AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20153


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20153.t1 MTR_8g101980 99.174 121 1 0 1 121 1 121 2.44e-84 241
MS.gene20153.t1 MTR_6g091630 96.694 121 4 0 1 121 1 121 3.27e-82 236
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20153.t1 AT5G56710 82.456 114 20 0 8 121 6 119 3.61e-66 196
MS.gene20153.t1 AT4G26230 81.579 114 21 0 8 121 6 119 1.18e-65 194
MS.gene20153.t1 AT2G19740 81.034 116 22 0 6 121 4 119 2.00e-65 194
MS.gene20153.t1 AT5G56710 58.772 114 13 1 8 121 6 85 6.95e-38 123

Find 51 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGATCTCCTTTATTGCTTT+AGG 0.186329 4.4:+3783285 None:intergenic
TCAAGTTGAACAAGGCTATT+TGG 0.242228 4.4:-3783215 MS.gene20153:CDS
CATTAGTTCCCATAGCCTTT+TGG 0.252576 4.4:+3783253 None:intergenic
CAATCCTTTGAGCTCTTCCT+TGG 0.276372 4.4:+3783077 None:intergenic
CTCCTCATCGTTCCTCTTGC+GGG 0.302912 4.4:+3783146 None:intergenic
GAAAGCTCCTAAAGCAATAA+AGG 0.311659 4.4:-3783292 MS.gene20153:CDS
AATCCTTTGAGCTCTTCCTT+GGG 0.346185 4.4:+3783078 None:intergenic
GAAGTGTCCCTAGGAGGGTT+AGG 0.392774 4.4:-3783179 MS.gene20153:CDS
GAGGCGTTTGTGGAGGTTGA+TGG 0.411978 4.4:+3783898 None:intergenic
GATCAGGAAGTTTGCCCAAA+AGG 0.422618 4.4:-3783268 MS.gene20153:CDS
ATGCGAACCCTAACCCTCCT+AGG 0.432434 4.4:+3783171 None:intergenic
CTAAAGCAATAAAGGAGATC+AGG 0.445899 4.4:-3783284 MS.gene20153:CDS
AAGGAAGAGCTCAAAGGATT+GGG 0.447041 4.4:-3783075 MS.gene20153:CDS
ACCAGCCATGGAGGCGTTTG+TGG 0.449631 4.4:+3783888 None:intergenic
CAAGGAAGAGCTCAAAGGAT+TGG 0.452186 4.4:-3783076 MS.gene20153:CDS
CCTCCTCATCGTTCCTCTTG+CGG 0.459607 4.4:+3783145 None:intergenic
GAACAAGGCTATTTGGAGCC+AGG 0.460263 4.4:-3783208 MS.gene20153:CDS
TCCACAAACGCCTCCATGGC+TGG 0.473615 4.4:-3783889 MS.gene20153:intron
TAGGGACACTTCTGATCCCC+TGG 0.478265 4.4:+3783190 None:intergenic
CTCTTCCTTCCTACCGGCGC+CGG 0.482937 4.4:+3783940 None:intergenic
GAAGTTTGCCCAAAAGGCTA+TGG 0.483900 4.4:-3783262 MS.gene20153:CDS
GTGAAAATGGTGGAGAAGAC+CGG 0.499433 4.4:-3783959 None:intergenic
GAGGTTGATGGTGTACTCTC+TGG 0.499941 4.4:+3783910 None:intergenic
AAGTGTCCCTAGGAGGGTTA+GGG 0.512529 4.4:-3783178 MS.gene20153:CDS
ATCCTTTGAGCTCTTCCTTG+GGG 0.520497 4.4:+3783079 None:intergenic
