtrunA17_Chr4g0049701 | 80.769 | 52 | 10 | 0 | 17 | 68 | 14 | 65 | 1.30e-22 | 87.8 |
| Msa0613870 | MtrunA17_Chr4g0049691 | 48.649 | 111 | 13 | 3 | 1 | 67 | 1 | 111 | 2.27e-20 | 77.4 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0613870 | AT1G74520.1 | 48.387 | 62 | 32 | 0 | 6 | 67 | 8 | 69 | 3.45e-12 | 58.2 |
| Msa0613870 | AT1G74520.2 | 48.387 | 62 | 32 | 0 | 6 | 67 | 8 | 69 | 3.45e-12 | 58.2 |
| Msa0613870 | AT5G62490.1 | 47.541 | 61 | 32 | 0 | 7 | 67 | 9 | 69 | 1.29e-11 | 56.6 |
Find 31 sgRNAs with CRISPR-Local
Find 54 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| TTCCATTCGGAGCTTGAATT+TGG | 0.152842 | 4_2:-62743829 | Msa0613870:five_prime_UTR |
| GAATTTGGGTTGGTAGTAAA+TGG | 0.202975 | 4_2:-62743814 | Msa0613870:exon |
| TTTATTCAGGTTGTAGGATT+TGG | 0.214942 | 4_2:-62744056 | Msa0613870:five_prime_UTR |
| TTATTCAGGTTGTAGGATTT+GGG | 0.230723 | 4_2:-62744055 | Msa0613870:five_prime_UTR |
| GTTATAGTACGGATTTATTC+AGG | 0.269672 | 4_2:-62744069 | Msa0613870:five_prime_UTR |
| CATACCATGCAAAATGATAA+AGG | 0.301623 | 4_2:+62743757 | None:intergenic |
| TTCTTCATGGTTTCTCAAAC+TGG | 0.304002 | 4_2:-62743790 | Msa0613870:CDS |
| CTCCGAATGGAAAAGGAAAA+TGG | 0.330831 | 4_2:+62743840 | None:intergenic |
| TTCTAGGCCTCTTGTTGCTC+TGG | 0.337704 | 4_2:-62743635 | Msa0613870:intron |
| CTAAGGATTTGATCTCATAT+TGG | 0.368288 | 4_2:-62743442 | Msa0613870:CDS |
| TCCATTCGGAGCTTGAATTT+GGG | 0.371252 | 4_2:-62743828 | Msa0613870:five_prime_UTR |
| ATATTCAAAGAGGTAAATTA+AGG | 0.374191 | 4_2:+62743409 | None:intergenic |
| GGTAGTAAATGGATTCTTCA+TGG | 0.377876 | 4_2:-62743803 | Msa0613870:exon |
| AAATAGTAAAGTAGCTTAGT+TGG | 0.385187 | 4_2:+62743894 | None:intergenic |
| TACGGATTTATTCAGGTTGT+AGG | 0.413492 | 4_2:-62744062 | Msa0613870:five_prime_UTR |
| GTCAGTTTCAATTGCTTGTA+CGG | 0.466858 | 4_2:+62743478 | None:intergenic |
| ATTCAAGCTCCGAATGGAAA+AGG | 0.483180 | 4_2:+62743833 | None:intergenic |
| AGTAAAGTAGCTTAGTTGGT+AGG | 0.504642 | 4_2:+62743898 | None:intergenic |
| TGACTCATATGCAGAAACTA+AGG | 0.505188 | 4_2:-62743459 | Msa0613870:CDS |
| GACACGGAGCAAAATGTCAT+TGG | 0.524996 | 4_2:+62743953 | None:intergenic |
| AAAGAATTTACCGTAGAAGA+AGG | 0.542698 | 4_2:+62743375 | None:intergenic |
| TTCGGAGCTTGAATTTGGGT+TGG | 0.553560 | 4_2:-62743824 | Msa0613870:five_prime_UTR |
| TATTCAGGTTGTAGGATTTG+GGG | 0.559272 | 4_2:-62744054 | Msa0613870:five_prime_UTR |
| CTTAGTTGGTAGGTTGCAAG+TGG | 0.575855 | 4_2:+62743908 | None:intergenic |
| ACCCAAATTCAAGCTCCGAA+TGG | 0.576931 | 4_2:+62743827 | None:intergenic |
| GTTGGTAGGTTGCAAGTGGG+AGG | 0.594166 | 4_2:+62743912 | None:intergenic |
| TCATAAAAGCATATTCAAAG+AGG | 0.621411 | 4_2:+62743399 | None:intergenic |
| GGATACACCAGAGCAACAAG+AGG | 0.670998 | 4_2:+62743628 | None:intergenic |
| TGTATTTAACATGCGAACGA+GGG | 0.671832 | 4_2:-62743977 | Msa0613870:intron |
| TTAGTTGGTAGGTTGCAAGT+GGG | 0.704476 | 4_2:+62743909 | None:intergenic |
| GAAAATAAGATATACCGACA+CGG | 0.773589 | 4_2:+62743937 | None:intergenic |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | TTTTTATTCTATCTACTTTT+GGG | + | chr4_2:62743393-62743412 | None:intergenic | 15.0% |
