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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0296230 | XP_013456902.1 | 98.718 | 78 | 1 | 0 | 28 | 105 | 405 | 482 | 1.75e-42 | 157 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0296230 | sp|Q6Z6S1|API5_ORYSJ | 55.128 | 78 | 35 | 0 | 28 | 105 | 387 | 464 | 9.92e-20 | 86.7 |
| Query id | Subject id | identity % | alignment length | mis matches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0296230 | A0A072UPJ9 | 98.718 | 78 | 1 | 0 | 28 | 105 | 405 | 482 | 8.35e-43 | 157 |
| Gene ID | Type | Classification |
|---|
| Gene ID | Type | Classification |
|---|
Co-expression Network
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| Msa0296230 | Msa1000860 | 0.800666 | 1.294681e-48 | -8.615850e-47 |
| Msa0296230 | Msa1171610 | 0.808673 | 2.758494e-50 | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0296230 | MtrunA17_Chr4g0046111 | 98.718 | 78 | 1 | 0 | 28 | 105 | 405 | 482 | 1.61e-46 | 157 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Msa0296230 | AT2G34040.3 | 72.368 | 76 | 21 | 0 | 31 | 106 | 396 | 471 | 4.75e-31 | 115 |
| Msa0296230 | AT2G34040.1 | 72.368 | 76 | 21 | 0 | 31 | 106 | 396 | 471 | 4.75e-31 | 115 |
| Msa0296230 | AT1G29030.1 | 67.089 | 79 | 26 | 0 | 28 | 106 | 393 | 471 | 1.34e-28 | 108 |
| Msa0296230 | AT1G29030.2 | 67.089 | 79 | 26 | 0 | 28 | 106 | 371 | 449 | 1.40e-28 | 108 |
| Msa0296230 | AT3G19515.2 | 38.961 | 77 | 45 | 1 | 28 | 102 | 240 | 316 | 4.27e-12 | 62.4 |
Find 17 sgRNAs with CRISPR-Local
Find 92 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| GGACCTTAAAATTGTATTTA+TGG | 0.116764 | 2_3:-49289987 | Msa0296230:CDS |
| AAATATTATTGATATATTTA+TGG | 0.127838 | 2_3:-49289913 | Msa0296230:three_prime_UTR |
| ATGAGAAGTGTATTAGTAAA+TGG | 0.267292 | 2_3:+49290607 | None:intergenic |
| GATGGTGAAAGCTCTTAATT+TGG | 0.296250 | 2_3:-49290641 | Msa0296230:CDS |
| CATTGTCAAAATATTATTGC+AGG | 0.335597 | 2_3:+49290224 | None:intergenic |
| GGCTGAAAACAACAAATCTA+TGG | 0.365544 | 2_3:-49290414 | Msa0296230:CDS |
| TGCTAAAACTGATGAAGAAA+AGG | 0.453582 | 2_3:-49290387 | Msa0296230:CDS |
| CTGTTTGTTGTTAGCAGCTG+AGG | 0.473094 | 2_3:-49290008 | Msa0296230:CDS |
| CTAACAACAAACAGCAAGAA+AGG | 0.490776 | 2_3:+49290017 | None:intergenic |
| TAGTTTCTTGATTGTAGCCC+GGG | 0.492094 | 2_3:+49290448 | None:intergenic |
| TTAGTTTCTTGATTGTAGCC+CGG | 0.527233 | 2_3:+49290447 | None:intergenic |
| CTCTTATCTCCAATAAAAGA+AGG | 0.529752 | 2_3:+49290046 | None:intergenic |
