AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0230880

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0230880 MtrunA17_Chr4g0046521 42.778 180 89 2 32 198 26 204 2.39e-48 157
Msa0230880 MtrunA17_Chr2g0282811 44.444 180 83 4 35 198 30 208 5.10e-48 156
Msa0230880 MtrunA17_Chr2g0282791 42.222 180 90 3 32 198 27 205 2.61e-46 152
Msa0230880 MtrunA17_Chr4g0040531 38.150 173 92 4 40 198 32 203 4.77e-39 133
Msa0230880 MtrunA17_Chr2g0286871 34.659 176 104 3 33 198 13 187 1.85e-31 113
Msa0230880 MtrunA17_Chr5g0419161 35.955 178 97 4 33 194 38 214 7.38e-31 112
Msa0230880 MtrunA17_Chr4g0066491 32.258 186 114 3 24 198 15 199 8.65e-31 112
Msa0230880 MtrunA17_Chr4g0066481 34.118 170 100 3 40 198 29 197 1.32e-30 112
Msa0230880 MtrunA17_Chr7g0217511 35.955 178 97 4 33 194 38 214 1.48e-29 109
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0230880 AT3G02430.1 47.115 208 94 3 6 198 7 213 2.54e-58 183
Msa0230880 AT4G24310.1 47.170 212 87 4 2 198 6 207 4.42e-56 177
Msa0230880 AT5G46090.1 37.569 181 99 2 31 198 33 212 1.12e-38 133
Msa0230880 AT4G18425.1 39.548 177 69 4 47 198 48 211 1.06e-37 130
Msa0230880 AT4G28485.2 39.785 186 95 5 29 198 14 198 1.03e-35 125
Msa0230880 AT3G21550.1 38.150 173 96 3 45 208 14 184 1.16e-29 108
Msa0230880 AT3G21520.1 33.333 177 106 4 43 208 26 201 1.08e-27 104
Msa0230880 AT1G09157.1 33.333 180 94 2 40 194 61 239 2.55e-25 99.4
Msa0230880 AT5G39650.1 33.333 180 94 2 40 194 62 240 8.75e-25 97.8
Msa0230880 AT5G27370.1 32.222 180 93 6 43 194 8 186 1.03e-17 77.8
Msa0230880 AT4G28485.1 50.000 50 25 0 149 198 114 163 7.61e-11 58.9

Find 51 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTTCAGATTGCTTATTAT+TGG 0.102422 2_2:+3079334 None:intergenic
CTTAGCTCATAGTAATTATT+TGG 0.136016 2_2:+3078667 None:intergenic
TCATAGTAATTATTTGGAAT+TGG 0.289611 2_2:+3078673 None:intergenic
GCAGCAGGTGCAGGTGTAAC+AGG 0.319770 2_2:+3078701 None:intergenic
GATATTGTGCCACTCGGAAT+TGG 0.345690 2_2:-3078782 Msa0230880:CDS
TGAAGACTGGCGTGAGAATC+TGG 0.355118 2_2:+3079171 None:intergenic
CATAGTAATTATTTGGAATT+GGG 0.358154 2_2:+3078674 None:intergenic
TAGTCACACGGCGTGGTTGC+GGG 0.359159 2_2:+3078816 None:intergenic
ATGCTTCCTTGCTTGTTTCA+CGG 0.371761 2_2:-3079078 Msa0230880:CDS
CCATGGCATCGCAACCTTCA+AGG 0.392282 2_2:-3079021 Msa0230880:CDS
GTAGTATCTGGAGCATTAAC+GGG 0.406461 2_2:-3079242 Msa0230880:CDS
AGTAGTATCTGGAGCATTAA+CGG 0.435471 2_2:-3079243 Msa0230880:CDS
CGACGGTCAGTAGTAGTATC+TGG 0.437746 2_2:-3079254 Msa0230880:CDS
TTGGAATTGGGTGCAGCAGC+AGG 0.443039 2_2:+3078686 None:intergenic
TTAGTCACACGGCGTGGTTG+CGG 0.444013 2_2:+3078815 None:intergenic
