AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0793390


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0793390 MtrunA17_Chr1g0198001 85.437 103 10 1 1 103 1 98 3.44e-45 141
Msa0793390 MtrunA17_Chr2g0317581 74.038 104 11 2 1 103 1 89 4.41e-39 125
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0793390 AT3G15352.4 88.889 45 5 0 59 103 53 97 6.47e-27 95.5
Msa0793390 AT3G15352.2 88.889 45 5 0 59 103 31 75 6.85e-27 94.7
Msa0793390 AT3G15352.1 88.889 45 5 0 59 103 30 74 7.60e-27 94.4
Msa0793390 AT3G15352.3 88.889 45 5 0 59 103 37 81 1.12e-26 94.4
Msa0793390 AT1G53030.1 82.222 45 8 0 59 103 28 72 1.71e-24 88.6

Find 24 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCCGGCGTTGCTGCAGTTGC+TGG 0.322432 5_3:-5363849 None:intergenic
GCTGGCGTTGCTGCTGTTGA+TGG 0.363493 5_3:-5363876 None:intergenic
ACCAGCAACTGCAGCAACGC+CGG 0.403671 5_3:+5363848 Msa0793390:CDS
AACGCCAGCGACGGCAGAAA+CGG 0.425755 5_3:+5363890 Msa0793390:CDS
TCTCGCAGCCTCTTCGTGTC+AGG 0.437710 5_3:-5363978 None:intergenic
CAGTTGCTGGTGCTGTTGGT+TGG 0.439790 5_3:-5363836 None:intergenic
CGAATTTGTCTTCGTGCTGA+AGG 0.441593 5_3:+5364056 Msa0793390:CDS
GCCGCCGTTTCTGCCGTCGC+TGG 0.445253 5_3:-5363894 None:intergenic
GCTGCTGTTGATGGCGCTGC+CGG 0.473729 5_3:-5363867 None:intergenic
GCTGCAGTTGCTGGTGCTGT+TGG 0.489129 5_3:-5363840 None:intergenic
AACAGCAGCAACGCCAGCGA+CGG 0.494709 5_3:+5363881 Msa0793390:CDS
TTTGACACTTCACATGCTGC+TGG 0.518991 5_3:-5363921 None:intergenic
GCCAGCGACGGCAGAAACGG+CGG 0.552546 5_3:+5363893 Msa0793390:CDS
TGGTTCGAAGCAGAGGAAGA+AGG 0.559341 5_3:-5363816 None:intergenic
TGTTGGTTGGTTCGAAGCAG+AGG 0.577421 5_3:-5363823 None:intergenic
GGTAACGCGCAAGTGCAAAA+CGG 0.577765 5_3:+5363783 Msa0793390:CDS
ATGAGTGCATAGTGGAACAC+GGG 0.582328 5_3:+5364000 Msa0793390:CDS
TCGATGAGCTTCAATCCACT+TGG 0.585020 5_3:-5364036 None:intergenic
GCGCTTGTCCTGACACGAAG+AGG 0.611666 5_3:+5363970 Msa0793390:CDS
GCTGCGAGATGAGTGCATAG+TGG 0.621172 5_3:+5363992 Msa0793390:CDS
GGGAGGATGCTTGTGCCAAG+TGG 0.626172 5_3:+5364021 Msa0793390:CDS
GATGAGTGCATAGTGGAACA+CGG 0.674556 5_3:+5363999 Msa0793390:CDS
GTGCATAGTGGAACACGGGG+AGG 0.723863 5_3:+5364004 Msa0793390:CDS
TGAGTGCATAGTGGAACACG+GGG 0.769217 5_3:+5364001 Msa0793390:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CAACAGATTTTCTTCTTCTT+CGG - chr5_3:5363951-5363970 None:intergenic 30.0%
TTTGACACTTCACATGCTGC+TGG - chr5_3:5363924-5363943 None:intergenic 45.0%
! GATGAGTGCATAGTGGAACA+CGG + chr5_3:5363999-5364018 Msa0793390:CDS 45.0%
