AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06169


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06169.t1 MTR_8g101980 100.000 121 0 0 1 121 1 121 5.31e-85 243
MS.gene06169.t1 MTR_6g091630 97.521 121 3 0 1 121 1 121 8.29e-83 238
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06169.t1 AT5G56710 83.333 114 19 0 8 121 6 119 5.84e-67 197
MS.gene06169.t1 AT4G26230 82.456 114 20 0 8 121 6 119 2.06e-66 196
MS.gene06169.t1 AT2G19740 81.897 116 21 0 6 121 4 119 2.90e-66 196
MS.gene06169.t1 AT5G56710 58.772 114 13 1 8 121 6 85 6.30e-38 123

Find 50 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGATCTCCTTTATTGCTTT+AGG 0.186329 4.2:+3257309 None:intergenic
TCAAGTTGAACAAGGCTATT+TGG 0.242228 4.2:-3257239 MS.gene06169:CDS
CATTAGTTCCCATAGCCTTT+TGG 0.252576 4.2:+3257277 None:intergenic
CAATCCTTTGAGCTCTTCCT+TGG 0.276372 4.2:+3257101 None:intergenic
GAAAGCTCCTAAAGCAATAA+AGG 0.311659 4.2:-3257316 MS.gene06169:CDS
CTCATCATCGTTCCTCTTGC+GGG 0.315756 4.2:+3257170 None:intergenic
AATCCTTTGAGCTCTTCCTT+GGG 0.346185 4.2:+3257102 None:intergenic
GAAGTGTCCCTAGGAGGGTT+AGG 0.392774 4.2:-3257203 MS.gene06169:CDS
GAGGCGTTTGTGGAGGTTGA+TGG 0.411978 4.2:+3257922 None:intergenic
GATCAGGAAGTTTGCCCAAA+AGG 0.422618 4.2:-3257292 MS.gene06169:CDS
ATGCGAACCCTAACCCTCCT+AGG 0.432434 4.2:+3257195 None:intergenic
CTAAAGCAATAAAGGAGATC+AGG 0.445899 4.2:-3257308 MS.gene06169:CDS
AAGGAAGAGCTCAAAGGATT+GGG 0.447041 4.2:-3257099 MS.gene06169:CDS
ACCAGCCATGGAGGCGTTTG+TGG 0.449631 4.2:+3257912 None:intergenic
CAAGGAAGAGCTCAAAGGAT+TGG 0.452186 4.2:-3257100 MS.gene06169:CDS
CCTCATCATCGTTCCTCTTG+CGG 0.459607 4.2:+3257169 None:intergenic
GAACAAGGCTATTTGGAGCC+AGG 0.460263 4.2:-3257232 MS.gene06169:CDS
TCCACAAACGCCTCCATGGC+TGG 0.473615 4.2:-3257913 MS.gene06169:intron
TAGGGACACTTCTGATCCCC+TGG 0.478265 4.2:+3257214 None:intergenic
CTCTTCCTTCCTACCGGCGC+CGG 0.482937 4.2:+3257964 None:intergenic
GAAGTTTGCCCAAAAGGCTA+TGG 0.483900 4.2:-3257286 MS.gene06169:CDS
GTGAAAATGGTGGAGAAGAC+CGG 0.499433 4.2:-3257983 None:intergenic
GAGGTTGATGGTGTACTCTC+TGG 0.499941 4.2:+3257934 None:intergenic
AAGTGTCCCTAGGAGGGTTA+GGG 0.512529 4.2:-3257202 MS.gene06169:CDS
ATCCTTTGAGCTCTTCCTTG+GGG 0.520497 4.2:+3257103 None:intergenic