TTGGGTGCAGCAGCAGGTGC+AGG 0.468002 2_2:+3078692 None:intergenic
TCGCAACCTTCAAGGGTCTC+TGG 0.469635 2_2:-3079013 Msa0230880:CDS
GCAGCAGCACATGGAATTAG+TGG 0.477735 2_2:-3079290 Msa0230880:CDS
GCAACCACGCCGTGTGACTA+AGG 0.489093 2_2:-3078813 Msa0230880:CDS
CATGGCATCGCAACCTTCAA+GGG 0.499059 2_2:-3079020 Msa0230880:CDS
GCTCCGTTGTTTGTGAAGAC+TGG 0.503057 2_2:+3079158 None:intergenic
AAATAGCCAGAGACCCTTGA+AGG 0.509853 2_2:+3079007 None:intergenic
CCAACCACTAGACATGGGAT+TGG 0.514072 2_2:-3078728 Msa0230880:CDS
TTATACTTGCTCAACTCAGC+TGG 0.520275 2_2:+3078930 None:intergenic
GGGAAGTAAGTTTGCCAAGT+TGG 0.532415 2_2:+3079214 None:intergenic
GCGTGAGAATCTGGAATGCT+AGG 0.537937 2_2:+3079180 None:intergenic
ATTAACGGGGACAGCCAACT+TGG 0.539398 2_2:-3079228 Msa0230880:CDS
AATAAGCAATCTGAAGCAGA+TGG 0.548858 2_2:-3079329 Msa0230880:CDS
TCCATGACATTGACATTGAC+TGG 0.556571 2_2:+3078975 None:intergenic
CCAATCCCATGTCTAGTGGT+TGG 0.561333 2_2:+3078728 None:intergenic
CCTTGAAGGTTGCGATGCCA+TGG 0.569779 2_2:+3079021 None:intergenic
ACCAGTCAATGTCAATGTCA+TGG 0.571952 2_2:-3078976 Msa0230880:CDS
GCATCAGCAGCAGCAGCACA+TGG 0.574320 2_2:-3079299 Msa0230880:CDS
ACAGTGAATAATGCATCAGA+TGG 0.586121 2_2:-3079053 Msa0230880:CDS
TTGGCAAACTTACTTCCCAC+AGG 0.590824 2_2:-3079209 Msa0230880:CDS
GAATGCTAGGAGTGTTCCTG+TGG 0.592747 2_2:+3079193 None:intergenic
CAGCAGGTGCAGGTGTAACA+GGG 0.600653 2_2:+3078702 None:intergenic
ATGAGATTGCAAGCAAGATG+AGG 0.612498 2_2:+3079099 None:intergenic
GTTCTTGATATTGTGCCACT+CGG 0.614142 2_2:-3078788 Msa0230880:CDS
GTAGCCAATCCCATGTCTAG+TGG 0.615835 2_2:+3078724 None:intergenic
AAGTGTGAGAATGCGAGTAA+CGG 0.616907 2_2:+3079127 None:intergenic
CAAGAACCTCCTTAGTCACA+CGG 0.627426 2_2:+3078804 None:intergenic
CTGTGTCCGTGAAACAAGCA+AGG 0.639798 2_2:+3079072 None:intergenic
ACCTCCTTAGTCACACGGCG+TGG 0.648095 2_2:+3078809 None:intergenic
ACGCCAGTCTTCACAAACAA+CGG 0.649231 2_2:-3079161 Msa0230880:CDS
GTGGTAGACGACGACGACGA+CGG 0.670485 2_2:-3079271 Msa0230880:CDS
TAGTATCTGGAGCATTAACG+GGG 0.687598 2_2:-3079241 Msa0230880:CDS
TCAGATGGAAGAATCTACCA+TGG 0.695565 2_2:-3079038 Msa0230880:CDS
ACCACGCCGTGTGACTAAGG+AGG 0.698128 2_2:-3078810 Msa0230880:CDS
AATGCTAGGAGTGTTCCTGT+GGG 0.719785 2_2:+3079194 None:intergenic
CATAGGAATCCAATTCCGAG+TGG 0.746885 2_2:+3078773 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGCTTCAGATTGCTTATTAT+TGG + chr2_2:3078707-3078726 None:intergenic 30.0%
AATGCATGTACAAAGTCAAT+GGG + chr2_2:3079141-3079160 None:intergenic 30.0%
AAATGCATGTACAAAGTCAA+TGG + chr2_2:3079142-3079161 None:intergenic 30.0%
! AATAAGCAATCTGAAGCAGA+TGG - chr2_2:3078709-3078728 Msa0230880:CDS 35.0%
! AGTAGTATCTGGAGCATTAA+CGG - chr2_2:3078795-3078814 Msa0230880:CDS 35.0%