! ATGAGTGCATAGTGGAACAC+GGG + chr5_3:5364000-5364019 Msa0793390:CDS 45.0%
TCGATGAGCTTCAATCCACT+TGG - chr5_3:5364039-5364058 None:intergenic 45.0%
CGAATTTGTCTTCGTGCTGA+AGG + chr5_3:5364056-5364075 Msa0793390:CDS 45.0%
GGTAACGCGCAAGTGCAAAA+CGG + chr5_3:5363783-5363802 Msa0793390:CDS 50.0%
TGGTTCGAAGCAGAGGAAGA+AGG - chr5_3:5363819-5363838 None:intergenic 50.0%
!! TGTTGGTTGGTTCGAAGCAG+AGG - chr5_3:5363826-5363845 None:intergenic 50.0%
! TGAGTGCATAGTGGAACACG+GGG + chr5_3:5364001-5364020 Msa0793390:CDS 50.0%
!! CAGTTGCTGGTGCTGTTGGT+TGG - chr5_3:5363839-5363858 None:intergenic 55.0%
GCTGCGAGATGAGTGCATAG+TGG + chr5_3:5363992-5364011 Msa0793390:CDS 55.0%
!! GCTGCAGTTGCTGGTGCTGT+TGG - chr5_3:5363843-5363862 None:intergenic 60.0%
ACCAGCAACTGCAGCAACGC+CGG + chr5_3:5363848-5363867 Msa0793390:CDS 60.0%
GCTGGCGTTGCTGCTGTTGA+TGG - chr5_3:5363879-5363898 None:intergenic 60.0%
AACAGCAGCAACGCCAGCGA+CGG + chr5_3:5363881-5363900 Msa0793390:CDS 60.0%
AACGCCAGCGACGGCAGAAA+CGG + chr5_3:5363890-5363909 Msa0793390:CDS 60.0%
GCGCTTGTCCTGACACGAAG+AGG + chr5_3:5363970-5363989 Msa0793390:CDS 60.0%
TCTCGCAGCCTCTTCGTGTC+AGG - chr5_3:5363981-5364000 None:intergenic 60.0%
! GTGCATAGTGGAACACGGGG+AGG + chr5_3:5364004-5364023 Msa0793390:CDS 60.0%
GGGAGGATGCTTGTGCCAAG+TGG + chr5_3:5364021-5364040 Msa0793390:CDS 60.0%
!! GCTGCTGTTGATGGCGCTGC+CGG - chr5_3:5363870-5363889 None:intergenic 65.0%
GCCGGCGTTGCTGCAGTTGC+TGG - chr5_3:5363852-5363871 None:intergenic 70.0%
GCCAGCGACGGCAGAAACGG+CGG + chr5_3:5363893-5363912 Msa0793390:CDS 70.0%
GCCGCCGTTTCTGCCGTCGC+TGG - chr5_3:5363897-5363916 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 5363780 5364091 5363780 ID=Msa0793390;Name=Msa0793390
chr5_3 mRNA 5363780 5364091 5363780 ID=Msa0793390-mRNA-1;Parent=Msa0793390;Name=Msa0793390-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|103
chr5_3 exon 5363780 5364091 5363780 ID=Msa0793390-mRNA-1:exon:2038;Parent=Msa0793390-mRNA-1
chr5_3 CDS 5363780 5364091 5363780 ID=Msa0793390-mRNA-1:cds;Parent=Msa0793390-mRNA-1
Gene Sequence

>Msa0793390

ATGGGTAACGCGCAAGTGCAAAACGGTGTTGCTGTTCCTTCTTCCTCTGCTTCGAACCAACCAACAGCACCAGCAACTGCAGCAACGCCGGCAGCGCCATCAACAGCAGCAACGCCAGCGACGGCAGAAACGGCGGCAACGCCAGCAGCATGTGAAGTGTCAAATGCTCCGAAGAAGAAGAAAATCTGTTGCGCTTGTCCTGACACGAAGAGGCTGCGAGATGAGTGCATAGTGGAACACGGGGAGGATGCTTGTGCCAAGTGGATTGAAGCTCATCGAATTTGTCTTCGTGCTGAAGGATTCAATGTTTGA

Protein sequence

>Msa0793390

MGNAQVQNGVAVPSSSASNQPTAPATAATPAAPSTAATPATAETAATPAACEVSNAPKKKKICCACPDTKRLRDECIVEHGEDACAKWIEAHRICLRAEGFNV*