| CAAGAAACTAACTCAAGGAA+TGG | 0.535136 | 2_3:-49290435 | Msa0296230:CDS |
| AAAACGTTGAGGAGTTCACC+CGG | 0.582162 | 2_3:-49290466 | Msa0296230:CDS |
| ACAATCAAGAAACTAACTCA+AGG | 0.609790 | 2_3:-49290440 | Msa0296230:CDS |
| AAACGTTGAGGAGTTCACCC+GGG | 0.696711 | 2_3:-49290465 | Msa0296230:CDS |
| AGGAAATATGGATACAAACG+AGG | 0.701472 | 2_3:+49290568 | None:intergenic |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | ACTAAATAGATTTTTGAAAA+AGG | + | chr2_3:49290300-49290319 | None:intergenic | 15.0% |
| !! | ATTCAATAATTAAAAGATCA+GGG | + | chr2_3:49290373-49290392 | None:intergenic | 15.0% |
| !! | AATTCAATAATTAAAAGATC+AGG | + | chr2_3:49290374-49290393 | None:intergenic | 15.0% |
| !!! | AAACCATAAATACAATTTTA+AGG | + | chr2_3:49290496-49290515 | None:intergenic | 15.0% |
| !!! | ACTAAATAGATTTTTGAAAA+AGG | + | chr2_3:49290300-49290319 | None:intergenic | 15.0% |
| !! | ATTCAATAATTAAAAGATCA+GGG | + | chr2_3:49290373-49290392 | None:intergenic | 15.0% |
| !! | AATTCAATAATTAAAAGATC+AGG | + | chr2_3:49290374-49290393 | None:intergenic | 15.0% |
| !!! | AAACCATAAATACAATTTTA+AGG | + | chr2_3:49290496-49290515 | None:intergenic | 15.0% |
| !! | TAATTGTTATGTTACATTTC+TGG | - | chr2_3:49289960-49289979 | Msa0296230:exon | 20.0% |
| !!! | TAATATTTTGACAATGACAA+AGG | - | chr2_3:49290260-49290279 | Msa0296230:CDS | 20.0% |
| !! | ATTGAATTGTTCAATTTGTA+TGG | - | chr2_3:49290386-49290405 | Msa0296230:CDS | 20.0% |
| !!! | TTTTGTACGAAATTGATTTA+TGG | - | chr2_3:49290587-49290606 | Msa0296230:CDS | 20.0% |
| !! | TAATTGTTATGTTACATTTC+TGG | - | chr2_3:49289960-49289979 | Msa0296230:exon | 20.0% |
| !!! | TAATATTTTGACAATGACAA+AGG | - | chr2_3:49290260-49290279 | Msa0296230:CDS | 20.0% |
| !! | ATTGAATTGTTCAATTTGTA+TGG | - | chr2_3:49290386-49290405 | Msa0296230:CDS | 20.0% |
| !!! | TTTTGTACGAAATTGATTTA+TGG | - | chr2_3:49290587-49290606 | Msa0296230:CDS | 20.0% |
| !! | ATGAGAAGTGTATTAGTAAA+TGG | + | chr2_3:49289873-49289892 | None:intergenic | 25.0% |
| ! | TTTGTATCCATATTTCCTTT+GGG | - | chr2_3:49289914-49289933 | Msa0296230:three_prime_UTR | 25.0% |
| ! | CATTGTCAAAATATTATTGC+AGG | + | chr2_3:49290256-49290275 | None:intergenic | 25.0% |
| ! | AATAATTAAAAGATCAGGGA+GGG | + | chr2_3:49290369-49290388 | None:intergenic | 25.0% |
| ! | GGACCTTAAAATTGTATTTA+TGG | - | chr2_3:49290490-49290509 | Msa0296230:intron | 25.0% |
| !! | ATGAGAAGTGTATTAGTAAA+TGG | + | chr2_3:49289873-49289892 | None:intergenic | 25.0% |
| ! | TTTGTATCCATATTTCCTTT+GGG | - | chr2_3:49289914-49289933 | Msa0296230:three_prime_UTR | 25.0% |
