AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene89046

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene89046.t1 MTR_2g103440 96.875 96 3 0 1 96 1 96 7.62e-64 188
MS.gene89046.t1 MTR_4g011030 56.250 96 30 3 1 95 1 85 3.25e-23 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene89046.t1 AT1G15385 57.778 45 16 1 51 95 31 72 4.96e-11 53.9

Find 15 sgRNAs with CRISPR-Local

Find 16 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCCTTCATCAAGAATTTC+AGG 0.206507 2.4:-2058909 MS.gene89046:CDS
CATCTTCTCTCTCAAGTTGA+TGG 0.263758 2.4:+2059050 None:intergenic
TTTCCTGAAATTCTTGATGA+AGG 0.417879 2.4:+2058906 None:intergenic
TAGCTTCTTATTTGTTTCAA+AGG 0.468483 2.4:+2058969 None:intergenic
ATTATGAGAAAATGCTTGCA+AGG 0.509016 2.4:-2058849 MS.gene89046:CDS
ATCAGATCTCAAGAAAATAG+AGG 0.513230 2.4:-2059082 MS.gene89046:CDS
CTTGATGAAGGCATCAGCAC+TGG 0.520908 2.4:+2058918 None:intergenic
GGAAACAACTCGTGATTCAA+AGG 0.528679 2.4:-2058888 MS.gene89046:CDS
TCTTGAGATCTGATGATGGT+TGG 0.529007 2.4:+2059091 None:intergenic
AAAGTCATATCAACATGAGA+AGG 0.558128 2.4:-2059122 None:intergenic
AAACAAATAAGAAGCTAGAG+AGG 0.570340 2.4:-2058963 MS.gene89046:CDS
TTATGAGAAAATGCTTGCAA+GGG 0.578068 2.4:-2058848 MS.gene89046:CDS
ATTATCATATGATCATAATG+AGG 0.611197 2.4:-2059010 MS.gene89046:CDS
TATGAGAAAATGCTTGCAAG+GGG 0.640051 2.4:-2058847 MS.gene89046:CDS
TAATGAGGTAAAGAAAGTTG+AGG 0.652046 2.4:-2058995 MS.gene89046:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATCATATGATCATAATG+AGG - chr2.4:2058938-2058957 MS.gene89046:CDS 20.0%
!! CATTTTCTCATAATTCTCAA+TGG + chr2.4:2059093-2059112 None:intergenic 25.0%
!! TAGCTTCTTATTTGTTTCAA+AGG + chr2.4:2058982-2059001 None:intergenic 25.0%
AAACAAATAAGAAGCTAGAG+AGG - chr2.4:2058985-2059004 MS.gene89046:CDS 30.0%
ATCAGATCTCAAGAAAATAG+AGG - chr2.4:2058866-2058885 MS.gene89046:CDS 30.0%
ATTATGAGAAAATGCTTGCA+AGG - chr2.4:2059099-2059118 MS.gene89046:CDS 30.0%
TAATGAGGTAAAGAAAGTTG+AGG - chr2.4:2058953-2058972 MS.gene89046:CDS 30.0%
TTATGAGAAAATGCTTGCAA+GGG - chr2.4:2059100-2059119 MS.gene89046:CDS 30.0%
TTTCCTGAAATTCTTGATGA+AGG + chr2.4:2059045-2059064 None:intergenic 30.0%
! ATTTTCTTGAGATCTGATGA+TGG + chr2.4:2058864-2058883 None:intergenic 30.0%
ATGCCTTCATCAAGAATTTC+AGG - chr2.4:2059039-2059058 MS.gene89046:CDS 35.0%
TATGAGAAAATGCTTGCAAG+GGG - chr2.4:2059101-2059120 MS.gene89046:CDS 35.0%
GGAAACAACTCGTGATTCAA+AGG - chr2.4:2059060-2059079 MS.gene89046:CDS 40.0%
!! CATCTTCTCTCTCAAGTTGA+TGG + chr2.4:2058901-2058920 None:intergenic 40.0%
!! TCTTGAGATCTGATGATGGT+TGG + chr2.4:2058860-2058879 None:intergenic 40.0%
!! CTTGATGAAGGCATCAGCAC+TGG + chr2.4:2059033-2059052 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 2058840 2059130 2058840 ID=MS.gene89046
chr2.4 mRNA 2058840 2059130 2058840 ID=MS.gene89046.t1;Parent=MS.gene89046
chr2.4 exon 2058840 2059130 2058840 ID=MS.gene89046.t1.exon1;Parent=MS.gene89046.t1
chr2.4 CDS 2058840 2059130 2058840 ID=cds.MS.gene89046.t1;Parent=MS.gene89046.t1
Gene Sequence

>MS.gene89046

ATGAGAAGGAGCTACATCCAACCATCATCAGATCTCAAGAAAATAGAGGAAAAAAGCACCATCAACTTGAGAGAGAAGATGAGAAACTCATCAACTTCATTATCATATGATCATAATGAGGTAAAGAAAGTTGAGGACTCCTTTGAAACAAATAAGAAGCTAGAGAGGAAGACTACAGAAGACATCAATGCCAGTGCTGATGCCTTCATCAAGAATTTCAGGAAACAACTCGTGATTCAAAGGCTTCAATCCATTGAGAATTATGAGAAAATGCTTGCAAGGGGTCTCTAG
Protein sequence

>MS.gene89046.t1

MRRSYIQPSSDLKKIEEKSTINLREKMRNSSTSLSYDHNEVKKVEDSFETNKKLERKTTEDINASADAFIKNFRKQLVIQRLQSIENYEKMLARGL