AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene026428

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene026428.t1 MTR_1g033750 92.377 223 17 0 1 223 1 223 4.27e-152 421
MS.gene026428.t1 MTR_1g114640 67.123 219 69 2 4 222 5 220 3.13e-100 290
MS.gene026428.t1 MTR_1g114690 53.778 225 86 3 4 222 5 217 6.06e-77 231
MS.gene026428.t1 MTR_1g114690 53.097 226 88 3 4 223 5 218 3.09e-76 229
MS.gene026428.t1 MTR_1g114750 51.131 221 103 3 4 223 5 221 6.98e-73 221
MS.gene026428.t1 MTR_1g114640 67.857 168 51 2 4 171 5 169 1.88e-71 215
MS.gene026428.t1 MTR_1g114690 46.154 260 88 4 4 223 5 252 1.29e-68 211
MS.gene026428.t1 MTR_1g115130 49.770 217 79 3 7 223 8 194 4.82e-63 195
MS.gene026428.t1 MTR_8g100065 49.727 183 91 1 42 223 3 185 4.85e-59 184
MS.gene026428.t1 MTR_6g077990 46.078 204 102 2 20 223 4 199 2.96e-58 183
MS.gene026428.t1 MTR_6g077990 53.704 162 75 0 62 223 37 198 5.69e-58 182
MS.gene026428.t1 MTR_8g100065 54.601 163 73 1 62 223 45 207 6.85e-58 182
MS.gene026428.t1 MTR_6g077990 55.705 149 66 0 75 223 8 156 1.10e-54 172
MS.gene026428.t1 MTR_1g114690 45.631 206 82 5 4 203 5 186 6.43e-48 156
MS.gene026428.t1 MTR_1g114680 68.468 111 35 0 113 223 53 163 8.46e-45 148
MS.gene026428.t1 MTR_3g100750 40.645 155 91 1 66 220 102 255 6.57e-41 140
MS.gene026428.t1 MTR_7g083570 37.143 175 110 0 48 222 102 276 4.15e-40 139
MS.gene026428.t1 MTR_8g069110 37.989 179 100 2 52 220 90 267 2.32e-39 137
MS.gene026428.t1 MTR_6g077990 52.778 108 51 0 62 169 37 144 6.96e-35 121
MS.gene026428.t1 MTR_8g100065 46.457 127 67 1 42 167 3 129 2.55e-32 114
MS.gene026428.t1 MTR_8g100065 53.271 107 49 1 62 167 45 151 2.13e-31 112
MS.gene026428.t1 MTR_2g076350 32.900 231 142 4 1 222 1 227 3.09e-31 115
MS.gene026428.t1 MTR_5g015750 49.296 71 33 2 4 74 5 72 4.62e-12 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene026428.t1 AT5G08350 52.857 210 85 3 15 223 19 215 7.72e-72 218
MS.gene026428.t1 AT5G23370 51.339 224 91 5 5 223 6 216 5.27e-71 216
MS.gene026428.t1 AT5G23350 48.869 221 95 4 5 220 6 213 1.41e-69 212
MS.gene026428.t1 AT5G23360 50.256 195 94 2 30 223 16 208 7.55e-67 205
MS.gene026428.t1 AT4G01600 36.279 215 123 4 23 223 13 227 1.96e-42 143
MS.gene026428.t1 AT4G01600 38.674 181 103 2 51 223 8 188 1.11e-41 140
MS.gene026428.t1 AT5G13200 33.816 207 132 2 16 221 59 261 2.81e-40 139