| ! | CATTGTCAAAATATTATTGC+AGG | + | chr2_3:49290256-49290275 | None:intergenic | 25.0% |
| ! | AATAATTAAAAGATCAGGGA+GGG | + | chr2_3:49290369-49290388 | None:intergenic | 25.0% |
| ! | GGACCTTAAAATTGTATTTA+TGG | - | chr2_3:49290490-49290509 | Msa0296230:intron | 25.0% |
| GTTTGTATCCATATTTCCTT+TGG | - | chr2_3:49289913-49289932 | Msa0296230:three_prime_UTR | 30.0% | |
| ACAATCAAGAAACTAACTCA+AGG | - | chr2_3:49290037-49290056 | Msa0296230:CDS | 30.0% | |
| TGCTAAAACTGATGAAGAAA+AGG | - | chr2_3:49290090-49290109 | Msa0296230:intron | 30.0% | |
| ! | AAATTGTGAGTCTTATCTTG+TGG | - | chr2_3:49290116-49290135 | Msa0296230:intron | 30.0% |
| AAAAAACAGAATGCTACAAC+TGG | - | chr2_3:49290222-49290241 | Msa0296230:CDS | 30.0% | |
| AAAAACAGAATGCTACAACT+GGG | - | chr2_3:49290223-49290242 | Msa0296230:CDS | 30.0% | |
| AATGAGTTATTGCGTATATG+AGG | - | chr2_3:49290321-49290340 | Msa0296230:intron | 30.0% | |
| ATGAGTTATTGCGTATATGA+GGG | - | chr2_3:49290322-49290341 | Msa0296230:intron | 30.0% | |
| CAATAATTAAAAGATCAGGG+AGG | + | chr2_3:49290370-49290389 | None:intergenic | 30.0% | |
| CTCTTATCTCCAATAAAAGA+AGG | + | chr2_3:49290434-49290453 | None:intergenic | 30.0% | |
| GTTTGTATCCATATTTCCTT+TGG | - | chr2_3:49289913-49289932 | Msa0296230:three_prime_UTR | 30.0% | |
| ACAATCAAGAAACTAACTCA+AGG | - | chr2_3:49290037-49290056 | Msa0296230:CDS | 30.0% | |
| TGCTAAAACTGATGAAGAAA+AGG | - | chr2_3:49290090-49290109 | Msa0296230:intron | 30.0% | |
| ! | AAATTGTGAGTCTTATCTTG+TGG | - | chr2_3:49290116-49290135 | Msa0296230:intron | 30.0% |
| AAAAAACAGAATGCTACAAC+TGG | - | chr2_3:49290222-49290241 | Msa0296230:CDS | 30.0% | |
| AAAAACAGAATGCTACAACT+GGG | - | chr2_3:49290223-49290242 | Msa0296230:CDS | 30.0% | |
| AATGAGTTATTGCGTATATG+AGG | - | chr2_3:49290321-49290340 | Msa0296230:intron | 30.0% | |
| ATGAGTTATTGCGTATATGA+GGG | - | chr2_3:49290322-49290341 | Msa0296230:intron | 30.0% | |
| CAATAATTAAAAGATCAGGG+AGG | + | chr2_3:49290370-49290389 | None:intergenic | 30.0% | |
| CTCTTATCTCCAATAAAAGA+AGG | + | chr2_3:49290434-49290453 | None:intergenic | 30.0% | |
| AGGAAATATGGATACAAACG+AGG | + | chr2_3:49289912-49289931 | None:intergenic | 35.0% | |
| !! | ATATTTCCTTTGGGATTTGC+CGG | - | chr2_3:49289923-49289942 | Msa0296230:three_prime_UTR | 35.0% |
| AATTAACAACCCAAAACGAC+CGG | + | chr2_3:49289945-49289964 | None:intergenic | 35.0% | |
| TTAGTTTCTTGATTGTAGCC+CGG | + | chr2_3:49290033-49290052 | None:intergenic | 35.0% | |
| CAAGAAACTAACTCAAGGAA+TGG | - | chr2_3:49290042-49290061 | Msa0296230:CDS | 35.0% | |
