AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053284


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053284.t1 MTR_4g005520 95.745 94 4 0 1 94 121 214 1.64e-60 183
MS.gene053284.t1 MTR_3g105100 47.368 76 35 3 12 86 120 191 4.60e-14 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053284.t1 AT4G27990 85.227 88 13 0 4 91 127 214 1.25e-51 161
MS.gene053284.t1 AT3G07430 83.908 87 14 0 4 90 141 227 9.49e-51 159
MS.gene053284.t1 AT5G21920 50.000 76 33 3 12 86 133 204 1.41e-14 66.6

Find 25 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACAACCATTGTCTGCAATT+AGG 0.283838 4.3:+88923778 MS.gene053284:CDS
ACAACCATTGTCTGCAATTA+GGG 0.307081 4.3:+88923779 MS.gene053284:CDS
ACAGTGGTGTGTTGTTGGTT+AGG 0.327645 4.3:+88923718 MS.gene053284:CDS
ATCCTTATCTAAGTTTGTTT+AGG 0.329465 4.3:+88923811 MS.gene053284:CDS
CAGTGGTGTGTTGTTGGTTA+GGG 0.363509 4.3:+88923719 MS.gene053284:CDS
TAGCGGCGGGGTTGAAGAAA+TGG 0.403666 4.3:+88923685 MS.gene053284:CDS
GGATGGGATGGGATCTAAAC+AGG 0.408629 4.3:-88923924 None:intergenic
TATTTACAGTGGTGTGTTGT+TGG 0.416695 4.3:+88923713 MS.gene053284:CDS
GACGGTGAACACGCCGTTGA+CGG 0.439588 4.3:+88923659 MS.gene053284:CDS
CCGTTGACGGTTGTAGCGGC+GGG 0.441420 4.3:+88923672 MS.gene053284:CDS
TGTCTTTCCCATGGAATGTT+GGG 0.454889 4.3:-88923759 None:intergenic
GTTGGTTTCCCAACATTCCA+TGG 0.512936 4.3:+88923751 MS.gene053284:CDS
GACAATGGTTGTCTTTCCCA+TGG 0.515980 4.3:-88923768 None:intergenic
TTCCTAAACAAACTTAGATA+AGG 0.528049 4.3:-88923813 None:intergenic
GCCGTTGACGGTTGTAGCGG+CGG 0.535668 4.3:+88923671 MS.gene053284:CDS
TTGGTTTCCCAACATTCCAT+GGG 0.548737 4.3:+88923752 MS.gene053284:CDS
CCCGCCGCTACAACCGTCAA+CGG 0.573983 4.3:-88923672 None:intergenic
TTGTCTTTCCCATGGAATGT+TGG 0.574451 4.3:-88923760 None:intergenic
AAAACAGCAAAAGCAAGAAG+AGG 0.574512 4.3:-88923873 None:intergenic
CACGCCGTTGACGGTTGTAG+CGG 0.575214 4.3:+88923668 MS.gene053284:CDS
CGTTGACGGTTGTAGCGGCG+GGG 0.610796 4.3:+88923673 MS.gene053284:CDS
GGCGGGGTTGAAGAAATGGT+TGG 0.623671 4.3:+88923689 MS.gene053284:CDS
AAATGGTTGGATATTTACAG+TGG 0.642279 4.3:+88923702 MS.gene053284:CDS
AGATCCCTAATTGCAGACAA+TGG 0.662621 4.3:-88923783 None:intergenic
GGATCTAAACAGGAACAGTG+AGG 0.722011 4.3:-88923914 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTCCTAAACAAACTTAGATA+AGG - chr4.3:88923816-88923835 None:intergenic 25.0%
!! ATCCTTATCTAAGTTTGTTT+AGG + chr4.3:88923811-88923830 MS.gene053284:CDS 25.0%
!!! ATATCAAGAGTATCAAAAAC+AGG - chr4.3:88923849-88923868 None:intergenic 25.0%
AAATGGTTGGATATTTACAG+TGG + chr4.3:88923702-88923721 MS.gene053284:CDS 30.0%
AAAACAGCAAAAGCAAGAAG+AGG - chr4.3:88923876-88923895 None:intergenic 35.0%