MS.gene026428.t1 AT4G01600 36.019 211 124 5 23 223 13 222 1.80e-38 133
MS.gene026428.t1 AT1G28200 36.478 159 100 1 62 220 97 254 6.25e-37 130
MS.gene026428.t1 AT1G28200 36.478 159 100 1 62 220 97 254 6.25e-37 130
MS.gene026428.t1 AT2G22475 35.152 165 106 1 56 220 128 291 1.72e-36 130
MS.gene026428.t1 AT5G13200 32.026 153 99 2 16 167 59 207 3.61e-22 90.5
MS.gene026428.t1 AT4G40100 34.328 134 59 1 87 220 112 216 5.65e-22 90.5
MS.gene026428.t1 AT2G22475 31.304 115 78 1 56 170 128 241 1.86e-17 79.0

Find 36 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGCAATTTCAATGTACTTT+TGG 0.206367 1.1:+18709768 None:intergenic
GTTCTAATAAAGTGGCCTTT+TGG 0.325622 1.1:+18710040 None:intergenic
TTTCTTCAAGAGCTATTAGT+TGG 0.372608 1.1:-18710988 MS.gene026428:CDS
CTCACTAGGATGAACAATCT+TGG 0.396062 1.1:-18710696 MS.gene026428:CDS
ATTCACCTCAGCAGCATACT+TGG 0.404852 1.1:-18710959 MS.gene026428:CDS
AATTGATCCCTCACTACAAA+AGG 0.422203 1.1:+18710075 None:intergenic
CTTTATTAGAACACATTACA+AGG 0.441996 1.1:-18710029 MS.gene026428:intron
TGGGTGATAATTCATCAAAT+AGG 0.448132 1.1:-18710939 MS.gene026428:CDS
ATTAAAATCTCTTCTCCAAA+AGG 0.451169 1.1:-18710055 MS.gene026428:CDS
TCACTAGGATGAACAATCTT+GGG 0.454379 1.1:-18710695 MS.gene026428:CDS
CTTATTGTAGTAGTTGGACT+TGG 0.459996 1.1:+18710900 None:intergenic
GCTTGACTTATTGTAGTAGT+TGG 0.460001 1.1:+18710894 None:intergenic
TTATTCCACTTGGCAAGATA+AGG 0.462580 1.1:-18709826 MS.gene026428:CDS
TTTAAAATGCAGTGAAACTA+GGG 0.462654 1.1:-18710294 MS.gene026428:intron
GTGAAAGGAAAACTGAGGTT+AGG 0.467486 1.1:-18710253 MS.gene026428:CDS
GGAGCTAGAATTCTTCAAGT+TGG 0.475294 1.1:-18710232 MS.gene026428:CDS
TGTTATCTATCAACAACAAT+GGG 0.480358 1.1:-18710139 MS.gene026428:CDS
TGTAATGTGTTCTAATAAAG+TGG 0.482439 1.1:+18710032 None:intergenic
TCAAGTTGGAGGAGTGGAAA+AGG 0.489991 1.1:-18710218 MS.gene026428:CDS
GCTAGAATTCTTCAAGTTGG+AGG 0.512754 1.1:-18710229 MS.gene026428:CDS
ACAACAATGGGTCCTCTAGC+AGG 0.513963 1.1:-18710127 MS.gene026428:CDS
ATGTTATCTATCAACAACAA+TGG 0.535398 1.1:-18710140 MS.gene026428:CDS
AAGTATGCTGCTGAGGTGAA+TGG 0.545777 1.1:+18710961 None:intergenic
TTGTAGGTCATTATTCCACT+TGG 0.560547 1.1:-18709836 MS.gene026428:intron
TTAGTGTAAAAGATGAAGAG+AGG 0.564160 1.1:-18710180 MS.gene026428:CDS
AATTCTTCAAGTTGGAGGAG+TGG 0.572161 1.1:-18710224 MS.gene026428:CDS
