Alfalfa Gene Editing Database
Alfalfa Gene Editing Database
Nr:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene062744.t1 | XP_003589266.1 | 95.6 | 183 | 8 | 0 | 3 | 185 | 30 | 212 | 1.70E-98 | 368.6 |
Swissprot:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene062744.t1 | Q8L3W1 | 36.4 | 118 | 63 | 3 | 3 | 112 | 21 | 134 | 3.5e-12 | 73.2 |
Trembl:
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene062744.t1 | G7I4K0 | 95.6 | 183 | 8 | 0 | 3 | 185 | 30 | 212 | 1.2e-98 | 368.6 |
TFs/TRs:
| Gene ID | Type | Classification |
|---|---|---|
| MS.gene062744.t1 | TF | B3 |
Protein Kinases:
| Gene ID | Type | Classification |
|---|
Network:
Co-expression Network:
| Gene1 | Gene2 | correlation coefficient | p_value | FDR |
|---|---|---|---|---|
| MS.gene049142 | MS.gene062744 | 0.806091 | 9.73E-50 | -1.69E-46 |
| MS.gene052609 | MS.gene062744 | 0.825695 | 4.07E-54 | -1.69E-46 |
| MS.gene053079 | MS.gene062744 | 0.809039 | 2.30E-50 | -1.69E-46 |
| MS.gene058010 | MS.gene062744 | 0.81516 | 1.07E-51 | -1.69E-46 |
| MS.gene058919 | MS.gene062744 | 0.804249 | 2.36E-49 | -1.69E-46 |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene062744.t1 | MTR_1g021270 | 95.628 | 183 | 8 | 0 | 3 | 185 | 30 | 212 | 6.67e-128 | 372 |
| MS.gene062744.t1 | MTR_4g068320 | 40.741 | 81 | 48 | 0 | 3 | 83 | 21 | 101 | 2.98e-16 | 75.9 |
| MS.gene062744.t1 | MTR_1g021320 | 40.698 | 86 | 50 | 1 | 4 | 88 | 198 | 283 | 3.04e-16 | 76.3 |
| MS.gene062744.t1 | MTR_1g021320 | 36.937 | 111 | 59 | 3 | 4 | 103 | 41 | 151 | 5.73e-16 | 75.5 |
| MS.gene062744.t1 | MTR_1g021290 | 34.532 | 139 | 71 | 4 | 4 | 130 | 171 | 301 | 3.77e-16 | 75.1 |
| MS.gene062744.t1 | MTR_1g021290 | 34.884 | 86 | 55 | 1 | 4 | 88 | 43 | 128 | 1.89e-11 | 62.0 |
| MS.gene062744.t1 | MTR_1g021440 | 28.758 | 153 | 102 | 2 | 4 | 149 | 38 | 190 | 7.49e-16 | 73.9 |
| MS.gene062744.t1 | MTR_1g021440 | 28.758 | 153 | 102 | 2 | 4 | 149 | 38 | 190 | 8.48e-16 | 73.9 |
| MS.gene062744.t1 | MTR_1g021440 | 28.758 | 153 | 102 | 2 | 4 | 149 | 38 | 190 | 1.68e-15 | 73.6 |
| MS.gene062744.t1 | MTR_1g021440 | 28.758 | 153 | 102 | 2 | 4 | 149 | 38 | 190 | 1.74e-15 | 73.6 |
| MS.gene062744.t1 | MTR_7g050710 | 34.615 | 104 | 65 | 1 | 3 | 106 | 28 | 128 | 1.95e-15 | 73.2 |
| MS.gene062744.t1 | MTR_1g021350 | 38.000 | 100 | 60 | 2 | 4 | 101 | 37 | 136 | 6.62e-15 | 71.6 |
| MS.gene062744.t1 | MTR_1g021410 | 29.870 | 154 | 100 | 5 | 4 | 153 | 38 | 187 | 9.72e-15 | 71.2 |
