AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0828490


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0828490 MtrunA17_Chr3g0093131 81.347 193 29 4 1 187 1 192 2.62e-100 287
Msa0828490 MtrunA17_Chr2g0302091 61.081 185 64 6 1 181 16 196 8.87e-59 182
Msa0828490 MtrunA17_Chr8g0345001 50.857 175 73 6 15 180 10 180 6.68e-47 152
Msa0828490 MtrunA17_Chr2g0333981 36.196 163 96 3 12 168 1 161 2.06e-24 94.0
Msa0828490 MtrunA17_Chr4g0018951 36.842 133 74 2 36 168 31 153 3.91e-22 87.8
Msa0828490 MtrunA17_Chr8g0379021 35.135 148 88 3 24 165 13 158 9.85e-20 82.0
Msa0828490 MtrunA17_Chr5g0422421 36.129 155 87 4 21 165 7 159 5.53e-18 78.6
Msa0828490 MtrunA17_Chr4g0071601 34.507 142 83 3 36 168 31 171 8.21e-18 77.0
Msa0828490 MtrunA17_Chr3g0099421 32.911 158 88 3 21 165 32 184 7.06e-16 73.2
Msa0828490 MtrunA17_Chr8g0355091 30.909 165 95 4 14 165 1 159 7.29e-16 72.8
Msa0828490 MtrunA17_Chr1g0149391 32.298 161 85 5 21 165 7 159 1.00e-15 72.4
Msa0828490 MtrunA17_Chr1g0206991 32.919 161 84 5 21 165 7 159 3.05e-15 70.1
Msa0828490 MtrunA17_Chr1g0206721 31.646 158 90 4 21 165 7 159 3.29e-15 71.2
Msa0828490 MtrunA17_Chr3g0089141 33.125 160 83 5 22 165 8 159 4.36e-15 70.9
Msa0828490 MtrunA17_Chr2g0292791 31.646 158 90 4 21 165 7 159 5.90e-15 70.5
Msa0828490 MtrunA17_Chr1g0206701 31.013 158 91 3 21 165 7 159 9.34e-15 70.1
Msa0828490 MtrunA17_Chr3g0119901 29.861 144 83 3 36 169 28 163 1.09e-14 69.3
Msa0828490 MtrunA17_Chr2g0317481 29.091 165 85 5 21 165 7 159 1.99e-14 68.9
Msa0828490 MtrunA17_Chr1g0208581 33.125 160 83 5 22 165 8 159 2.11e-14 68.9
Msa0828490 MtrunA17_Chr2g0317451 29.091 165 85 5 21 165 7 159 2.13e-14 68.9
Msa0828490 MtrunA17_Chr1g0208561 32.500 160 84 5 22 165 8 159 3.75e-14 68.2
Msa0828490 MtrunA17_Chr3g0085241 27.273 176 107 5 1 169 34 195 6.49e-14 67.8
Msa0828490 MtrunA17_Chr5g0422941 31.757 148 83 3 21 155 7 149 9.91e-14 67.0
Msa0828490 MtrunA17_Chr8g0356071 42.466 73 36 1 24 90 3 75 2.08e-13 65.1
Msa0828490 MtrunA17_Chr2g0300441 33.824 136 78 4 37 165 29 159 3.37e-12 62.8
Msa0828490 MtrunA17_Chr2g0325971 31.210 157 90 4 22 165 8 159 6.35e-12 62.0
Msa0828490 MtrunA17_Chr3g0099411 43.056 72 35 1 21 86 7 78 8.53e-12 61.6
Msa0828490 MtrunA17_Chr8g0357771 46.552 58 31 0 36 93 21 78 8.91e-12 60.8
Msa0828490 MtrunA17_Chr1g0169761 33.654 104 61 2 24 119 3 106 1.75e-11 60.1
Msa0828490 MtrunA17_Chr1g0206691 30.216 139 79 4 36 164 11 141 2.06e-11 60.5
Msa0828490 MtrunA17_Chr8g0376821 42.647 68 33 1 24 85 3 70 3.37e-11 59.3
Msa0828490 MtrunA17_Chr7g0238991 33.577 137 79 3 36 165 40 171 6.03e-11 59.7
Msa0828490 MtrunA17_Chr5g0419601 27.273 165 88 5 21 165 7 159 9.71e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0828490 AT5G60440.1 31.757 148 92 4 36 177 26 170 2.40e-16 75.5
Msa0828490 AT2G24840.1 28.090 178 106 6 8 175 63 228 3.31e-16 74.7
Msa0828490 AT3G66656.1 51.020 49 24 0 36 84 21 69 4.11e-12 62.0
Msa0828490 AT1G65360.1 29.747 158 92 5 21 165 5 156 8.74e-12 62.0
Msa0828490 AT4G36590.1 28.571 161 97 5 21 165 5 163 1.49e-11 61.6
Msa0828490 AT2G34440.1 29.508 122 80 2 36 154 21 139 3.35e-11 59.7