AACAAGGCTATTTGGAGCCA+GGG 0.528204 4.4:-3783207 MS.gene20153:CDS
GAACGATGAGGAGGATGCTA+AGG 0.531511 4.4:-3783136 MS.gene20153:CDS
AGAGAGAGAATTACCAGCCA+TGG 0.536558 4.4:+3783876 None:intergenic
CACAAAGGTTATTGATGATG+AGG 0.542190 4.4:-3783052 MS.gene20153:CDS
GAAGACCGGCGCCGGTAGGA+AGG 0.546764 4.4:-3783945 MS.gene20153:CDS
CGGCGCCGGTAGGAAGGAAG+AGG 0.547239 4.4:-3783939 MS.gene20153:CDS
AACCTCCACAAACGCCTCCA+TGG 0.560698 4.4:-3783893 MS.gene20153:CDS
AGGGGATCAGAAGTGTCCCT+AGG 0.578761 4.4:-3783188 MS.gene20153:CDS
GACAACCTCTTCCTTCCTAC+CGG 0.582542 4.4:+3783934 None:intergenic
AAGTTTGCCCAAAAGGCTAT+GGG 0.584767 4.4:-3783261 MS.gene20153:CDS
AGCCATGGAGGCGTTTGTGG+AGG 0.589507 4.4:+3783891 None:intergenic
TACTGTTGTTGAAATCCCCA+AGG 0.603575 4.4:-3783094 MS.gene20153:CDS
TGGAGAAGACCGGCGCCGGT+AGG 0.608791 4.4:-3783949 MS.gene20153:CDS
GATCAGAAGTGTCCCTAGGA+GGG 0.609828 4.4:-3783184 MS.gene20153:CDS
ATGGTGGAGAAGACCGGCGC+CGG 0.610511 4.4:-3783953 MS.gene20153:CDS
TGCGAACCCTAACCCTCCTA+GGG 0.611019 4.4:+3783172 None:intergenic
GGGTTCGCATTGCCCGCAAG+AGG 0.617342 4.4:-3783158 MS.gene20153:CDS
GGATCAGAAGTGTCCCTAGG+AGG 0.618801 4.4:-3783185 MS.gene20153:CDS
CCGCAAGAGGAACGATGAGG+AGG 0.619270 4.4:-3783145 MS.gene20153:CDS
ATCCCCAAGGAAGAGCTCAA+AGG 0.635127 4.4:-3783081 MS.gene20153:CDS
GAGAGAATTACCAGCCATGG+AGG 0.648989 4.4:+3783879 None:intergenic
ACAAGGCTATTTGGAGCCAG+GGG 0.649532 4.4:-3783206 MS.gene20153:CDS
GCTCAAAGGATTGGGCACAA+AGG 0.653987 4.4:-3783067 MS.gene20153:CDS
AGTGGACGTCAAGTTGAACA+AGG 0.683327 4.4:-3783223 MS.gene20153:CDS
GGGAACTAATGATGTCAGAG+TGG 0.705766 4.4:-3783241 MS.gene20153:CDS
TGCCCGCAAGAGGAACGATG+AGG 0.726992 4.4:-3783148 MS.gene20153:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTTTAATCTCTTTAGA+AGG - chr4.4:3783254-3783273 MS.gene20153:CDS 15.0%
!!! TTTACAATTATTTTGATAAC+CGG - chr4.4:3783499-3783518 MS.gene20153:intron 15.0%
!! ATCAGTTAAAATAACATCTA+CGG + chr4.4:3783480-3783499 None:intergenic 20.0%
!!! TTACAATTATTTTGATAACC+GGG - chr4.4:3783500-3783519 MS.gene20153:intron 20.0%
! TAAATAGCATATCACAGAAA+TGG - chr4.4:3783423-3783442 MS.gene20153:intron 25.0%
!! AAACAAAACATTTGCTAGAT+AGG + chr4.4:3783184-3783203 None:intergenic 25.0%
!! AACAAAACATTTGCTAGATA+GGG + chr4.4:3783183-3783202 None:intergenic 25.0%
