AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0289260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0289260 MtrunA17_Chr1g0160961 49.065 214 57 7 1 169 1108 1314 1.01e-45 159
Msa0289260 MtrunA17_Chr5g0419891 48.598 214 58 7 1 169 984 1190 4.89e-45 157
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGATTCTATCATCTCATTTC+AGG 0.217727 2_3:-35468132 Msa0289260:CDS
GTTGTCAATTCCTTGAAAAC+TGG 0.305092 2_3:+35467795 None:intergenic
TTGGACAGGACCTGGGGATA+TGG 0.313019 2_3:-35468304 Msa0289260:CDS
GGCAACTTCAAGCAAATTAG+TGG 0.357784 2_3:+35467858 None:intergenic
CATCTCATTTCAGGAGTAGA+TGG 0.362782 2_3:-35468123 Msa0289260:CDS
AAGACAACATGCACTTTACT+AGG 0.368570 2_3:-35468153 Msa0289260:CDS
AGGCCACTCTGATGCGCATT+TGG 0.371819 2_3:-35468045 Msa0289260:CDS
AACAAAGAAAAGTCCACATT+TGG 0.394798 2_3:+35467837 None:intergenic
TTCATATTGCTGCCACCTAC+AGG 0.401617 2_3:+35468177 None:intergenic
ACACTGCCTTGGACAGGACC+TGG 0.477027 2_3:-35468312 Msa0289260:CDS
GTCAATGATGCATGCTGAAT+AGG 0.489388 2_3:+35467763 None:intergenic
CACTGCCTTGGACAGGACCT+GGG 0.509070 2_3:-35468311 Msa0289260:CDS
GCATTTGGATACGATATATG+AGG 0.530559 2_3:-35468030 Msa0289260:CDS
GCAGCGGATTAACACTGCCT+TGG 0.543231 2_3:-35468323 Msa0289260:CDS
GAGTAGATGGTTGTCTGTAA+AGG 0.545061 2_3:-35468110 Msa0289260:CDS
CAAGCTGGTCCTCTAAAAGT+TGG 0.547141 2_3:-35467895 Msa0289260:CDS
GGATTAACACTGCCTTGGAC+AGG 0.550002 2_3:-35468318 Msa0289260:CDS
TTGCTTGAAGTTGCCAAATG+TGG 0.554295 2_3:-35467850 Msa0289260:CDS
GCAACTTCAAGCAAATTAGT+GGG 0.566368 2_3:+35467859 None:intergenic
GGCAGTGTTAATCCGCTGCA+TGG 0.594322 2_3:+35468327 None:intergenic
ATATCCCCAGGTCCTGTCCA+AGG 0.597750 2_3:+35468306 None:intergenic
GTAAAATCTAAAGCCGTGGA+TGG 0.599176 2_3:-35468088 Msa0289260:CDS
GATGCATGCTGAATAGGAGA+AGG 0.600149 2_3:+35467769 None:intergenic
TTTCACTATACCAAGCAAGC+TGG 0.602071 2_3:-35467910 Msa0289260:CDS
TCTATAGCAACCATATCCCC+AGG 0.613424 2_3:+35468294 None:intergenic
AAAGGTAAAATCTAAAGCCG+TGG 0.614741 2_3:-35468092 Msa0289260:CDS
GGTTGCTATAGAGCAAACAT+TGG 0.621396 2_3:-35468283 Msa0289260:CDS
AAAAGAACTAATGCCATCCA+CGG 0.628505 2_3:+35468075 None:intergenic
ACTGCCTTGGACAGGACCTG+GGG 0.640697 2_3:-35468310 Msa0289260:CDS
TACTTCAAAATAGAGAGACA+TGG 0.684859 2_3:+35468250 None:intergenic
AAACAACCTTCACCATGCAG+CGG 0.695848 2_3:-35468339 None:intergenic
TATCCAAATGCGCATCAGAG+TGG 0.708943 2_3:+35468042 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTGTATACAAAGTTCA+AGG + chr2_3:35467860-35467879 None:intergenic 20.0%
!!! CATTAGTTCTTTTAGCATTA+AGG - chr2_3:35468019-35468038 Msa0289260:intron 25.0%
! AGAAGTCTTCAATAATAGAA+TGG - chr2_3:35468097-35468116 Msa0289260:CDS 25.0%
! GAAGTCTTCAATAATAGAAT+GGG - chr2_3:35468098-35468117 Msa0289260:CDS 25.0%
TACTTCAAAATAGAGAGACA+TGG + chr2_3:35467837-35467856 None:intergenic 30.0%
AAAAATTTCTCCGTAACAAG+AGG - chr2_3:35467874-35467893 Msa0289260:CDS 30.0%
!!! CTTTTTTACTCCTCTTGTTA+CGG + chr2_3:35467887-35467906 None:intergenic 30.0%
AACAAAGAAAAGTCCACATT+TGG + chr2_3:35468250-35468269 None:intergenic 30.0%
!!! TGTGGACTTTTCTTTGTTTT+TGG - chr2_3:35468252-35468271 Msa0289260:CDS 30.0%
AAGACAACATGCACTTTACT+AGG - chr2_3:35467931-35467950 Msa0289260:intron 35.0%
GGATTCTATCATCTCATTTC+AGG - chr2_3:35467952-35467971 Msa0289260:intron 35.0%
! AAAGGTAAAATCTAAAGCCG+TGG - chr2_3:35467992-35468011 Msa0289260:intron 35.0%
