AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene43899


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43899.t1 MTR_5g035010 93.590 156 10 0 1 156 1 156 2.26e-110 310
MS.gene43899.t1 MTR_8g012550 29.801 151 105 1 1 151 1 150 1.23e-19 80.5
MS.gene43899.t1 MTR_1g030810 32.026 153 97 5 3 151 1 150 2.32e-15 69.3
MS.gene43899.t1 MTR_1g030820 30.968 155 96 6 3 151 1 150 4.13e-14 65.9
MS.gene43899.t1 MTR_1g030840 30.827 133 86 3 3 130 1 132 2.16e-12 61.6
MS.gene43899.t1 MTR_1g031640 29.630 135 86 5 9 141 7 134 2.36e-12 61.2
MS.gene43899.t1 MTR_8g045520 27.097 155 109 4 3 155 1 153 6.55e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43899.t1 AT1G24020 51.678 149 72 0 3 151 1 149 2.71e-55 171
MS.gene43899.t1 AT1G24020 51.678 149 72 0 3 151 1 149 2.71e-55 171
MS.gene43899.t1 AT1G70830 34.868 152 96 2 2 151 19 169 2.11e-22 88.2
MS.gene43899.t1 AT1G70830 34.868 152 96 2 2 151 19 169 3.89e-22 88.2
MS.gene43899.t1 AT1G70840 36.667 150 92 2 4 151 19 167 4.13e-22 87.4
MS.gene43899.t1 AT1G70830 34.868 152 96 2 2 151 19 169 1.43e-21 87.8
MS.gene43899.t1 AT1G70850 34.416 154 98 2 2 153 6 158 1.93e-21 87.0
MS.gene43899.t1 AT1G70830 34.868 152 96 2 2 151 19 169 3.52e-21 88.2
MS.gene43899.t1 AT1G70830 33.333 150 97 2 4 151 183 331 1.72e-19 83.6
MS.gene43899.t1 AT1G70850 34.416 154 98 2 2 153 6 158 6.02e-21 87.0
MS.gene43899.t1 AT1G70850 33.813 139 89 2 15 151 175 312 2.28e-17 77.4
MS.gene43899.t1 AT1G70850 34.416 154 98 2 2 153 6 158 6.02e-21 87.0
MS.gene43899.t1 AT1G70850 33.813 139 89 2 15 151 175 312 2.28e-17 77.4
MS.gene43899.t1 AT1G70890 36.184 152 94 3 2 151 4 154 7.39e-21 83.6
MS.gene43899.t1 AT1G70830 33.333 150 97 2 4 151 136 284 8.27e-20 83.6
MS.gene43899.t1 AT1G70830 36.471 85 52 1 69 151 38 122 9.82e-11 58.9
MS.gene43899.t1 AT5G28010 31.579 152 101 2 4 153 14 164 2.62e-19 79.7
MS.gene43899.t1 AT5G28010 31.579 152 101 2 4 153 14 164 2.62e-19 79.7
MS.gene43899.t1 AT5G28000 32.237 152 100 2 4 153 12 162 5.46e-18 76.3
MS.gene43899.t1 AT1G70880 31.169 154 103 3 2 153 5 157 4.68e-17 73.9
MS.gene43899.t1 AT1G14930 28.289 152 102 3 3 151 1 148 7.33e-14 65.5
MS.gene43899.t1 AT1G35260 31.081 148 96 4 9 153 6 150 2.50e-13 63.9
MS.gene43899.t1 AT3G26460 25.333 150 110 2 3 151 1 149 7.23e-11 57.4