AACAAGGCTATTTGGAGCCA+GGG 0.528204 4.2:-3257231 MS.gene06169:CDS
AGAGAGAGAATTACCAGCCA+TGG 0.536558 4.2:+3257900 None:intergenic
CACAAAGGTTATTGATGATG+AGG 0.542190 4.2:-3257076 MS.gene06169:CDS
GAACGATGATGAGGATGCTA+AGG 0.543980 4.2:-3257160 MS.gene06169:CDS
GAAGACCGGCGCCGGTAGGA+AGG 0.546764 4.2:-3257969 MS.gene06169:CDS
CGGCGCCGGTAGGAAGGAAG+AGG 0.547239 4.2:-3257963 MS.gene06169:CDS
AACCTCCACAAACGCCTCCA+TGG 0.560698 4.2:-3257917 MS.gene06169:CDS
AGGGGATCAGAAGTGTCCCT+AGG 0.578761 4.2:-3257212 MS.gene06169:CDS
GACAACCTCTTCCTTCCTAC+CGG 0.582542 4.2:+3257958 None:intergenic
AAGTTTGCCCAAAAGGCTAT+GGG 0.584767 4.2:-3257285 MS.gene06169:CDS
AGCCATGGAGGCGTTTGTGG+AGG 0.589507 4.2:+3257915 None:intergenic
TACTGTTGTTGAAATCCCCA+AGG 0.603575 4.2:-3257118 MS.gene06169:CDS
CCGCAAGAGGAACGATGATG+AGG 0.607958 4.2:-3257169 MS.gene06169:CDS
TGGAGAAGACCGGCGCCGGT+AGG 0.608791 4.2:-3257973 MS.gene06169:CDS
GATCAGAAGTGTCCCTAGGA+GGG 0.609828 4.2:-3257208 MS.gene06169:CDS
ATGGTGGAGAAGACCGGCGC+CGG 0.610511 4.2:-3257977 MS.gene06169:CDS
TGCGAACCCTAACCCTCCTA+GGG 0.611019 4.2:+3257196 None:intergenic
GGGTTCGCATTGCCCGCAAG+AGG 0.617342 4.2:-3257182 MS.gene06169:CDS
GGATCAGAAGTGTCCCTAGG+AGG 0.618801 4.2:-3257209 MS.gene06169:CDS
ATCCCCAAGGAAGAGCTCAA+AGG 0.635127 4.2:-3257105 MS.gene06169:CDS
GAGAGAATTACCAGCCATGG+AGG 0.648989 4.2:+3257903 None:intergenic
ACAAGGCTATTTGGAGCCAG+GGG 0.649532 4.2:-3257230 MS.gene06169:CDS
GCTCAAAGGATTGGGCACAA+AGG 0.653987 4.2:-3257091 MS.gene06169:CDS
AGTGGACGTCAAGTTGAACA+AGG 0.683327 4.2:-3257247 MS.gene06169:CDS
GGGAACTAATGATGTCAGAG+TGG 0.705766 4.2:-3257265 MS.gene06169:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTTTAATCTCTTTAGA+AGG - chr4.2:3257278-3257297 MS.gene06169:CDS 15.0%
!!! TTTACAAATATTTTGATAAC+CGG - chr4.2:3257523-3257542 MS.gene06169:intron 15.0%
!! ATCAGTTAAAATAACATCTA+CGG + chr4.2:3257504-3257523 None:intergenic 20.0%
!!! TTACAAATATTTTGATAACC+GGG - chr4.2:3257524-3257543 MS.gene06169:intron 20.0%
! TAAATAGCATATCACAGAAA+TGG - chr4.2:3257447-3257466 MS.gene06169:intron 25.0%
!! AAACAAAACATTTGCTAGAT+AGG + chr4.2:3257208-3257227 None:intergenic 25.0%
!! AACAAAACATTTGCTAGATA+GGG + chr4.2:3257207-3257226 None:intergenic 25.0%
