AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene037362

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene037362.t1 MTR_1g114500 99.342 152 1 0 1 152 1 152 8.12e-109 306
MS.gene037362.t1 MTR_1g114500 90.345 145 4 1 1 145 1 135 6.83e-91 260
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene037362.t1 AT5G23290 72.368 152 39 2 1 152 1 149 2.79e-73 216

Find 29 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCACGTTCTCGTCGATAT+CGG 0.346200 1.3:+77592235 MS.gene037362:CDS
AGTTAAGGAACAAGCAGATA+TGG 0.392343 1.3:+77592048 MS.gene037362:CDS
TCGCAGTAATCCTTTCCTTC+AGG 0.397139 1.3:-77592399 None:intergenic
TGAACAGTTGAAAGCAGTTA+AGG 0.432363 1.3:+77592033 MS.gene037362:CDS
GATCTCTCTCTCCGTTCTCT+CGG 0.450391 1.3:+77592151 MS.gene037362:CDS
CGGAAGCGGAGCGATGACTC+TGG 0.463988 1.3:+77591997 MS.gene037362:CDS
CAAGACAGTCTCAACAATAT+CGG 0.466377 1.3:+77592085 MS.gene037362:CDS
TGTTGAGACTGTCTTGAAGA+AGG 0.480129 1.3:-77592078 None:intergenic
GTTCTCGTCGATATCGGAAC+TGG 0.508671 1.3:+77592241 MS.gene037362:CDS
TGAGGATCTTGAAGAGTAGC+AGG 0.512402 1.3:-77592214 None:intergenic
GAGATCGTTGAGAGCGGTGG+TGG 0.515505 1.3:-77592134 None:intergenic
GAAAACCATGCCTGAAGGAA+AGG 0.522733 1.3:+77592389 MS.gene037362:intron
GCTTCGTCGAAGAGCGGAAG+CGG 0.528323 1.3:+77591983 MS.gene037362:CDS
AAAACGTTGCGGATGAAGCT+GGG 0.534177 1.3:+77592798 MS.gene037362:CDS
GTAATCCTTTCCTTCAGGCA+TGG 0.536343 1.3:-77592394 None:intergenic
TAACTTCGATCAACTTGTTG+AGG 0.544631 1.3:+77592446 MS.gene037362:CDS
GAGTTCAAGACGAGTGGTGG+CGG 0.544654 1.3:-77592110 None:intergenic
GGCGAGTTCAAGACGAGTGG+TGG 0.560196 1.3:-77592113 None:intergenic
CGGAACTGGTTATTTCGTTG+AGG 0.563029 1.3:+77592255 MS.gene037362:CDS
AGAGAGATCGTTGAGAGCGG+TGG 0.573255 1.3:-77592137 None:intergenic
GAGAAGCGGTGAGAGGAACA+AGG 0.602439 1.3:-77592183 None:intergenic
AAAATGGCTTCGTCGAAGAG+CGG 0.608939 1.3:+77591977 None:intergenic
ATATCGACGAGAACGTGATG+AGG 0.609043 1.3:-77592232 None:intergenic
ACATAGAGAGAAGCGGTGAG+AGG 0.615765 1.3:-77592190 None:intergenic
AAACAGAAAACCATGCCTGA+AGG 0.621995 1.3:+77592384 MS.gene037362:intron
AGCAGGAACATAGAGAGAAG+CGG 0.640463 1.3:-77592197 None:intergenic
GCGGAGCGATGACTCTGGAG+AGG 0.643180 1.3:+77592002 MS.gene037362:CDS
GAGAGAGAGATCGTTGAGAG+CGG 0.661545 1.3:-77592140 None:intergenic
GGTGGCGAGTTCAAGACGAG+TGG 0.675476 1.3:-77592116 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAGATCTAAATAAATTAAT+CGG - chr1.3:77592298-77592317 None:intergenic 15.0%
!! TACATATATCAAAATCAAAT+AGG - chr1.3:77592500-77592519 None:intergenic 15.0%
!! AAAAATATCAAAGAGAAAAC+TGG - chr1.3:77592704-77592723 None:intergenic 20.0%
!! AGATCTAAATAAATTAATCG+GGG - chr1.3:77592296-77592315 None:intergenic 20.0%
!! CAGATCTAAATAAATTAATC+GGG - chr1.3:77592297-77592316 None:intergenic 20.0%
!! CTAGACAAAATATCAAATTA+GGG - chr1.3:77592669-77592688 None:intergenic 20.0%
!!! AGTTTTCTCTTTGATATTTT+TGG + chr1.3:77592703-77592722 MS.gene037362:intron 20.0%
! CCTAGACAAAATATCAAATT+AGG - chr1.3:77592670-77592689 None:intergenic 25.0%
!! ATCGTATATGCTTCTTTTTA+GGG + chr1.3:77592318-77592337 MS.gene037362:intron 25.0%
!! CCTAATTTGATATTTTGTCT+AGG + chr1.3:77592667-77592686 MS.gene037362:intron 25.0%
!! TATCGTATATGCTTCTTTTT+AGG + chr1.3:77592317-77592336 MS.gene037362:intron 25.0%
!!! GTGTTAGTTTTATACTAATG+TGG + chr1.3:77592592-77592611 MS.gene037362:intron 25.0%
CTTGATGTAATTACAAATGC+AGG + chr1.3:77592760-77592779 MS.gene037362:intron 30.0%
