AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene25230

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25230.t1 MTR_2g025410 95.161 62 3 0 1 62 1 62 6.40e-37 122
MS.gene25230.t1 MTR_4g132880 75.926 54 12 1 1 53 1 54 1.03e-23 87.4
MS.gene25230.t1 MTR_6g453350 60.377 53 21 0 1 53 1 53 2.05e-16 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25230.t1 AT1G12020 64.815 54 16 1 1 51 1 54 1.18e-15 67.8
MS.gene25230.t1 AT1G62422 68.627 51 12 2 1 47 1 51 1.28e-14 64.3

Find 27 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGATGAACCGTCGCTTTA+TGG 0.220331 2.3:+63512825 None:intergenic
GCTAAGACTTCTCTGTCTTC+AGG 0.378513 2.3:+63512731 None:intergenic
CAGGTGATAGCGCCGCCGCT+AGG 0.396501 2.3:+63512750 None:intergenic
TTTATGGTAGAGCTTCTTCA+TGG 0.396994 2.3:+63512841 None:intergenic
GATGAAAGTTGGTGGGGTTG+TGG 0.429398 2.3:+63512685 None:intergenic
ATAGCGCCGCCGCTAGGGTT+AGG 0.446267 2.3:+63512756 None:intergenic
TAGGATGGTTGCGGGAAGGA+AGG 0.465653 2.3:+63512775 None:intergenic
CCAACTTTCATCAATTTGTC+CGG 0.468567 2.3:-63512674 None:intergenic
GCTAGGGTTAGGATGGTTGC+GGG 0.469356 2.3:+63512767 None:intergenic
GAAAGTTGGTGGGGTTGTGG+TGG 0.470051 2.3:+63512688 None:intergenic
CCGGACAAATTGATGAAAGT+TGG 0.505144 2.3:+63512674 None:intergenic
CGCTAGGGTTAGGATGGTTG+CGG 0.505574 2.3:+63512766 None:intergenic
TCGGTTATCACCGGTGGTGA+TGG 0.517567 2.3:+63512806 None:intergenic
GACAAATTGATGAAAGTTGG+TGG 0.528605 2.3:+63512677 None:intergenic
AGGTGATAGCGCCGCCGCTA+GGG 0.532801 2.3:+63512751 None:intergenic
ACAAATTGATGAAAGTTGGT+GGG 0.555489 2.3:+63512678 None:intergenic
TTGCGGGAAGGAAGGAAAGT+TGG 0.558904 2.3:+63512783 None:intergenic
CGCCGCCGCTAGGGTTAGGA+TGG 0.565059 2.3:+63512760 None:intergenic
GAAAGTTGGTCGGTTATCAC+CGG 0.579949 2.3:+63512797 None:intergenic
GGGTTAGGATGGTTGCGGGA+AGG 0.591167 2.3:+63512771 None:intergenic
AACCATCCTAACCCTAGCGG+CGG 0.614685 2.3:-63512762 MS.gene25230:CDS
GACGGTTCATCCATCACCAC+CGG 0.616178 2.3:-63512816 MS.gene25230:CDS
AGTTGGTCGGTTATCACCGG+TGG 0.641033 2.3:+63512800 None:intergenic
CAAATTGATGAAAGTTGGTG+GGG 0.641144 2.3:+63512679 None:intergenic
GGGAAGGAAGGAAAGTTGGT+CGG 0.644008 2.3:+63512787 None:intergenic
GAAGCTCTACCATAAAGCGA+CGG 0.694050 2.3:-63512834 MS.gene25230:CDS
CGCAACCATCCTAACCCTAG+CGG 0.725015 2.3:-63512765 MS.gene25230:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACAAATTGATGAAAGTTGGT+GGG + chr2.3:63512839-63512858 None:intergenic 30.0%
