AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0146050

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0146050 MtrunA17_Chr1g0152661 94.142 239 4 4 1 236 1 232 3.36e-164 452
Msa0146050 MtrunA17_Chr3g0134711 58.065 248 76 9 1 234 1 234 4.22e-83 247
Msa0146050 MtrunA17_Chr1g0207451 42.857 266 85 13 1 225 3 242 2.46e-47 157
Msa0146050 MtrunA17_Chr1g0180311 35.938 192 92 8 43 204 81 271 4.39e-21 89.4
Msa0146050 MtrunA17_Chr1g0197281 29.730 222 109 7 21 197 81 300 9.50e-18 80.9
Msa0146050 MtrunA17_Chr7g0263121 36.975 119 56 2 43 161 15 114 3.46e-17 76.3
Msa0146050 MtrunA17_Chr4g0012691 49.425 87 41 2 78 164 220 303 7.69e-17 78.6
Msa0146050 MtrunA17_Chr7g0263131 35.246 122 67 2 78 199 34 143 1.05e-15 72.4
Msa0146050 MtrunA17_Chr5g0425411 46.154 91 45 2 77 163 118 208 2.32e-15 72.8
Msa0146050 MtrunA17_Chr5g0448611 41.026 117 31 4 78 165 130 237 5.71e-15 72.4
Msa0146050 MtrunA17_Chr1g0212561 41.667 84 39 1 78 161 45 118 1.83e-14 69.7
Msa0146050 MtrunA17_Chr7g0222831 35.036 137 66 4 32 168 2 115 3.13e-14 68.6
Msa0146050 MtrunA17_Chr1g0182161 31.214 173 83 7 32 195 3 148 1.68e-13 66.2
Msa0146050 MtrunA17_Chr1g0182181 36.735 98 47 2 76 172 33 116 8.14e-13 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0146050 AT1G27730.1 50.607 247 87 11 1 232 1 227 7.43e-61 191
Msa0146050 AT5G04340.1 54.348 230 88 9 1 216 1 227 7.13e-51 166
Msa0146050 AT3G19580.1 40.551 254 104 8 1 213 1 248 3.07e-46 155
Msa0146050 AT3G19580.2 40.551 254 104 8 1 213 1 248 3.07e-46 155
Msa0146050 AT5G43170.1 47.034 236 69 12 1 224 1 192 4.31e-43 144
Msa0146050 AT5G67450.1 40.249 241 96 8 1 197 1 237 5.49e-36 127
Msa0146050 AT3G49930.1 43.500 200 70 8 25 210 36 206 1.60e-35 125
Msa0146050 AT2G28200.1 34.872 195 94 7 37 200 70 262 9.89e-24 96.7
Msa0146050 AT2G45120.1 37.791 172 78 5 38 197 146 300 2.39e-22 93.6
Msa0146050 AT3G60580.1 38.378 185 79 7 38 210 122 283 3.64e-21 89.7
Msa0146050 AT1G49900.1 42.149 121 37 3 63 168 172 274 5.32e-21 92.0
Msa0146050 AT1G49900.1 45.714 105 43 2 77 180 749 840 9.32e-20 88.2
Msa0146050 AT5G03510.1 31.443 194 98 5 39 200 69 259 6.84e-19 84.0
Msa0146050 AT5G04390.1 29.565 230 113 7 39 232 96 312 3.95e-18 82.4
Msa0146050 AT5G56200.1 41.525 118 55 2 80 186 344 458 6.18e-17 79.7
Msa0146050 AT1G02040.1 31.795 195 89 7 5 162 61 248 8.01e-17 78.6
Msa0146050 AT2G37430.1 38.060 134 60 4 32 161 2 116 3.42e-16 74.3
Msa0146050 AT4G35280.1 39.844 128 55 5 39 163 138 246 6.98e-16 75.5
Msa0146050 AT3G46090.1 35.878 131 58 4 38 168 11 115 3.55e-15 71.2
Msa0146050 AT1G02030.1 35.938 128 67 3 34 161 119 231 1.06e-14 72.0
Msa0146050 AT2G17180.1 29.268 164 79 4 39 197 121 252 1.45e-14 71.6
