AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1305190


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 12 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACAATTTATGGGATTAAA+TGG 0.170061 8_3:-68522616 Msa1305190:CDS
AGAGTTTATAGAACAATTTA+TGG 0.254847 8_3:-68522626 Msa1305190:CDS
AAAGATCAACTTAGCATTGT+TGG 0.297378 8_3:+68522649 None:intergenic
AGTTCATCGGATTCTGCATT+TGG 0.303861 8_3:-68522709 Msa1305190:CDS
ATCAAGAGAATGCTTCAAAC+TGG 0.364802 8_3:-68522676 Msa1305190:CDS
GAGTTTATAGAACAATTTAT+GGG 0.389704 8_3:-68522625 Msa1305190:CDS
GTTCATCGGATTCTGCATTT+GGG 0.414475 8_3:-68522708 Msa1305190:CDS
TCTTGTTCTTATGTTGAAGC+TGG 0.444656 8_3:-68522591 Msa1305190:CDS
AAATGCAGAATCCGATGAAC+TGG 0.458650 8_3:+68522711 None:intergenic
GGTCTTAATTGTAGTATGAT+AGG 0.475415 8_3:-68523214 None:intergenic
ATCGGATTCTGCATTTGGGA+TGG 0.499346 8_3:-68522704 Msa1305190:CDS
TCAAGAGAATGCTTCAAACT+GGG 0.611932 8_3:-68522675 Msa1305190:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCAAAACATAACTTATTATT+TGG - chr8_3:68522872-68522891 Msa1305190:intron 15.0%
!!! TACATATGTTCTCAAAATTT+TGG + chr8_3:68522965-68522984 None:intergenic 20.0%
!!! AATTTTGAGAACATATGTAT+TGG - chr8_3:68522966-68522985 Msa1305190:intron 20.0%
!!! ATTTTGAGAACATATGTATT+GGG - chr8_3:68522967-68522986 Msa1305190:intron 20.0%
!! AGAGTTTATAGAACAATTTA+TGG - chr8_3:68523150-68523169 Msa1305190:intron 20.0%
!! GAGTTTATAGAACAATTTAT+GGG - chr8_3:68523151-68523170 Msa1305190:intron 20.0%
! TAAATTAGTGACATCAGAAT+AGG + chr8_3:68522630-68522649 None:intergenic 25.0%
!! TTTACAGAATTCTTTTCCAA+TGG + chr8_3:68522676-68522695 None:intergenic 25.0%
!! AATCAACAAGTTGAATGTTT+AGG - chr8_3:68522694-68522713 Msa1305190:CDS 25.0%
!! ATCAACAAGTTGAATGTTTA+GGG - chr8_3:68522695-68522714 Msa1305190:CDS 25.0%
! GAACAATTTATGGGATTAAA+TGG - chr8_3:68523160-68523179 Msa1305190:intron 25.0%
!! ACAGTTATTTTGTGAAAACC+CGG + chr8_3:68522722-68522741 None:intergenic 30.0%
GCAACGATGAAAATTTGAAA+AGG + chr8_3:68522904-68522923 None:intergenic 30.0%
! TCAAATTTTCATCGTTGCAT+TGG - chr8_3:68522906-68522925 Msa1305190:intron 30.0%
!!! GATGTTTTTTACCAGTTCAT+CGG - chr8_3:68523054-68523073 Msa1305190:intron 30.0%
AAAGATCAACTTAGCATTGT+TGG + chr8_3:68523130-68523149 None:intergenic 30.0%
TAACTGTATGATATCTGTCC+TGG - chr8_3:68522735-68522754 Msa1305190:intron 35.0%
TTAATGACACTTCAGCAGTT+CGG + chr8_3:68522777-68522796 None:intergenic 35.0%