| MS.gene062744.t1 | MTR_1g021435 | 28.169 | 142 | 95 | 2 | 4 | 138 | 38 | 179 | 1.27e-14 | 71.2 |
| MS.gene062744.t1 | MTR_1g035460 | 30.894 | 123 | 81 | 1 | 4 | 126 | 2 | 120 | 3.20e-14 | 70.1 |
| MS.gene062744.t1 | MTR_1g021360 | 38.372 | 86 | 52 | 1 | 4 | 88 | 41 | 126 | 4.17e-14 | 69.7 |
| MS.gene062744.t1 | MTR_1g021360 | 37.209 | 86 | 53 | 1 | 4 | 88 | 198 | 283 | 6.85e-14 | 69.3 |
| MS.gene062744.t1 | MTR_1g021400 | 31.387 | 137 | 87 | 2 | 4 | 133 | 46 | 182 | 5.14e-14 | 69.3 |
| MS.gene062744.t1 | MTR_1g021380 | 39.535 | 86 | 51 | 1 | 4 | 88 | 37 | 122 | 3.06e-13 | 67.0 |
| MS.gene062744.t1 | MTR_1g021330 | 38.372 | 86 | 52 | 1 | 4 | 88 | 42 | 127 | 7.26e-13 | 66.2 |
| MS.gene062744.t1 | MTR_1g034240 | 25.954 | 131 | 97 | 0 | 3 | 133 | 22 | 152 | 8.46e-13 | 65.9 |
| MS.gene062744.t1 | MTR_8g103940 | 28.916 | 83 | 59 | 0 | 3 | 85 | 54 | 136 | 5.17e-12 | 63.9 |
| MS.gene062744.t1 | MTR_7g050640 | 32.941 | 85 | 57 | 0 | 4 | 88 | 29 | 113 | 5.78e-12 | 60.1 |
| MS.gene062744.t1 | MTR_7g050590 | 32.941 | 85 | 57 | 0 | 4 | 88 | 2 | 86 | 1.07e-11 | 62.4 |
| MS.gene062744.t1 | MTR_7g050580 | 35.000 | 80 | 52 | 0 | 4 | 83 | 29 | 108 | 1.81e-11 | 62.0 |
| MS.gene062744.t1 | MTR_7g050720 | 26.380 | 163 | 114 | 3 | 4 | 166 | 26 | 182 | 2.33e-11 | 61.6 |
| MS.gene062744.t1 | MTR_1g034210 | 36.000 | 75 | 48 | 0 | 3 | 77 | 22 | 96 | 2.85e-11 | 61.2 |
| MS.gene062744.t1 | MTR_1g034210 | 36.000 | 75 | 48 | 0 | 3 | 77 | 22 | 96 | 3.45e-11 | 61.2 |
| MS.gene062744.t1 | MTR_3g061310 | 27.338 | 139 | 87 | 4 | 1 | 137 | 21 | 147 | 4.73e-11 | 60.5 |
| Query id | Subject id | identity % | alignment length | mismatches | gap openings | q. start | q. end | s. start | s. end | e-value | bit score |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MS.gene062744.t1 | AT3G18990 | 36.441 | 118 | 63 | 3 | 3 | 112 | 21 | 134 | 7.01e-17 | 77.4 |
| MS.gene062744.t1 | AT3G18990 | 36.441 | 118 | 63 | 3 | 3 | 112 | 21 | 134 | 1.29e-16 | 76.6 |
| MS.gene062744.t1 | AT5G66980 | 24.828 | 145 | 102 | 3 | 4 | 142 | 25 | 168 | 8.60e-13 | 65.9 |
| MS.gene062744.t1 | AT4G01580 | 32.530 | 83 | 56 | 0 | 1 | 83 | 43 | 125 | 1.37e-11 | 60.8 |
| MS.gene062744.t1 | AT4G33280 | 35.238 | 105 | 60 | 3 | 4 | 100 | 39 | 143 | 2.70e-11 | 61.6 |
| MS.gene062744.t1 | AT3G06220 | 25.581 | 129 | 87 | 2 | 4 | 131 | 25 | 145 | 3.00e-11 | 59.7 |
| MS.gene062744.t1 | AT4G33280 | 35.238 | 105 | 60 | 3 | 4 | 100 | 39 | 143 | 3.59e-11 | 60.8 |
Find 37 sgRNAs with CRISPR-Local