Msa0146050 AT2G28710.1 36.134 119 44 4 43 161 14 100 1.69e-14 69.3
Msa0146050 AT3G46080.1 42.529 87 37 2 75 161 34 107 6.97e-13 65.1
Msa0146050 AT3G10470.1 38.235 102 45 2 78 161 182 283 1.63e-12 66.6
Msa0146050 AT5G61470.1 39.535 86 35 2 78 162 228 297 3.10e-12 65.5
Msa0146050 AT3G46070.1 38.462 91 45 2 71 161 29 108 2.93e-11 60.8
Msa0146050 AT5G59820.1 32.593 135 61 4 46 179 18 123 3.46e-11 60.5

Find 60 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTCATCGAAGGTGAATTT+AGG 0.257514 1_4:+5774327 None:intergenic
CGTTTAGTCCATGGAAGATT+TGG 0.286174 1_4:+5774306 None:intergenic
AAAATTCGGAATTTCAATCT+TGG 0.317164 1_4:+5773684 None:intergenic
AGAACATTTGTAACTGAGTT+TGG 0.333314 1_4:+5774146 None:intergenic
CCGGAGTTTGCTAATAAGAT+TGG 0.334097 1_4:-5773772 Msa0146050:CDS
ATTATTCATCACTGAAAATT+CGG 0.339013 1_4:+5773670 None:intergenic
TTGTCAATGGTTGTTGGTGG+TGG 0.368111 1_4:+5774174 None:intergenic
TTTCCGACAGGACAAGCTTT+GGG 0.386450 1_4:-5773925 Msa0146050:CDS
AAATTCGGAATTTCAATCTT+GGG 0.411878 1_4:+5773685 None:intergenic
TCTGAATATCCCGGCTTATC+CGG 0.414206 1_4:-5773791 Msa0146050:CDS
AACTCCGTCGGTGGCGGTGT+TGG 0.416768 1_4:-5774060 Msa0146050:CDS
GTTTCCGACAGGACAAGCTT+TGG 0.428305 1_4:-5773926 Msa0146050:CDS
GATTCAAAGGCTTGAAATCA+TGG 0.448405 1_4:+5774196 None:intergenic
TTCTTCATCATCACAGGATG+AGG 0.458403 1_4:+5773730 None:intergenic
GAGTTTGGTGTTGTTGTCAA+TGG 0.463877 1_4:+5774161 None:intergenic
GTGTTGTTGTCAATGGTTGT+TGG 0.486272 1_4:+5774168 None:intergenic
AATTTAGGAGTAGTAGAAGT+GGG 0.488875 1_4:+5774342 None:intergenic
GCTTTCTTCTTCATCATCAC+AGG 0.490449 1_4:+5773724 None:intergenic
TTAGCAAACTCCGGATAAGC+CGG 0.495798 1_4:+5773781 None:intergenic
GAATTTAGGAGTAGTAGAAG+TGG 0.499359 1_4:+5774341 None:intergenic
ATGAGTGTTCGATTTGTCAT+AGG 0.501927 1_4:-5773951 Msa0146050:CDS
ACTTGCTTTGTGTCCACCGA+GGG 0.502207 1_4:+5774092 None:intergenic
GTCGGTGGCGGTGTTGGTGT+TGG 0.503000 1_4:-5774054 Msa0146050:CDS
TGTCATAGGTCGTTTCCGAC+AGG 0.511441 1_4:-5773937 Msa0146050:CDS
GAACGTTTACGTTTAGTCCA+TGG 0.526324 1_4:+5774297 None:intergenic
TTGTTGTCAATGGTTGTTGG+TGG 0.527436 1_4:+5774171 None:intergenic
GTGGCAGCTGAGGAAGTTGA+TGG 0.530856 1_4:+5774018 None:intergenic
GGTGGCGGTGTTGGTGTTGG+TGG 0.533807 1_4:-5774051 Msa0146050:CDS
GTTGTTGGTGGTGGATTCAA+AGG 0.535966 1_4:+5774183 None:intergenic
GCCAACACAAACGGTGGCGG+TGG 0.536836 1_4:-5773985 Msa0146050:CDS
TGTCACTACGAAGGTGTTGT+TGG 0.546239 1_4:-5773889 Msa0146050:CDS
TCGATGAACCAAATCTTCCA+TGG 0.550148 1_4:-5774314 Msa0146050:CDS
TGTAACTGTCTCTGAAGGTG+TGG 0.551186 1_4:-5773845 Msa0146050:CDS
CCAATCTTATTAGCAAACTC+CGG 0.554584 1_4:+5773772 None:intergenic