| GGCTGAAAACAACAAATCTA+TGG | - | chr2_3:49290063-49290082 | Msa0296230:CDS | 35.0% | |
| !!! | GCAAAAGCACCTTCTTTTAT+TGG | - | chr2_3:49290422-49290441 | Msa0296230:CDS | 35.0% |
| CTAACAACAAACAGCAAGAA+AGG | + | chr2_3:49290463-49290482 | None:intergenic | 35.0% | |
| AGGAAATATGGATACAAACG+AGG | + | chr2_3:49289912-49289931 | None:intergenic | 35.0% | |
| !! | ATATTTCCTTTGGGATTTGC+CGG | - | chr2_3:49289923-49289942 | Msa0296230:three_prime_UTR | 35.0% |
| AATTAACAACCCAAAACGAC+CGG | + | chr2_3:49289945-49289964 | None:intergenic | 35.0% | |
| TTAGTTTCTTGATTGTAGCC+CGG | + | chr2_3:49290033-49290052 | None:intergenic | 35.0% | |
| CAAGAAACTAACTCAAGGAA+TGG | - | chr2_3:49290042-49290061 | Msa0296230:CDS | 35.0% | |
| GGCTGAAAACAACAAATCTA+TGG | - | chr2_3:49290063-49290082 | Msa0296230:CDS | 35.0% | |
| !!! | GCAAAAGCACCTTCTTTTAT+TGG | - | chr2_3:49290422-49290441 | Msa0296230:CDS | 35.0% |
| CTAACAACAAACAGCAAGAA+AGG | + | chr2_3:49290463-49290482 | None:intergenic | 35.0% | |
| GGCAAATCCCAAAGGAAATA+TGG | + | chr2_3:49289924-49289943 | None:intergenic | 40.0% | |
| CTCCAGATTGAAAAACGTTG+AGG | - | chr2_3:49290000-49290019 | Msa0296230:CDS | 40.0% | |
| !! | CTCCTCAACGTTTTTCAATC+TGG | + | chr2_3:49290005-49290024 | None:intergenic | 40.0% |
| TAGTTTCTTGATTGTAGCCC+GGG | + | chr2_3:49290032-49290051 | None:intergenic | 40.0% | |
| GGCAAATCCCAAAGGAAATA+TGG | + | chr2_3:49289924-49289943 | None:intergenic | 40.0% | |
| CTCCAGATTGAAAAACGTTG+AGG | - | chr2_3:49290000-49290019 | Msa0296230:CDS | 40.0% | |
| !! | CTCCTCAACGTTTTTCAATC+TGG | + | chr2_3:49290005-49290024 | None:intergenic | 40.0% |
| TAGTTTCTTGATTGTAGCCC+GGG | + | chr2_3:49290032-49290051 | None:intergenic | 40.0% | |
| AAAACGTTGAGGAGTTCACC+CGG | - | chr2_3:49290011-49290030 | Msa0296230:CDS | 45.0% | |
| !! | CTGTTTGTTGTTAGCAGCTG+AGG | - | chr2_3:49290469-49290488 | Msa0296230:CDS | 45.0% |
| AAAACGTTGAGGAGTTCACC+CGG | - | chr2_3:49290011-49290030 | Msa0296230:CDS | 45.0% | |
| !! | CTGTTTGTTGTTAGCAGCTG+AGG | - | chr2_3:49290469-49290488 | Msa0296230:CDS | 45.0% |
| !!! | TTTAATCTTTTATTTTATTA+TGG | - | chr2_3:49290159-49290178 | Msa0296230:intron | 5.0% |
| !!! | TTAATCTTTTATTTTATTAT+GGG | - | chr2_3:49290160-49290179 | Msa0296230:intron | 5.0% |
| !! | AAATATTATTGATATATTTA+TGG | - | chr2_3:49290564-49290583 | Msa0296230:intron | 5.0% |
| !!! | TTTAATCTTTTATTTTATTA+TGG | - | chr2_3:49290159-49290178 | Msa0296230:intron | 5.0% |
| !!! | TTAATCTTTTATTTTATTAT+GGG | - | chr2_3:49290160-49290179 | Msa0296230:intron | 5.0% |