Find 69 sgRNAs with CRISPR-GE
CRISPR-Local
| sgRNA_sequence | on_target_score | Position | Region |
|---|---|---|---|
| TGCTGATGTGATTTCTTCTT+TGG | 0.171504 | 1.4:-3013598 | MS.gene062744:CDS |
| CATTTCACCGTGCAAGTATT+TGG | 0.220691 | 1.4:-3013711 | MS.gene062744:CDS |
| TGCGGATTAGTTTCATTAAC+TGG | 0.303142 | 1.4:-3013873 | MS.gene062744:CDS |
| TGGTCTAACCAACTCATAAT+TGG | 0.316491 | 1.4:+3013488 | None:intergenic |
| ACTAGCTGAACATTCTTTGC+AGG | 0.330880 | 1.4:+3013437 | None:intergenic |
| TTTACAATATGGCGACCTTT+TGG | 0.367843 | 1.4:-3013757 | MS.gene062744:CDS |
| GGAGATCATCATTTACAATA+TGG | 0.369169 | 1.4:-3013768 | MS.gene062744:CDS |
| GTTTCTCTGATCATACTGAT+TGG | 0.381923 | 1.4:+3013468 | None:intergenic |
| GAGCCTGAGTTGGCTATTGC+TGG | 0.383202 | 1.4:-3013522 | MS.gene062744:CDS |
| ATTTCTTCTTTGGATGTTGT+TGG | 0.389381 | 1.4:-3013588 | MS.gene062744:CDS |
| TTAAACTTCAATAATATTGA+AGG | 0.413589 | 1.4:-3013633 | MS.gene062744:CDS |
| ATGCCGTGCCCTCCATTTGA+TGG | 0.415676 | 1.4:+3013895 | None:intergenic |
| TTACTATTTCCTGTTTGAAA+AGG | 0.440868 | 1.4:+3013402 | None:intergenic |
| TCATGGATGGTCAACATTTG+TGG | 0.468855 | 1.4:-3013790 | MS.gene062744:CDS |
| CTGGTCCTAGTGGAAATACT+TGG | 0.471402 | 1.4:-3013854 | MS.gene062744:CDS |
| ATTTGATGGACAAAACCATC+TGG | 0.494945 | 1.4:+3013909 | None:intergenic |
| AATCATCTGTTCTTCCATCA+TGG | 0.499739 | 1.4:-3013807 | MS.gene062744:CDS |
| GCAAGTTCGATTAGTTGAGC+AGG | 0.500057 | 1.4:-3013832 | MS.gene062744:CDS |
| GTGCGACGCCATTGAGAACC+AGG | 0.505570 | 1.4:-3013544 | MS.gene062744:CDS |
| GGAAATAGTAATGAAGTTGA+AGG | 0.516580 | 1.4:-3013390 | MS.gene062744:intron |
| CATGGATGGTCAACATTTGT+GGG | 0.520091 | 1.4:-3013789 | MS.gene062744:CDS |
| CTCAGGCTCCTGGTTCTCAA+TGG | 0.520233 | 1.4:+3013536 | None:intergenic |
| CAATAGCCAACTCAGGCTCC+TGG | 0.530813 | 1.4:+3013526 | None:intergenic |
| AAATCTATCCAATTATGAGT+TGG | 0.532358 | 1.4:-3013496 | MS.gene062744:CDS |
| CAAATGGAGGGCACGGCATG+CGG | 0.548985 | 1.4:-3013891 | MS.gene062744:CDS |
| CAAATGTTGACCATCCATGA+TGG | 0.553915 | 1.4:+3013793 | None:intergenic |
| CCTCGTATCTGAAAACCAAA+AGG | 0.559251 | 1.4:+3013742 | None:intergenic |
| TTCCTGTTTGAAAAGGAACA+TGG | 0.559808 | 1.4:+3013409 | None:intergenic |
| ATCTGTTCTTCCATCATGGA+TGG | 0.561421 | 1.4:-3013803 | MS.gene062744:CDS |
| TGTCCATCAAATGGAGGGCA+CGG | 0.563910 | 1.4:-3013898 | MS.gene062744:CDS |
| TTACCAGCAATAGCCAACTC+AGG | 0.564889 | 1.4:+3013519 | None:intergenic |