GACAAATTGATGAAAGTTGG+TGG + chr2.3:63512840-63512859 None:intergenic 35.0%
TTATGGTAGAGCTTCTTCAT+CGG + chr2.3:63512675-63512694 None:intergenic 35.0%
!! CAAATTGATGAAAGTTGGTG+GGG + chr2.3:63512838-63512857 None:intergenic 35.0%
GAAGCTCTACCATAAAGCGA+CGG - chr2.3:63512680-63512699 MS.gene25230:CDS 45.0%
GCTAAGACTTCTCTGTCTTC+AGG + chr2.3:63512786-63512805 None:intergenic 45.0%
! ATGGATGAACCGTCGCTTTA+TGG + chr2.3:63512692-63512711 None:intergenic 45.0%
! GAAAGTTGGTCGGTTATCAC+CGG + chr2.3:63512720-63512739 None:intergenic 45.0%
TTGCGGGAAGGAAGGAAAGT+TGG + chr2.3:63512734-63512753 None:intergenic 50.0%
! GGGAAGGAAGGAAAGTTGGT+CGG + chr2.3:63512730-63512749 None:intergenic 50.0%
!! GATGAAAGTTGGTGGGGTTG+TGG + chr2.3:63512832-63512851 None:intergenic 50.0%
AACCATCCTAACCCTAGCGG+CGG - chr2.3:63512752-63512771 MS.gene25230:CDS 55.0%
AGTTGGTCGGTTATCACCGG+TGG + chr2.3:63512717-63512736 None:intergenic 55.0%
CGCAACCATCCTAACCCTAG+CGG - chr2.3:63512749-63512768 MS.gene25230:CDS 55.0%
CGCTAGGGTTAGGATGGTTG+CGG + chr2.3:63512751-63512770 None:intergenic 55.0%
GACGGTTCATCCATCACCAC+CGG - chr2.3:63512698-63512717 MS.gene25230:CDS 55.0%
GCTAGGGTTAGGATGGTTGC+GGG + chr2.3:63512750-63512769 None:intergenic 55.0%
TAGGATGGTTGCGGGAAGGA+AGG + chr2.3:63512742-63512761 None:intergenic 55.0%
TCGGTTATCACCGGTGGTGA+TGG + chr2.3:63512711-63512730 None:intergenic 55.0%
!! GAAAGTTGGTGGGGTTGTGG+TGG + chr2.3:63512829-63512848 None:intergenic 55.0%
GGGTTAGGATGGTTGCGGGA+AGG + chr2.3:63512746-63512765 None:intergenic 60.0%
ATAGCGCCGCCGCTAGGGTT+AGG + chr2.3:63512761-63512780 None:intergenic 65.0%
! AGGTGATAGCGCCGCCGCTA+GGG + chr2.3:63512766-63512785 None:intergenic 65.0%
CGCCGCCGCTAGGGTTAGGA+TGG + chr2.3:63512757-63512776 None:intergenic 70.0%
! CAGGTGATAGCGCCGCCGCT+AGG + chr2.3:63512767-63512786 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 63512675 63512861 63512675 ID=MS.gene25230
chr2.3 mRNA 63512675 63512861 63512675 ID=MS.gene25230.t1;Parent=MS.gene25230
chr2.3 exon 63512675 63512861 63512675 ID=MS.gene25230.t1.exon1;Parent=MS.gene25230.t1
chr2.3 CDS 63512675 63512861 63512675 ID=cds.MS.gene25230.t1;Parent=MS.gene25230.t1
Gene Sequence

>MS.gene25230

ATGAAGAAGCTCTACCATAAAGCGACGGTTCATCCATCACCACCGGTGATAACCGACCAACTTTCCTTCCTTCCCGCAACCATCCTAACCCTAGCGGCGGCGCTATCACCTGAAGACAGAGAAGTCTTAGCTTATCTCATCTATTGTTCATCCACCACAACCCCACCAACTTTCATCAATTTGTCCG
Protein sequence

>MS.gene25230.t1

MKKLYHKATVHPSPPVITDQLSFLPATILTLAAALSPEDREVLAYLIYCSSTTTPPTFINLS