!! GATATAGAGGAAAATTTTTG+TGG - chr4.4:3783215-3783234 MS.gene20153:CDS 25.0%
!!! TCTTTAGAAGGTTTTTTCAA+TGG - chr4.4:3783266-3783285 MS.gene20153:CDS 25.0%
! AAAAGTCATTTCAGGTAAAG+GGG + chr4.4:3783574-3783593 None:intergenic 30.0%
! AGAAAAGTCATTTCAGGTAA+AGG + chr4.4:3783576-3783595 None:intergenic 30.0%
! CATCAAAATGAAAAGCACAA+GGG + chr4.4:3783304-3783323 None:intergenic 30.0%
! CTTTTCTATGGAGATTGTTT+CGG - chr4.4:3783589-3783608 MS.gene20153:intron 30.0%
! GAAAAGTCATTTCAGGTAAA+GGG + chr4.4:3783575-3783594 None:intergenic 30.0%
! TACCTGAAATGACTTTTCTA+TGG - chr4.4:3783577-3783596 MS.gene20153:intron 30.0%
! TCATCAAAATGAAAAGCACA+AGG + chr4.4:3783305-3783324 None:intergenic 30.0%
! TTGTTTTCGATCAGATATAG+AGG - chr4.4:3783202-3783221 MS.gene20153:CDS 30.0%
!! GCTGTTTTGCATAATAACAA+AGG + chr4.4:3783677-3783696 None:intergenic 30.0%
ATAGCATATCACAGAAATGG+TGG - chr4.4:3783426-3783445 MS.gene20153:intron 35.0%
CTAAAGCAATAAAGGAGATC+AGG - chr4.4:3783716-3783735 MS.gene20153:intron 35.0%
CTCCATAGAAAAGTCATTTC+AGG + chr4.4:3783582-3783601 None:intergenic 35.0%
CTGATCTCCTTTATTGCTTT+AGG + chr4.4:3783718-3783737 None:intergenic 35.0%
GAAAGCTCCTAAAGCAATAA+AGG - chr4.4:3783708-3783727 MS.gene20153:intron 35.0%
! ATTAGTTCCCATAGCCTTTT+GGG + chr4.4:3783749-3783768 None:intergenic 35.0%
!! CACAAAGGTTATTGATGATG+AGG - chr4.4:3783948-3783967 MS.gene20153:CDS 35.0%
!! TCAAGTTGAACAAGGCTATT+TGG - chr4.4:3783785-3783804 MS.gene20153:intron 35.0%
!!! CAATTATTTTGATAACCGGG+AGG - chr4.4:3783503-3783522 MS.gene20153:intron 35.0%
AAGGAAGAGCTCAAAGGATT+GGG - chr4.4:3783925-3783944 MS.gene20153:CDS 40.0%
AAGTTTGCCCAAAAGGCTAT+GGG - chr4.4:3783739-3783758 MS.gene20153:intron 40.0%
AATCCTTTGAGCTCTTCCTT+GGG + chr4.4:3783925-3783944 None:intergenic 40.0%
CAAAACTATATTCCTCCTCC+CGG + chr4.4:3783521-3783540 None:intergenic 40.0%
TACTGTTGTTGAAATCCCCA+AGG - chr4.4:3783906-3783925 MS.gene20153:CDS 40.0%
! CATTAGTTCCCATAGCCTTT+TGG + chr4.4:3783750-3783769 None:intergenic 40.0%
!!! TTATTTTGATAACCGGGAGG+AGG - chr4.4:3783506-3783525 MS.gene20153:intron 40.0%
AGAGAGAGAATTACCAGCCA+TGG + chr4.4:3783127-3783146 None:intergenic 45.0%
ATCCTTTGAGCTCTTCCTTG+GGG + chr4.4:3783924-3783943 None:intergenic 45.0%