| GTTTCATTAACTGGTCCTAG+TGG | 0.577634 | 1.4:-3013864 | MS.gene062744:CDS |
| TGAGAACCAGGAGCCTGAGT+TGG | 0.586623 | 1.4:-3013532 | MS.gene062744:CDS |
| GAGATGTTCCGAAGAAAATG+AGG | 0.590900 | 1.4:-3013566 | MS.gene062744:CDS |
| ACTTGCCAAGTATTTCCACT+AGG | 0.637449 | 1.4:+3013849 | None:intergenic |
| ATTCTCACCAAATACTTGCA+CGG | 0.664539 | 1.4:+3013704 | None:intergenic |
| TTAATGCAGAGAGTTCCAGA+TGG | 0.692519 | 1.4:-3013924 | MS.gene062744:CDS |
CRISPR-GE
| badsite warning | sgRNA_sequence | Strand | Position | Region | GC_content |
|---|---|---|---|---|---|
| !!! | TTGATTATTTTAACAAAATA+TGG | + | chr1.4:3013803-3013822 | None:intergenic | 10.0% |
| !! | GATAAATTATAAATGACAAA+AGG | + | chr1.4:3013868-3013887 | None:intergenic | 15.0% |
| !! | TTAAACTTCAATAATATTGA+AGG | - | chr1.4:3013238-3013257 | MS.gene062744:intron | 15.0% |
| !! | AAGATAAAACAGCATTATTT+GGG | + | chr1.4:3013892-3013911 | None:intergenic | 20.0% |
| !! | TTAAATAAAATGATAAGCTC+TGG | + | chr1.4:3013628-3013647 | None:intergenic | 20.0% |
| !! | TTTAACAAAATATGGAAAAG+AGG | + | chr1.4:3013795-3013814 | None:intergenic | 20.0% |
| ! | AAATCTATCCAATTATGAGT+TGG | - | chr1.4:3013375-3013394 | MS.gene062744:intron | 25.0% |
| ! | GAAGATAAAACAGCATTATT+TGG | + | chr1.4:3013893-3013912 | None:intergenic | 25.0% |
| ! | TTACTATTTCCTGTTTGAAA+AGG | + | chr1.4:3013472-3013491 | None:intergenic | 25.0% |
| AAAAGAGGACGTAAATGATT+GGG | + | chr1.4:3013780-3013799 | None:intergenic | 30.0% | |
| AGCAAATTCGATTTCATTCT+GGG | - | chr1.4:3013507-3013526 | MS.gene062744:CDS | 30.0% | |
| ATTTCTTCTTTGGATGTTGT+TGG | - | chr1.4:3013283-3013302 | MS.gene062744:intron | 30.0% | |
| GGAAATAGTAATGAAGTTGA+AGG | - | chr1.4:3013481-3013500 | MS.gene062744:CDS | 30.0% | |
| GGAGATCATCATTTACAATA+TGG | - | chr1.4:3013103-3013122 | MS.gene062744:intron | 30.0% | |
| TAGCAAATTCGATTTCATTC+TGG | - | chr1.4:3013506-3013525 | MS.gene062744:CDS | 30.0% | |
| ! | AGACAAGTATCAGTTTTCTA+GGG | + | chr1.4:3013567-3013586 | None:intergenic | 30.0% |
| ! | TAAGCTCTGGCATAAATATA+AGG | + | chr1.4:3013615-3013634 | None:intergenic | 30.0% |
| ! | TAGACAAGTATCAGTTTTCT+AGG | + | chr1.4:3013568-3013587 | None:intergenic | 30.0% |
| AATCATCTGTTCTTCCATCA+TGG | - | chr1.4:3013064-3013083 | MS.gene062744:intron | 35.0% | |
| ATCAAAACCTTCAATGTCAG+TGG | - | chr1.4:3013818-3013837 | MS.gene062744:CDS | 35.0% | |
| ATCTTCTTGAGAAACTGATC+TGG | - | chr1.4:3013907-3013926 | MS.gene062744:CDS | 35.0% | |
| ATTCTCACCAAATACTTGCA+CGG | + | chr1.4:3013170-3013189 | None:intergenic | 35.0% | |