ACAACCATTGTCTGCAATTA+GGG + chr4.3:88923779-88923798 MS.gene053284:CDS 35.0%
TATTTACAGTGGTGTGTTGT+TGG + chr4.3:88923713-88923732 MS.gene053284:CDS 35.0%
!! TCAAGAGTATCAAAAACAGG+TGG - chr4.3:88923846-88923865 None:intergenic 35.0%
!!! CTTCTTGCTTTTGCTGTTTT+GGG + chr4.3:88923876-88923895 MS.gene053284:CDS 35.0%
!!! TCTTCTTGCTTTTGCTGTTT+TGG + chr4.3:88923875-88923894 MS.gene053284:CDS 35.0%
AGATCCCTAATTGCAGACAA+TGG - chr4.3:88923786-88923805 None:intergenic 40.0%
GACAACCATTGTCTGCAATT+AGG + chr4.3:88923778-88923797 MS.gene053284:CDS 40.0%
TGTCTTTCCCATGGAATGTT+GGG - chr4.3:88923762-88923781 None:intergenic 40.0%
TTGGTTTCCCAACATTCCAT+GGG + chr4.3:88923752-88923771 MS.gene053284:CDS 40.0%
TTGTCTTTCCCATGGAATGT+TGG - chr4.3:88923763-88923782 None:intergenic 40.0%
!!! TGGTTAGGGTTTTGTTGAGT+TGG + chr4.3:88923733-88923752 MS.gene053284:CDS 40.0%
GACAATGGTTGTCTTTCCCA+TGG - chr4.3:88923771-88923790 None:intergenic 45.0%
! ACAGTGGTGTGTTGTTGGTT+AGG + chr4.3:88923718-88923737 MS.gene053284:CDS 45.0%
! CAGTGGTGTGTTGTTGGTTA+GGG + chr4.3:88923719-88923738 MS.gene053284:CDS 45.0%
! GTTGGTTTCCCAACATTCCA+TGG + chr4.3:88923751-88923770 MS.gene053284:CDS 45.0%
!! GCTGTTTTGGGTACTCTTGC+TGG + chr4.3:88923888-88923907 MS.gene053284:CDS 50.0%
GGCGGGGTTGAAGAAATGGT+TGG + chr4.3:88923689-88923708 MS.gene053284:CDS 55.0%
TAGCGGCGGGGTTGAAGAAA+TGG + chr4.3:88923685-88923704 MS.gene053284:CDS 55.0%
CACGCCGTTGACGGTTGTAG+CGG + chr4.3:88923668-88923687 MS.gene053284:CDS 60.0%
GACGGTGAACACGCCGTTGA+CGG + chr4.3:88923659-88923678 MS.gene053284:CDS 60.0%
CCCGCCGCTACAACCGTCAA+CGG - chr4.3:88923675-88923694 None:intergenic 65.0%
CCGTTGACGGTTGTAGCGGC+GGG + chr4.3:88923672-88923691 MS.gene053284:CDS 65.0%
CGTTGACGGTTGTAGCGGCG+GGG + chr4.3:88923673-88923692 MS.gene053284:CDS 65.0%
GCCGTTGACGGTTGTAGCGG+CGG + chr4.3:88923671-88923690 MS.gene053284:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 88923648 88923932 88923648 ID=MS.gene053284
chr4.3 mRNA 88923648 88923932 88923648 ID=MS.gene053284.t1;Parent=MS.gene053284
chr4.3 exon 88923648 88923932 88923648 ID=MS.gene053284.t1.exon1;Parent=MS.gene053284.t1
chr4.3 CDS 88923648 88923932 88923648 ID=cds.MS.gene053284.t1;Parent=MS.gene053284.t1
Gene Sequence

>MS.gene053284

ACTAGGACGGGGACGGTGAACACGCCGTTGACGGTTGTAGCGGCGGGGTTGAAGAAATGGTTGGATATTTACAGTGGTGTGTTGTTGGTTAGGGTTTTGTTGAGTTGGTTTCCCAACATTCCATGGGAAAGACAACCATTGTCTGCAATTAGGGATCTTTGTGATCCTTATCTAAGTTTGTTTAGGAATGTTGTTCCACCTGTTTTTGATACTCTTGATATTAGTCCTCTTCTTGCTTTTGCTGTTTTGGGTACTCTTGCTGGTCTCCTCACTGTTCCTGTTTAG

Protein sequence

>MS.gene053284.t1

TRTGTVNTPLTVVAAGLKKWLDIYSGVLLVRVLLSWFPNIPWERQPLSAIRDLCDPYLSLFRNVVPPVFDTLDISPLLAFAVLGTLAGLLTVPV