!! GATATAGAGGAAAATTTTTG+TGG - chr4.2:3257239-3257258 MS.gene06169:CDS 25.0%
!!! TCTTTAGAAGGTTTTTTCAA+TGG - chr4.2:3257290-3257309 MS.gene06169:CDS 25.0%
! AAAAGTCATTTCAGGTAAAG+GGG + chr4.2:3257598-3257617 None:intergenic 30.0%
! AGAAAAGTCATTTCAGGTAA+AGG + chr4.2:3257600-3257619 None:intergenic 30.0%
! CATCAAAATGAAAAGCACAA+GGG + chr4.2:3257328-3257347 None:intergenic 30.0%
! CTTTTCTATGGAGATTGTTT+CGG - chr4.2:3257613-3257632 MS.gene06169:intron 30.0%
! GAAAAGTCATTTCAGGTAAA+GGG + chr4.2:3257599-3257618 None:intergenic 30.0%
! TACCTGAAATGACTTTTCTA+TGG - chr4.2:3257601-3257620 MS.gene06169:intron 30.0%
! TCATCAAAATGAAAAGCACA+AGG + chr4.2:3257329-3257348 None:intergenic 30.0%
! TTGTTTTCGATCAGATATAG+AGG - chr4.2:3257226-3257245 MS.gene06169:CDS 30.0%
!! GCTGTTTTGCATAATAACAA+AGG + chr4.2:3257701-3257720 None:intergenic 30.0%
ATAGCATATCACAGAAATGG+TGG - chr4.2:3257450-3257469 MS.gene06169:intron 35.0%
CTAAAGCAATAAAGGAGATC+AGG - chr4.2:3257740-3257759 MS.gene06169:intron 35.0%
CTCCATAGAAAAGTCATTTC+AGG + chr4.2:3257606-3257625 None:intergenic 35.0%
CTGATCTCCTTTATTGCTTT+AGG + chr4.2:3257742-3257761 None:intergenic 35.0%
GAAAGCTCCTAAAGCAATAA+AGG - chr4.2:3257732-3257751 MS.gene06169:intron 35.0%
! ATTAGTTCCCATAGCCTTTT+GGG + chr4.2:3257773-3257792 None:intergenic 35.0%
!! CACAAAGGTTATTGATGATG+AGG - chr4.2:3257972-3257991 MS.gene06169:CDS 35.0%
!! TCAAGTTGAACAAGGCTATT+TGG - chr4.2:3257809-3257828 MS.gene06169:intron 35.0%
!!! CAAATATTTTGATAACCGGG+AGG - chr4.2:3257527-3257546 MS.gene06169:intron 35.0%
AAGGAAGAGCTCAAAGGATT+GGG - chr4.2:3257949-3257968 MS.gene06169:CDS 40.0%
AAGTTTGCCCAAAAGGCTAT+GGG - chr4.2:3257763-3257782 MS.gene06169:intron 40.0%
AATCCTTTGAGCTCTTCCTT+GGG + chr4.2:3257949-3257968 None:intergenic 40.0%
CAAAACTATATTCCTCCTCC+CGG + chr4.2:3257545-3257564 None:intergenic 40.0%
TACTGTTGTTGAAATCCCCA+AGG - chr4.2:3257930-3257949 MS.gene06169:CDS 40.0%
! CATTAGTTCCCATAGCCTTT+TGG + chr4.2:3257774-3257793 None:intergenic 40.0%
!!! ATATTTTGATAACCGGGAGG+AGG - chr4.2:3257530-3257549 MS.gene06169:intron 40.0%
AGAGAGAGAATTACCAGCCA+TGG + chr4.2:3257151-3257170 None:intergenic 45.0%
ATCCTTTGAGCTCTTCCTTG+GGG + chr4.2:3257948-3257967 None:intergenic 45.0%