Find 35 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGTCATGTGGGAAGGCCTT+AGG 0.333006 5.2:-25485276 None:intergenic
AATAGTTGTAGAATCCCTTA+TGG 0.338562 5.2:-25485250 None:intergenic
GCAAAATCTTTGACAATAGT+TGG 0.338740 5.2:-25486041 None:intergenic
ATCCCCTTCAATTATACAAT+AGG 0.381348 5.2:-25485904 None:intergenic
ATCTCACATCCTTCTCCAAC+TGG 0.381866 5.2:-25485972 None:intergenic
CCTTGAATGATTTGTAGTAT+TGG 0.436050 5.2:-25485932 None:intergenic
CCAATACTACAAATCATTCA+AGG 0.446219 5.2:+25485932 MS.gene43899:CDS
AGTCTAATGCAGACAAGTAC+TGG 0.454231 5.2:+25485223 MS.gene43899:CDS
AGTCATGTGGGAAGGCCTTA+GGG 0.459268 5.2:-25485275 None:intergenic
GAGAAGGATGTGAGATGAAA+TGG 0.470943 5.2:+25485979 MS.gene43899:CDS
ACAAGTACTGGCAAACCATA+AGG 0.476885 5.2:+25485235 MS.gene43899:CDS
GAGGGTGATGGTAAAGCTCC+TGG 0.482745 5.2:+25485318 MS.gene43899:CDS
TCTTTGACAATAGTTGGATC+AGG 0.487708 5.2:-25486035 None:intergenic
GTGAAGTGGCGGATAGAGCC+AGG 0.488549 5.2:-25485336 None:intergenic
GCAACCTATTGTATAATTGA+AGG 0.505768 5.2:+25485900 MS.gene43899:CDS
AAAAGCATTGAGGTCCTTGA+GGG 0.507266 5.2:+25485300 MS.gene43899:CDS
CAAGTACTGGCAAACCATAA+GGG 0.509772 5.2:+25485236 MS.gene43899:CDS
ATCATGGCTGTAGCTCTTCG+TGG 0.517791 5.2:+25485174 None:intergenic
CAACCTATTGTATAATTGAA+GGG 0.524179 5.2:+25485901 MS.gene43899:CDS
TACCTTCAGCATAAGTGAAG+TGG 0.548909 5.2:-25485350 None:intergenic
TGCAGTCAAGAACTTCATTG+AGG 0.557320 5.2:+25486061 MS.gene43899:CDS
CAAAAGCATTGAGGTCCTTG+AGG 0.558857 5.2:+25485299 MS.gene43899:CDS
CGCCACTTCACTTATGCTGA+AGG 0.559188 5.2:+25485348 MS.gene43899:CDS
ATTGAGGTCCTTGAGGGTGA+TGG 0.560374 5.2:+25485306 MS.gene43899:CDS
CATCTTGCTGTAACACCAGT+TGG 0.560972 5.2:+25485957 MS.gene43899:CDS
CAATACTACAAATCATTCAA+GGG 0.584423 5.2:+25485933 MS.gene43899:CDS
GCTGTAACACCAGTTGGAGA+AGG 0.585512 5.2:+25485963 MS.gene43899:CDS
AACCTATTGTATAATTGAAG+GGG 0.589185 5.2:+25485902 MS.gene43899:CDS
GAGCTTTACCATCACCCTCA+AGG 0.617751 5.2:-25485314 None:intergenic
ATGCTGCTGATGATGAAAAG+AGG 0.618271 5.2:+25485874 MS.gene43899:CDS
AGTCAAGAACTTCATTGAGG+TGG 0.628959 5.2:+25486064 MS.gene43899:CDS
CTTCAGCATAAGTGAAGTGG+CGG 0.638511 5.2:-25485347 None:intergenic
AAAACTCGCGAAGTCTTCGA+CGG 0.651660 5.2:+25485842 MS.gene43899:CDS
AGCTCTTCGTGGAAAGCTAG+AGG 0.660101 5.2:+25485185 MS.gene43899:CDS
ACATGACTACAAAAGCATTG+AGG 0.674108 5.2:+25485290 MS.gene43899:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGATGAAATTCAATAAATA+AGG + chr5.2:25485540-25485559 MS.gene43899:intron 15.0%
!! TGATGAAATTCAATAAATAA+GGG + chr5.2:25485541-25485560 MS.gene43899:intron 15.0%
!! TTGATCCTACAATATATTAT+AGG - chr5.2:25485824-25485843 None:intergenic 20.0%
!!! AATAAATAAGGGTATATCAA+TGG + chr5.2:25485552-25485571 MS.gene43899:intron 20.0%
! AACCTATTGTATAATTGAAG+GGG + chr5.2:25485902-25485921 MS.gene43899:CDS 25.0%
! AATTTAGAGACTTTCTTCTT+TGG + chr5.2:25485374-25485393 MS.gene43899:intron 25.0%
! CAACCTATTGTATAATTGAA+GGG + chr5.2:25485901-25485920 MS.gene43899:CDS 25.0%
! CAATACTACAAATCATTCAA+GGG + chr5.2:25485933-25485952 MS.gene43899:CDS 25.0%
! TCATACATTCTTATCTGATT+TGG + chr5.2:25485795-25485814 MS.gene43899:intron 25.0%
! TGTTAAATCGATGATTAAAG+AGG + chr5.2:25485639-25485658 MS.gene43899:intron 25.0%
AATAGTTGTAGAATCCCTTA+TGG - chr5.2:25485253-25485272 None:intergenic 30.0%
ATCCCCTTCAATTATACAAT+AGG - chr5.2:25485907-25485926 None:intergenic 30.0%
CCAATACTACAAATCATTCA+AGG + chr5.2:25485932-25485951 MS.gene43899:CDS 30.0%
GCAAAATCTTTGACAATAGT+TGG - chr5.2:25486044-25486063 None:intergenic 30.0%
GCAACCTATTGTATAATTGA+AGG + chr5.2:25485900-25485919 MS.gene43899:CDS 30.0%
! CCTTGAATGATTTGTAGTAT+TGG - chr5.2:25485935-25485954 None:intergenic 30.0%
