AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene68338


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene68338.t1 MTR_5g035010 93.590 156 10 0 1 156 1 156 2.26e-110 310
MS.gene68338.t1 MTR_8g012550 29.801 151 105 1 1 151 1 150 1.23e-19 80.5
MS.gene68338.t1 MTR_1g030810 32.026 153 97 5 3 151 1 150 2.32e-15 69.3
MS.gene68338.t1 MTR_1g030820 30.968 155 96 6 3 151 1 150 4.13e-14 65.9
MS.gene68338.t1 MTR_1g030840 30.827 133 86 3 3 130 1 132 2.16e-12 61.6
MS.gene68338.t1 MTR_1g031640 29.630 135 86 5 9 141 7 134 2.36e-12 61.2
MS.gene68338.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.gene68338.t1 AT1G24020 51.678 149 72 0 3 151 1 149 2.71e-55 171
MS.gene68338.t1 AT1G24020 51.678 149 72 0 3 151 1 149 2.71e-55 171
MS.gene68338.t1 AT1G70830 34.868 152 96 2 2 151 19 169 2.11e-22 88.2
MS.gene68338.t1 AT1G70830 34.868 152 96 2 2 151 19 169 3.89e-22 88.2
MS.gene68338.t1 AT1G70840 36.667 150 92 2 4 151 19 167 4.13e-22 87.4
MS.gene68338.t1 AT1G70830 34.868 152 96 2 2 151 19 169 1.43e-21 87.8
MS.gene68338.t1 AT1G70850 34.416 154 98 2 2 153 6 158 1.93e-21 87.0
MS.gene68338.t1 AT1G70830 34.868 152 96 2 2 151 19 169 3.52e-21 88.2
MS.gene68338.t1 AT1G70830 33.333 150 97 2 4 151 183 331 1.72e-19 83.6
MS.gene68338.t1 AT1G70850 34.416 154 98 2 2 153 6 158 6.02e-21 87.0
MS.gene68338.t1 AT1G70850 33.813 139 89 2 15 151 175 312 2.28e-17 77.4
MS.gene68338.t1 AT1G70850 34.416 154 98 2 2 153 6 158 6.02e-21 87.0
MS.gene68338.t1 AT1G70850 33.813 139 89 2 15 151 175 312 2.28e-17 77.4
MS.gene68338.t1 AT1G70890 36.184 152 94 3 2 151 4 154 7.39e-21 83.6
MS.gene68338.t1 AT1G70830 33.333 150 97 2 4 151 136 284 8.27e-20 83.6
MS.gene68338.t1 AT1G70830 36.471 85 52 1 69 151 38 122 9.82e-11 58.9
MS.gene68338.t1 AT5G28010 31.579 152 101 2 4 153 14 164 2.62e-19 79.7
MS.gene68338.t1 AT5G28010 31.579 152 101 2 4 153 14 164 2.62e-19 79.7
MS.gene68338.t1 AT5G28000 32.237 152 100 2 4 153 12 162 5.46e-18 76.3
MS.gene68338.t1 AT1G70880 31.169 154 103 3 2 153 5 157 4.68e-17 73.9
MS.gene68338.t1 AT1G14930 28.289 152 102 3 3 151 1 148 7.33e-14 65.5
MS.gene68338.t1 AT1G35260 31.081 148 96 4 9 153 6 150 2.50e-13 63.9
MS.gene68338.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:+25563673 None:intergenic
AATAGTTGTAGAATCCCTTA+TGG 0.338562 5.2:+25563699 None:intergenic
GCAAAATCTTTGACAATAGT+TGG 0.338740 5.2:+25562908 None:intergenic
ATCCCCTTCAATTATACAAT+AGG 0.381348 5.2:+25563045 None:intergenic
ATCTCACATCCTTCTCCAAC+TGG 0.381866 5.2:+25562977 None:intergenic
CCTTGAATGATTTGTAGTAT+TGG 0.436050 5.2:+25563017 None:intergenic
CCAATACTACAAATCATTCA+AGG 0.446219 5.2:-25563017 MS.gene68338:CDS