CAAGGAAGAGCTCAAAGGAT+TGG - chr4.2:3257948-3257967 MS.gene06169:CDS 45.0%
CAATCCTTTGAGCTCTTCCT+TGG + chr4.2:3257950-3257969 None:intergenic 45.0%
GAACGATGATGAGGATGCTA+AGG - chr4.2:3257888-3257907 MS.gene06169:intron 45.0%
GAAGTTTGCCCAAAAGGCTA+TGG - chr4.2:3257762-3257781 MS.gene06169:intron 45.0%
GATCAGGAAGTTTGCCCAAA+AGG - chr4.2:3257756-3257775 MS.gene06169:intron 45.0%
GGGAACTAATGATGTCAGAG+TGG - chr4.2:3257783-3257802 MS.gene06169:intron 45.0%
! AACAAGGCTATTTGGAGCCA+GGG - chr4.2:3257817-3257836 MS.gene06169:intron 45.0%
!! AGTGGACGTCAAGTTGAACA+AGG - chr4.2:3257801-3257820 MS.gene06169:intron 45.0%
AAGTGTCCCTAGGAGGGTTA+GGG - chr4.2:3257846-3257865 MS.gene06169:intron 50.0%
ATCCCCAAGGAAGAGCTCAA+AGG - chr4.2:3257943-3257962 MS.gene06169:CDS 50.0%
CCTCATCATCGTTCCTCTTG+CGG + chr4.2:3257882-3257901 None:intergenic 50.0%
CTCATCATCGTTCCTCTTGC+GGG + chr4.2:3257881-3257900 None:intergenic 50.0%
GACAACCTCTTCCTTCCTAC+CGG + chr4.2:3257093-3257112 None:intergenic 50.0%
GAGAGAATTACCAGCCATGG+AGG + chr4.2:3257148-3257167 None:intergenic 50.0%
GCTCAAAGGATTGGGCACAA+AGG - chr4.2:3257957-3257976 MS.gene06169:CDS 50.0%
! ACAAGGCTATTTGGAGCCAG+GGG - chr4.2:3257818-3257837 MS.gene06169:intron 50.0%
! GAACAAGGCTATTTGGAGCC+AGG - chr4.2:3257816-3257835 MS.gene06169:intron 50.0%
!! GAGGTTGATGGTGTACTCTC+TGG + chr4.2:3257117-3257136 None:intergenic 50.0%
!! GATCAGAAGTGTCCCTAGGA+GGG - chr4.2:3257840-3257859 MS.gene06169:intron 50.0%
AACCTCCACAAACGCCTCCA+TGG - chr4.2:3257131-3257150 MS.gene06169:CDS 55.0%
ATGCGAACCCTAACCCTCCT+AGG + chr4.2:3257856-3257875 None:intergenic 55.0%
CCGCAAGAGGAACGATGATG+AGG - chr4.2:3257879-3257898 MS.gene06169:intron 55.0%
TAGGGACACTTCTGATCCCC+TGG + chr4.2:3257837-3257856 None:intergenic 55.0%
TGCGAACCCTAACCCTCCTA+GGG + chr4.2:3257855-3257874 None:intergenic 55.0%
! GAAGTGTCCCTAGGAGGGTT+AGG - chr4.2:3257845-3257864 MS.gene06169:intron 55.0%
! GAGGCGTTTGTGGAGGTTGA+TGG + chr4.2:3257129-3257148 None:intergenic 55.0%
!! AGGGGATCAGAAGTGTCCCT+AGG - chr4.2:3257836-3257855 MS.gene06169:intron 55.0%
!! GGATCAGAAGTGTCCCTAGG+AGG - chr4.2:3257839-3257858 MS.gene06169:intron 55.0%
TCCACAAACGCCTCCATGGC+TGG - chr4.2:3257135-3257154 MS.gene06169:CDS 60.0%