Find 26 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGCTTCATATCGAAGTCTT+AGG 0.201474 5_4:+1074113 None:intergenic
TAACACACATTCTCTTGAAT+TGG 0.284587 5_4:+1073887 None:intergenic
GAATAAATCTATTGATGATA+TGG 0.314688 5_4:-1074002 Msa0828490:CDS
TGAATGACAGCATCATAGTT+AGG 0.369392 5_4:+1074205 None:intergenic
CGCTTCATATCGAAGTCTTA+GGG 0.401643 5_4:+1074114 None:intergenic
TTGTTTCTCTCGGCCGCCAT+TGG 0.404729 5_4:+1074391 None:intergenic
CTTCCGTGTGTTGTTTCTCT+CGG 0.413838 5_4:+1074381 None:intergenic
CCCTTCTCAAAACTCAAACT+TGG 0.422835 5_4:-1074325 Msa0828490:CDS
CGATGAGTGCAGTTTCTGAT+TGG 0.423120 5_4:+1074266 None:intergenic
CTCATCCTCGTCCATATGTC+CGG 0.445428 5_4:+1074171 None:intergenic
CTTCTTCGCTTCGCTTGCTA+CGG 0.451335 5_4:+1073922 None:intergenic
CTTCGATATGAAGCGATTCA+AGG 0.460946 5_4:-1074106 Msa0828490:CDS
GAAGGATGAAATCAAGAAAG+AGG 0.477445 5_4:-1074353 Msa0828490:CDS
GATTTATTCCACCAATCAGC+AGG 0.485193 5_4:+1074016 None:intergenic
GAATGACAGCATCATAGTTA+GGG 0.520135 5_4:+1074206 None:intergenic
CATGCATAGAACTTGTTGTT+GGG 0.522753 5_4:+1074235 None:intergenic
AGGAAAACTTAAAGAAGAGA+AGG 0.524858 5_4:-1074086 Msa0828490:CDS
CAACACACGGAAGAGAAAGA+AGG 0.527351 5_4:-1074371 Msa0828490:CDS
TTGATTTGCCTGCTGATTGG+TGG 0.538450 5_4:-1074024 Msa0828490:CDS
TGGGACAACATGAATAAGAA+TGG 0.556319 5_4:-1074436 None:intergenic
ACATGCATAGAACTTGTTGT+TGG 0.594378 5_4:+1074234 None:intergenic
AACAACAAGTTCTATGCATG+TGG 0.619639 5_4:-1074232 Msa0828490:CDS
GTCTAAGAAGAAAATTCCAA+TGG 0.626985 5_4:-1074407 Msa0828490:CDS
TAAGAAGAAAATTCCAATGG+CGG 0.679668 5_4:-1074404 Msa0828490:CDS
CGGCCGAGAGAAACAACACA+CGG 0.685523 5_4:-1074384 Msa0828490:CDS
TCTGACCGGACATATGGACG+AGG 0.696130 5_4:-1074176 Msa0828490:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAATAAATCTATTGATGATA+TGG - chr5_4:1074311-1074330 Msa0828490:CDS 20.0%
GTCTAAGAAGAAAATTCCAA+TGG - chr5_4:1073906-1073925 Msa0828490:CDS 30.0%
TAAGAAGAAAATTCCAATGG+CGG - chr5_4:1073909-1073928 Msa0828490:CDS 30.0%
AGGAAAACTTAAAGAAGAGA+AGG - chr5_4:1074227-1074246 Msa0828490:CDS 30.0%
TAACACACATTCTCTTGAAT+TGG + chr5_4:1074429-1074448 None:intergenic 30.0%
GAAGGATGAAATCAAGAAAG+AGG - chr5_4:1073960-1073979 Msa0828490:CDS 35.0%
!!! CCAAGTTTGAGTTTTGAGAA+GGG + chr5_4:1073991-1074010 None:intergenic 35.0%
!!! TCCAAGTTTGAGTTTTGAGA+AGG + chr5_4:1073992-1074011 None:intergenic 35.0%
!! CATGCATAGAACTTGTTGTT+GGG + chr5_4:1074081-1074100 None:intergenic 35.0%
!! ACATGCATAGAACTTGTTGT+TGG + chr5_4:1074082-1074101 None:intergenic 35.0%
AACAACAAGTTCTATGCATG+TGG - chr5_4:1074081-1074100 Msa0828490:CDS 35.0%
GAATGACAGCATCATAGTTA+GGG + chr5_4:1074110-1074129 None:intergenic 35.0%
TGAATGACAGCATCATAGTT+AGG + chr5_4:1074111-1074130 None:intergenic 35.0%
!!! ATTTTGATTTGCCTGCTGAT+TGG - chr5_4:1074286-1074305 Msa0828490:CDS 35.0%
CCCTTCTCAAAACTCAAACT+TGG - chr5_4:1073988-1074007 Msa0828490:CDS 40.0%
CGCTTCATATCGAAGTCTTA+GGG + chr5_4:1074202-1074221 None:intergenic 40.0%
TCGCTTCATATCGAAGTCTT+AGG + chr5_4:1074203-1074222 None:intergenic 40.0%
CTTCGATATGAAGCGATTCA+AGG - chr5_4:1074207-1074226 Msa0828490:CDS 40.0%
GATTTATTCCACCAATCAGC+AGG + chr5_4:1074300-1074319 None:intergenic 40.0%
!! CTTCCGTGTGTTGTTTCTCT+CGG + chr5_4:1073935-1073954 None:intergenic 45.0%
CAACACACGGAAGAGAAAGA+AGG - chr5_4:1073942-1073961 Msa0828490:CDS 45.0%
CGATGAGTGCAGTTTCTGAT+TGG + chr5_4:1074050-1074069 None:intergenic 45.0%
! GTCATTCAGCGTTTTCTGAC+CGG - chr5_4:1074123-1074142 Msa0828490:CDS 45.0%
!! TTGATTTGCCTGCTGATTGG+TGG - chr5_4:1074289-1074308 Msa0828490:CDS 45.0%
! GCGTTTTCTGACCGGACATA+TGG - chr5_4:1074131-1074150 Msa0828490:CDS 50.0%
CTCATCCTCGTCCATATGTC+CGG + chr5_4:1074145-1074164 None:intergenic 50.0%
! CTTCTTCGCTTCGCTTGCTA+CGG + chr5_4:1074394-1074413 None:intergenic 50.0%
! TTGTTTCTCTCGGCCGCCAT+TGG + chr5_4:1073925-1073944 None:intergenic 55.0%
CGGCCGAGAGAAACAACACA+CGG - chr5_4:1073929-1073948 Msa0828490:CDS 55.0%
TCTGACCGGACATATGGACG+AGG - chr5_4:1074137-1074156 Msa0828490:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 1073886 1074449 1073886 ID=Msa0828490;Name=Msa0828490
chr5_4 mRNA 1073886 1074449 1073886 ID=Msa0828490-mRNA-1;Parent=Msa0828490;Name=Msa0828490-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|187
chr5_4 exon 1073886 1074449 1073886 ID=Msa0828490-mRNA-1:exon:216;Parent=Msa0828490-mRNA-1
chr5_4 CDS 1073886 1074449 1073886 ID=Msa0828490-mRNA-1:cds;Parent=Msa0828490-mRNA-1
Gene Sequence