AGTCTAATGCAGACAAGTAC+TGG 0.454231 5.2:-25563726 MS.gene68338:CDS
AGTCATGTGGGAAGGCCTTA+GGG 0.459268 5.2:+25563674 None:intergenic
GAGAAGGATGTGAGATGAAA+TGG 0.470943 5.2:-25562970 MS.gene68338:CDS
ACAAGTACTGGCAAACCATA+AGG 0.476885 5.2:-25563714 MS.gene68338:CDS
GAGGGTGATGGTAAAGCTCC+TGG 0.482745 5.2:-25563631 MS.gene68338:CDS
TCTTTGACAATAGTTGGATC+AGG 0.487708 5.2:+25562914 None:intergenic
GTGAAGTGGCGGATAGAGCC+AGG 0.488549 5.2:+25563613 None:intergenic
GCAACCTATTGTATAATTGA+AGG 0.505768 5.2:-25563049 MS.gene68338:CDS
AAAAGCATTGAGGTCCTTGA+GGG 0.507266 5.2:-25563649 MS.gene68338:CDS
CAAGTACTGGCAAACCATAA+GGG 0.509772 5.2:-25563713 MS.gene68338:CDS
ATCATGGCTGTAGCTCTTCG+TGG 0.517791 5.2:-25563775 MS.gene68338:CDS
CAACCTATTGTATAATTGAA+GGG 0.524179 5.2:-25563048 MS.gene68338:CDS
TACCTTCAGCATAAGTGAAG+TGG 0.548909 5.2:+25563599 None:intergenic
TGCAGTCAAGAACTTCATTG+AGG 0.557320 5.2:-25562888 MS.gene68338:CDS
CAAAAGCATTGAGGTCCTTG+AGG 0.558857 5.2:-25563650 MS.gene68338:CDS
CGCCACTTCACTTATGCTGA+AGG 0.559188 5.2:-25563601 MS.gene68338:intron
ATTGAGGTCCTTGAGGGTGA+TGG 0.560374 5.2:-25563643 MS.gene68338:CDS
CATCTTGCTGTAACACCAGT+TGG 0.560972 5.2:-25562992 MS.gene68338:CDS
CAATACTACAAATCATTCAA+GGG 0.584423 5.2:-25563016 MS.gene68338:CDS
GCTGTAACACCAGTTGGAGA+AGG 0.585512 5.2:-25562986 MS.gene68338:CDS
AACCTATTGTATAATTGAAG+GGG 0.589185 5.2:-25563047 MS.gene68338:CDS
GAGCTTTACCATCACCCTCA+AGG 0.617751 5.2:+25563635 None:intergenic
ATGCTGCTGATGATGAAAAG+AGG 0.618271 5.2:-25563075 MS.gene68338:CDS
AGTCAAGAACTTCATTGAGG+TGG 0.628959 5.2:-25562885 MS.gene68338:CDS
CTTCAGCATAAGTGAAGTGG+CGG 0.638511 5.2:+25563602 None:intergenic
AAAACTCGCGAAGTCTTCGA+CGG 0.651660 5.2:-25563107 MS.gene68338:CDS
AGCTCTTCGTGGAAAGCTAG+AGG 0.660101 5.2:-25563764 MS.gene68338:CDS
ACATGACTACAAAAGCATTG+AGG 0.674108 5.2:-25563659 MS.gene68338:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGATGAAATTCAATAAATA+AGG - chr5.2:25563219-25563238 MS.gene68338:intron 15.0%
!! TGATGAAATTCAATAAATAA+GGG - chr5.2:25563220-25563239 MS.gene68338:intron 15.0%
!! TTGATCCTACAATATATTAT+AGG + chr5.2:25563503-25563522 None:intergenic 20.0%
!!! AATAAATAAGGGTATATCAA+TGG - chr5.2:25563231-25563250 MS.gene68338:intron 20.0%
! AACCTATTGTATAATTGAAG+GGG - chr5.2:25563581-25563600 MS.gene68338:intron 25.0%
! AATTTAGAGACTTTCTTCTT+TGG - chr5.2:25563053-25563072 MS.gene68338:CDS 25.0%
! CAACCTATTGTATAATTGAA+GGG - chr5.2:25563580-25563599 MS.gene68338:intron 25.0%
! CAATACTACAAATCATTCAA+GGG - chr5.2:25563612-25563631 MS.gene68338:CDS 25.0%
! TCATACATTCTTATCTGATT+TGG - chr5.2:25563474-25563493 MS.gene68338:intron 25.0%