ACAGTGAATAATGCATCAGA+TGG - chr2_2:3078985-3079004 Msa0230880:CDS 35.0%
AGTTGAGCAAGTATAAGATC+AGG - chr2_2:3079115-3079134 Msa0230880:CDS 35.0%
!! TGTTCTTTGCTGTTGCATTA+AGG - chr2_2:3079173-3079192 Msa0230880:CDS 35.0%
!! GTTCTTTGCTGTTGCATTAA+GGG - chr2_2:3079174-3079193 Msa0230880:CDS 35.0%
! TTTTTCCAACCACTAGACAT+GGG - chr2_2:3079305-3079324 Msa0230880:CDS 35.0%
! GTAGTATCTGGAGCATTAAC+GGG - chr2_2:3078796-3078815 Msa0230880:CDS 40.0%
! TAGTATCTGGAGCATTAACG+GGG - chr2_2:3078797-3078816 Msa0230880:CDS 40.0%
AAGTGTGAGAATGCGAGTAA+CGG + chr2_2:3078914-3078933 None:intergenic 40.0%
ATGAGATTGCAAGCAAGATG+AGG + chr2_2:3078942-3078961 None:intergenic 40.0%
ATGCTTCCTTGCTTGTTTCA+CGG - chr2_2:3078960-3078979 Msa0230880:CDS 40.0%
TCAGATGGAAGAATCTACCA+TGG - chr2_2:3079000-3079019 Msa0230880:CDS 40.0%
ACCAGTCAATGTCAATGTCA+TGG - chr2_2:3079062-3079081 Msa0230880:CDS 40.0%
TCCATGACATTGACATTGAC+TGG + chr2_2:3079066-3079085 None:intergenic 40.0%
TTATACTTGCTCAACTCAGC+TGG + chr2_2:3079111-3079130 None:intergenic 40.0%
! GTTCTTGATATTGTGCCACT+CGG - chr2_2:3079250-3079269 Msa0230880:CDS 40.0%
CGACAAAAAGCAAAGTGCAT+AGG + chr2_2:3079285-3079304 None:intergenic 40.0%
! GTTTTTCCAACCACTAGACA+TGG - chr2_2:3079304-3079323 Msa0230880:CDS 40.0%
GGGAAGTAAGTTTGCCAAGT+TGG + chr2_2:3078827-3078846 None:intergenic 45.0%
TTGGCAAACTTACTTCCCAC+AGG - chr2_2:3078829-3078848 Msa0230880:CDS 45.0%
!! AATGCTAGGAGTGTTCCTGT+GGG + chr2_2:3078847-3078866 None:intergenic 45.0%
ACGCCAGTCTTCACAAACAA+CGG - chr2_2:3078877-3078896 Msa0230880:intron 45.0%
AAATAGCCAGAGACCCTTGA+AGG + chr2_2:3079034-3079053 None:intergenic 45.0%
CAAGAACCTCCTTAGTCACA+CGG + chr2_2:3079237-3079256 None:intergenic 45.0%
! GATATTGTGCCACTCGGAAT+TGG - chr2_2:3079256-3079275 Msa0230880:CDS 45.0%
CATAGGAATCCAATTCCGAG+TGG + chr2_2:3079268-3079287 None:intergenic 45.0%
GCAGCAGCACATGGAATTAG+TGG - chr2_2:3078748-3078767 Msa0230880:CDS 50.0%
CGACGGTCAGTAGTAGTATC+TGG - chr2_2:3078784-3078803 Msa0230880:CDS 50.0%
ATTAACGGGGACAGCCAACT+TGG - chr2_2:3078810-3078829 Msa0230880:CDS 50.0%
!! GAATGCTAGGAGTGTTCCTG+TGG + chr2_2:3078848-3078867 None:intergenic 50.0%
! GCGTGAGAATCTGGAATGCT+AGG + chr2_2:3078861-3078880 None:intergenic 50.0%
TGAAGACTGGCGTGAGAATC+TGG + chr2_2:3078870-3078889 None:intergenic 50.0%
GCTCCGTTGTTTGTGAAGAC+TGG + chr2_2:3078883-3078902 None:intergenic 50.0%
CTGTGTCCGTGAAACAAGCA+AGG + chr2_2:3078969-3078988 None:intergenic 50.0%
CATGGCATCGCAACCTTCAA+GGG - chr2_2:3079018-3079037 Msa0230880:CDS 50.0%
CCAATCCCATGTCTAGTGGT+TGG + chr2_2:3079313-3079332 None:intergenic 50.0%
