AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0306980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0306980 MtrunA17_Chr5g0395021 90.566 53 5 0 2 54 24 76 1.55e-28 98.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 19 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGATGTTGAGCTCTATGCTT+TGG 0.339133 2_3:+66317972 Msa0306980:CDS
CAGAAGGTAGTTTGCAATAG+TGG 0.373095 2_3:-66318132 None:intergenic
GAAGAGAGGCTTCTTAGTCT+TGG 0.409377 2_3:-66317789 None:intergenic
GATGTTGAGCTCTATGCTTT+GGG 0.462010 2_3:+66317973 Msa0306980:CDS
AATTCAGAAACACTTGAAGC+TGG 0.479335 2_3:+66317945 Msa0306980:intron
TGAATACCTTAGCGAGATTG+AGG 0.487915 2_3:-66317817 None:intergenic
ATGAAGAATGTGAAGATCAA+TGG 0.502380 2_3:+66317722 Msa0306980:CDS
TCAGAGATGAGTATGATAGT+TGG 0.532402 2_3:-66318004 None:intergenic
GCCTTCCTTTGTATCAACAG+TGG 0.538665 2_3:-66318074 None:intergenic
GTCATCCACTGTTGATACAA+AGG 0.593976 2_3:+66318069 Msa0306980:three_prime_UTR
CTGCTACCTCAATCTCGCTA+AGG 0.595774 2_3:+66317811 Msa0306980:CDS
TCCACTGTTGATACAAAGGA+AGG 0.621515 2_3:+66318073 Msa0306980:three_prime_UTR
AGATTGAGGTAGCAGAAGAG+AGG 0.631106 2_3:-66317803 None:intergenic
TGTCGTGGAACTCTAAAGTG+TGG 0.638989 2_3:+66318103 Msa0306980:three_prime_UTR
AAGGAAGGCAAAGAATGTCG+TGG 0.649842 2_3:+66318088 Msa0306980:three_prime_UTR
CGTGGAACTCTAAAGTGTGG+AGG 0.661706 2_3:+66318106 Msa0306980:three_prime_UTR
AAGAATGTGAAGATCAATGG+CGG 0.680804 2_3:+66317725 Msa0306980:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATGAAGAATGTGAAGATCAA+TGG + chr2_3:66317722-66317741 Msa0306980:CDS 30.0%
AAGAATGTGAAGATCAATGG+CGG + chr2_3:66317725-66317744 Msa0306980:CDS 35.0%
AATTCAGAAACACTTGAAGC+TGG + chr2_3:66317945-66317964 Msa0306980:intron 35.0%
TCAGAGATGAGTATGATAGT+TGG - chr2_3:66318007-66318026 None:intergenic 35.0%
!!! CTCATCTCTGAGATTTTGAA+CGG + chr2_3:66318016-66318035 Msa0306980:exon 35.0%
TGAATACCTTAGCGAGATTG+AGG - chr2_3:66317820-66317839 None:intergenic 40.0%
GATGTTGAGCTCTATGCTTT+GGG + chr2_3:66317973-66317992 Msa0306980:CDS 40.0%
! AGATTTTGAACGGCAGTAGA+TGG + chr2_3:66318026-66318045 Msa0306980:exon 40.0%
! GATTTTGAACGGCAGTAGAT+GGG + chr2_3:66318027-66318046 Msa0306980:three_prime_UTR 40.0%
GTCATCCACTGTTGATACAA+AGG + chr2_3:66318069-66318088 Msa0306980:three_prime_UTR 40.0%
TCCACTGTTGATACAAAGGA+AGG + chr2_3:66318073-66318092 Msa0306980:three_prime_UTR 40.0%
GAAGAGAGGCTTCTTAGTCT+TGG - chr2_3:66317792-66317811 None:intergenic 45.0%
AGATTGAGGTAGCAGAAGAG+AGG - chr2_3:66317806-66317825 None:intergenic 45.0%
CGATGTTGAGCTCTATGCTT+TGG + chr2_3:66317972-66317991 Msa0306980:CDS 45.0%
GCCTTCCTTTGTATCAACAG+TGG - chr2_3:66318077-66318096 None:intergenic 45.0%
AAGGAAGGCAAAGAATGTCG+TGG + chr2_3:66318088-66318107 Msa0306980:three_prime_UTR 45.0%
!! TGTCGTGGAACTCTAAAGTG+TGG + chr2_3:66318103-66318122 Msa0306980:three_prime_UTR 45.0%
CTGCTACCTCAATCTCGCTA+AGG + chr2_3:66317811-66317830 Msa0306980:CDS 50.0%
!! CGTGGAACTCTAAAGTGTGG+AGG + chr2_3:66318106-66318125 Msa0306980:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 66317716 66318146 66317716 ID=Msa0306980;Name=Msa0306980
chr2_3 mRNA 66317716 66318146 66317716 ID=Msa0306980-mRNA-1;Parent=Msa0306980;Name=Msa0306980-mRNA-1;_AED=0.15;_eAED=0.15;_QI=6|1|1|1|1|1|2|120|61
chr2_3 exon 66317716 66317832 66317716 ID=Msa0306980-mRNA-1:exon:22040;Parent=Msa0306980-mRNA-1
chr2_3 exon 66317952 66318146 66317952 ID=Msa0306980-mRNA-1:exon:22041;Parent=Msa0306980-mRNA-1
chr2_3 five_prime_UTR 66317716 66317721 66317716 ID=Msa0306980-mRNA-1:five_prime_utr;Parent=Msa0306980-mRNA-1
chr2_3 CDS 66317722 66317832 66317722 ID=Msa0306980-mRNA-1:cds;Parent=Msa0306980-mRNA-1
chr2_3 CDS 66317952 66318026 66317952 ID=Msa0306980-mRNA-1:cds;Parent=Msa0306980-mRNA-1
chr2_3 three_prime_UTR 66318027 66318146 66318027 ID=Msa0306980-mRNA-1:three_prime_utr;Parent=Msa0306980-mRNA-1
Gene Sequence

>Msa0306980

ATGAAGAATGTGAAGATCAATGGCGGCGAGATTGAGAAAGAGAAGAAGTTCTTTCGTATTCAAGTTTCCAAGACTAAGAAGCCTCTCTTCTGCTACCTCAATCTCGCTAAGAAACACTTGAAGCTGGATAACGATGTTGAGCTCTATGCTTTGGGAACTGCTTCCAACTATCATACTCATCTCTGA

Protein sequence

>Msa0306980

MKNVKINGGEIEKEKKFFRIQVSKTKKPLFCYLNLAKKHLKLDNDVELYALGTASNYHTHL*