!! ACCAGCCATGGAGGCGTTTG+TGG + chr4.2:3257139-3257158 None:intergenic 60.0%
!! AGCCATGGAGGCGTTTGTGG+AGG + chr4.2:3257136-3257155 None:intergenic 60.0%
CTCTTCCTTCCTACCGGCGC+CGG + chr4.2:3257087-3257106 None:intergenic 65.0%
GGGTTCGCATTGCCCGCAAG+AGG - chr4.2:3257866-3257885 MS.gene06169:intron 65.0%
! ATGGTGGAGAAGACCGGCGC+CGG - chr4.2:3257071-3257090 MS.gene06169:CDS 65.0%
!! CGGCGCCGGTAGGAAGGAAG+AGG - chr4.2:3257085-3257104 MS.gene06169:CDS 70.0%
!! GAAGACCGGCGCCGGTAGGA+AGG - chr4.2:3257079-3257098 MS.gene06169:CDS 70.0%
!! TGGAGAAGACCGGCGCCGGT+AGG - chr4.2:3257075-3257094 MS.gene06169:CDS 70.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 3257071 3257999 3257071 ID=MS.gene06169
chr4.2 mRNA 3257071 3257999 3257071 ID=MS.gene06169.t1;Parent=MS.gene06169
chr4.2 exon 3257914 3257999 3257914 ID=MS.gene06169.t1.exon1;Parent=MS.gene06169.t1
chr4.2 CDS 3257914 3257999 3257914 ID=cds.MS.gene06169.t1;Parent=MS.gene06169.t1
chr4.2 exon 3257071 3257350 3257071 ID=MS.gene06169.t1.exon2;Parent=MS.gene06169.t1
chr4.2 CDS 3257071 3257350 3257071 ID=cds.MS.gene06169.t1;Parent=MS.gene06169.t1
Gene Sequence

>MS.gene06169

ATGGTGGAGAAGACCGGCGCCGGTAGGAAGGAAGAGGTTGTCACCAGAGAGTACACCATCAACCTCCACAAACGCCTCCATGGCTGGTAATTCTCTCTCTATTGTTCATTTTTGTTTTTTTCGTTTGTCTAAACCCTATCTAGCAAATGTTTTGTTTGTTTTCGATCAGATATAGAGGAAAATTTTTGTGGATTTTTTATTTATTATATTTTTTTAATCTCTTTAGAAGGTTTTTTCAATGGCAGTAAAATAGTCCCTTGTGCTTTTCATTTTGATGATATTGTAATTAAGCTGTTTGAATGTTTAAATGTTCTGTGTCTTTGATATTAATGTTGTCAATTGTGCAATAATGCTGTTAGTTAGCACAATTTTAAGCTAAATAGCATATCACAGAAATGGTGGTTTGCTATGCACTGCGTTTCTAGCAACTCCGTAGATGTTATTTTAACTGATTTACAAATATTTTGATAACCGGGAGGAGGAATATAGTTTTGTGCGACAATACTTTGATGTAACAAACATATCCCCTTTACCTGAAATGACTTTTCTATGGAGATTGTTTCGGCTGATATCTCGTTTGTATTATTTGTTTGTTTTAACTTTATGAAATTCTAACAGTCATTTTTTCCTTTGTTATTATGCAAAACAGCACATTTAAGAAGAAAGCTCCTAAAGCAATAAAGGAGATCAGGAAGTTTGCCCAAAAGGCTATGGGAACTAATGATGTCAGAGTGGACGTCAAGTTGAACAAGGCTATTTGGAGCCAGGGGATCAGAAGTGTCCCTAGGAGGGTTAGGGTTCGCATTGCCCGCAAGAGGAACGATGATGAGGATGCTAAGGAAGAGCTCTACTCACTTGTTACTGTTGTTGAAATCCCCAAGGAAGAGCTCAAAGGATTGGGCACAAAGGTTATTGATGATGAGGATTGA

Protein sequence

>MS.gene06169.t1

MVEKTGAGRKEEVVTREYTINLHKRLHGCTFKKKAPKAIKEIRKFAQKAMGTNDVRVDVKLNKAIWSQGIRSVPRRVRVRIARKRNDDEDAKEELYSLVTVVEIPKEELKGLGTKVIDDED