!!! TATGCTTCTTTTTAGGGTTA+TGG + chr1.3:77592324-77592343 MS.gene037362:intron 30.0%
AGTTAAGGAACAAGCAGATA+TGG + chr1.3:77592048-77592067 MS.gene037362:CDS 35.0%
CAAGACAGTCTCAACAATAT+CGG + chr1.3:77592085-77592104 MS.gene037362:CDS 35.0%
CTAATGTGGTTATTCTGTTG+TGG + chr1.3:77592606-77592625 MS.gene037362:intron 35.0%
TGAACAGTTGAAAGCAGTTA+AGG + chr1.3:77592033-77592052 MS.gene037362:CDS 35.0%
!! TAACTTCGATCAACTTGTTG+AGG + chr1.3:77592446-77592465 MS.gene037362:CDS 35.0%
AAACAGAAAACCATGCCTGA+AGG + chr1.3:77592384-77592403 MS.gene037362:intron 40.0%
GTCCAAGAAGAAAAACGTTG+CGG + chr1.3:77592787-77592806 MS.gene037362:CDS 40.0%
TGTTGAGACTGTCTTGAAGA+AGG - chr1.3:77592081-77592100 None:intergenic 40.0%
! ATCCGCAACGTTTTTCTTCT+TGG - chr1.3:77592792-77592811 None:intergenic 40.0%
!!! TGAAGCTGGGCTTATTTTAC+AGG + chr1.3:77592811-77592830 MS.gene037362:CDS 40.0%
AAAAACGTTGCGGATGAAGC+TGG + chr1.3:77592797-77592816 MS.gene037362:CDS 45.0%
AAAACGTTGCGGATGAAGCT+GGG + chr1.3:77592798-77592817 MS.gene037362:CDS 45.0%
AGCAGGAACATAGAGAGAAG+CGG - chr1.3:77592200-77592219 None:intergenic 45.0%
ATATCGACGAGAACGTGATG+AGG - chr1.3:77592235-77592254 None:intergenic 45.0%
CATCACGTTCTCGTCGATAT+CGG + chr1.3:77592235-77592254 MS.gene037362:CDS 45.0%
GAAAACCATGCCTGAAGGAA+AGG + chr1.3:77592389-77592408 MS.gene037362:intron 45.0%
GTAATCCTTTCCTTCAGGCA+TGG - chr1.3:77592397-77592416 None:intergenic 45.0%
TCGCAGTAATCCTTTCCTTC+AGG - chr1.3:77592402-77592421 None:intergenic 45.0%
TGAGGATCTTGAAGAGTAGC+AGG - chr1.3:77592217-77592236 None:intergenic 45.0%
! CGGAACTGGTTATTTCGTTG+AGG + chr1.3:77592255-77592274 MS.gene037362:CDS 45.0%
! GGATTTTACTGCCGAGAGAA+CGG - chr1.3:77592165-77592184 None:intergenic 45.0%
ACATAGAGAGAAGCGGTGAG+AGG - chr1.3:77592193-77592212 None:intergenic 50.0%
GAGAGAGAGATCGTTGAGAG+CGG - chr1.3:77592143-77592162 None:intergenic 50.0%
GATCTCTCTCTCCGTTCTCT+CGG + chr1.3:77592151-77592170 MS.gene037362:CDS 50.0%
GTTCTCGTCGATATCGGAAC+TGG + chr1.3:77592241-77592260 MS.gene037362:CDS 50.0%
AGAGAGATCGTTGAGAGCGG+TGG - chr1.3:77592140-77592159 None:intergenic 55.0%
GAGAAGCGGTGAGAGGAACA+AGG - chr1.3:77592186-77592205 None:intergenic 55.0%
GAGTTCAAGACGAGTGGTGG+CGG - chr1.3:77592113-77592132 None:intergenic 55.0%
GAGATCGTTGAGAGCGGTGG+TGG - chr1.3:77592137-77592156 None:intergenic 60.0%
GCTTCGTCGAAGAGCGGAAG+CGG + chr1.3:77591983-77592002 MS.gene037362:CDS 60.0%
GGCGAGTTCAAGACGAGTGG+TGG - chr1.3:77592116-77592135 None:intergenic 60.0%
GGTGGCGAGTTCAAGACGAG+TGG - chr1.3:77592119-77592138 None:intergenic 60.0%
CGGAAGCGGAGCGATGACTC+TGG + chr1.3:77591997-77592016 MS.gene037362:CDS 65.0%
! GCGGAGCGATGACTCTGGAG+AGG + chr1.3:77592002-77592021 MS.gene037362:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 77591980 77592865 77591980 ID=MS.gene037362
chr1.3 mRNA 77591980 77592865 77591980 ID=MS.gene037362.t1;Parent=MS.gene037362
chr1.3 exon 77591980 77592276 77591980 ID=MS.gene037362.t1.exon1;Parent=MS.gene037362.t1
chr1.3 CDS 77591980 77592276 77591980 ID=cds.MS.gene037362.t1;Parent=MS.gene037362.t1
chr1.3 exon 77592390 77592467 77592390 ID=MS.gene037362.t1.exon2;Parent=MS.gene037362.t1
chr1.3 CDS 77592390 77592467 77592390 ID=cds.MS.gene037362.t1;Parent=MS.gene037362.t1
chr1.3 exon 77592782 77592865 77592782 ID=MS.gene037362.t1.exon3;Parent=MS.gene037362.t1
chr1.3 CDS 77592782 77592865 77592782 ID=cds.MS.gene037362.t1;Parent=MS.gene037362.t1
Gene Sequence