| !!! | TTTTTTATTCTATCTACTTT+TGG | + | chr4_2:62743394-62743413 | None:intergenic | 15.0% |
| !! | GAATAAAAAAAGTTATAGTA+CGG | - | chr4_2:62743404-62743423 | Msa0613870:CDS | 15.0% |
| !!! | TTTTATTCTATCTACTTTTG+GGG | + | chr4_2:62743392-62743411 | None:intergenic | 20.0% |
| !! | GAAAAAGATGAAGAAAATAA+AGG | + | chr4_2:62743775-62743794 | None:intergenic | 20.0% |
| !! | ATATTCAAAGAGGTAAATTA+AGG | + | chr4_2:62744078-62744097 | None:intergenic | 20.0% |
| ! | AAATAGTAAAGTAGCTTAGT+TGG | + | chr4_2:62743593-62743612 | None:intergenic | 25.0% |
| ! | AAGATGAAGAAAATAAAGGA+GGG | + | chr4_2:62743771-62743790 | None:intergenic | 25.0% |
| ! | AAAGATGAAGAAAATAAAGG+AGG | + | chr4_2:62743772-62743791 | None:intergenic | 25.0% |
| !! | TTATTTCCTTCTCTTTTTCT+AGG | - | chr4_2:62743833-62743852 | Msa0613870:five_prime_UTR | 25.0% |
| ! | TGTCAAGACAATAATGTAAA+AGG | + | chr4_2:62743929-62743948 | None:intergenic | 25.0% |
| !! | TCATAAAAGCATATTCAAAG+AGG | + | chr4_2:62744088-62744107 | None:intergenic | 25.0% |
| GTTATAGTACGGATTTATTC+AGG | - | chr4_2:62743415-62743434 | Msa0613870:CDS | 30.0% | |
| !! | TTTATTCAGGTTGTAGGATT+TGG | - | chr4_2:62743428-62743447 | Msa0613870:CDS | 30.0% |
| !! | TTATTCAGGTTGTAGGATTT+GGG | - | chr4_2:62743429-62743448 | Msa0613870:CDS | 30.0% |
| GTTAAATACACACTTCAAGT+AGG | + | chr4_2:62743497-62743516 | None:intergenic | 30.0% | |
| GAAAATAAGATATACCGACA+CGG | + | chr4_2:62743550-62743569 | None:intergenic | 30.0% | |
| ! | TTCCATTTTCCTTTTCCATT+CGG | - | chr4_2:62743642-62743661 | Msa0613870:intron | 30.0% |
| ! | AATGCCTTTATCATTTTGCA+TGG | - | chr4_2:62743723-62743742 | Msa0613870:intron | 30.0% |
| CATACCATGCAAAATGATAA+AGG | + | chr4_2:62743730-62743749 | None:intergenic | 30.0% | |
| !!! | TTTGTGATTACTGTTTTGAC+AGG | - | chr4_2:62743976-62743995 | Msa0613870:intron | 30.0% |
| CTAAGGATTTGATCTCATAT+TGG | - | chr4_2:62744042-62744061 | Msa0613870:five_prime_UTR | 30.0% | |
| !! | TACGGATTTATTCAGGTTGT+AGG | - | chr4_2:62743422-62743441 | Msa0613870:CDS | 35.0% |
| !! | TATTCAGGTTGTAGGATTTG+GGG | - | chr4_2:62743430-62743449 | Msa0613870:CDS | 35.0% |
| ! | GGATGAGAAGCATAAAAAAC+AGG | - | chr4_2:62743451-62743470 | Msa0613870:CDS | 35.0% |
| TGTATTTAACATGCGAACGA+GGG | - | chr4_2:62743507-62743526 | Msa0613870:intron | 35.0% | |
| AGTAAAGTAGCTTAGTTGGT+AGG | + | chr4_2:62743589-62743608 | None:intergenic | 35.0% | |
| !! | GAATTTGGGTTGGTAGTAAA+TGG | - | chr4_2:62743670-62743689 | Msa0613870:intron | 35.0% |
| ! | GGTAGTAAATGGATTCTTCA+TGG | - | chr4_2:62743681-62743700 | Msa0613870:intron | 35.0% |
| TTCTTCATGGTTTCTCAAAC+TGG | - | chr4_2:62743694-62743713 | Msa0613870:intron | 35.0% | |
| GTCAGTTTCAATTGCTTGTA+CGG | + | chr4_2:62744009-62744028 | None:intergenic | 35.0% | |
| TGACTCATATGCAGAAACTA+AGG | - | chr4_2:62744025-62744044 | Msa0613870:intron | 35.0% | |
| ! | CTTTTATGAGCCTTCTTCTA+CGG | - | chr4_2:62744099-62744118 | Msa0613870:five_prime_UTR | 35.0% |
| ACAGGAAAATTCACAACGAG+AGG | - | chr4_2:62743469-62743488 | Msa0613870:CDS | 40.0% | |
| CAGGAAAATTCACAACGAGA+GGG | - | chr4_2:62743470-62743489 | Msa0613870:CDS | 40.0% | |