! TGTTAAATCGATGATTAAAG+AGG - chr5.2:25563318-25563337 MS.gene68338:intron 25.0%
AATAGTTGTAGAATCCCTTA+TGG + chr5.2:25562932-25562951 None:intergenic 30.0%
ATCCCCTTCAATTATACAAT+AGG + chr5.2:25563586-25563605 None:intergenic 30.0%
CCAATACTACAAATCATTCA+AGG - chr5.2:25563611-25563630 MS.gene68338:CDS 30.0%
GCAAAATCTTTGACAATAGT+TGG + chr5.2:25563723-25563742 None:intergenic 30.0%
GCAACCTATTGTATAATTGA+AGG - chr5.2:25563579-25563598 MS.gene68338:intron 30.0%
! CCTTGAATGATTTGTAGTAT+TGG + chr5.2:25563614-25563633 None:intergenic 30.0%
! TTCTACAACTATTTTCCCTA+AGG - chr5.2:25562939-25562958 MS.gene68338:CDS 30.0%
!! TACATTCTTATCTGATTTGG+TGG - chr5.2:25563477-25563496 MS.gene68338:intron 30.0%
AAAGCGATACATGAATCTCT+TGG + chr5.2:25563411-25563430 None:intergenic 35.0%
ATTAAAGAGGTAGAGACACT+AGG - chr5.2:25563331-25563350 MS.gene68338:intron 35.0%
CTTCTTTGGTAGAGAATGAA+GGG - chr5.2:25563067-25563086 MS.gene68338:CDS 35.0%
GGTGGCCTATAATATATTGT+AGG - chr5.2:25563495-25563514 MS.gene68338:intron 35.0%
GTCAAATGCAACGAATATTG+TGG + chr5.2:25563174-25563193 None:intergenic 35.0%
TCTTCTTTGGTAGAGAATGA+AGG - chr5.2:25563066-25563085 MS.gene68338:CDS 35.0%
TCTTTGACAATAGTTGGATC+AGG + chr5.2:25563717-25563736 None:intergenic 35.0%
! CAATGCTTTTGTAGTCATGT+GGG + chr5.2:25562969-25562988 None:intergenic 35.0%
! TCAATGCTTTTGTAGTCATG+TGG + chr5.2:25562970-25562989 None:intergenic 35.0%
!! ACATGACTACAAAAGCATTG+AGG - chr5.2:25562969-25562988 MS.gene68338:CDS 35.0%
!!! TAGAGAATGAAGGGCATTTT+GGG - chr5.2:25563076-25563095 MS.gene68338:CDS 35.0%
AGTCAAGAACTTCATTGAGG+TGG - chr5.2:25563743-25563762 MS.gene68338:CDS 40.0%
AGTCTAATGCAGACAAGTAC+TGG - chr5.2:25562902-25562921 MS.gene68338:CDS 40.0%
GAGAAGGATGTGAGATGAAA+TGG - chr5.2:25563658-25563677 MS.gene68338:CDS 40.0%
TACCTTCAGCATAAGTGAAG+TGG + chr5.2:25563032-25563051 None:intergenic 40.0%
TGCAGTCAAGAACTTCATTG+AGG - chr5.2:25563740-25563759 MS.gene68338:CDS 40.0%
! ATGCTGCTGATGATGAAAAG+AGG - chr5.2:25563553-25563572 MS.gene68338:intron 40.0%
!! AAAAGCATTGAGGTCCTTGA+GGG - chr5.2:25562979-25562998 MS.gene68338:CDS 40.0%
!! ACAAGTACTGGCAAACCATA+AGG - chr5.2:25562914-25562933 MS.gene68338:CDS 40.0%
!! CAAGTACTGGCAAACCATAA+GGG - chr5.2:25562915-25562934 MS.gene68338:CDS 40.0%
!!! GTAGAGAATGAAGGGCATTT+TGG - chr5.2:25563075-25563094 MS.gene68338:CDS 40.0%
AAAACTCGCGAAGTCTTCGA+CGG - chr5.2:25563521-25563540 MS.gene68338:intron 45.0%
ATCTCACATCCTTCTCCAAC+TGG + chr5.2:25563654-25563673 None:intergenic 45.0%
CATGAATCTCTTGGAACGCT+AGG + chr5.2:25563402-25563421 None:intergenic 45.0%
CTTCAGCATAAGTGAAGTGG+CGG + chr5.2:25563029-25563048 None:intergenic 45.0%