| GAAAAGAGGACGTAAATGAT+TGG | + | chr1.4:3013781-3013800 | None:intergenic | 35.0% | |
| GTTTCTCTGATCATACTGAT+TGG | + | chr1.4:3013406-3013425 | None:intergenic | 35.0% | |
| TGCTGATGTGATTTCTTCTT+TGG | - | chr1.4:3013273-3013292 | MS.gene062744:intron | 35.0% | |
| TGGTCTAACCAACTCATAAT+TGG | + | chr1.4:3013386-3013405 | None:intergenic | 35.0% | |
| TTCCTGTTTGAAAAGGAACA+TGG | + | chr1.4:3013465-3013484 | None:intergenic | 35.0% | |
| ! | ATTTGATGGACAAAACCATC+TGG | + | chr1.4:3012965-3012984 | None:intergenic | 35.0% |
| ! | TTTACAATATGGCGACCTTT+TGG | - | chr1.4:3013114-3013133 | MS.gene062744:intron | 35.0% |
| !! | TGCGGATTAGTTTCATTAAC+TGG | - | chr1.4:3012998-3013017 | MS.gene062744:intron | 35.0% |
| !!! | AGATGGTTTTGTCCATCAAA+TGG | - | chr1.4:3012964-3012983 | MS.gene062744:intron | 35.0% |
| !!! | CTTTTGGTTTTCAGATACGA+GGG | - | chr1.4:3013130-3013149 | MS.gene062744:intron | 35.0% |
| AATCCTGTATAGAAGTGGGA+AGG | - | chr1.4:3013685-3013704 | MS.gene062744:CDS | 40.0% | |
| ACTAGCTGAACATTCTTTGC+AGG | + | chr1.4:3013437-3013456 | None:intergenic | 40.0% | |
| ACTTGCCAAGTATTTCCACT+AGG | + | chr1.4:3013025-3013044 | None:intergenic | 40.0% | |
| ATACGAACCACTGACATTGA+AGG | + | chr1.4:3013828-3013847 | None:intergenic | 40.0% | |
| ATCTGTTCTTCCATCATGGA+TGG | - | chr1.4:3013068-3013087 | MS.gene062744:intron | 40.0% | |
| CAAATGTTGACCATCCATGA+TGG | + | chr1.4:3013081-3013100 | None:intergenic | 40.0% | |
| CAGCAATCCTGTATAGAAGT+GGG | - | chr1.4:3013681-3013700 | MS.gene062744:CDS | 40.0% | |
| CATGGATGGTCAACATTTGT+GGG | - | chr1.4:3013082-3013101 | MS.gene062744:intron | 40.0% | |
| CATTTCACCGTGCAAGTATT+TGG | - | chr1.4:3013160-3013179 | MS.gene062744:intron | 40.0% | |
| CCTCGTATCTGAAAACCAAA+AGG | + | chr1.4:3013132-3013151 | None:intergenic | 40.0% | |
| CTTGAGAAACTGATCTGGTT+GGG | - | chr1.4:3013912-3013931 | MS.gene062744:CDS | 40.0% | |
| GAGATGTTCCGAAGAAAATG+AGG | - | chr1.4:3013305-3013324 | MS.gene062744:intron | 40.0% | |
| GTTTCATTAACTGGTCCTAG+TGG | - | chr1.4:3013007-3013026 | MS.gene062744:intron | 40.0% | |
| TCATGGATGGTCAACATTTG+TGG | - | chr1.4:3013081-3013100 | MS.gene062744:intron | 40.0% | |
| TCTTGAGAAACTGATCTGGT+TGG | - | chr1.4:3013911-3013930 | MS.gene062744:CDS | 40.0% | |
| TTGAGAAACTGATCTGGTTG+GGG | - | chr1.4:3013913-3013932 | MS.gene062744:CDS | 40.0% | |
| ! | GTCCATGTTCCTTTTCAAAC+AGG | - | chr1.4:3013460-3013479 | MS.gene062744:CDS | 40.0% |