| GTGTATTTAACATGCGAACG+AGG | - | chr4_2:62743506-62743525 | Msa0613870:intron | 40.0% | |
| ! | AATGACATTTTGCTCCGTGT+CGG | - | chr4_2:62743533-62743552 | Msa0613870:intron | 40.0% |
| !! | TTAGTTGGTAGGTTGCAAGT+GGG | + | chr4_2:62743578-62743597 | None:intergenic | 40.0% |
| CTCCGAATGGAAAAGGAAAA+TGG | + | chr4_2:62743647-62743666 | None:intergenic | 40.0% | |
| ATTCAAGCTCCGAATGGAAA+AGG | + | chr4_2:62743654-62743673 | None:intergenic | 40.0% | |
| TTCCATTCGGAGCTTGAATT+TGG | - | chr4_2:62743655-62743674 | Msa0613870:intron | 40.0% | |
| TCCATTCGGAGCTTGAATTT+GGG | - | chr4_2:62743656-62743675 | Msa0613870:intron | 40.0% | |
| AAGAGGCCTAGAAAAAGAGA+AGG | + | chr4_2:62743842-62743861 | None:intergenic | 40.0% | |
| TCCCATGTAAGTTCTTGATC+TGG | - | chr4_2:62743876-62743895 | Msa0613870:five_prime_UTR | 40.0% | |
| GCCAGATCAAGAACTTACAT+GGG | + | chr4_2:62743880-62743899 | None:intergenic | 40.0% | |
| AGCCAGATCAAGAACTTACA+TGG | + | chr4_2:62743881-62743900 | None:intergenic | 40.0% | |
| AAGTTCTTGATCTGGCTGTT+TGG | - | chr4_2:62743884-62743903 | Msa0613870:five_prime_UTR | 40.0% | |
| GACACGGAGCAAAATGTCAT+TGG | + | chr4_2:62743534-62743553 | None:intergenic | 45.0% | |
| !! | CTTAGTTGGTAGGTTGCAAG+TGG | + | chr4_2:62743579-62743598 | None:intergenic | 45.0% |
| ACCCAAATTCAAGCTCCGAA+TGG | + | chr4_2:62743660-62743679 | None:intergenic | 45.0% | |
| TTCGGAGCTTGAATTTGGGT+TGG | - | chr4_2:62743660-62743679 | Msa0613870:intron | 45.0% | |
| TTCTAGGCCTCTTGTTGCTC+TGG | - | chr4_2:62743849-62743868 | Msa0613870:five_prime_UTR | 50.0% | |
| GGATACACCAGAGCAACAAG+AGG | + | chr4_2:62743859-62743878 | None:intergenic | 50.0% | |
| ! | GTTGGTAGGTTGCAAGTGGG+AGG | + | chr4_2:62743575-62743594 | None:intergenic | 55.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr4_2 | gene | 62743382 | 62744124 | 62743382 | ID=Msa0613870;Name=Msa0613870 |
| chr4_2 | mRNA | 62743382 | 62744124 | 62743382 | ID=Msa0613870-mRNA-1;Parent=Msa0613870;Name=Msa0613870-mRNA-1;_AED=0.48;_eAED=0.48;_QI=257|1|0.75|1|0.66|0.5|4|0|69 |
| chr4_2 | exon | 62743382 | 62743508 | 62743382 | ID=Msa0613870-mRNA-1:exon:17345;Parent=Msa0613870-mRNA-1 |
| chr4_2 | exon | 62743625 | 62743651 | 62743625 | ID=Msa0613870-mRNA-1:exon:17344;Parent=Msa0613870-mRNA-1 |
| chr4_2 | exon | 62743762 | 62743984 | 62743762 | ID=Msa0613870-mRNA-1:exon:17343;Parent=Msa0613870-mRNA-1 |
| chr4_2 | exon | 62744035 | 62744124 | 62744035 | ID=Msa0613870-mRNA-1:exon:17342;Parent=Msa0613870-mRNA-1 |
| chr4_2 | five_prime_UTR | 62744035 | 62744124 | 62744035 | ID=Msa0613870-mRNA-1:five_prime_utr;Parent=Msa0613870-mRNA-1 |
| chr4_2 | five_prime_UTR | 62743818 | 62743984 | 62743818 | ID=Msa0613870-mRNA-1:five_prime_utr;Parent=Msa0613870-mRNA-1 |
| chr4_2 | CDS | 62743762 | 62743817 | 62743762 | ID=Msa0613870-mRNA-1:cds;Parent=Msa0613870-mRNA-1 |
| chr4_2 | CDS | 62743625 | 62743651 | 62743625 | ID=Msa0613870-mRNA-1:cds;Parent=Msa0613870-mRNA-1 |
| chr4_2 | CDS | 62743382 | 62743508 | 62743382 | ID=Msa0613870-mRNA-1:cds;Parent=Msa0613870-mRNA-1 |
| Gene Sequence |
| Protein sequence |