! CATCTTGCTGTAACACCAGT+TGG - chr5.2:25563636-25563655 MS.gene68338:CDS 45.0%
! GCTTTTGTAGTCATGTGGGA+AGG + chr5.2:25562965-25562984 None:intergenic 45.0%
!! CAAAAGCATTGAGGTCCTTG+AGG - chr5.2:25562978-25562997 MS.gene68338:CDS 45.0%
AGCTCTTCGTGGAAAGCTAG+AGG - chr5.2:25562864-25562883 MS.gene68338:CDS 50.0%
AGTCATGTGGGAAGGCCTTA+GGG + chr5.2:25562957-25562976 None:intergenic 50.0%
ATTGAGGTCCTTGAGGGTGA+TGG - chr5.2:25562985-25563004 MS.gene68338:CDS 50.0%
CGCCACTTCACTTATGCTGA+AGG - chr5.2:25563027-25563046 MS.gene68338:CDS 50.0%
GAGCTTTACCATCACCCTCA+AGG + chr5.2:25562996-25563015 None:intergenic 50.0%
GCTGTAACACCAGTTGGAGA+AGG - chr5.2:25563642-25563661 MS.gene68338:CDS 50.0%
TAGTCATGTGGGAAGGCCTT+AGG + chr5.2:25562958-25562977 None:intergenic 50.0%
AACGCTAGGCACTAGTGCAG+TGG + chr5.2:25563388-25563407 None:intergenic 55.0%
! GAGGGTGATGGTAAAGCTCC+TGG - chr5.2:25562997-25563016 MS.gene68338:CDS 55.0%
!! GTGAAGTGGCGGATAGAGCC+AGG + chr5.2:25563018-25563037 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 25562856 25563794 25562856 ID=MS.gene68338
chr5.2 mRNA 25562856 25563794 25562856 ID=MS.gene68338.t1;Parent=MS.gene68338
chr5.2 exon 25563602 25563794 25563602 ID=MS.gene68338.t1.exon1;Parent=MS.gene68338.t1
chr5.2 CDS 25563602 25563794 25563602 ID=cds.MS.gene68338.t1;Parent=MS.gene68338.t1
chr5.2 exon 25562856 25563133 25562856 ID=MS.gene68338.t1.exon2;Parent=MS.gene68338.t1
chr5.2 CDS 25562856 25563133 25562856 ID=cds.MS.gene68338.t1;Parent=MS.gene68338.t1
Gene Sequence

>MS.gene68338

ATGGCTGTAGCTCTTCGTGGAAAGCTAGAGGTAGACATTGAACTCAAGTCTAATGCAGACAAGTACTGGCAAACCATAAGGGATTCTACAACTATTTTCCCTAAGGCCTTCCCACATGACTACAAAAGCATTGAGGTCCTTGAGGGTGATGGTAAAGCTCCTGGCTCTATCCGCCACTTCACTTATGCTGAAGGTAAAATTTAGAGACTTTCTTCTTTGGTAGAGAATGAAGGGCATTTTGGGTATAAATGAAAGTTTCATTTATTTTCTGCTTTGTTTTTTACTCTTATATACATACATAATACTCACTTTGTACCACAATATTCGTTGCATTTGACAATTTCACACAAGTTAAGAAAAAAAATGATGAAATTCAATAAATAAGGGTATATCAATGGAAAATAATAATAAATTTTGCATTGATATTCTAAAGTGAAAATTAATTTGAGACATAGAAAAAAATGTTAAATCGATGATTAAAGAGGTAGAGACACTAGGTCATACATTAGATTAGAAAGCTAGACAGTTGCCACTGCACTAGTGCCTAGCGTTCCAAGAGATTCATGTATCGCTTTAGTTTATGTGAGCACTGATAAAAGAGTGAGAGATTGAAAAACTTCATACATTCTTATCTGATTTGGTGGCCTATAATATATTGTAGGATCAAAACTCGCGAAGTCTTCGACGGAGAAGATTGATGCTGCTGATGATGAAAAGAGGACAGCAACCTATTGTATAATTGAAGGGGATCTTCTCCAATACTACAAATCATTCAAGGGACATCTTGCTGTAACACCAGTTGGAGAAGGATGTGAGATGAAATGGTGTGCTGAGTATATTAAAGTTAGTAATGATATTCCTGATCCAACTATTGTCAAAGATTTTGCAGTCAAGAACTTCATTGAGGTGGATGACTATGTTCAATCACTTGCTGCATAG

Protein sequence

>MS.gene68338.t1

MAVALRGKLEVDIELKSNADKYWQTIRDSTTIFPKAFPHDYKSIEVLEGDGKAPGSIRHFTYAEGSKLAKSSTEKIDAADDEKRTATYCIIEGDLLQYYKSFKGHLAVTPVGEGCEMKWCAEYIKVSNDIPDPTIVKDFAVKNFIEVDDYVQSLAA