CAAGGAAGAGCTCAAAGGAT+TGG - chr4.4:3783924-3783943 MS.gene20153:CDS 45.0%
CAATCCTTTGAGCTCTTCCT+TGG + chr4.4:3783926-3783945 None:intergenic 45.0%
GAAGTTTGCCCAAAAGGCTA+TGG - chr4.4:3783738-3783757 MS.gene20153:intron 45.0%
GATCAGGAAGTTTGCCCAAA+AGG - chr4.4:3783732-3783751 MS.gene20153:intron 45.0%
GGGAACTAATGATGTCAGAG+TGG - chr4.4:3783759-3783778 MS.gene20153:intron 45.0%
! AACAAGGCTATTTGGAGCCA+GGG - chr4.4:3783793-3783812 MS.gene20153:intron 45.0%
!! AGTGGACGTCAAGTTGAACA+AGG - chr4.4:3783777-3783796 MS.gene20153:intron 45.0%
AAGTGTCCCTAGGAGGGTTA+GGG - chr4.4:3783822-3783841 MS.gene20153:intron 50.0%
ATCCCCAAGGAAGAGCTCAA+AGG - chr4.4:3783919-3783938 MS.gene20153:CDS 50.0%
GAACGATGAGGAGGATGCTA+AGG - chr4.4:3783864-3783883 MS.gene20153:intron 50.0%
GACAACCTCTTCCTTCCTAC+CGG + chr4.4:3783069-3783088 None:intergenic 50.0%
GAGAGAATTACCAGCCATGG+AGG + chr4.4:3783124-3783143 None:intergenic 50.0%
GCTCAAAGGATTGGGCACAA+AGG - chr4.4:3783933-3783952 MS.gene20153:CDS 50.0%
! ACAAGGCTATTTGGAGCCAG+GGG - chr4.4:3783794-3783813 MS.gene20153:intron 50.0%
! GAACAAGGCTATTTGGAGCC+AGG - chr4.4:3783792-3783811 MS.gene20153:intron 50.0%
!! GAGGTTGATGGTGTACTCTC+TGG + chr4.4:3783093-3783112 None:intergenic 50.0%
!! GATCAGAAGTGTCCCTAGGA+GGG - chr4.4:3783816-3783835 MS.gene20153:intron 50.0%
AACCTCCACAAACGCCTCCA+TGG - chr4.4:3783107-3783126 MS.gene20153:CDS 55.0%
ATGCGAACCCTAACCCTCCT+AGG + chr4.4:3783832-3783851 None:intergenic 55.0%
CCTCCTCATCGTTCCTCTTG+CGG + chr4.4:3783858-3783877 None:intergenic 55.0%
CTCCTCATCGTTCCTCTTGC+GGG + chr4.4:3783857-3783876 None:intergenic 55.0%
TAGGGACACTTCTGATCCCC+TGG + chr4.4:3783813-3783832 None:intergenic 55.0%
TGCGAACCCTAACCCTCCTA+GGG + chr4.4:3783831-3783850 None:intergenic 55.0%
! GAAGTGTCCCTAGGAGGGTT+AGG - chr4.4:3783821-3783840 MS.gene20153:intron 55.0%
! GAGGCGTTTGTGGAGGTTGA+TGG + chr4.4:3783105-3783124 None:intergenic 55.0%
!! AGGGGATCAGAAGTGTCCCT+AGG - chr4.4:3783812-3783831 MS.gene20153:intron 55.0%
!! GGATCAGAAGTGTCCCTAGG+AGG - chr4.4:3783815-3783834 MS.gene20153:intron 55.0%
CCGCAAGAGGAACGATGAGG+AGG - chr4.4:3783855-3783874 MS.gene20153:intron 60.0%
TCCACAAACGCCTCCATGGC+TGG - chr4.4:3783111-3783130 MS.gene20153:CDS 60.0%
TGCCCGCAAGAGGAACGATG+AGG - chr4.4:3783852-3783871 MS.gene20153:intron 60.0%
