AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31523

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31523.t1 MTR_2g090020 97.701 87 2 0 1 87 1 87 6.71e-61 180
MS.gene31523.t1 MTR_2g090010 81.111 90 14 2 1 87 1 90 3.08e-48 148
MS.gene31523.t1 MTR_2g090015 75.824 91 18 2 1 87 1 91 1.24e-45 141
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31523.t1 AT4G28240 46.739 92 38 3 1 87 1 86 3.56e-20 77.4

Find 30 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAGAGACGAGTTCGGTTT+TGG 0.305492 2.4:+11086245 None:intergenic
AAGTTATGTACATGAATTGC+TGG 0.397828 2.4:-11086117 MS.gene31523:CDS
TCCGATCTCCGTCCGTTGTC+CGG 0.406922 2.4:-11086208 MS.gene31523:CDS
TGAGTTACTTGAACCGTGTT+TGG 0.412758 2.4:-11086345 MS.gene31523:CDS
GCGCAAGGCCACACCGATCC+AGG 0.445476 2.4:-11086301 MS.gene31523:CDS
CGGCAGAGAAGAGACGAGTT+CGG 0.471245 2.4:+11086239 None:intergenic
ACGGAGATCGGATAAACTTC+CGG 0.486636 2.4:+11086219 None:intergenic
GTTGTCCGGCGTCGTTGTAT+CGG 0.492908 2.4:-11086194 MS.gene31523:CDS
GTGGCCTTGCGCCACAGCTA+CGG 0.499116 2.4:+11086312 None:intergenic
TTTGCACTTGTGGCCTGGAT+CGG 0.503366 2.4:+11086288 None:intergenic
GCCGGACAACGGACGGAGAT+CGG 0.505197 2.4:+11086207 None:intergenic
GAAGAACCGATGATTCTCTT+CGG 0.508064 2.4:-11086141 MS.gene31523:CDS
AGTTATGTACATGAATTGCT+GGG 0.535583 2.4:-11086116 MS.gene31523:CDS
CAACGACGCCGGACAACGGA+CGG 0.536509 2.4:+11086200 None:intergenic
CGAACTCGTCTCTTCTCTGC+CGG 0.543523 2.4:-11086238 MS.gene31523:CDS
AACTTTCCGAAGAGAATCAT+CGG 0.563956 2.4:+11086135 None:intergenic
CTTGAACCGTGTTTGGATGG+CGG 0.571348 2.4:-11086338 MS.gene31523:CDS
GCAACCGTAGCTGTGGCGCA+AGG 0.574484 2.4:-11086316 MS.gene31523:CDS
TTACTTGAACCGTGTTTGGA+TGG 0.584544 2.4:-11086341 MS.gene31523:CDS
GATGGCGGCAACCGTAGCTG+TGG 0.585844 2.4:-11086323 MS.gene31523:CDS
TACATGAATTGCTGGGGTCA+AGG 0.586623 2.4:-11086109 MS.gene31523:CDS
GATACAACGACGCCGGACAA+CGG 0.587431 2.4:+11086196 None:intergenic
CACAAGTGCAAAACAGCCGT+TGG 0.609626 2.4:-11086277 MS.gene31523:CDS
GTCCGGCGTCGTTGTATCGG+AGG 0.612227 2.4:-11086191 MS.gene31523:CDS
CGGTTGCCGCCATCCAAACA+CGG 0.636549 2.4:+11086332 None:intergenic
TGTATCGGAGGTGAGTTCTG+AGG 0.650249 2.4:-11086179 MS.gene31523:CDS
ATCGGAGGTGAGTTCTGAGG+CGG 0.654083 2.4:-11086176 MS.gene31523:CDS
CACCTCCGATACAACGACGC+CGG 0.661000 2.4:+11086189 None:intergenic
ACTTGTGGCCTGGATCGGTG+TGG 0.680459 2.4:+11086293 None:intergenic
GTTATGTACATGAATTGCTG+GGG 0.680638 2.4:-11086115 MS.gene31523:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGTTATGTACATGAATTGC+TGG - chr2.4:11086334-11086353 MS.gene31523:CDS 30.0%
AGTTATGTACATGAATTGCT+GGG - chr2.4:11086335-11086354 MS.gene31523:CDS 30.0%
AACTTTCCGAAGAGAATCAT+CGG + chr2.4:11086319-11086338 None:intergenic 35.0%
GTTATGTACATGAATTGCTG+GGG - chr2.4:11086336-11086355 MS.gene31523:CDS 35.0%
!! GTTTTGGTGAATAGATCCAA+CGG + chr2.4:11086193-11086212 None:intergenic 35.0%
