AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0793270


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0793270 MtrunA17_Chr7g0222831 93.064 173 12 0 1 173 12 184 4.48e-101 288
Msa0793270 MtrunA17_Chr1g0212561 57.895 190 58 6 1 172 16 201 5.07e-58 180
Msa0793270 MtrunA17_Chr1g0182161 48.428 159 66 2 1 159 16 158 6.06e-41 135
Msa0793270 MtrunA17_Chr7g0263121 45.614 171 73 5 1 168 15 168 4.68e-36 123
Msa0793270 MtrunA17_Chr1g0182181 42.236 161 73 4 1 159 11 153 1.40e-33 116
Msa0793270 MtrunA17_Chr7g0263131 45.223 157 59 5 2 155 15 147 1.02e-32 114
Msa0793270 MtrunA17_Chr2g0327901 43.590 156 51 3 3 158 12 130 1.83e-30 107
Msa0793270 MtrunA17_Chr1g0197281 37.383 214 64 7 1 155 102 304 3.27e-29 110
Msa0793270 MtrunA17_Chr1g0180311 38.693 199 68 5 1 155 81 269 9.47e-26 100
Msa0793270 MtrunA17_Chr2g0320311 36.937 222 60 11 1 156 75 282 2.89e-22 90.5
Msa0793270 MtrunA17_Chr4g0027991 31.390 223 62 5 2 156 67 266 5.88e-22 89.7
Msa0793270 MtrunA17_Chr1g0207451 41.414 99 51 3 1 97 60 153 2.40e-16 73.9
Msa0793270 MtrunA17_Chr7g0231181 43.478 92 44 3 12 97 219 308 2.27e-15 72.4
Msa0793270 MtrunA17_Chr4g0012691 46.988 83 28 2 29 97 220 300 2.48e-15 72.4
Msa0793270 MtrunA17_Chr3g0134711 31.765 170 83 3 1 154 52 204 1.86e-14 68.6
Msa0793270 MtrunA17_Chr1g0152661 30.233 172 80 5 1 152 43 194 2.39e-14 68.2
Msa0793270 MtrunA17_Chr1g0188901 44.944 89 32 3 28 99 59 147 3.09e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0793270 AT2G28710.1 45.238 168 59 6 1 163 14 153 1.77e-35 121
Msa0793270 AT2G37430.1 42.775 173 80 4 1 170 17 173 5.51e-33 115
Msa0793270 AT3G53600.1 41.714 175 76 6 1 170 17 170 2.67e-30 108
Msa0793270 AT2G28200.1 38.785 214 80 6 1 170 77 283 8.86e-30 110
Msa0793270 AT5G59820.1 56.122 98 34 4 2 98 16 105 3.80e-27 100
Msa0793270 AT3G46090.1 40.127 157 60 5 2 148 17 149 5.88e-27 100
Msa0793270 AT3G46080.1 41.333 150 65 4 2 146 16 147 4.46e-25 95.5
Msa0793270 AT5G04390.1 35.268 224 73 8 1 155 100 320 4.85e-25 99.4
Msa0793270 AT5G03510.1 41.333 150 43 5 1 105 73 222 1.55e-24 97.1
Msa0793270 AT3G46070.1 41.290 155 66 6 2 148 16 153 4.07e-22 87.8
Msa0793270 AT3G10470.1 37.791 172 63 6 28 155 181 352 2.28e-21 89.7
Msa0793270 AT5G43170.1 44.898 98 46 3 1 97 50 140 1.34e-17 76.6
Msa0793270 AT2G45120.1 39.655 116 50 3 1 97 151 265 1.66e-17 78.6
Msa0793270 AT1G49900.1 36.364 121 69 4 29 143 750 868 9.47e-17 77.4
Msa0793270 AT1G49900.1 30.968 155 89 4 8 146 172 324 1.86e-15 73.6
Msa0793270 AT1G02030.1 49.367 79 37 1 26 101 157 235 1.45e-16 75.1
Msa0793270 AT3G49930.1 37.719 114 52 3 1 97 60 171 6.44e-16 72.8
Msa0793270 AT3G60580.1 37.594 133 54 5 1 107 127 256 3.53e-15 71.6
Msa0793270 AT3G19580.1 36.752 117 54 3 1 97 71 187 9.55e-15 70.5
Msa0793270 AT3G19580.2 36.752 117 54 3 1 97 71 187 9.55e-15 70.5
Msa0793270 AT5G04340.1 35.294 119 55 2 1 97 52 170 1.30e-14 69.7
Msa0793270 AT1G27730.1 35.185 162 75 6 1 152 55 196 2.70e-14 68.6
Msa0793270 AT5G67450.1 34.146 123 55 2 1 97 64 186 2.20e-13 66.2
Msa0793270 AT5G61470.1 44.928 69 38 0 29 97 228 296 7.63e-12 62.8
Msa0793270 AT4G35280.1 37.719 114 43 4 1 97 142 244 5.66e-11 60.1
Msa0793270 AT5G56200.1 29.927 137 73 2 31 144 344 480 5.93e-11 60.5
Msa0793270 AT2G17180.1 35.246 122 57 5 1 105 125 241 8.26e-11 59.3