CCACCCAAAGCTTGTCCTGT+CGG 0.557784 1_4:+5773922 None:intergenic
ACCACCGCCACCGTTTGTGT+TGG 0.559183 1_4:+5773984 None:intergenic
CACTACGAAGGTGTTGTTGG+TGG 0.560111 1_4:-5773886 Msa0146050:CDS
TACGAAGGTGTTGTTGGTGG+TGG 0.560220 1_4:-5773883 Msa0146050:CDS
ACTAGCTCAGCCAACACAAA+CGG 0.565002 1_4:-5773994 Msa0146050:CDS
GTAACTGTCTCTGAAGGTGT+GGG 0.567359 1_4:-5773844 Msa0146050:CDS
TGAGCTAGTGGTGGCAGCTG+AGG 0.573892 1_4:+5774008 None:intergenic
TGATTTCGATCTGAATATCC+CGG 0.576158 1_4:-5773800 Msa0146050:CDS
CCGACAGGACAAGCTTTGGG+TGG 0.581171 1_4:-5773922 Msa0146050:CDS
TGAAATCATGGCGGTTGGTG+TGG 0.583151 1_4:+5774208 None:intergenic
TAGCAAACTCCGGATAAGCC+GGG 0.583949 1_4:+5773782 None:intergenic
AGGCTTGAAATCATGGCGGT+TGG 0.583949 1_4:+5774203 None:intergenic
TCTGCTGTAACTGTCTCTGA+AGG 0.589059 1_4:-5773850 Msa0146050:CDS
TGTCTCATCATGCTCGCTCG+TGG 0.591916 1_4:-5774231 Msa0146050:CDS
TGGAAGATTTGGTTCATCGA+AGG 0.595055 1_4:+5774317 None:intergenic
TCAGCCAACACAAACGGTGG+CGG 0.600998 1_4:-5773988 Msa0146050:CDS
AACACCAACACCGCCACCGA+CGG 0.603987 1_4:+5774056 None:intergenic
GACTTGCTTTGTGTCCACCG+AGG 0.621099 1_4:+5774091 None:intergenic
GTTTGTGTTGGCTGAGCTAG+TGG 0.622781 1_4:+5773996 None:intergenic
TCTTCTTATCAAGCCCTCGG+TGG 0.636904 1_4:-5774105 Msa0146050:CDS
ATCACGTTGATGACTATGTG+TGG 0.647702 1_4:+5773819 None:intergenic
TGTGTTGGCTGAGCTAGTGG+TGG 0.672396 1_4:+5773999 None:intergenic
TGGCAGCTGAGGAAGTTGAT+GGG 0.673304 1_4:+5774019 None:intergenic
CACAAACGTTGTCACTACGA+AGG 0.683725 1_4:-5773898 Msa0146050:CDS
AGCTCAGCCAACACAAACGG+TGG 0.690830 1_4:-5773991 Msa0146050:CDS
TCAAAGGCTTGAAATCATGG+CGG 0.753429 1_4:+5774199 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAATTCGGAATTTCAATCTT+GGG + chr1_4:5774362-5774381 None:intergenic 25.0%
! AAAATTCGGAATTTCAATCT+TGG + chr1_4:5774363-5774382 None:intergenic 25.0%
AATTTAGGAGTAGTAGAAGT+GGG + chr1_4:5773705-5773724 None:intergenic 30.0%
AGAACATTTGTAACTGAGTT+TGG + chr1_4:5773901-5773920 None:intergenic 30.0%
GAATTTAGGAGTAGTAGAAG+TGG + chr1_4:5773706-5773725 None:intergenic 35.0%
GATTCAAAGGCTTGAAATCA+TGG + chr1_4:5773851-5773870 None:intergenic 35.0%
! TTTTCTTCTTATCAAGCCCT+CGG - chr1_4:5773936-5773955 Msa0146050:CDS 35.0%
! ATGAGTGTTCGATTTGTCAT+AGG - chr1_4:5774093-5774112 Msa0146050:CDS 35.0%
TGATTTCGATCTGAATATCC+CGG - chr1_4:5774244-5774263 Msa0146050:CDS 35.0%
CCAATCTTATTAGCAAACTC+CGG + chr1_4:5774275-5774294 None:intergenic 35.0%
GGTTCATCGAAGGTGAATTT+AGG + chr1_4:5773720-5773739 None:intergenic 40.0%
! TGGAAGATTTGGTTCATCGA+AGG + chr1_4:5773730-5773749 None:intergenic 40.0%
TCGATGAACCAAATCTTCCA+TGG - chr1_4:5773730-5773749 Msa0146050:CDS 40.0%
