AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene026342

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene026342.t1 MTR_1g035520 93.443 122 8 0 1 122 262 383 1.03e-79 239
MS.gene026342.t1 MTR_6g061070 77.049 122 27 1 1 122 350 470 7.55e-63 198
MS.gene026342.t1 MTR_1g035490 44.681 94 46 4 30 122 240 328 1.30e-17 77.0
MS.gene026342.t1 MTR_1g035570 42.222 90 48 2 33 122 309 394 2.97e-15 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGAATATGCGGGCAATTT+TGG 0.164513 1.2:-20355412 MS.gene026342:CDS
TATAATGAACATCTCGACTA+TGG 0.280428 1.2:-20355010 MS.gene026342:CDS
AAGAAGCATGTTATATTTAG+TGG 0.292603 1.2:-20355085 MS.gene026342:CDS
TACTGCAGATTCTGTAAGTC+TGG 0.316891 1.2:-20355262 MS.gene026342:intron
ATTCAGTGGAGTTGAGAGTA+GGG 0.448522 1.2:-20355060 MS.gene026342:CDS
TGCTTCTTCAACAGCTCACT+TGG 0.474225 1.2:+20355100 None:intergenic
GGGTTTACATGAGATGTTCA+AGG 0.483513 1.2:-20355241 MS.gene026342:CDS
TGAGAGTAGGGGAAGGAACA+TGG 0.483751 1.2:-20355048 MS.gene026342:CDS
GACTATGGGTGGTTCACTAA+AGG 0.507216 1.2:-20354995 MS.gene026342:CDS
AGAGATTGCAAAGTAAAGAC+TGG 0.515563 1.2:-20354956 MS.gene026342:CDS
ACTGCAGATTCTGTAAGTCT+GGG 0.516733 1.2:-20355261 MS.gene026342:intron
TATTCAGTGGAGTTGAGAGT+AGG 0.518002 1.2:-20355061 MS.gene026342:CDS
TATATTTAGTGGATATTCAG+TGG 0.520038 1.2:-20355074 MS.gene026342:CDS
TGTGCAAAATCATGTGTTCA+AGG 0.521657 1.2:-20354906 MS.gene026342:CDS
TTCAGTGGAGTTGAGAGTAG+GGG 0.529294 1.2:-20355059 MS.gene026342:CDS
ATAATGAACATCTCGACTAT+GGG 0.547880 1.2:-20355009 MS.gene026342:CDS
ATGGGTGGTTCACTAAAGGC+TGG 0.558556 1.2:-20354991 MS.gene026342:CDS
GTAAAAGATATGGAATATGC+GGG 0.574921 1.2:-20355421 None:intergenic
CGTAAAAGATATGGAATATG+CGG 0.600766 1.2:-20355422 None:intergenic
GGAAGGAACATGGTTTGTAG+AGG 0.629163 1.2:-20355038 MS.gene026342:CDS
ATGAACATCTCGACTATGGG+TGG 0.635276 1.2:-20355006 MS.gene026342:CDS
GTGGAGTTGAGAGTAGGGGA+AGG 0.647557 1.2:-20355055 MS.gene026342:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAAAGAAAACATAGTTTA+AGG + chr1.2:20355016-20355035 None:intergenic 20.0%
! TTTGTTCATATATATGCAGT+TGG - chr1.2:20355173-20355192 MS.gene026342:intron 25.0%
!! AAGAAGCATGTTATATTTAG+TGG - chr1.2:20355219-20355238 MS.gene026342:CDS 25.0%
!! TATATTTAGTGGATATTCAG+TGG - chr1.2:20355230-20355249 MS.gene026342:CDS 25.0%
!! TTTTATAACATCATCAGACA+AGG - chr1.2:20355087-20355106 MS.gene026342:CDS 25.0%
ATAATGAACATCTCGACTAT+GGG - chr1.2:20355295-20355314 MS.gene026342:intron 30.0%
TATAATGAACATCTCGACTA+TGG - chr1.2:20355294-20355313 MS.gene026342:intron 30.0%
!! ATTTTGGAGATGGAATTTCA+AGG - chr1.2:20354908-20354927 MS.gene026342:CDS 30.0%
!! CACAAAAACACATGGTTTTA+GGG - chr1.2:20354936-20354955 MS.gene026342:CDS 30.0%
!!! ACAAAAACACATGGTTTTAG+GGG - chr1.2:20354937-20354956 MS.gene026342:CDS 30.0%
AGAGATTGCAAAGTAAAGAC+TGG - chr1.2:20355348-20355367 MS.gene026342:intron 35.0%
CACACACATAGCTATATACA+TGG + chr1.2:20355137-20355156 None:intergenic 35.0%
TGTGCAAAATCATGTGTTCA+AGG - chr1.2:20355398-20355417 MS.gene026342:CDS 35.0%
! GCACAAAAACACATGGTTTT+AGG - chr1.2:20354935-20354954 MS.gene026342:CDS 35.0%
ACTGCAGATTCTGTAAGTCT+GGG - chr1.2:20355043-20355062 MS.gene026342:CDS 40.0%
ATTCAGTGGAGTTGAGAGTA+GGG - chr1.2:20355244-20355263 MS.gene026342:CDS 40.0%
GGGTTTACATGAGATGTTCA+AGG - chr1.2:20355063-20355082 MS.gene026342:CDS 40.0%
TACTGCAGATTCTGTAAGTC+TGG - chr1.2:20355042-20355061 MS.gene026342:CDS 40.0%
TATTCAGTGGAGTTGAGAGT+AGG - chr1.2:20355243-20355262 MS.gene026342:CDS 40.0%
! ATGGAATATGCGGGCAATTT+TGG - chr1.2:20354892-20354911 MS.gene026342:CDS 40.0%
AGGAGCTGCACAAAAACACA+TGG - chr1.2:20354928-20354947 MS.gene026342:CDS 45.0%
ATGAACATCTCGACTATGGG+TGG - chr1.2:20355298-20355317 MS.gene026342:intron 45.0%
GACTATGGGTGGTTCACTAA+AGG - chr1.2:20355309-20355328 MS.gene026342:intron 45.0%
TGCTTCTTCAACAGCTCACT+TGG + chr1.2:20355207-20355226 None:intergenic 45.0%
TTCAGTGGAGTTGAGAGTAG+GGG - chr1.2:20355245-20355264 MS.gene026342:CDS 45.0%
! GGAAGGAACATGGTTTGTAG+AGG - chr1.2:20355266-20355285 MS.gene026342:intron 45.0%
!! TATGCGGGCAATTTTGGAGA+TGG - chr1.2:20354898-20354917 MS.gene026342:CDS 45.0%
ATGGGTGGTTCACTAAAGGC+TGG - chr1.2:20355313-20355332 MS.gene026342:intron 50.0%
TGAGAGTAGGGGAAGGAACA+TGG - chr1.2:20355256-20355275 MS.gene026342:CDS 50.0%
GTGGAGTTGAGAGTAGGGGA+AGG - chr1.2:20355249-20355268 MS.gene026342:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 20354892 20355434 20354892 ID=MS.gene026342
chr1.2 mRNA 20354892 20355434 20354892 ID=MS.gene026342.t1;Parent=MS.gene026342
chr1.2 exon 20355368 20355434 20355368 ID=MS.gene026342.t1.exon1;Parent=MS.gene026342.t1
chr1.2 CDS 20355368 20355434 20355368 ID=cds.MS.gene026342.t1;Parent=MS.gene026342.t1
chr1.2 exon 20355218 20355276 20355218 ID=MS.gene026342.t1.exon2;Parent=MS.gene026342.t1
chr1.2 CDS 20355218 20355276 20355218 ID=cds.MS.gene026342.t1;Parent=MS.gene026342.t1
chr1.2 exon 20354892 20355134 20354892 ID=MS.gene026342.t1.exon3;Parent=MS.gene026342.t1
chr1.2 CDS 20354892 20355134 20354892 ID=cds.MS.gene026342.t1;Parent=MS.gene026342.t1
Gene Sequence