TTCACCTCAGCAGCATACTT+GGG 0.589074 1.1:-18710958 MS.gene026428:CDS
GAGCAAATTCAGTTCTCACT+AGG 0.589590 1.1:-18710710 MS.gene026428:CDS
AAAATAACTGATACAGTGAA+AGG 0.595974 1.1:-18710268 MS.gene026428:CDS
AAAGTACATTGAAATTGCTA+CGG 0.602017 1.1:-18709765 MS.gene026428:CDS
ACAAACCTTATCTTGCCAAG+TGG 0.607201 1.1:+18709821 None:intergenic
ATCACCCAAGTATGCTGCTG+AGG 0.611603 1.1:+18710954 None:intergenic
GTACATTGAAATTGCTACGG+TGG 0.620058 1.1:-18709762 MS.gene026428:CDS
GCAACTGGACTCAAAGAACA+TGG 0.622654 1.1:-18710654 MS.gene026428:intron
ATGAAGAGTAAGCCTGCTAG+AGG 0.652380 1.1:+18710115 None:intergenic
ATACAGTGAAAGGAAAACTG+AGG 0.714258 1.1:-18710258 MS.gene026428:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACTAATTATATTAGTATA+TGG + chr1.1:18710070-18710089 None:intergenic 10.0%
!! GAAGATTAAATTTAAATTAA+AGG + chr1.1:18709833-18709852 None:intergenic 10.0%
!! AAAAAATAACGTTATAAATG+AGG + chr1.1:18710364-18710383 None:intergenic 15.0%
!!! AAGTTTTTCTTTATATTTCT+TGG + chr1.1:18709872-18709891 None:intergenic 15.0%
!! TGAAAAAAAAAATGTCTAAG+AGG + chr1.1:18710266-18710285 None:intergenic 20.0%
!! TTAAAAATCATATGAAGCAA+AGG + chr1.1:18710792-18710811 None:intergenic 20.0%
!!! ACATTTTTTTTTTCATCTAG+AGG - chr1.1:18710271-18710290 MS.gene026428:CDS 20.0%
!!! ATTTTCTTTAACCCTATTAT+TGG - chr1.1:18710176-18710195 MS.gene026428:CDS 20.0%
!!! CATTTTTTTTTTCATCTAGA+GGG - chr1.1:18710272-18710291 MS.gene026428:CDS 20.0%
! AAAATAACTGATACAGTGAA+AGG - chr1.1:18710408-18710427 MS.gene026428:intron 25.0%
! AAAGTACATTGAAATTGCTA+CGG - chr1.1:18710911-18710930 MS.gene026428:CDS 25.0%
! ATGTTATCTATCAACAACAA+TGG - chr1.1:18710536-18710555 MS.gene026428:intron 25.0%
! ATTAAAATCTCTTCTCCAAA+AGG - chr1.1:18710621-18710640 MS.gene026428:intron 25.0%
! CTTTATTAGAACACATTACA+AGG - chr1.1:18710647-18710666 MS.gene026428:intron 25.0%
! GATAAATCTCACCAATAATA+GGG + chr1.1:18710190-18710209 None:intergenic 25.0%
! TGTAATGTGTTCTAATAAAG+TGG + chr1.1:18710647-18710666 None:intergenic 25.0%
! TGTAATTTATCTATCCTTGT+AGG - chr1.1:18710824-18710843 MS.gene026428:intron 25.0%
! TGTTATCTATCAACAACAAT+GGG - chr1.1:18710537-18710556 MS.gene026428:intron 25.0%
!! AGCAATTTCAATGTACTTTT+GGG + chr1.1:18710910-18710929 None:intergenic 25.0%
!! TAGCAATTTCAATGTACTTT+TGG + chr1.1:18710911-18710930 None:intergenic 25.0%
