AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene066167

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066167.t1 MTR_2g069400 98.276 58 1 0 1 58 1 58 1.75e-37 119
MS.gene066167.t1 MTR_2g069430 57.377 61 22 1 1 57 1 61 1.13e-15 64.3
MS.gene066167.t1 MTR_4g091090 57.377 61 19 3 4 57 5 65 2.25e-13 58.5
MS.gene066167.t1 MTR_2g069420 54.688 64 21 3 1 57 1 63 1.57e-12 56.2
MS.gene066167.t1 MTR_1g040735 48.333 60 22 3 6 57 63 121 6.26e-11 53.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAGCAGGGGTGATGGTTTC+TGG 0.154253 2.3:-26702738 MS.gene066167:CDS
TTTAATTGGAACACTTTGTT+GGG 0.371717 2.3:+26702765 None:intergenic
AGCTGTTCCACCACCACCTA+TGG 0.399384 2.3:-26702809 MS.gene066167:CDS
ACTTTGTTGGGGATCATCCT+TGG 0.445500 2.3:+26702777 None:intergenic
TTGTTGGGGATCATCCTTGG+AGG 0.481114 2.3:+26702780 None:intergenic
GGGTTGTTCTGACTCACTGC+TGG 0.483166 2.3:+26702835 None:intergenic
TTCCAATTAAAACAACTAGC+AGG 0.486226 2.3:-26702753 MS.gene066167:CDS
GGATAACCCATAGGTGGTGG+TGG 0.506331 2.3:+26702802 None:intergenic
AAAACAACTAGCAGGGGTGA+TGG 0.528737 2.3:-26702745 MS.gene066167:CDS
ATCAATCAACAACAATCTCC+TGG 0.529469 2.3:-26703069 MS.gene066167:intron
GGTGGTGGTGGAACAGCTTG+AGG 0.543912 2.3:+26702814 None:intergenic
GTGGTGGTGGAACAGCTTGA+GGG 0.555087 2.3:+26702815 None:intergenic
GAGGGATAACCCATAGGTGG+TGG 0.556470 2.3:+26702799 None:intergenic
TCCAATTAAAACAACTAGCA+GGG 0.562056 2.3:-26702752 MS.gene066167:CDS
AGGGGTGATGGTTTCTGGAA+AGG 0.573043 2.3:-26702733 MS.gene066167:CDS
GCTGTTCCACCACCACCTAT+GGG 0.592890 2.3:-26702808 MS.gene066167:CDS
ACCTATGGGTTATCCCTCCA+AGG 0.593969 2.3:-26702794 MS.gene066167:CDS
GTGATGGTTTCTGGAAAGGA+TGG 0.594474 2.3:-26702729 MS.gene066167:CDS
TGTTGGGGATCATCCTTGGA+GGG 0.597882 2.3:+26702781 None:intergenic
TTAATTGGAACACTTTGTTG+GGG 0.602125 2.3:+26702766 None:intergenic
CCAATTAAAACAACTAGCAG+GGG 0.643519 2.3:-26702751 MS.gene066167:CDS
TCCTTGGAGGGATAACCCAT+AGG 0.667495 2.3:+26702793 None:intergenic
TTGGAGGGATAACCCATAGG+TGG 0.675232 2.3:+26702796 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATTAAAAAAAACTTACC+AGG + chr2.3:26702759-26702778 None:intergenic 15.0%
!! CATTTCTATAAGAAATAATT+TGG - chr2.3:26702895-26702914 MS.gene066167:intron 15.0%
!! CAAAAAAATTAAACGATTCT+AGG + chr2.3:26702861-26702880 None:intergenic 20.0%
! TTTAATTGGAACACTTTGTT+GGG + chr2.3:26703045-26703064 None:intergenic 25.0%
!!! TTTTAATTGGAACACTTTGT+TGG + chr2.3:26703046-26703065 None:intergenic 25.0%
CTAGGCTTGAATATAAAACA+TGG + chr2.3:26702843-26702862 None:intergenic 30.0%
TCCAATTAAAACAACTAGCA+GGG - chr2.3:26703055-26703074 MS.gene066167:intron 30.0%
TTAATTGGAACACTTTGTTG+GGG + chr2.3:26703044-26703063 None:intergenic 30.0%
