AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0178590


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0178590 MtrunA17_Chr1g0208371 48.529 68 13 1 2 47 251 318 7.02e-15 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 14 sgRNAs with CRISPR-Local

Find 17 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATATATTGTACTTTGATTAC+TGG 0.275088 1_4:-65946208 Msa0178590:CDS
TGAGCCTGACGCGGTTACTA+TGG 0.420376 1_4:-65946327 Msa0178590:intron
TGTACTTTGATTACTGGTCT+TGG 0.428132 1_4:-65946202 Msa0178590:CDS
TGTAGGGAGATGAAGGATGA+TGG 0.433447 1_4:-65946353 Msa0178590:intron
TTGATTACTGGTCTTGGTAA+TGG 0.438096 1_4:-65946196 Msa0178590:CDS
TGAAGTTTGTAGGGAGATGA+AGG 0.454618 1_4:-65946360 Msa0178590:intron
TATACCATAGTAACCGCGTC+AGG 0.499602 1_4:+65946323 None:intergenic
TTTATCATGAGATACAATCA+AGG 0.522069 1_4:-65946252 Msa0178590:intron
GCTATGCAAAATGAAGAAGA+AGG 0.531029 1_4:-65946157 Msa0178590:CDS
CTATGCAAAATGAAGAAGAA+GGG 0.588304 1_4:-65946156 Msa0178590:CDS
AAATGAAGAAGAAGGGGCAA+AGG 0.592568 1_4:-65946149 Msa0178590:CDS
GTACAATATATATGAAGACT+AGG 0.609451 1_4:+65946220 None:intergenic
TCTTGGTAATGGTAGTCGAA+TGG 0.610381 1_4:-65946185 Msa0178590:CDS
TATGCAAAATGAAGAAGAAG+GGG 0.633838 1_4:-65946155 Msa0178590:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATATTGTACTTTGATTAC+TGG - chr1_4:65946261-65946280 Msa0178590:intron 20.0%
! AATCATCAATGCATATTGTA+TGG - chr1_4:65946168-65946187 Msa0178590:CDS 25.0%
! TTTATCATGAGATACAATCA+AGG - chr1_4:65946217-65946236 Msa0178590:CDS 25.0%
! GTACAATATATATGAAGACT+AGG + chr1_4:65946252-65946271 None:intergenic 25.0%
CTATGCAAAATGAAGAAGAA+GGG - chr1_4:65946313-65946332 Msa0178590:intron 30.0%
TATGCAAAATGAAGAAGAAG+GGG - chr1_4:65946314-65946333 Msa0178590:intron 30.0%
! TGTACTTTGATTACTGGTCT+TGG - chr1_4:65946267-65946286 Msa0178590:intron 35.0%
!! TTGATTACTGGTCTTGGTAA+TGG - chr1_4:65946273-65946292 Msa0178590:intron 35.0%
GCTATGCAAAATGAAGAAGA+AGG - chr1_4:65946312-65946331 Msa0178590:intron 35.0%
!!! GCGTTCTCTCTTACATTTTT+TGG - chr1_4:65946351-65946370 Msa0178590:CDS 35.0%
TGAAGTTTGTAGGGAGATGA+AGG - chr1_4:65946109-65946128 Msa0178590:CDS 40.0%
!! TCTTGGTAATGGTAGTCGAA+TGG - chr1_4:65946284-65946303 Msa0178590:intron 40.0%
AAATGAAGAAGAAGGGGCAA+AGG - chr1_4:65946320-65946339 Msa0178590:intron 40.0%
TGTAGGGAGATGAAGGATGA+TGG - chr1_4:65946116-65946135 Msa0178590:CDS 45.0%
TATACCATAGTAACCGCGTC+AGG + chr1_4:65946149-65946168 None:intergenic 45.0%
!!! TGATGGTTTTGAGCCTGACG+CGG - chr1_4:65946133-65946152 Msa0178590:CDS 50.0%
TGAGCCTGACGCGGTTACTA+TGG - chr1_4:65946142-65946161 Msa0178590:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 65946108 65946383 65946108 ID=Msa0178590;Name=Msa0178590
chr1_4 mRNA 65946108 65946383 65946108 ID=Msa0178590-mRNA-1;Parent=Msa0178590;Name=Msa0178590-mRNA-1;_AED=0.62;_eAED=0.66;_QI=0|0|0|1|0|0|3|0|67
chr1_4 exon 65946379 65946383 65946379 ID=Msa0178590-mRNA-1:exon:21528;Parent=Msa0178590-mRNA-1
chr1_4 exon 65946328 65946370 65946328 ID=Msa0178590-mRNA-1:exon:21527;Parent=Msa0178590-mRNA-1
chr1_4 exon 65946108 65946263 65946108 ID=Msa0178590-mRNA-1:exon:21526;Parent=Msa0178590-mRNA-1
chr1_4 CDS 65946379 65946383 65946379 ID=Msa0178590-mRNA-1:cds;Parent=Msa0178590-mRNA-1
chr1_4 CDS 65946328 65946370 65946328 ID=Msa0178590-mRNA-1:cds;Parent=Msa0178590-mRNA-1
chr1_4 CDS 65946108 65946263 65946108 ID=Msa0178590-mRNA-1:cds;Parent=Msa0178590-mRNA-1
Gene Sequence

>Msa0178590

ATGAAGGAGATGAAGGATGATGGTTTTGAGCCTGACGCGGTTACTATGATACAATCAAGGAATATAAATCCTAGTCTTCATATATATTGTACTTTGATTACTGGTCTTGGTAATGGTAGTCGAATGGACAAAGCTATGCAAAATGAAGAAGAAGGGGCAAAGGAAAGTCAAGCGTTCTCTCTTACATTTTTTGGTTATTTTTAA

Protein sequence

>Msa0178590

MKEMKDDGFEPDAVTMIQSRNINPSLHIYCTLITGLGNGSRMDKAMQNEEEGAKESQAFSLTFFGYF*