!! TTTAAAATGCAGTGAAACTA+GGG - chr1.1:18710382-18710401 MS.gene026428:intron 25.0%
!!! AATCGTTATTTTTTCTCTTC+AGG - chr1.1:18709941-18709960 MS.gene026428:intron 25.0%
!!! GATTTTGAGTTTTGGTTTAT+GGG - chr1.1:18710939-18710958 MS.gene026428:CDS 25.0%
!!! TGATTTTGAGTTTTGGTTTA+TGG - chr1.1:18710938-18710957 MS.gene026428:CDS 25.0%
!!! TTTTAAAATGCAGTGAAACT+AGG - chr1.1:18710381-18710400 MS.gene026428:intron 25.0%
GGATAAATCTCACCAATAAT+AGG + chr1.1:18710191-18710210 None:intergenic 30.0%
TGGGTGATAATTCATCAAAT+AGG - chr1.1:18709737-18709756 MS.gene026428:CDS 30.0%
TTAGTGTAAAAGATGAAGAG+AGG - chr1.1:18710496-18710515 MS.gene026428:intron 30.0%
TTTCTTCAAGAGCTATTAGT+TGG - chr1.1:18709688-18709707 MS.gene026428:CDS 30.0%
! AAAATTGCCTTTTGTAGTGA+GGG - chr1.1:18710594-18710613 MS.gene026428:intron 30.0%
! AAAGCTAACAATTTTGCAAC+TGG - chr1.1:18710007-18710026 MS.gene026428:intron 30.0%
! TAAAATTGCCTTTTGTAGTG+AGG - chr1.1:18710593-18710612 MS.gene026428:intron 30.0%
!! ATTTCAATGTACTTTTGGGT+AGG + chr1.1:18710906-18710925 None:intergenic 30.0%
AAGTGGAATAATGACCTACA+AGG + chr1.1:18710841-18710860 None:intergenic 35.0%
AATTGATCCCTCACTACAAA+AGG + chr1.1:18710604-18710623 None:intergenic 35.0%
AGGAGAGACTTCACTAAAAA+TGG + chr1.1:18710246-18710265 None:intergenic 35.0%
ATACAGTGAAAGGAAAACTG+AGG - chr1.1:18710418-18710437 MS.gene026428:intron 35.0%
ATAGCCGTTAAGTACATGTT+TGG - chr1.1:18710699-18710718 MS.gene026428:CDS 35.0%
CAAAGGATTTAGTATCTGCA+TGG + chr1.1:18710775-18710794 None:intergenic 35.0%
CGATCCAAACATGTACTTAA+CGG + chr1.1:18710706-18710725 None:intergenic 35.0%
CTTATTGTAGTAGTTGGACT+TGG + chr1.1:18709779-18709798 None:intergenic 35.0%
GATTTAGTATCTGCATGGAT+TGG + chr1.1:18710770-18710789 None:intergenic 35.0%
GCTTGACTTATTGTAGTAGT+TGG + chr1.1:18709785-18709804 None:intergenic 35.0%
TAACGTTATAAATGAGGTCG+AGG + chr1.1:18710358-18710377 None:intergenic 35.0%
TCACTAGGATGAACAATCTT+GGG - chr1.1:18709981-18710000 MS.gene026428:intron 35.0%
TTATTCCACTTGGCAAGATA+AGG - chr1.1:18710850-18710869 MS.gene026428:intron 35.0%
TTGTAGGTCATTATTCCACT+TGG - chr1.1:18710840-18710859 MS.gene026428:intron 35.0%
! ACAAGAGCATATGAGAAGAA+CGG + chr1.1:18709903-18709922 None:intergenic 35.0%
! GTTCTAATAAAGTGGCCTTT+TGG + chr1.1:18710639-18710658 None:intergenic 35.0%
