AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0931100


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0931100 MtrunA17_CPg0492871 65.278 144 2 1 1 96 86 229 7.78e-55 169
Msa0931100 MtrunA17_Chr4g0015721 65.278 144 2 1 1 96 86 229 7.78e-55 169
Msa0931100 MtrunA17_Chr4g0016811 65.278 144 2 1 1 96 95 238 8.15e-55 170
Msa0931100 MtrunA17_Chr5g0403621 73.333 75 17 1 1 72 86 160 1.06e-31 109
Msa0931100 MtrunA17_Chr3g0141111 96.154 52 2 0 1 52 15 66 2.88e-31 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0931100 ATCG00530.1 47.917 144 27 1 1 96 86 229 1.42e-35 120

Find 16 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTAAGTGGTTATTCTATT+AGG 0.170612 6_2:+80330668 Msa0931100:CDS
TCTAAGTGGTTATTCTATTA+GGG 0.213858 6_2:+80330669 Msa0931100:CDS
TAGAATAACCACTTAGAATA+AGG 0.296044 6_2:-80330663 None:intergenic
AACTCATTATTCTTAACTCT+TGG 0.323937 6_2:+80330701 Msa0931100:CDS
GGTTGTTCGTCTCTATCAAT+TGG 0.367131 6_2:-80330591 None:intergenic
CAGAATGATCAAATTATATC+TGG 0.400622 6_2:+80330865 Msa0931100:intron
ACTCATTATTCTTAACTCTT+GGG 0.414290 6_2:+80330702 Msa0931100:CDS
AAATCGTATGGATACGGTCT+TGG 0.446811 6_2:-80330612 None:intergenic
AAAATTGTATCTAAAATGAC+TGG 0.459050 6_2:-80330904 None:intergenic
ATATGTTTCCTTATTCTAAG+TGG 0.468100 6_2:+80330655 Msa0931100:CDS
ATCTAAAATGACTGGAAAAG+TGG 0.472631 6_2:-80330896 None:intergenic
TACAGAAATGCAAAATCGTA+TGG 0.481344 6_2:-80330624 None:intergenic
GAGATACACGATTTAAATAA+CGG 0.522190 6_2:-80330942 None:intergenic
CTAAGTGGTTATTCTATTAG+GGG 0.545375 6_2:+80330670 Msa0931100:CDS
AATGCAAAATCGTATGGATA+CGG 0.548969 6_2:-80330618 None:intergenic
TGATAAATCACTACAAGTGA+CGG 0.591823 6_2:-80330964 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TACATAAATCAGTTAATAAA+AGG - chr6_2:80330777-80330796 None:intergenic 15.0%
!!! TTATTAACTGATTTATGTAT+AGG + chr6_2:80330778-80330797 Msa0931100:intron 15.0%
!!! TAGATACAATTTTAAAATAC+TGG + chr6_2:80330914-80330933 Msa0931100:CDS 15.0%
!!! AAAATTGTATCTAAAATGAC+TGG - chr6_2:80330907-80330926 None:intergenic 20.0%
! ATATGTTTCCTTATTCTAAG+TGG + chr6_2:80330655-80330674 Msa0931100:CDS 25.0%
! TAGAATAACCACTTAGAATA+AGG - chr6_2:80330666-80330685 None:intergenic 25.0%
! TTCTAAGTGGTTATTCTATT+AGG + chr6_2:80330668-80330687 Msa0931100:CDS 25.0%
! TCTAAGTGGTTATTCTATTA+GGG + chr6_2:80330669-80330688 Msa0931100:CDS 25.0%
! AACTCATTATTCTTAACTCT+TGG + chr6_2:80330701-80330720 Msa0931100:CDS 25.0%
! ACTCATTATTCTTAACTCTT+GGG + chr6_2:80330702-80330721 Msa0931100:CDS 25.0%
! CAGAATGATCAAATTATATC+TGG + chr6_2:80330865-80330884 Msa0931100:intron 25.0%
! GAGATACACGATTTAAATAA+CGG - chr6_2:80330945-80330964 None:intergenic 25.0%
AATGCAAAATCGTATGGATA+CGG - chr6_2:80330621-80330640 None:intergenic 30.0%
TACAGAAATGCAAAATCGTA+TGG - chr6_2:80330627-80330646 None:intergenic 30.0%
CTAAGTGGTTATTCTATTAG+GGG + chr6_2:80330670-80330689 Msa0931100:CDS 30.0%
! ATCTAAAATGACTGGAAAAG+TGG - chr6_2:80330899-80330918 None:intergenic 30.0%
TGATAAATCACTACAAGTGA+CGG - chr6_2:80330967-80330986 None:intergenic 30.0%
ATAGGATTCCATTCAACTCA+TGG + chr6_2:80330796-80330815 Msa0931100:intron 35.0%
ATTCCATTCAACTCATGGTT+GGG + chr6_2:80330801-80330820 Msa0931100:intron 35.0%
ATGGTTGGGAACTAATGATT+GGG + chr6_2:80330815-80330834 Msa0931100:intron 35.0%
! GGGTCTGTCTATAAAGATTT+TGG + chr6_2:80330835-80330854 Msa0931100:intron 35.0%
GGTTGTTCGTCTCTATCAAT+TGG - chr6_2:80330594-80330613 None:intergenic 40.0%
AAATCGTATGGATACGGTCT+TGG - chr6_2:80330615-80330634 None:intergenic 40.0%
GATTCCATTCAACTCATGGT+TGG + chr6_2:80330800-80330819 Msa0931100:intron 40.0%
CATGGTTGGGAACTAATGAT+TGG + chr6_2:80330814-80330833 Msa0931100:intron 40.0%
! GTTCCCAACCATGAGTTGAA+TGG - chr6_2:80330807-80330826 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 80330568 80331002 80330568 ID=Msa0931100;Name=Msa0931100
chr6_2 mRNA 80330568 80331002 80330568 ID=Msa0931100-mRNA-1;Parent=Msa0931100;Name=Msa0931100-mRNA-1;_AED=0.55;_eAED=0.55;_QI=0|0|0|1|0|0|2|0|96
chr6_2 exon 80330568 80330723 80330568 ID=Msa0931100-mRNA-1:exon:14079;Parent=Msa0931100-mRNA-1
chr6_2 exon 80330868 80331002 80330868 ID=Msa0931100-mRNA-1:exon:14080;Parent=Msa0931100-mRNA-1
chr6_2 CDS 80330568 80330723 80330568 ID=Msa0931100-mRNA-1:cds;Parent=Msa0931100-mRNA-1
chr6_2 CDS 80330868 80331002 80330868 ID=Msa0931100-mRNA-1:cds;Parent=Msa0931100-mRNA-1
Gene Sequence

>Msa0931100

ATGGAAATCTACAAAGAAAGCATCCAATTGATAGAGACGAACAACCAAGACCGTATCCATACGATTTTGCATTTCTGTACAAATATAATATGTTTCCTTATTCTAAGTGGTTATTCTATTAGGGGTAATCAAGAACTCATTATTCTTAACTCTTGGAATGATCAAATTATATCTGGTCTTGTTTCCACTTTTCCAGTCATTTTAGATACAATTTTAAAATACTGGATTTTCCGTTATTTAAATCGTGTATCTCCGTCACTTGTAGTGATTTATCATTCAATGAATGACTGA

Protein sequence

>Msa0931100

MEIYKESIQLIETNNQDRIHTILHFCTNIICFLILSGYSIRGNQELIILNSWNDQIISGLVSTFPVILDTILKYWIFRYLNRVSPSLVVIYHSMND*