AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0083760

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0083760 MtrunA17_Chr2g0287651 41.317 167 93 2 43 205 68 233 2.79e-38 140
Msa0083760 MtrunA17_Chr1g0203051 29.518 166 114 1 43 205 72 237 3.71e-24 99.4
Msa0083760 MtrunA17_Chr5g0448761 33.974 156 98 2 52 202 62 217 3.20e-19 85.5
Msa0083760 MtrunA17_Chr2g0290391 29.032 186 122 5 27 205 29 211 2.52e-18 82.8
Msa0083760 MtrunA17_Chr2g0276841 34.091 132 81 4 56 181 76 207 2.98e-16 76.6
Msa0083760 MtrunA17_Chr6g0458391 36.283 113 70 2 54 165 95 206 2.98e-16 76.6
Msa0083760 MtrunA17_Chr6g0458391 34.266 143 84 6 43 177 216 356 1.36e-13 68.9
Msa0083760 MtrunA17_Chr7g0258861 31.737 167 102 4 47 205 4 166 6.70e-15 71.6
Msa0083760 MtrunA17_Chr3g0082121 30.719 153 104 2 54 204 47 199 8.49e-15 72.4
Msa0083760 MtrunA17_Chr1g0171741 30.645 124 78 2 51 169 134 254 4.32e-14 68.9
Msa0083760 MtrunA17_Chr1g0202341 33.544 158 95 5 49 201 50 202 5.49e-14 70.1
Msa0083760 MtrunA17_Chr3g0078041 34.211 152 88 6 28 172 24 170 6.65e-14 68.2
Msa0083760 MtrunA17_Chr2g0294841 33.113 151 88 5 56 195 51 199 2.87e-13 68.2
Msa0083760 MtrunA17_Chr2g0324011 29.139 151 103 2 54 202 14 162 1.44e-11 62.8
Msa0083760 MtrunA17_Chr1g0203721 37.500 96 57 3 56 149 69 163 7.11e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0083760 AT4G38180.1 33.766 154 96 3 54 202 77 229 7.62e-18 81.6
Msa0083760 AT5G28530.3 29.677 155 104 3 56 205 61 215 3.78e-16 76.6
Msa0083760 AT5G28530.2 29.677 155 104 3 56 205 61 215 3.78e-16 76.6
Msa0083760 AT5G28530.1 29.677 155 104 3 56 205 61 215 3.97e-16 76.6
Msa0083760 AT5G28530.5 29.677 155 104 3 56 205 61 215 4.63e-16 76.6
Msa0083760 AT5G28530.4 29.677 155 104 3 56 205 61 215 4.64e-16 76.6
Msa0083760 AT1G10240.2 32.414 145 92 4 56 194 54 198 7.73e-16 75.9
Msa0083760 AT1G10240.1 32.414 145 92 4 56 194 54 198 7.73e-16 75.9
Msa0083760 AT3G07500.1 34.247 146 85 6 24 164 4 143 1.89e-13 67.0