CGTTTAGTCCATGGAAGATT+TGG + chr1_4:5773741-5773760 None:intergenic 40.0%
GAACGTTTACGTTTAGTCCA+TGG + chr1_4:5773750-5773769 None:intergenic 40.0%
TCAAAGGCTTGAAATCATGG+CGG + chr1_4:5773848-5773867 None:intergenic 40.0%
TTGTTGTCAATGGTTGTTGG+TGG + chr1_4:5773876-5773895 None:intergenic 40.0%
! GTGTTGTTGTCAATGGTTGT+TGG + chr1_4:5773879-5773898 None:intergenic 40.0%
!! GAGTTTGGTGTTGTTGTCAA+TGG + chr1_4:5773886-5773905 None:intergenic 40.0%
!! ATCACGTTGATGACTATGTG+TGG + chr1_4:5774228-5774247 None:intergenic 40.0%
!! CCGGAGTTTGCTAATAAGAT+TGG - chr1_4:5774272-5774291 Msa0146050:CDS 40.0%
TTCTTCATCATCACAGGATG+AGG + chr1_4:5774317-5774336 None:intergenic 40.0%
GCTTTCTTCTTCATCATCAC+AGG + chr1_4:5774323-5774342 None:intergenic 40.0%
!! GTTGTTGGTGGTGGATTCAA+AGG + chr1_4:5773864-5773883 None:intergenic 45.0%
! TTGTCAATGGTTGTTGGTGG+TGG + chr1_4:5773873-5773892 None:intergenic 45.0%
ACTAGCTCAGCCAACACAAA+CGG - chr1_4:5774050-5774069 Msa0146050:CDS 45.0%
TTTCCGACAGGACAAGCTTT+GGG - chr1_4:5774119-5774138 Msa0146050:CDS 45.0%
CACAAACGTTGTCACTACGA+AGG - chr1_4:5774146-5774165 Msa0146050:CDS 45.0%
!! TGTCACTACGAAGGTGTTGT+TGG - chr1_4:5774155-5774174 Msa0146050:CDS 45.0%
TCTGCTGTAACTGTCTCTGA+AGG - chr1_4:5774194-5774213 Msa0146050:CDS 45.0%
! TGTAACTGTCTCTGAAGGTG+TGG - chr1_4:5774199-5774218 Msa0146050:CDS 45.0%
! GTAACTGTCTCTGAAGGTGT+GGG - chr1_4:5774200-5774219 Msa0146050:CDS 45.0%
TCTGAATATCCCGGCTTATC+CGG - chr1_4:5774253-5774272 Msa0146050:CDS 45.0%
TTAGCAAACTCCGGATAAGC+CGG + chr1_4:5774266-5774285 None:intergenic 45.0%
! GAAGAAAGCTCGTGTTTTCG+TGG - chr1_4:5774334-5774353 Msa0146050:CDS 45.0%
! TGAAATCATGGCGGTTGGTG+TGG + chr1_4:5773839-5773858 None:intergenic 50.0%
AGGCTTGAAATCATGGCGGT+TGG + chr1_4:5773844-5773863 None:intergenic 50.0%
TCTTCTTATCAAGCCCTCGG+TGG - chr1_4:5773939-5773958 Msa0146050:CDS 50.0%
ACTTGCTTTGTGTCCACCGA+GGG + chr1_4:5773955-5773974 None:intergenic 50.0%
AGTCACCGCAAAAACTCCGT+CGG - chr1_4:5773972-5773991 Msa0146050:CDS 50.0%
! TGGCAGCTGAGGAAGTTGAT+GGG + chr1_4:5774028-5774047 None:intergenic 50.0%
!! GTTTGTGTTGGCTGAGCTAG+TGG + chr1_4:5774051-5774070 None:intergenic 50.0%
TGTCATAGGTCGTTTCCGAC+AGG - chr1_4:5774107-5774126 Msa0146050:CDS 50.0%
GTTTCCGACAGGACAAGCTT+TGG - chr1_4:5774118-5774137 Msa0146050:CDS 50.0%
!! CACTACGAAGGTGTTGTTGG+TGG - chr1_4:5774158-5774177 Msa0146050:CDS 50.0%
!! TACGAAGGTGTTGTTGGTGG+TGG - chr1_4:5774161-5774180 Msa0146050:CDS 50.0%
TAGCAAACTCCGGATAAGCC+GGG + chr1_4:5774265-5774284 None:intergenic 50.0%
TGTCTCATCATGCTCGCTCG+TGG - chr1_4:5773813-5773832 Msa0146050:CDS 55.0%
! GACTTGCTTTGTGTCCACCG+AGG + chr1_4:5773956-5773975 None:intergenic 55.0%