>MS.gene037362

ATGGCTTCGTCGAAGAGCGGAAGCGGAGCGATGACTCTGGAGAGGATGAGCGTTGAACAGTTGAAAGCAGTTAAGGAACAAGCAGATATGGAAGTTAACCTTCTTCAAGACAGTCTCAACAATATCGGCACCGCCACCACTCGTCTTGAACTCGCCACCACCGCTCTCAACGATCTCTCTCTCCGTTCTCTCGGCAGTAAAATCCTTGTTCCTCTCACCGCTTCTCTCTATGTTCCTGCTACTCTTCAAGATCCTCATCACGTTCTCGTCGATATCGGAACTGGTTATTTCGTTGAGGTGAGCTCAACTCTTTCCCCGATTAATTTATTTAGATCTGTATCGTATATGCTTCTTTTTAGGGTTATGGAATATTAATTTTAATTTGAATGTTGTGTTGATGTTGAAAACAGAAAACCATGCCTGAAGGAAAGGATTACTGCGAGCGCAAAATCAACTTACTCAAATCTAACTTCGATCAACTTGTTGAGGTAATTAATTTTCTTATTAATTAAGTACTCCTATTTGATTTTGATATATGTATTTCTACTGAATTTGTTTATTCACGATATATATAGATTATACTAGAATAATTGTCATTTGTACTCGATCATTGTGTTAGTTTTATACTAATGTGGTTATTCTGTTGTGGAGAGTGATTATTCATATAACACTTATTTTAGTTTAAACCCTAATTTGATATTTTGTCTAGGAAATGAGCTTACCAGTTTTCTCTTTGATATTTTTGGCTCAACTATAATGAAATCGTGTTCAAGAAAAAATCTTGATGTAATTACAAATGCAGGTTGCGTCCAAGAAGAAAAACGTTGCGGATGAAGCTGGGCTTATTTTACAGGCAAAATTGAAGCAATTAGCATCTTCATCCTAA
Protein sequence

>MS.gene037362.t1

MASSKSGSGAMTLERMSVEQLKAVKEQADMEVNLLQDSLNNIGTATTRLELATTALNDLSLRSLGSKILVPLTASLYVPATLQDPHHVLVDIGTGYFVEKTMPEGKDYCERKINLLKSNFDQLVEVASKKKNVADEAGLILQAKLKQLASSS