TTCCAATTAAAACAACTAGC+AGG - chr2.3:26703054-26703073 MS.gene066167:intron 30.0%
ATCAATCAACAACAATCTCC+TGG - chr2.3:26702738-26702757 MS.gene066167:CDS 35.0%
CCAATTAAAACAACTAGCAG+GGG - chr2.3:26703056-26703075 MS.gene066167:intron 35.0%
CGAAATACACAACACAAGTT+AGG + chr2.3:26702933-26702952 None:intergenic 35.0%
!!! CCCCTGCTAGTTGTTTTAAT+TGG + chr2.3:26703059-26703078 None:intergenic 40.0%
AAAACAACTAGCAGGGGTGA+TGG - chr2.3:26703062-26703081 MS.gene066167:intron 45.0%
ACTTTGTTGGGGATCATCCT+TGG + chr2.3:26703033-26703052 None:intergenic 45.0%
! GTGATGGTTTCTGGAAAGGA+TGG - chr2.3:26703078-26703097 MS.gene066167:CDS 45.0%
TCCTTGGAGGGATAACCCAT+AGG + chr2.3:26703017-26703036 None:intergenic 50.0%
TGTTGGGGATCATCCTTGGA+GGG + chr2.3:26703029-26703048 None:intergenic 50.0%
TTGGAGGGATAACCCATAGG+TGG + chr2.3:26703014-26703033 None:intergenic 50.0%
TTGTTGGGGATCATCCTTGG+AGG + chr2.3:26703030-26703049 None:intergenic 50.0%
! ACCTATGGGTTATCCCTCCA+AGG - chr2.3:26703013-26703032 MS.gene066167:intron 50.0%
! AGGGGTGATGGTTTCTGGAA+AGG - chr2.3:26703074-26703093 MS.gene066167:CDS 50.0%
AGCTGTTCCACCACCACCTA+TGG - chr2.3:26702998-26703017 MS.gene066167:intron 55.0%
GAGGGATAACCCATAGGTGG+TGG + chr2.3:26703011-26703030 None:intergenic 55.0%
GCTGTTCCACCACCACCTAT+GGG - chr2.3:26702999-26703018 MS.gene066167:intron 55.0%
GGGTTGTTCTGACTCACTGC+TGG + chr2.3:26702975-26702994 None:intergenic 55.0%
! CTAGCAGGGGTGATGGTTTC+TGG - chr2.3:26703069-26703088 MS.gene066167:intron 55.0%
! GGATAACCCATAGGTGGTGG+TGG + chr2.3:26703008-26703027 None:intergenic 55.0%
!! GTGGTGGTGGAACAGCTTGA+GGG + chr2.3:26702995-26703014 None:intergenic 55.0%
!! GGTGGTGGTGGAACAGCTTG+AGG + chr2.3:26702996-26703015 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 26702726 26703103 26702726 ID=MS.gene066167
chr2.3 mRNA 26702726 26703103 26702726 ID=MS.gene066167.t1;Parent=MS.gene066167
chr2.3 exon 26703070 26703103 26703070 ID=MS.gene066167.t1.exon1;Parent=MS.gene066167.t1
chr2.3 CDS 26703070 26703103 26703070 ID=cds.MS.gene066167.t1;Parent=MS.gene066167.t1
chr2.3 exon 26702726 26702868 26702726 ID=MS.gene066167.t1.exon2;Parent=MS.gene066167.t1
chr2.3 CDS 26702726 26702868 26702726 ID=cds.MS.gene066167.t1;Parent=MS.gene066167.t1
Gene Sequence

>MS.gene066167

ATGAGTCACAATATCAATCAACAACAATCTCCTGGTAAGTTTTTTTTAATTATTTCAATTGAATATACTTAAATATTAATCAATCAACAATCATATTTGAGTGCAAAAAAATATCCATGTTTTATATTCAAGCCTAGAATCGTTTAATTTTTTTGTTGCTAGAATTTTTCATTTCTATAAGAAATAATTTGGATTTTTATTTAACCTAACTTGTGTTGTGTATTTCGATGATCAGTTACTGCATATCCAGCAGTGAGTCAGAACAACCCTCAAGCTGTTCCACCACCACCTATGGGTTATCCCTCCAAGGATGATCCCCAACAAAGTGTTCCAATTAAAACAACTAGCAGGGGTGATGGTTTCTGGAAAGGATGGTGA
Protein sequence

>MS.gene066167.t1

MSHNINQQQSPVTAYPAVSQNNPQAVPPPPMGYPSKDDPQQSVPIKTTSRGDGFWKGW