CCAACCACTAGACATGGGAT+TGG - chr2_2:3079310-3079329 Msa0230880:CDS 50.0%
GTAGCCAATCCCATGTCTAG+TGG + chr2_2:3079317-3079336 None:intergenic 50.0%
CCTTGAAGGTTGCGATGCCA+TGG + chr2_2:3079020-3079039 None:intergenic 55.0%
CCATGGCATCGCAACCTTCA+AGG - chr2_2:3079017-3079036 Msa0230880:CDS 55.0%
TCGCAACCTTCAAGGGTCTC+TGG - chr2_2:3079025-3079044 Msa0230880:CDS 55.0%
TTAGTCACACGGCGTGGTTG+CGG + chr2_2:3079226-3079245 None:intergenic 55.0%
CAGCAGGTGCAGGTGTAACA+GGG + chr2_2:3079339-3079358 None:intergenic 55.0%
TTGGAATTGGGTGCAGCAGC+AGG + chr2_2:3079355-3079374 None:intergenic 55.0%
GCATCAGCAGCAGCAGCACA+TGG - chr2_2:3078739-3078758 Msa0230880:CDS 60.0%
GTGGTAGACGACGACGACGA+CGG - chr2_2:3078767-3078786 Msa0230880:CDS 60.0%
TAGTCACACGGCGTGGTTGC+GGG + chr2_2:3079225-3079244 None:intergenic 60.0%
GCAACCACGCCGTGTGACTA+AGG - chr2_2:3079225-3079244 Msa0230880:CDS 60.0%
ACCACGCCGTGTGACTAAGG+AGG - chr2_2:3079228-3079247 Msa0230880:CDS 60.0%
ACCTCCTTAGTCACACGGCG+TGG + chr2_2:3079232-3079251 None:intergenic 60.0%
GCAGCAGGTGCAGGTGTAAC+AGG + chr2_2:3079340-3079359 None:intergenic 60.0%
TTGGGTGCAGCAGCAGGTGC+AGG + chr2_2:3079349-3079368 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 3078682 3079378 3078682 ID=Msa0230880;Name=Msa0230880
chr2_2 mRNA 3078682 3079378 3078682 ID=Msa0230880-mRNA-1;Parent=Msa0230880;Name=Msa0230880-mRNA-1;_AED=0.18;_eAED=0.18;_QI=0|0|0|1|1|1|2|0|208
chr2_2 exon 3078936 3079378 3078936 ID=Msa0230880-mRNA-1:exon:1119;Parent=Msa0230880-mRNA-1
chr2_2 exon 3078682 3078865 3078682 ID=Msa0230880-mRNA-1:exon:1118;Parent=Msa0230880-mRNA-1
chr2_2 CDS 3078936 3079378 3078936 ID=Msa0230880-mRNA-1:cds;Parent=Msa0230880-mRNA-1
chr2_2 CDS 3078682 3078865 3078682 ID=Msa0230880-mRNA-1:cds;Parent=Msa0230880-mRNA-1
Gene Sequence

>Msa0230880

ATGTCGGTTACACAACGTCGATCCAATAATAAGCAATCTGAAGCAGATGGATCATCAGCATCAGCAGCAGCAGCACATGGAATTAGTGGTAGACGACGACGACGACGGTCAGTAGTAGTATCTGGAGCATTAACGGGGACAGCCAACTTGGCAAACTTACTTCCCACAGGAACACTCCTAGCATTCCAGATTCTCACGCCAGTCTTCACAAACAACGGAGCTTGTGACTCCGTTACTCGCATTCTCACACTTGTACTCCTCATCTTGCTTGCAATCTCATGCTTCCTTGCTTGTTTCACGGACACAGTGAATAATGCATCAGATGGAAGAATCTACCATGGCATCGCAACCTTCAAGGGTCTCTGGCTATTTGATTACTCACCAGTCAATGTCAATGTCATGGACAGTAGTAGTACAATAATATTACCAGCTGAGTTGAGCAAGGATAACAATGTGTTGACATGTTATTACCCGCAACCACGCCGTGTGACTAAGGAGGTTCTTGATATTGTGCCACTCGGAATTGGATTCCTATGCACTTTGCTTTTTGTCGTTTTTCCAACCACTAGACATGGGATTGGCTACCCTGTTACACCTGCACCTGCTGCTGCACCCAATTCCAAATAA
Protein sequence

>Msa0230880

MSVTQRRSNNKQSEADGSSASAAAAHGISGRRRRRRSVVVSGALTGTANLANLLPTGTLLAFQILTPVFTNNGACDSVTRILTLVLLILLAISCFLACFTDTVNNASDGRIYHGIATFKGLWLFDYSPVNVNVMDSSSTIILPAELSKDNNVLTCYYPQPRRVTKEVLDIVPLGIGFLCTLLFVVFPTTRHGIGYPVTPAPAAAPNSK*