Find 34 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCTAGAAACAAGAGAGTTT+TGG 0.329211 5_3:-5250150 Msa0793270:CDS
GACTCCCTTTGAGAATGATT+TGG 0.338834 5_3:-5250105 Msa0793270:CDS
GATTTGGAGTTTCTGAAGAT+TGG 0.360026 5_3:-5250089 Msa0793270:CDS
TTTGCAATAGGACAAGCTTT+AGG 0.385361 5_3:-5250302 Msa0793270:CDS
TGTGGATTGGAGTTTGCAAT+AGG 0.393580 5_3:-5250314 Msa0793270:CDS
ACACATGAGTGTTCTATTTG+TGG 0.398280 5_3:-5250332 Msa0793270:CDS
TGTAGCAGTGGTGGTGGTGG+TGG 0.405921 5_3:-5250206 Msa0793270:CDS
TTCAAGCCCTAGGTGGTCAT+AGG 0.408731 5_3:-5250430 Msa0793270:CDS
TCACAAGAAGCCAAGGTTGA+TGG 0.443193 5_3:-5250402 Msa0793270:CDS
CCACCTAGGGCTTGAAATGA+AGG 0.446333 5_3:+5250437 None:intergenic
CATAGAGCTTCAAATATGAA+TGG 0.476589 5_3:-5250263 Msa0793270:CDS
TTGATGGGAGAAAATATTGA+TGG 0.490093 5_3:-5250386 Msa0793270:CDS
AACTCCAAATCATTCTCAAA+GGG 0.502858 5_3:+5250101 None:intergenic
TGAGTGTTCTATTTGTGGAT+TGG 0.512248 5_3:-5250327 Msa0793270:CDS
CACAAGAAGCCAAGGTTGAT+GGG 0.513592 5_3:-5250401 Msa0793270:CDS
AGTTGTAGCAGTGGTGGTGG+TGG 0.515605 5_3:-5250209 Msa0793270:CDS
AAACTCCAAATCATTCTCAA+AGG 0.533957 5_3:+5250100 None:intergenic
TTTCCTTCATTTCAAGCCCT+AGG 0.534557 5_3:-5250440 Msa0793270:CDS
TCAAGCCCTAGGTGGTCATA+GGG 0.557115 5_3:-5250429 Msa0793270:CDS
ATGAGTTGTAGCAGTGGTGG+TGG 0.557976 5_3:-5250212 Msa0793270:CDS
AAGCTCTATGTCTCCTCATG+TGG 0.562112 5_3:+5250276 None:intergenic
GGAGTTTCTGAAGATTGGAA+AGG 0.563168 5_3:-5250084 Msa0793270:CDS
AAGCTTTAGGTGGCCACATG+AGG 0.574238 5_3:-5250289 Msa0793270:CDS
TGTTTGATGTTACTTTCTCG+TGG 0.575084 5_3:-5250542 Msa0793270:CDS
TAACATCAAACAATTTGCCA+TGG 0.576305 5_3:+5250553 None:intergenic
ACTTGCCCTATGACCACCTA+GGG 0.582911 5_3:+5250424 None:intergenic
TGAAGTGGTAGATGAATATG+TGG 0.588513 5_3:+5250502 None:intergenic
AAACACACGATTGTTTGAAG+TGG 0.591898 5_3:+5250487 None:intergenic
GCAATAGGACAAGCTTTAGG+TGG 0.602680 5_3:-5250299 Msa0793270:CDS
GGGCAAGTCACAAGAAGCCA+AGG 0.614071 5_3:-5250409 Msa0793270:CDS
GACTTGCCCTATGACCACCT+AGG 0.633456 5_3:+5250423 None:intergenic
CCTTCATTTCAAGCCCTAGG+TGG 0.640290 5_3:-5250437 Msa0793270:CDS
AATACTATGAGTTGTAGCAG+TGG 0.665691 5_3:-5250218 Msa0793270:CDS
ACTATGAGTTGTAGCAGTGG+TGG 0.688595 5_3:-5250215 Msa0793270:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TTGATGGGAGAAAATATTGA+TGG - chr5_3:5250217-5250236 Msa0793270:CDS 30.0%
! ATAGAACACTCATGTGTTTT+AGG + chr5_3:5250268-5250287 None:intergenic 30.0%
CATAGAGCTTCAAATATGAA+TGG - chr5_3:5250340-5250359 Msa0793270:CDS 30.0%
!!! AAACAAGAGAGTTTTGGTTT+TGG - chr5_3:5250459-5250478 Msa0793270:CDS 30.0%
AACTCCAAATCATTCTCAAA+GGG + chr5_3:5250505-5250524 None:intergenic 30.0%
AAACTCCAAATCATTCTCAA+AGG + chr5_3:5250506-5250525 None:intergenic 30.0%
!! TGTTTGATGTTACTTTCTCG+TGG - chr5_3:5250061-5250080 Msa0793270:CDS 35.0%
TGAAGTGGTAGATGAATATG+TGG + chr5_3:5250104-5250123 None:intergenic 35.0%
AAACACACGATTGTTTGAAG+TGG + chr5_3:5250119-5250138 None:intergenic 35.0%