GAAGAACCGATGATTCTCTT+CGG - chr2.4:11086310-11086329 MS.gene31523:CDS 40.0%
TGAGTTACTTGAACCGTGTT+TGG - chr2.4:11086106-11086125 MS.gene31523:CDS 40.0%
TTACTTGAACCGTGTTTGGA+TGG - chr2.4:11086110-11086129 MS.gene31523:CDS 40.0%
ACGGAGATCGGATAAACTTC+CGG + chr2.4:11086235-11086254 None:intergenic 45.0%
TACATGAATTGCTGGGGTCA+AGG - chr2.4:11086342-11086361 MS.gene31523:CDS 45.0%
! AGAAGAGACGAGTTCGGTTT+TGG + chr2.4:11086209-11086228 None:intergenic 45.0%
CACAAGTGCAAAACAGCCGT+TGG - chr2.4:11086174-11086193 MS.gene31523:CDS 50.0%
CTTGAACCGTGTTTGGATGG+CGG - chr2.4:11086113-11086132 MS.gene31523:CDS 50.0%
TGTATCGGAGGTGAGTTCTG+AGG - chr2.4:11086272-11086291 MS.gene31523:CDS 50.0%
TTTGCACTTGTGGCCTGGAT+CGG + chr2.4:11086166-11086185 None:intergenic 50.0%
!! CAACGGCTGTTTTGCACTTG+TGG + chr2.4:11086176-11086195 None:intergenic 50.0%
CGAACTCGTCTCTTCTCTGC+CGG - chr2.4:11086213-11086232 MS.gene31523:CDS 55.0%
CGGCAGAGAAGAGACGAGTT+CGG + chr2.4:11086215-11086234 None:intergenic 55.0%
GATACAACGACGCCGGACAA+CGG + chr2.4:11086258-11086277 None:intergenic 55.0%
GTTGTCCGGCGTCGTTGTAT+CGG - chr2.4:11086257-11086276 MS.gene31523:CDS 55.0%
!! ATCGGAGGTGAGTTCTGAGG+CGG - chr2.4:11086275-11086294 MS.gene31523:CDS 55.0%
!! GCTGTTTTGCACTTGTGGCC+TGG + chr2.4:11086171-11086190 None:intergenic 55.0%
ACTTGTGGCCTGGATCGGTG+TGG + chr2.4:11086161-11086180 None:intergenic 60.0%
CACCTCCGATACAACGACGC+CGG + chr2.4:11086265-11086284 None:intergenic 60.0%
CGGTTGCCGCCATCCAAACA+CGG + chr2.4:11086122-11086141 None:intergenic 60.0%
TCCGATCTCCGTCCGTTGTC+CGG - chr2.4:11086243-11086262 MS.gene31523:CDS 60.0%
CAACGACGCCGGACAACGGA+CGG + chr2.4:11086254-11086273 None:intergenic 65.0%
GCAACCGTAGCTGTGGCGCA+AGG - chr2.4:11086135-11086154 MS.gene31523:CDS 65.0%
GCCGGACAACGGACGGAGAT+CGG + chr2.4:11086247-11086266 None:intergenic 65.0%
GTCCGGCGTCGTTGTATCGG+AGG - chr2.4:11086260-11086279 MS.gene31523:CDS 65.0%
! GATGGCGGCAACCGTAGCTG+TGG - chr2.4:11086128-11086147 MS.gene31523:CDS 65.0%
! GTGGCCTTGCGCCACAGCTA+CGG + chr2.4:11086142-11086161 None:intergenic 65.0%
GCGCAAGGCCACACCGATCC+AGG - chr2.4:11086150-11086169 MS.gene31523:CDS 70.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 11086105 11086368 11086105 ID=MS.gene31523
chr2.4 mRNA 11086105 11086368 11086105 ID=MS.gene31523.t1;Parent=MS.gene31523
chr2.4 exon 11086105 11086368 11086105 ID=MS.gene31523.t1.exon1;Parent=MS.gene31523.t1
chr2.4 CDS 11086105 11086368 11086105 ID=cds.MS.gene31523.t1;Parent=MS.gene31523.t1
Gene Sequence

>MS.gene31523

ATGAGTTACTTGAACCGTGTTTGGATGGCGGCAACCGTAGCTGTGGCGCAAGGCCACACCGATCCAGGCCACAAGTGCAAAACAGCCGTTGGATCTATTCACCAAAACCGAACTCGTCTCTTCTCTGCCGGAAGTTTATCCGATCTCCGTCCGTTGTCCGGCGTCGTTGTATCGGAGGTGAGTTCTGAGGCGGATGAGAAGTTAAGAAGAACCGATGATTCTCTTCGGAAAGTTATGTACATGAATTGCTGGGGTCAAGGCTGA
Protein sequence

>MS.gene31523.t1

MSYLNRVWMAATVAVAQGHTDPGHKCKTAVGSIHQNRTRLFSAGSLSDLRPLSGVVVSEVSSEADEKLRRTDDSLRKVMYMNCWGQG