AAAAGAACTAATGCCATCCA+CGG + chr2_3:35468012-35468031 None:intergenic 35.0%
GCATTTGGATACGATATATG+AGG - chr2_3:35468054-35468073 Msa0289260:CDS 35.0%
AAACTGAACCAAGGAAAAAG+TGG + chr2_3:35468149-35468168 None:intergenic 35.0%
GAAATGTTGAAACTGAACCA+AGG + chr2_3:35468158-35468177 None:intergenic 35.0%
! TCTACACTACCAACTTTTAG+AGG + chr2_3:35468201-35468220 None:intergenic 35.0%
GCAACTTCAAGCAAATTAGT+GGG + chr2_3:35468228-35468247 None:intergenic 35.0%
! GAAAGAATGTCCAGTTTTCA+AGG - chr2_3:35468279-35468298 Msa0289260:CDS 35.0%
GTTGTCAATTCCTTGAAAAC+TGG + chr2_3:35468292-35468311 None:intergenic 35.0%
GGTTGCTATAGAGCAAACAT+TGG - chr2_3:35467801-35467820 Msa0289260:CDS 40.0%
AGAGGAGTAAAAAAGCCTGT+AGG - chr2_3:35467892-35467911 Msa0289260:CDS 40.0%
CATCTCATTTCAGGAGTAGA+TGG - chr2_3:35467961-35467980 Msa0289260:intron 40.0%
GAGTAGATGGTTGTCTGTAA+AGG - chr2_3:35467974-35467993 Msa0289260:intron 40.0%
! GTAAAATCTAAAGCCGTGGA+TGG - chr2_3:35467996-35468015 Msa0289260:intron 40.0%
TTTCACTATACCAAGCAAGC+TGG - chr2_3:35468174-35468193 Msa0289260:CDS 40.0%
GGCAACTTCAAGCAAATTAG+TGG + chr2_3:35468229-35468248 None:intergenic 40.0%
TTGCTTGAAGTTGCCAAATG+TGG - chr2_3:35468234-35468253 Msa0289260:CDS 40.0%
GTCAATGATGCATGCTGAAT+AGG + chr2_3:35468324-35468343 None:intergenic 40.0%
TCTATAGCAACCATATCCCC+AGG + chr2_3:35467793-35467812 None:intergenic 45.0%
GGAGTAAAAAAGCCTGTAGG+TGG - chr2_3:35467895-35467914 Msa0289260:CDS 45.0%
TTCATATTGCTGCCACCTAC+AGG + chr2_3:35467910-35467929 None:intergenic 45.0%
TATCCAAATGCGCATCAGAG+TGG + chr2_3:35468045-35468064 None:intergenic 45.0%
!! AGGAAAAAGTGGACTGGAAG+TGG + chr2_3:35468138-35468157 None:intergenic 45.0%
!!! CTTCCAGTCCACTTTTTCCT+TGG - chr2_3:35468138-35468157 Msa0289260:CDS 45.0%
GAACCAAGGAAAAAGTGGAC+TGG + chr2_3:35468144-35468163 None:intergenic 45.0%
!! TTTTAGAGGACCAGCTTGCT+TGG + chr2_3:35468187-35468206 None:intergenic 45.0%
! CAAGCTGGTCCTCTAAAAGT+TGG - chr2_3:35468189-35468208 Msa0289260:CDS 45.0%
GATGCATGCTGAATAGGAGA+AGG + chr2_3:35468318-35468337 None:intergenic 45.0%
GGATTAACACTGCCTTGGAC+AGG - chr2_3:35467766-35467785 Msa0289260:CDS 50.0%
!! GCAGCGGATTAACACTGCCT+TGG - chr2_3:35467761-35467780 Msa0289260:CDS 55.0%
ATATCCCCAGGTCCTGTCCA+AGG + chr2_3:35467781-35467800 None:intergenic 55.0%
TTGGACAGGACCTGGGGATA+TGG - chr2_3:35467780-35467799 Msa0289260:CDS 55.0%
AGGCCACTCTGATGCGCATT+TGG - chr2_3:35468039-35468058 Msa0289260:CDS 55.0%
ACACTGCCTTGGACAGGACC+TGG - chr2_3:35467772-35467791 Msa0289260:CDS 60.0%
CACTGCCTTGGACAGGACCT+GGG - chr2_3:35467773-35467792 Msa0289260:CDS 60.0%
ACTGCCTTGGACAGGACCTG+GGG - chr2_3:35467774-35467793 Msa0289260:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 35467759 35468347 35467759 ID=Msa0289260;Name=Msa0289260
chr2_3 mRNA 35467759 35468347 35467759 ID=Msa0289260-mRNA-1;Parent=Msa0289260;Name=Msa0289260-mRNA-1;_AED=0.45;_eAED=0.50;_QI=0|0|0|1|1|1|2|0|169
chr2_3 exon 35468020 35468347 35468020 ID=Msa0289260-mRNA-1:exon:11473;Parent=Msa0289260-mRNA-1
chr2_3 exon 35467759 35467940 35467759 ID=Msa0289260-mRNA-1:exon:11472;Parent=Msa0289260-mRNA-1
chr2_3 CDS 35468020 35468347 35468020 ID=Msa0289260-mRNA-1:cds;Parent=Msa0289260-mRNA-1
chr2_3 CDS 35467759 35467940 35467759 ID=Msa0289260-mRNA-1:cds;Parent=Msa0289260-mRNA-1
Gene Sequence