! ATATTTTCTCCCATCAACCT+TGG + chr5_3:5250214-5250233 None:intergenic 35.0%
!! ACTCATGTGTTTTAGGCTTT+GGG + chr5_3:5250261-5250280 None:intergenic 35.0%
ACACATGAGTGTTCTATTTG+TGG - chr5_3:5250271-5250290 Msa0793270:CDS 35.0%
TGAGTGTTCTATTTGTGGAT+TGG - chr5_3:5250276-5250295 Msa0793270:CDS 35.0%
TTTGCAATAGGACAAGCTTT+AGG - chr5_3:5250301-5250320 Msa0793270:CDS 35.0%
AATACTATGAGTTGTAGCAG+TGG - chr5_3:5250385-5250404 Msa0793270:CDS 35.0%
! AGCTAGAAACAAGAGAGTTT+TGG - chr5_3:5250453-5250472 Msa0793270:CDS 35.0%
!!! GAGAGTTTTGGTTTTGGATT+TGG - chr5_3:5250465-5250484 Msa0793270:CDS 35.0%
! GATTTGGAGTTTCTGAAGAT+TGG - chr5_3:5250514-5250533 Msa0793270:CDS 35.0%
TTTCCTTCATTTCAAGCCCT+AGG - chr5_3:5250163-5250182 Msa0793270:CDS 40.0%
!! TCATGTGTTTTAGGCTTTGG+GGG + chr5_3:5250259-5250278 None:intergenic 40.0%
!! CTCATGTGTTTTAGGCTTTG+GGG + chr5_3:5250260-5250279 None:intergenic 40.0%
!! CACTCATGTGTTTTAGGCTT+TGG + chr5_3:5250262-5250281 None:intergenic 40.0%
!! TGTGGATTGGAGTTTGCAAT+AGG - chr5_3:5250289-5250308 Msa0793270:CDS 40.0%
! GACTCCCTTTGAGAATGATT+TGG - chr5_3:5250498-5250517 Msa0793270:CDS 40.0%
! GGAGTTTCTGAAGATTGGAA+AGG - chr5_3:5250519-5250538 Msa0793270:CDS 40.0%
TCACAAGAAGCCAAGGTTGA+TGG - chr5_3:5250201-5250220 Msa0793270:CDS 45.0%
! CACAAGAAGCCAAGGTTGAT+GGG - chr5_3:5250202-5250221 Msa0793270:CDS 45.0%
!! GCAATAGGACAAGCTTTAGG+TGG - chr5_3:5250304-5250323 Msa0793270:CDS 45.0%
AAGCTCTATGTCTCCTCATG+TGG + chr5_3:5250330-5250349 None:intergenic 45.0%
ACTATGAGTTGTAGCAGTGG+TGG - chr5_3:5250388-5250407 Msa0793270:CDS 45.0%
CCACCTAGGGCTTGAAATGA+AGG + chr5_3:5250169-5250188 None:intergenic 50.0%
CCTTCATTTCAAGCCCTAGG+TGG - chr5_3:5250166-5250185 Msa0793270:CDS 50.0%
TTCAAGCCCTAGGTGGTCAT+AGG - chr5_3:5250173-5250192 Msa0793270:CDS 50.0%
TCAAGCCCTAGGTGGTCATA+GGG - chr5_3:5250174-5250193 Msa0793270:CDS 50.0%
ACTTGCCCTATGACCACCTA+GGG + chr5_3:5250182-5250201 None:intergenic 50.0%
!! AAGCTTTAGGTGGCCACATG+AGG - chr5_3:5250314-5250333 Msa0793270:CDS 50.0%
ATGAGTTGTAGCAGTGGTGG+TGG - chr5_3:5250391-5250410 Msa0793270:CDS 50.0%
GACTTGCCCTATGACCACCT+AGG + chr5_3:5250183-5250202 None:intergenic 55.0%
GGGCAAGTCACAAGAAGCCA+AGG - chr5_3:5250194-5250213 Msa0793270:CDS 55.0%
!! AGTTGTAGCAGTGGTGGTGG+TGG - chr5_3:5250394-5250413 Msa0793270:CDS 55.0%
!! TGTAGCAGTGGTGGTGGTGG+TGG - chr5_3:5250397-5250416 Msa0793270:CDS 60.0%
!! AGCAGTGGTGGTGGTGGTGG+TGG - chr5_3:5250400-5250419 Msa0793270:CDS 65.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 5250052 5250573 5250052 ID=Msa0793270;Name=Msa0793270
chr5_3 mRNA 5250052 5250573 5250052 ID=Msa0793270-mRNA-1;Parent=Msa0793270;Name=Msa0793270-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|-1|0|1|-1|1|1|0|173
chr5_3 exon 5250052 5250573 5250052 ID=Msa0793270-mRNA-1:exon:2032;Parent=Msa0793270-mRNA-1
chr5_3 CDS 5250052 5250573 5250052 ID=Msa0793270-mRNA-1:cds;Parent=Msa0793270-mRNA-1
Gene Sequence