! TTCTACAACTATTTTCCCTA+AGG + chr5.2:25485260-25485279 MS.gene43899:CDS 30.0%
!! TACATTCTTATCTGATTTGG+TGG + chr5.2:25485798-25485817 MS.gene43899:intron 30.0%
AAAGCGATACATGAATCTCT+TGG - chr5.2:25485732-25485751 None:intergenic 35.0%
ATTAAAGAGGTAGAGACACT+AGG + chr5.2:25485652-25485671 MS.gene43899:intron 35.0%
CTTCTTTGGTAGAGAATGAA+GGG + chr5.2:25485388-25485407 MS.gene43899:intron 35.0%
GGTGGCCTATAATATATTGT+AGG + chr5.2:25485816-25485835 MS.gene43899:intron 35.0%
GTCAAATGCAACGAATATTG+TGG - chr5.2:25485495-25485514 None:intergenic 35.0%
TCTTCTTTGGTAGAGAATGA+AGG + chr5.2:25485387-25485406 MS.gene43899:intron 35.0%
TCTTTGACAATAGTTGGATC+AGG - chr5.2:25486038-25486057 None:intergenic 35.0%
! CAATGCTTTTGTAGTCATGT+GGG - chr5.2:25485290-25485309 None:intergenic 35.0%
! TCAATGCTTTTGTAGTCATG+TGG - chr5.2:25485291-25485310 None:intergenic 35.0%
!! ACATGACTACAAAAGCATTG+AGG + chr5.2:25485290-25485309 MS.gene43899:CDS 35.0%
!!! TAGAGAATGAAGGGCATTTT+GGG + chr5.2:25485397-25485416 MS.gene43899:intron 35.0%
AGTCAAGAACTTCATTGAGG+TGG + chr5.2:25486064-25486083 MS.gene43899:CDS 40.0%
AGTCTAATGCAGACAAGTAC+TGG + chr5.2:25485223-25485242 MS.gene43899:CDS 40.0%
GAGAAGGATGTGAGATGAAA+TGG + chr5.2:25485979-25485998 MS.gene43899:CDS 40.0%
TACCTTCAGCATAAGTGAAG+TGG - chr5.2:25485353-25485372 None:intergenic 40.0%
TGCAGTCAAGAACTTCATTG+AGG + chr5.2:25486061-25486080 MS.gene43899:CDS 40.0%
! ATGCTGCTGATGATGAAAAG+AGG + chr5.2:25485874-25485893 MS.gene43899:CDS 40.0%
!! AAAAGCATTGAGGTCCTTGA+GGG + chr5.2:25485300-25485319 MS.gene43899:CDS 40.0%
!! ACAAGTACTGGCAAACCATA+AGG + chr5.2:25485235-25485254 MS.gene43899:CDS 40.0%
!! CAAGTACTGGCAAACCATAA+GGG + chr5.2:25485236-25485255 MS.gene43899:CDS 40.0%
!!! GTAGAGAATGAAGGGCATTT+TGG + chr5.2:25485396-25485415 MS.gene43899:intron 40.0%
AAAACTCGCGAAGTCTTCGA+CGG + chr5.2:25485842-25485861 MS.gene43899:CDS 45.0%
ATCTCACATCCTTCTCCAAC+TGG - chr5.2:25485975-25485994 None:intergenic 45.0%
CATGAATCTCTTGGAACGCT+AGG - chr5.2:25485723-25485742 None:intergenic 45.0%
CTTCAGCATAAGTGAAGTGG+CGG - chr5.2:25485350-25485369 None:intergenic 45.0%
! CATCTTGCTGTAACACCAGT+TGG + chr5.2:25485957-25485976 MS.gene43899:CDS 45.0%
! GCTTTTGTAGTCATGTGGGA+AGG - chr5.2:25485286-25485305 None:intergenic 45.0%
!! CAAAAGCATTGAGGTCCTTG+AGG + chr5.2:25485299-25485318 MS.gene43899:CDS 45.0%
AGCTCTTCGTGGAAAGCTAG+AGG + chr5.2:25485185-25485204 MS.gene43899:CDS 50.0%
AGTCATGTGGGAAGGCCTTA+GGG - chr5.2:25485278-25485297 None:intergenic 50.0%
ATTGAGGTCCTTGAGGGTGA+TGG + chr5.2:25485306-25485325 MS.gene43899:CDS 50.0%
CGCCACTTCACTTATGCTGA+AGG + chr5.2:25485348-25485367 MS.gene43899:CDS 50.0%
GAGCTTTACCATCACCCTCA+AGG - chr5.2:25485317-25485336 None:intergenic 50.0%
GCTGTAACACCAGTTGGAGA+AGG + chr5.2:25485963-25485982 MS.gene43899:CDS 50.0%
TAGTCATGTGGGAAGGCCTT+AGG - chr5.2:25485279-25485298 None:intergenic 50.0%
AACGCTAGGCACTAGTGCAG+TGG - chr5.2:25485709-25485728 None:intergenic 55.0%
! GAGGGTGATGGTAAAGCTCC+TGG + chr5.2:25485318-25485337 MS.gene43899:CDS 55.0%
!! GTGAAGTGGCGGATAGAGCC+AGG - chr5.2:25485339-25485358 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 25485177 25486115 25485177 ID=MS.gene43899
chr5.2 mRNA 25485177 25486115 25485177 ID=MS.gene43899.t1;Parent=MS.gene43899
chr5.2 exon 25485177 25485369 25485177 ID=MS.gene43899.t1.exon1;Parent=MS.gene43899.t1
chr5.2 CDS 25485177 25485369 25485177 ID=cds.MS.gene43899.t1;Parent=MS.gene43899.t1
chr5.2 exon 25485838 25486115 25485838 ID=MS.gene43899.t1.exon2;Parent=MS.gene43899.t1
chr5.2 CDS 25485838 25486115 25485838 ID=cds.MS.gene43899.t1;Parent=MS.gene43899.t1
Gene Sequence