>Msa0828490

ATGAATAAGAATGGTGAAACGTCTAAGAAGAAAATTCCAATGGCGGCCGAGAGAAACAACACACGGAAGAGAAAGAAGGATGAAATCAAGAAAGAGGAAAAGCCCTTCTCAAAACTCAAACTTGGAATTTTCAACAAAGCAATAGAGCTATCTATTCTATGCCAATCAGAAACTGCACTCATCGTAACATCACCCAACAACAAGTTCTATGCATGTGGCTACCCTAACTATGATGCTGTCATTCAGCGTTTTCTGACCGGACATATGGACGAGGATGAGAAAAAGAAGCAAGAAGATGATGACGTTGTTGAAACCCTAAGACTTCGATATGAAGCGATTCAAGGAAAACTTAAAGAAGAGAAGGAGAAATTGCAAGCTGTCAAAGATGCACACAAGAGTAATTTTGATTTGCCTGCTGATTGGTGGAATAAATCTATTGATGATATGGATTTAACATCTCTTGAAGATATTACGACTTCGTTGAATAAATTGAAGATTAATTTGTCCGTAGCAAGCGAAGCGAAGAAGTTCAATTTACATCCAATTCAAGAGAATGTGTGTTAA

Protein sequence

>Msa0828490

MNKNGETSKKKIPMAAERNNTRKRKKDEIKKEEKPFSKLKLGIFNKAIELSILCQSETALIVTSPNNKFYACGYPNYDAVIQRFLTGHMDEDEKKKQEDDDVVETLRLRYEAIQGKLKEEKEKLQAVKDAHKSNFDLPADWWNKSIDDMDLTSLEDITTSLNKLKINLSVASEAKKFNLHPIQENVC*