>Msa0793270

ATGGCAAATTGTTTGATGTTACTTTCTCGTGGAAGTGATCAATTTGAAGCCACATATTCATCTACCACTTCAAACAATCGTGTGTTTGAATGTAAAACATGCAATAGACAATTTCCTTCATTTCAAGCCCTAGGTGGTCATAGGGCAAGTCACAAGAAGCCAAGGTTGATGGGAGAAAATATTGATGGTCAATTGCTACATACACCCCCAAAGCCTAAAACACATGAGTGTTCTATTTGTGGATTGGAGTTTGCAATAGGACAAGCTTTAGGTGGCCACATGAGGAGACATAGAGCTTCAAATATGAATGGAAATAACAAGATGCACAATTCTAATACTATGAGTTGTAGCAGTGGTGGTGGTGGTGGTGGTAGTAGTATTGATTCTTCACAAAATATGAAAGCTAGAAACAAGAGAGTTTTGGTTTTGGATTTGGATTTGAATTTGACTCCCTTTGAGAATGATTTGGAGTTTCTGAAGATTGGAAAGGCAACTGCTAATTTGATTGATTATTTTCATTGA

Protein sequence

>Msa0793270

MANCLMLLSRGSDQFEATYSSTTSNNRVFECKTCNRQFPSFQALGGHRASHKKPRLMGENIDGQLLHTPPKPKTHECSICGLEFAIGQALGGHMRRHRASNMNGNNKMHNSNTMSCSSGGGGGGSSIDSSQNMKARNKRVLVLDLDLNLTPFENDLEFLKIGKATANLIDYFH*