ATCAAGAGAATGCTTCAAAC+TGG - chr8_3:68523100-68523119 Msa1305190:intron 35.0%
TCAAGAGAATGCTTCAAACT+GGG - chr8_3:68523101-68523120 Msa1305190:intron 35.0%
TCTTGTTCTTATGTTGAAGC+TGG - chr8_3:68523185-68523204 Msa1305190:intron 35.0%
AAGGTCTGGAAGACTATGAT+TGG + chr8_3:68522599-68522618 None:intergenic 40.0%
ATCAGAATAGGCGATAGTGA+AGG + chr8_3:68522618-68522637 None:intergenic 40.0%
TTACTGACATGTTGAGCCAT+TGG - chr8_3:68522657-68522676 Msa1305190:CDS 40.0%
! CAAGTTGAATGTTTAGGGTC+CGG - chr8_3:68522700-68522719 Msa1305190:CDS 40.0%
! AAGTTGAATGTTTAGGGTCC+GGG - chr8_3:68522701-68522720 Msa1305190:CDS 40.0%
!! ATTTTCATCGTTGCATTGGC+TGG - chr8_3:68522910-68522929 Msa1305190:intron 40.0%
TGGGTGAAGATTTCTACTGT+AGG - chr8_3:68522986-68523005 Msa1305190:intron 40.0%
GGGTGAAGATTTCTACTGTA+GGG - chr8_3:68522987-68523006 Msa1305190:intron 40.0%
AAATGCAGAATCCGATGAAC+TGG + chr8_3:68523068-68523087 None:intergenic 40.0%
AGTTCATCGGATTCTGCATT+TGG - chr8_3:68523067-68523086 Msa1305190:intron 40.0%
GTTCATCGGATTCTGCATTT+GGG - chr8_3:68523068-68523087 Msa1305190:intron 40.0%
AATAGGCGATAGTGAAGGTC+TGG + chr8_3:68522613-68522632 None:intergenic 45.0%
! ATGATATCTGTCCTGGTTCG+TGG - chr8_3:68522742-68522761 Msa1305190:intron 45.0%
ATCGGATTCTGCATTTGGGA+TGG - chr8_3:68523072-68523091 Msa1305190:intron 45.0%
!! GTCCTGGTTCGTGGAACTTT+TGG - chr8_3:68522751-68522770 Msa1305190:intron 50.0%
GGCCAAAAGTTCCACGAACC+AGG + chr8_3:68522756-68522775 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 68522577 68523221 68522577 ID=Msa1305190;Name=Msa1305190
chr8_3 mRNA 68522577 68523221 68522577 ID=Msa1305190-mRNA-1;Parent=Msa1305190;Name=Msa1305190-mRNA-1;_AED=0.54;_eAED=1.00;_QI=0|0|0|0.5|1|1|2|0|60
chr8_3 exon 68523215 68523221 68523215 ID=Msa1305190-mRNA-1:exon:21217;Parent=Msa1305190-mRNA-1
chr8_3 exon 68522577 68522752 68522577 ID=Msa1305190-mRNA-1:exon:21216;Parent=Msa1305190-mRNA-1
chr8_3 CDS 68523215 68523221 68523215 ID=Msa1305190-mRNA-1:cds;Parent=Msa1305190-mRNA-1
chr8_3 CDS 68522577 68522752 68522577 ID=Msa1305190-mRNA-1:cds;Parent=Msa1305190-mRNA-1
Gene Sequence

>Msa1305190

ATGATAGTTAACACTGATGTTTTTTACCAGTTCATCGGATTCTGCATTTGGGATGGACATGATCAAGAGAATGCTTCAAACTGGGCATCCAACAATGCTAAGTTGATCTTTAGAGTTTATAGAACAATTTATGGGATTAAATGGATTCTTGTTCTTATGTTGAAGCTGGAAATCTGTTGCTAA

Protein sequence

>Msa1305190

MIVNTDVFYQFIGFCIWDGHDQENASNWASNNAKLIFRVYRTIYGIKWILVLMLKLEICC*