GTGGCAGCTGAGGAAGTTGA+TGG + chr1_4:5774029-5774048 None:intergenic 55.0%
!! TGTGTTGGCTGAGCTAGTGG+TGG + chr1_4:5774048-5774067 None:intergenic 55.0%
AGCTCAGCCAACACAAACGG+TGG - chr1_4:5774053-5774072 Msa0146050:CDS 55.0%
TCAGCCAACACAAACGGTGG+CGG - chr1_4:5774056-5774075 Msa0146050:CDS 55.0%
CCACCCAAAGCTTGTCCTGT+CGG + chr1_4:5774125-5774144 None:intergenic 55.0%
CACCGCAAAAACTCCGTCGG+TGG - chr1_4:5773975-5773994 Msa0146050:CDS 60.0%
! CGCCACCGACGGAGTTTTTG+CGG + chr1_4:5773980-5773999 None:intergenic 60.0%
CGCAAAAACTCCGTCGGTGG+CGG - chr1_4:5773978-5773997 Msa0146050:CDS 60.0%
AACACCAACACCGCCACCGA+CGG + chr1_4:5773991-5774010 None:intergenic 60.0%
TGAGCTAGTGGTGGCAGCTG+AGG + chr1_4:5774039-5774058 None:intergenic 60.0%
ACCACCGCCACCGTTTGTGT+TGG + chr1_4:5774063-5774082 None:intergenic 60.0%
!! CCGACAGGACAAGCTTTGGG+TGG - chr1_4:5774122-5774141 Msa0146050:CDS 60.0%
! AACTCCGTCGGTGGCGGTGT+TGG - chr1_4:5773984-5774003 Msa0146050:CDS 65.0%
!! GTCGGTGGCGGTGTTGGTGT+TGG - chr1_4:5773990-5774009 Msa0146050:CDS 65.0%
!! GGTGGCGGTGTTGGTGTTGG+TGG - chr1_4:5773993-5774012 Msa0146050:CDS 65.0%
! GCCAACACAAACGGTGGCGG+TGG - chr1_4:5774059-5774078 Msa0146050:CDS 65.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 5773678 5774388 5773678 ID=Msa0146050;Name=Msa0146050
chr1_4 mRNA 5773678 5774388 5773678 ID=Msa0146050-mRNA-1;Parent=Msa0146050;Name=Msa0146050-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|236
chr1_4 exon 5773678 5774388 5773678 ID=Msa0146050-mRNA-1:exon:2436;Parent=Msa0146050-mRNA-1
chr1_4 CDS 5773678 5774388 5773678 ID=Msa0146050-mRNA-1:cds;Parent=Msa0146050-mRNA-1
Gene Sequence

>Msa0146050

ATGGCTCTTGAAGCACTTAACTCACCCACTTCTACTACTCCTAAATTCACCTTCGATGAACCAAATCTTCCATGGACTAAACGTAAACGTTCTAAACGTTCACGTTCATGCACTGAAGAAGAGTATCTTGCTCTCTGTCTCATCATGCTCGCTCGTGGCCACACCAACCGCCATGATTTCAAGCCTTTGAATCCACCACCAACAACCATTGACAACAACACCAAACTCAGTTACAAATGTTCTGTCTGTAACAAAGAGTTTTCTTCTTATCAAGCCCTCGGTGGACACAAAGCAAGTCACCGCAAAAACTCCGTCGGTGGCGGTGTTGGTGTTGGTGGTGATGATCACCCATCAACTTCCTCAGCTGCCACCACTAGCTCAGCCAACACAAACGGTGGCGGTGGTGTTAGATCTCATGAGTGTTCGATTTGTCATAGGTCGTTTCCGACAGGACAAGCTTTGGGTGGACACAAACGTTGTCACTACGAAGGTGTTGTTGGTGGTGGTGCTTCTGCTTCTGCTGTAACTGTCTCTGAAGGTGTGGGATCCACACATAGTCATCAACGTGATTTCGATCTGAATATCCCGGCTTATCCGGAGTTTGCTAATAAGATTGGAGAAGATGAAGTTGAAAGTCCTCATCCTGTGATGATGAAGAAGAAAGCTCGTGTTTTCGTGGTGCCCAAGATTGAAATTCCGAATTTTCAGTGA
Protein sequence

>Msa0146050

MALEALNSPTSTTPKFTFDEPNLPWTKRKRSKRSRSCTEEEYLALCLIMLARGHTNRHDFKPLNPPPTTIDNNTKLSYKCSVCNKEFSSYQALGGHKASHRKNSVGGGVGVGGDDHPSTSSAATTSSANTNGGGGVRSHECSICHRSFPTGQALGGHKRCHYEGVVGGGASASAVTVSEGVGSTHSHQRDFDLNIPAYPEFANKIGEDEVESPHPVMMKKKARVFVVPKIEIPNFQ*