Find 37 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATTTGATTCCGAATTAT+AGG 0.217986 1_2:+62879381 Msa0083760:CDS
ATGATTTCATTCAGAAGATT+TGG 0.259205 1_2:+62879303 Msa0083760:CDS
TCATATACTAGGTTTCTTAA+TGG 0.276146 1_2:+62879466 Msa0083760:CDS
TTCAGTAGTGATAATGGTTT+TGG 0.283086 1_2:+62878972 Msa0083760:CDS
GGAATCAAATGAACAAGATT+TGG 0.284026 1_2:-62879371 None:intergenic
AGAAGAATGAAGATAGTAAT+AGG 0.287511 1_2:+62879237 Msa0083760:CDS
TCACTCAATTTCCTATAATT+CGG 0.322105 1_2:-62879392 None:intergenic
CATATACTAGGTTTCTTAAT+GGG 0.328869 1_2:+62879467 Msa0083760:CDS
GGTTTCTTAATGGGCCAAAA+AGG 0.332076 1_2:+62879476 Msa0083760:CDS
GTAGAATTCAGTAGTGATAA+TGG 0.335573 1_2:+62878966 Msa0083760:CDS
ACTTAGTTCATGGTTGTGAT+TGG 0.386513 1_2:-62879345 None:intergenic
AATCTTCTGAATGAAATCAT+AGG 0.410758 1_2:-62879300 None:intergenic
AAAGGAGGACATGAAAATCT+TGG 0.412933 1_2:+62879494 Msa0083760:CDS
GATTTGGAAGACTTAGTTCA+TGG 0.421801 1_2:-62879355 None:intergenic
CTTAGTTCATGGTTGTGATT+GGG 0.422729 1_2:-62879344 None:intergenic
TCGGATAAACAGATTGTTAG+TGG 0.430560 1_2:+62879416 Msa0083760:CDS
AAAGCGTATGCTCGTTTCCA+TGG 0.435800 1_2:+62879113 Msa0083760:CDS
GTTTCCATGGGTTTGTCGTA+AGG 0.452072 1_2:+62879126 Msa0083760:CDS
AATAGGCAAACCATGCGAAC+TGG 0.460478 1_2:+62879254 Msa0083760:CDS
GTTAGTGGTTTGCATTCTCA+AGG 0.476835 1_2:+62879431 Msa0083760:CDS
ATGCTGAGTTGCTTCACTAT+AGG 0.481546 1_2:-62878922 None:intergenic
GCGATTACTTTGCAATAAAG+AGG 0.481547 1_2:+62879193 Msa0083760:CDS
AAATGATGATATAAAAGCTA+TGG 0.514775 1_2:+62879055 Msa0083760:CDS
TTATAGGAAATTGAGTGAAT+CGG 0.515530 1_2:+62879397 Msa0083760:CDS
AAGGAATGATGATGTGGTAA+AGG 0.518755 1_2:+62879145 Msa0083760:CDS
GTAAGAACCTGTCATATACT+AGG 0.532163 1_2:+62879455 Msa0083760:CDS
AAGCGTATGCTCGTTTCCAT+GGG 0.546934 1_2:+62879114 Msa0083760:CDS
TAAGAAACCTAGTATATGAC+AGG 0.549198 1_2:-62879462 None:intergenic
AGCAAGACATCCAGTTCGCA+TGG 0.572129 1_2:-62879264 None:intergenic
CGATTACTTTGCAATAAAGA+GGG 0.582695 1_2:+62879194 Msa0083760:CDS
CATTCCTTACGACAAACCCA+TGG 0.631728 1_2:-62879130 None:intergenic
AGAAAGACAGAGAATTGCAA+TGG 0.633911 1_2:+62879008 Msa0083760:CDS
TCTCGATAATGATATTGTAG+AGG 0.641611 1_2:+62878944 Msa0083760:CDS
TGTCGTAAGGAATGATGATG+TGG 0.665073 1_2:+62879139 Msa0083760:CDS
TGATGTGGTAAAGGATCACG+AGG 0.682414 1_2:+62879154 Msa0083760:CDS
AGCTATGGAGTTTAGCACAG+AGG 0.706449 1_2:+62879070 Msa0083760:CDS
GATGTGGTAAAGGATCACGA+GGG 0.845291 1_2:+62879155 Msa0083760:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATCTTGGATTTATAAAAAA+AGG + chr1_2:62879509-62879528 Msa0083760:CDS 15.0%
!! AAATGATGATATAAAAGCTA+TGG + chr1_2:62879055-62879074 Msa0083760:CDS 20.0%
! AGAAGAATGAAGATAGTAAT+AGG + chr1_2:62879237-62879256 Msa0083760:CDS 25.0%
! AATCTTCTGAATGAAATCAT+AGG - chr1_2:62879303-62879322 None:intergenic 25.0%
! ATGATTTCATTCAGAAGATT+TGG + chr1_2:62879303-62879322 Msa0083760:CDS 25.0%
! TTCATTTGATTCCGAATTAT+AGG + chr1_2:62879381-62879400 Msa0083760:CDS 25.0%
! TCACTCAATTTCCTATAATT+CGG - chr1_2:62879395-62879414 None:intergenic 25.0%
! TTATAGGAAATTGAGTGAAT+CGG + chr1_2:62879397-62879416 Msa0083760:CDS 25.0%
! TCATATACTAGGTTTCTTAA+TGG + chr1_2:62879466-62879485 Msa0083760:CDS 25.0%
! CATATACTAGGTTTCTTAAT+GGG + chr1_2:62879467-62879486 Msa0083760:CDS 25.0%
TCTCGATAATGATATTGTAG+AGG + chr1_2:62878944-62878963 Msa0083760:CDS 30.0%
GTAGAATTCAGTAGTGATAA+TGG + chr1_2:62878966-62878985 Msa0083760:CDS 30.0%
!!! TTCAGTAGTGATAATGGTTT+TGG + chr1_2:62878972-62878991 Msa0083760:CDS 30.0%
!!! GATAATGGTTTTGGTAATGA+TGG + chr1_2:62878981-62879000 Msa0083760:CDS 30.0%
CGATTACTTTGCAATAAAGA+GGG + chr1_2:62879194-62879213 Msa0083760:CDS 30.0%
GGAATCAAATGAACAAGATT+TGG - chr1_2:62879374-62879393 None:intergenic 30.0%
TAAGAAACCTAGTATATGAC+AGG - chr1_2:62879465-62879484 None:intergenic 30.0%
AGAAAGACAGAGAATTGCAA+TGG + chr1_2:62879008-62879027 Msa0083760:CDS 35.0%
! AAGGAATGATGATGTGGTAA+AGG + chr1_2:62879145-62879164 Msa0083760:CDS 35.0%
GCGATTACTTTGCAATAAAG+AGG + chr1_2:62879193-62879212 Msa0083760:CDS 35.0%
CTTAGTTCATGGTTGTGATT+GGG - chr1_2:62879347-62879366 None:intergenic 35.0%
ACTTAGTTCATGGTTGTGAT+TGG - chr1_2:62879348-62879367 None:intergenic 35.0%
GATTTGGAAGACTTAGTTCA+TGG - chr1_2:62879358-62879377 None:intergenic 35.0%
TCGGATAAACAGATTGTTAG+TGG + chr1_2:62879416-62879435 Msa0083760:CDS 35.0%
GTAAGAACCTGTCATATACT+AGG + chr1_2:62879455-62879474 Msa0083760:CDS 35.0%
! GATTTTCATGTCCTCCTTTT+TGG - chr1_2:62879493-62879512 None:intergenic 35.0%
AAAGGAGGACATGAAAATCT+TGG + chr1_2:62879494-62879513 Msa0083760:CDS 35.0%
ATGCTGAGTTGCTTCACTAT+AGG - chr1_2:62878925-62878944 None:intergenic 40.0%
! TGTCGTAAGGAATGATGATG+TGG + chr1_2:62879139-62879158 Msa0083760:CDS 40.0%
! GTTAGTGGTTTGCATTCTCA+AGG + chr1_2:62879431-62879450 Msa0083760:CDS 40.0%
! GGTTTCTTAATGGGCCAAAA+AGG + chr1_2:62879476-62879495 Msa0083760:CDS 40.0%
! TTCTTAATGGGCCAAAAAGG+AGG + chr1_2:62879479-62879498 Msa0083760:CDS 40.0%
AGCTATGGAGTTTAGCACAG+AGG + chr1_2:62879070-62879089 Msa0083760:CDS 45.0%
AAAGCGTATGCTCGTTTCCA+TGG + chr1_2:62879113-62879132 Msa0083760:CDS 45.0%
AAGCGTATGCTCGTTTCCAT+GGG + chr1_2:62879114-62879133 Msa0083760:CDS 45.0%
GTTTCCATGGGTTTGTCGTA+AGG + chr1_2:62879126-62879145 Msa0083760:CDS 45.0%
CATTCCTTACGACAAACCCA+TGG - chr1_2:62879133-62879152 None:intergenic 45.0%
TGATGTGGTAAAGGATCACG+AGG + chr1_2:62879154-62879173 Msa0083760:CDS 45.0%
GATGTGGTAAAGGATCACGA+GGG + chr1_2:62879155-62879174 Msa0083760:CDS 45.0%
ACGAGGGAAAAATTGTTGCG+CGG + chr1_2:62879171-62879190 Msa0083760:CDS 45.0%
AATAGGCAAACCATGCGAAC+TGG + chr1_2:62879254-62879273 Msa0083760:CDS 45.0%
AGCAAGACATCCAGTTCGCA+TGG - chr1_2:62879267-62879286 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 62878915 62879541 62878915 ID=Msa0083760;Name=Msa0083760
chr1_2 mRNA 62878915 62879541 62878915 ID=Msa0083760-mRNA-1;Parent=Msa0083760;Name=Msa0083760-mRNA-1;_AED=0.31;_eAED=0.33;_QI=0|-1|0|1|-1|1|1|0|208
chr1_2 exon 62878915 62879541 62878915 ID=Msa0083760-mRNA-1:exon:20979;Parent=Msa0083760-mRNA-1
chr1_2 CDS 62878915 62879541 62878915 ID=Msa0083760-mRNA-1:cds;Parent=Msa0083760-mRNA-1
Gene Sequence