>Msa0289260

ATGCAGCGGATTAACACTGCCTTGGACAGGACCTGGGGATATGGTTGCTATAGAGCAAACATTGGATCTATTGTTCCATGTCTCTCTATTTTGAAGTACCTTGAACTTTGTATACAAAAATTTCTCCGTAACAAGAGGAGTAAAAAAGCCTGTAGGTGGCAGCAATATGAAGAAGACAACATGCACTTTACTAGGATTCTATCATCTCATTTCAGGAGTAGATGGTTGTCTGTAAAGGTAAAATCTAAAGCCGTGGATGGCATTAGTTCTTTTAGCATTAAGGCCACTCTGATGCGCATTTGGATACGATATATGAGGACTCAGACATTTTCAACATTTCACTATACCAAGCAAGCTGGTCCTCTAAAAGTTGGTAGTGTAGATGATCCCACTAATTTGCTTGAAGTTGCCAAATGTGGACTTTTCTTTGTTTTTGGCATTGAAAGAATGTCCAGTTTTCAAGGAATTGACAACATTCCTTCTCCTATTCAGCATGCATCATTGACATGA

Protein sequence

>Msa0289260

MQRINTALDRTWGYGCYRANIGSIVPCLSILKYLELCIQKFLRNKRSKKACRWQQYEEDNMHFTRILSSHFRSRWLSVKVKSKAVDGISSFSIKATLMRIWIRYMRTQTFSTFHYTKQAGPLKVGSVDDPTNLLEVAKCGLFFVFGIERMSSFQGIDNIPSPIQHASLT*