ACAAACCTTATCTTGCCAAG+TGG + chr1.1:18710858-18710877 None:intergenic 40.0%
CTCACTAGGATGAACAATCT+TGG - chr1.1:18709980-18709999 MS.gene026428:intron 40.0%
GAGCAAATTCAGTTCTCACT+AGG - chr1.1:18709966-18709985 MS.gene026428:intron 40.0%
GGAGCTAGAATTCTTCAAGT+TGG - chr1.1:18710444-18710463 MS.gene026428:intron 40.0%
GTACATTGAAATTGCTACGG+TGG - chr1.1:18710914-18710933 MS.gene026428:CDS 40.0%
GTATCGCATAGGCAATGTTT+CGG + chr1.1:18710305-18710324 None:intergenic 40.0%
GTGAAAGGAAAACTGAGGTT+AGG - chr1.1:18710423-18710442 MS.gene026428:intron 40.0%
GTTAATTCCTCGCTAGTCAT+AGG + chr1.1:18710224-18710243 None:intergenic 40.0%
TATCGCATAGGCAATGTTTC+GGG + chr1.1:18710304-18710323 None:intergenic 40.0%
!! AATTCTTCAAGTTGGAGGAG+TGG - chr1.1:18710452-18710471 MS.gene026428:intron 40.0%
!! GCTAGAATTCTTCAAGTTGG+AGG - chr1.1:18710447-18710466 MS.gene026428:intron 40.0%
!! TTAGTATCTGCATGGATTGG+CGG + chr1.1:18710767-18710786 None:intergenic 40.0%
!!! CGGTGGATGATTTTGAGTTT+TGG - chr1.1:18710931-18710950 MS.gene026428:CDS 40.0%
AAGTATGCTGCTGAGGTGAA+TGG + chr1.1:18709718-18709737 None:intergenic 45.0%
ATGAAGAGTAAGCCTGCTAG+AGG + chr1.1:18710564-18710583 None:intergenic 45.0%
ATTCACCTCAGCAGCATACT+TGG - chr1.1:18709717-18709736 MS.gene026428:CDS 45.0%
GCAACTGGACTCAAAGAACA+TGG - chr1.1:18710022-18710041 MS.gene026428:intron 45.0%
TCGCTAGTCATAGGCAACAT+CGG + chr1.1:18710215-18710234 None:intergenic 45.0%
TTCACCTCAGCAGCATACTT+GGG - chr1.1:18709718-18709737 MS.gene026428:CDS 45.0%
! TCCTTTGACTCGTATCGCAT+AGG + chr1.1:18710316-18710335 None:intergenic 45.0%
!! TCAAGTTGGAGGAGTGGAAA+AGG - chr1.1:18710458-18710477 MS.gene026428:intron 45.0%
ACAACAATGGGTCCTCTAGC+AGG - chr1.1:18710549-18710568 MS.gene026428:intron 50.0%
ATCACCCAAGTATGCTGCTG+AGG + chr1.1:18709725-18709744 None:intergenic 50.0%
CTAGTCATAGGCAACATCGG+TGG + chr1.1:18710212-18710231 None:intergenic 50.0%
GATGTTGCCTATGACTAGCG+AGG - chr1.1:18710214-18710233 MS.gene026428:CDS 50.0%
GCCTATGCGATACGAGTCAA+AGG - chr1.1:18710312-18710331 MS.gene026428:intron 50.0%
!! GCATGGATTGGCGGTGAGTT+TGG + chr1.1:18710758-18710777 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 18709679 18711019 18709679 ID=MS.gene026428
chr1.1 mRNA 18709679 18711019 18709679 ID=MS.gene026428.t1;Parent=MS.gene026428
chr1.1 exon 18710878 18711019 18710878 ID=MS.gene026428.t1.exon1;Parent=MS.gene026428.t1