| !! | GGTTTTGTCCATCAAATGGA+GGG | - | chr1.4:3012968-3012987 | MS.gene062744:intron | 40.0% |
| !!! | CCTTTTGGTTTTCAGATACG+AGG | - | chr1.4:3013129-3013148 | MS.gene062744:intron | 40.0% |
| !!! | TGGTTTTGTCCATCAAATGG+AGG | - | chr1.4:3012967-3012986 | MS.gene062744:intron | 40.0% |
| CTGGTCCTAGTGGAAATACT+TGG | - | chr1.4:3013017-3013036 | MS.gene062744:intron | 45.0% | |
| CTTCCTTCCCACTTCTATAC+AGG | + | chr1.4:3013691-3013710 | None:intergenic | 45.0% | |
| GATGACCACGATATTCTCAG+CGG | - | chr1.4:3013710-3013729 | MS.gene062744:CDS | 45.0% | |
| GCAGCAATCCTGTATAGAAG+TGG | - | chr1.4:3013680-3013699 | MS.gene062744:CDS | 45.0% | |
| TGTCAGTGGTTCGTATACTC+TGG | - | chr1.4:3013832-3013851 | MS.gene062744:CDS | 45.0% | |
| TTACCAGCAATAGCCAACTC+AGG | + | chr1.4:3013355-3013374 | None:intergenic | 45.0% | |
| ! | GCAAGTTCGATTAGTTGAGC+AGG | - | chr1.4:3013039-3013058 | MS.gene062744:intron | 45.0% |
| AAGCTCCGCTGAGAATATCG+TGG | + | chr1.4:3013718-3013737 | None:intergenic | 50.0% | |
| TGTCCATCAAATGGAGGGCA+CGG | - | chr1.4:3012973-3012992 | MS.gene062744:intron | 50.0% | |
| ! | GCGTCGCACCTCATTTTCTT+CGG | + | chr1.4:3013316-3013335 | None:intergenic | 50.0% |
| ATGCCGTGCCCTCCATTTGA+TGG | + | chr1.4:3012979-3012998 | None:intergenic | 55.0% | |
| CAATAGCCAACTCAGGCTCC+TGG | + | chr1.4:3013348-3013367 | None:intergenic | 55.0% | |
| TGAGAACCAGGAGCCTGAGT+TGG | - | chr1.4:3013339-3013358 | MS.gene062744:intron | 55.0% | |
| ! | CTCAGGCTCCTGGTTCTCAA+TGG | + | chr1.4:3013338-3013357 | None:intergenic | 55.0% |
| ! | GAGCCTGAGTTGGCTATTGC+TGG | - | chr1.4:3013349-3013368 | MS.gene062744:intron | 55.0% |
| GTGCGACGCCATTGAGAACC+AGG | - | chr1.4:3013327-3013346 | MS.gene062744:intron | 60.0% | |
| ! | CAAATGGAGGGCACGGCATG+CGG | - | chr1.4:3012980-3012999 | MS.gene062744:intron | 60.0% |
| Chromosome | Type | Strat | End | Strand | Name |
|---|---|---|---|---|---|
| chr1.4 | gene | 3012950 | 3013943 | 3012950 | ID=MS.gene062744 |
| chr1.4 | mRNA | 3012950 | 3013943 | 3012950 | ID=MS.gene062744.t1;Parent=MS.gene062744 |
| chr1.4 | exon | 3013391 | 3013943 | 3013391 | ID=MS.gene062744.t1.exon1;Parent=MS.gene062744.t1 |
| chr1.4 | CDS | 3013391 | 3013943 | 3013391 | ID=cds.MS.gene062744.t1;Parent=MS.gene062744.t1 |
| chr1.4 | exon | 3012950 | 3012954 | 3012950 | ID=MS.gene062744.t1.exon2;Parent=MS.gene062744.t1 |
| chr1.4 | CDS | 3012950 | 3012954 | 3012950 | ID=cds.MS.gene062744.t1;Parent=MS.gene062744.t1 |
| Gene Sequence |
| Protein sequence |