!! ACCAGCCATGGAGGCGTTTG+TGG + chr4.4:3783115-3783134 None:intergenic 60.0%
!! AGCCATGGAGGCGTTTGTGG+AGG + chr4.4:3783112-3783131 None:intergenic 60.0%
CTCTTCCTTCCTACCGGCGC+CGG + chr4.4:3783063-3783082 None:intergenic 65.0%
GGGTTCGCATTGCCCGCAAG+AGG - chr4.4:3783842-3783861 MS.gene20153:intron 65.0%
! ATGGTGGAGAAGACCGGCGC+CGG - chr4.4:3783047-3783066 MS.gene20153:CDS 65.0%
!! CGGCGCCGGTAGGAAGGAAG+AGG - chr4.4:3783061-3783080 MS.gene20153:CDS 70.0%
!! GAAGACCGGCGCCGGTAGGA+AGG - chr4.4:3783055-3783074 MS.gene20153:CDS 70.0%
!! TGGAGAAGACCGGCGCCGGT+AGG - chr4.4:3783051-3783070 MS.gene20153:CDS 70.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 3783047 3783975 3783047 ID=MS.gene20153
chr4.4 mRNA 3783047 3783975 3783047 ID=MS.gene20153.t1;Parent=MS.gene20153
chr4.4 exon 3783890 3783975 3783890 ID=MS.gene20153.t1.exon1;Parent=MS.gene20153.t1
chr4.4 CDS 3783890 3783975 3783890 ID=cds.MS.gene20153.t1;Parent=MS.gene20153.t1
chr4.4 exon 3783047 3783326 3783047 ID=MS.gene20153.t1.exon2;Parent=MS.gene20153.t1
chr4.4 CDS 3783047 3783326 3783047 ID=cds.MS.gene20153.t1;Parent=MS.gene20153.t1
Gene Sequence

>MS.gene20153

ATGGTGGAGAAGACCGGCGCCGGTAGGAAGGAAGAGGTTGTCACCAGAGAGTACACCATCAACCTCCACAAACGCCTCCATGGCTGGTAATTCTCTCTCTATTGTTCATTTTTGTTTTTTTCGTTTGTCTAAACCCTATCTAGCAAATGTTTTGTTTGTTTTCGATCAGATATAGAGGAAAATTTTTGTGGATTTTTTATTTATTATATTTTTTTAATCTCTTTAGAAGGTTTTTTCAATGGCAGTAAAATAGTCCCTTGTGCTTTTCATTTTGATGATATTGTAATTAAGCTGTTTGAATGTTTAAATGTTCTGTGTCTTTGATATTAATGTTGTCAATTGTGCAATAATGCTGTTAGTTAGCACAATTTTAAGCTAAATAGCATATCACAGAAATGGTGGTTTGCTATGCACTGCGTTTCTAGCAACTCCGTAGATGTTATTTTAACTGATTTACAATTATTTTGATAACCGGGAGGAGGAATATAGTTTTGTGCGACAATACTTTGATGTAACAAACATATCCCCTTTACCTGAAATGACTTTTCTATGGAGATTGTTTCGGCTGATATCTCGTTTGTATTATTTGTTTGTTTTAACTTTATGAAATTCTAACAGTCATTTTTTCCTTTGTTATTATGCAAAACAGCACATTTAAGAAGAAAGCTCCTAAAGCAATAAAGGAGATCAGGAAGTTTGCCCAAAAGGCTATGGGAACTAATGATGTCAGAGTGGACGTCAAGTTGAACAAGGCTATTTGGAGCCAGGGGATCAGAAGTGTCCCTAGGAGGGTTAGGGTTCGCATTGCCCGCAAGAGGAACGATGAGGAGGATGCTAAGGAAGAGCTCTACTCACTTGTTACTGTTGTTGAAATCCCCAAGGAAGAGCTCAAAGGATTGGGCACAAAGGTTATTGATGATGAGGATTGA

Protein sequence

>MS.gene20153.t1

MVEKTGAGRKEEVVTREYTINLHKRLHGCTFKKKAPKAIKEIRKFAQKAMGTNDVRVDVKLNKAIWSQGIRSVPRRVRVRIARKRNDEEDAKEELYSLVTVVEIPKEELKGLGTKVIDDED