>Msa0083760

ATGTCAGCCTATAGTGAAGCAACTCAGCATCTCGATAATGATATTGTAGAGGTAGAATTCAGTAGTGATAATGGTTTTGGTAATGATGGAGATAGAAAGACAGAGAATTGCAATGGTCAGAAAAGTTTAAGTGAAATTACAAATGATGATATAAAAGCTATGGAGTTTAGCACAGAGGAAGAAGCTATACAATTTTACAAAGCGTATGCTCGTTTCCATGGGTTTGTCGTAAGGAATGATGATGTGGTAAAGGATCACGAGGGAAAAATTGTTGCGCGGCGATTACTTTGCAATAAAGAGGGAAAGAGTGAAACTAAAAATAAGAAGAATGAAGATAGTAATAGGCAAACCATGCGAACTGGATGTCTTGCTAGACTTCGAGTAGCCTATGATTTCATTCAGAAGATTTGGAAAGTTACTAATTTTGAGCCCAATCACAACCATGAACTAAGTCTTCCAAATCTTGTTCATTTGATTCCGAATTATAGGAAATTGAGTGAATCGGATAAACAGATTGTTAGTGGTTTGCATTCTCAAGGTGTAAGAACCTGTCATATACTAGGTTTCTTAATGGGCCAAAAAGGAGGACATGAAAATCTTGGATTTATAAAAAAAGGATCTATATAA
Protein sequence

>Msa0083760

MSAYSEATQHLDNDIVEVEFSSDNGFGNDGDRKTENCNGQKSLSEITNDDIKAMEFSTEEEAIQFYKAYARFHGFVVRNDDVVKDHEGKIVARRLLCNKEGKSETKNKKNEDSNRQTMRTGCLARLRVAYDFIQKIWKVTNFEPNHNHELSLPNLVHLIPNYRKLSESDKQIVSGLHSQGVRTCHILGFLMGQKGGHENLGFIKKGSI*