| !! | AAATATTATTGATATATTTA+TGG | - | chr2_3:49290564-49290583 | Msa0296230:intron | 5.0% |
| AAACGACCGGCAAATCCCAA+AGG | + | chr2_3:49289932-49289951 | None:intergenic | 50.0% | |
| ! | TTGGGATTTGCCGGTCGTTT+TGG | - | chr2_3:49289932-49289951 | Msa0296230:three_prime_UTR | 50.0% |
| !! | TGGGATTTGCCGGTCGTTTT+GGG | - | chr2_3:49289933-49289952 | Msa0296230:three_prime_UTR | 50.0% |
| AAACGTTGAGGAGTTCACCC+GGG | - | chr2_3:49290012-49290031 | Msa0296230:CDS | 50.0% | |
| !!! | GAAGGTGCTTTTGCGTGCAA+TGG | + | chr2_3:49290416-49290435 | None:intergenic | 50.0% |
| AAACGACCGGCAAATCCCAA+AGG | + | chr2_3:49289932-49289951 | None:intergenic | 50.0% | |
| ! | TTGGGATTTGCCGGTCGTTT+TGG | - | chr2_3:49289932-49289951 | Msa0296230:three_prime_UTR | 50.0% |
| !! | TGGGATTTGCCGGTCGTTTT+GGG | - | chr2_3:49289933-49289952 | Msa0296230:three_prime_UTR | 50.0% |
| AAACGTTGAGGAGTTCACCC+GGG | - | chr2_3:49290012-49290031 | Msa0296230:CDS | 50.0% | |
| !!! | GAAGGTGCTTTTGCGTGCAA+TGG | + | chr2_3:49290416-49290435 | None:intergenic | 50.0% |
| ! | GTGCTTTTGCGTGCAATGGC+TGG | + | chr2_3:49290412-49290431 | None:intergenic | 55.0% |
| ! | GTGCTTTTGCGTGCAATGGC+TGG | + | chr2_3:49290412-49290431 | None:intergenic | 55.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr2_3 | gene | 49289837 | 49290662 | 49289837 | ID=Msa0296230;Name=Msa0296230 |
| chr2_3 | mRNA | 49289837 | 49290662 | 49289837 | ID=Msa0296230-mRNA-1;Parent=Msa0296230;Name=Msa0296230-mRNA-1;_AED=0.38;_eAED=0.38;_QI=0|0.66|0.75|1|1|1|4|124|128 |
| chr2_3 | exon | 49289837 | 49290086 | 49289837 | ID=Msa0296230-mRNA-1:exon:15543;Parent=Msa0296230-mRNA-1 |
| chr2_3 | exon | 49290218 | 49290283 | 49290218 | ID=Msa0296230-mRNA-1:exon:15542;Parent=Msa0296230-mRNA-1 |
| chr2_3 | exon | 49290379 | 49290493 | 49290379 | ID=Msa0296230-mRNA-1:exon:15541;Parent=Msa0296230-mRNA-1 |
| chr2_3 | exon | 49290583 | 49290662 | 49290583 | ID=Msa0296230-mRNA-1:exon:15540;Parent=Msa0296230-mRNA-1 |
| chr2_3 | CDS | 49290583 | 49290662 | 49290583 | ID=Msa0296230-mRNA-1:cds;Parent=Msa0296230-mRNA-1 |
| chr2_3 | CDS | 49290379 | 49290493 | 49290379 | ID=Msa0296230-mRNA-1:cds;Parent=Msa0296230-mRNA-1 |
| chr2_3 | CDS | 49290218 | 49290283 | 49290218 | ID=Msa0296230-mRNA-1:cds;Parent=Msa0296230-mRNA-1 |
| chr2_3 | CDS | 49289961 | 49290086 | 49289961 | ID=Msa0296230-mRNA-1:cds;Parent=Msa0296230-mRNA-1 |
| chr2_3 | three_prime_UTR | 49289837 | 49289960 | 49289837 | ID=Msa0296230-mRNA-1:three_prime_utr;Parent=Msa0296230-mRNA-1 |
| Gene Sequence |
| Protein sequence |