>MS.gene026342

ATGGAATATGCGGGCAATTTTGGAGATGGAATTTCAAGGAGCTGCACAAAAACACATGGTTTTAGGGGTATTCATCTTAATTTTGTTTTTGTGTTTTTTTGTGTACAATTCATGCAAATCTCCTTAAACTATGTTTTCTTTGTTGTTAATTACTGCAGATTCTGTAAGTCTGGGTTTACATGAGATGTTCAAGGTTTTTATAACATCATCAGACAAGGTATGAATTACGTAAAATGCTGTTACCATGTATATAGCTATGTGTGTGAATGTATAAAATTTAATTTGTTCATATATATGCAGTTGGTTGTACTACCAAGTGAGCTGTTGAAGAAGCATGTTATATTTAGTGGATATTCAGTGGAGTTGAGAGTAGGGGAAGGAACATGGTTTGTAGAGGTGAATTATAATGAACATCTCGACTATGGGTGGTTCACTAAAGGCTGGCAAGAATTTGTGAGAGATTGCAAAGTAAAGACTGGAGACACTTGCTTGTTTGAGACGATTGATGTGCAAAATCATGTGTTCAAGGTTTCAATTGTTTAG
Protein sequence

>MS.gene026342.t1

MEYAGNFGDGISRSCTKTHGFRDSVSLGLHEMFKVFITSSDKLVVLPSELLKKHVIFSGYSVELRVGEGTWFVEVNYNEHLDYGWFTKGWQEFVRDCKVKTGDTCLFETIDVQNHVFKVSIV