chr1.1 CDS 18710878 18711019 18710878 ID=cds.MS.gene026428.t1;Parent=MS.gene026428.t1
chr1.1 exon 18710655 18710735 18710655 ID=MS.gene026428.t1.exon2;Parent=MS.gene026428.t1
chr1.1 CDS 18710655 18710735 18710655 ID=cds.MS.gene026428.t1;Parent=MS.gene026428.t1
chr1.1 exon 18710030 18710304 18710030 ID=MS.gene026428.t1.exon3;Parent=MS.gene026428.t1
chr1.1 CDS 18710030 18710304 18710030 ID=cds.MS.gene026428.t1;Parent=MS.gene026428.t1
chr1.1 exon 18709679 18709852 18709679 ID=MS.gene026428.t1.exon4;Parent=MS.gene026428.t1
chr1.1 CDS 18709679 18709852 18709679 ID=cds.MS.gene026428.t1;Parent=MS.gene026428.t1
Gene Sequence

>MS.gene026428

ATGGCTTATTTTCTTCAAGAGCTATTAGTTGGATTTCCATTCACCTCAGCAGCATACTTGGGTGATAATTCATCAAATAGGTACTTAATAAATTCTTCCAAGTCCAACTACTACAATAAGTCAAGCACAAATTCAAATCAAAGTAAGACATCCTTTAATTTAAATTTAATCTTCATTGATCAAGTTTTTACCAAGAAATATAAAGAAAAACTTTATTTGATCCGTTCTTCTCATATGCTCTTGTTGTATTCACAATATTGAAAATCGTTATTTTTTCTCTTCAGGTAGAGCAAATTCAGTTCTCACTAGGATGAACAATCTTGGGAGAAAAGCTAACAATTTTGCAACTGGACTCAAAGAACATGGTATATACATATACTCATCGAAACCATATACTAATATAATTAGTTTGCACATGTCTAAATAATTTACTAAATTTTAGAACTTGAACTTGTATATTAGTATTTCTCAACAATATAATATACAATAAATTTGTAATTTTCTTTAACCCTATTATTGGTGAGATTTATCCACCGATGTTGCCTATGACTAGCGAGGAATTAACCATTTTTAGTGAAGTCTCTCCTCTTAGACATTTTTTTTTTCATCTAGAGGGCTTAAACCCGAAACATTGCCTATGCGATACGAGTCAAAGGATTCTAGTCTAGAATCGAGACCTCGACCTCATTTATAACGTTATTTTTTTAAAATGCAGTGAAACTAGGGCAAAAAATAACTGATACAGTGAAAGGAAAACTGAGGTTAGGAGCTAGAATTCTTCAAGTTGGAGGAGTGGAAAAGGTGTTCATGCAACTTTTTAGTGTAAAAGATGAAGAGAGGCTACTAAAAGCATCTTTATGTTATCTATCAACAACAATGGGTCCTCTAGCAGGCTTACTCTTCATATCAACTAATAAAATTGCCTTTTGTAGTGAGGGATCAATTAAAATCTCTTCTCCAAAAGGCCACTTTATTAGAACACATTACAAGGTAATAATACACATATTGATTTGTACAAAAATAGCCGTTAAGTACATGTTTGGATCGATAGTGAGTTTGACTAAATCGTGATTTCTCCAAACTCACCGCCAATCCATGCAGATACTAAATCCTTTGCTTCATATGATTTTTAATCTCATAAACATTGTAATTTATCTATCCTTGTAGGTCATTATTCCACTTGGCAAGATAAGGTTTGTTAATCAAAGTGAGCATGTGAAGAAGCCTACCCAAAAGTACATTGAAATTGCTACGGTGGATGATTTTGAGTTTTGGTTTATGGGTTTCTTAAATCATCAGCAAGCTTTCAAATATTTGAAGCAAGCTATCTCTCAATCTTAG
Protein sequence

>MS.gene026428.t1

MAYFLQELLVGFPFTSAAYLGDNSSNRYLINSSKSNYYNKSSTNSNQSRANSVLTRMNNLGRKANNFATGLKEHVKLGQKITDTVKGKLRLGARILQVGGVEKVFMQLFSVKDEERLLKASLCYLSTTMGPLAGLLFISTNKIAFCSEGSIKISSPKGHFIRTHYKVIIPLGKIRFVNQSEHVKKPTQKYIEIATVDDFEFWFMGFLNHQQAFKYLKQAISQS