>MS.gene43899

ATGGCTGTAGCTCTTCGTGGAAAGCTAGAGGTAGACATTGAACTCAAGTCTAATGCAGACAAGTACTGGCAAACCATAAGGGATTCTACAACTATTTTCCCTAAGGCCTTCCCACATGACTACAAAAGCATTGAGGTCCTTGAGGGTGATGGTAAAGCTCCTGGCTCTATCCGCCACTTCACTTATGCTGAAGGTAAAATTTAGAGACTTTCTTCTTTGGTAGAGAATGAAGGGCATTTTGGGTATAAATGAAAGTTTCATTTATTTTCTGCTTTGTTTTTTACTCTTATATACATACATAATACTCACTTTGTACCACAATATTCGTTGCATTTGACAATTTCACACAAGTTAAGAAAAAAAATGATGAAATTCAATAAATAAGGGTATATCAATGGAAAATAATAATAAATTTTGCATTGATATTCTAAAGTGAAAATTAATTTGAGACATAGAAAAAAATGTTAAATCGATGATTAAAGAGGTAGAGACACTAGGTCATACATTAGATTAGAAAGCTAGACAGTTGCCACTGCACTAGTGCCTAGCGTTCCAAGAGATTCATGTATCGCTTTAGTTTATGTGAGCACTGATAAAAGAGTGAGAGATTGAAAAACTTCATACATTCTTATCTGATTTGGTGGCCTATAATATATTGTAGGATCAAAACTCGCGAAGTCTTCGACGGAGAAGATTGATGCTGCTGATGATGAAAAGAGGACAGCAACCTATTGTATAATTGAAGGGGATCTTCTCCAATACTACAAATCATTCAAGGGACATCTTGCTGTAACACCAGTTGGAGAAGGATGTGAGATGAAATGGTGTGCTGAGTATATTAAAGTTAGTAATGATATTCCTGATCCAACTATTGTCAAAGATTTTGCAGTCAAGAACTTCATTGAGGTGGATGACTATGTTCAATCACTTGCTGCATAG

Protein sequence

>MS.gene43899.t1

MAVALRGKLEVDIELKSNADKYWQTIRDSTTIFPKAFPHDYKSIEVLEGDGKAPGSIRHFTYAEGSKLAKSSTEKIDAADDEKRTATYCIIEGDLLQYYKSFKGHLAVTPVGEGCEMKWCAEYIKVSNDIPDPTIVKDFAVKNFIEVDDYVQSLAA