AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1459960


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1459960 MtrunA17_Chr2g0285861 84.416 77 3 2 1 75 1 70 3.76e-38 121
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1459960 AT2G34585.1 76.190 42 10 0 1 42 1 42 9.84e-19 73.2

Find 19 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCGTTAGGGGCGGGGTTGAG+TGG 0.375759 tig0040567:-15070 None:intergenic
TCGTCGTCGGGATCGTAATC+AGG 0.386527 tig0040567:-15028 None:intergenic
TTGACGACCTTGTTCGAGGC+AGG 0.394231 tig0040567:-14984 None:intergenic
GCAGTGGTAGCAGTGATTCT+AGG 0.395537 tig0040567:+14932 Msa1459960:CDS
GCAGCGGTGGTGGAGGCGAC+GGG 0.399580 tig0040567:-15094 None:intergenic
AGCAGCGGTGGTGGAGGCGA+CGG 0.425781 tig0040567:-15095 None:intergenic
AGGATTGAGATTGCGATCAA+TGG 0.439079 tig0040567:-15008 None:intergenic
ACTGCGTTGTCTTCGTCGTC+GGG 0.450375 tig0040567:-15040 None:intergenic
AACTGCGTTGTCTTCGTCGT+CGG 0.458028 tig0040567:-15041 None:intergenic
AGTGAATACCACTTATGAAA+CGG 0.507725 tig0040567:-15122 None:intergenic
CAGCGGTGGTGGAGGCGACG+GGG 0.518735 tig0040567:-15093 None:intergenic
TGGCTTGACGACCTTGTTCG+AGG 0.522648 tig0040567:-14988 None:intergenic
GGGATCATGGGAGCAATCAC+CGG 0.545095 tig0040567:+14899 None:intergenic
TGACGACCTTGTTCGAGGCA+GGG 0.551454 tig0040567:-14983 None:intergenic
TGTAAACCCTGCCTCGAACA+AGG 0.577165 tig0040567:+14977 Msa1459960:CDS
TACCACTGCTATCACTGCAC+CGG 0.586478 tig0040567:-14918 None:intergenic
AGCGGTGGTGGAGGCGACGG+GGG 0.608456 tig0040567:-15092 None:intergenic
TGGTAGCAGTGATTCTAGGT+TGG 0.618694 tig0040567:+14936 Msa1459960:CDS
CACCGGTGCAGTGATAGCAG+TGG 0.664884 tig0040567:+14916 Msa1459960:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATGAAACGGTTTTAGCAG+CGG - tig0040567:15113-15132 None:intergenic 35.0%
AGGATTGAGATTGCGATCAA+TGG - tig0040567:15011-15030 None:intergenic 40.0%
TGGTAGCAGTGATTCTAGGT+TGG + tig0040567:14936-14955 Msa1459960:CDS 45.0%
TACCACTGCTATCACTGCAC+CGG - tig0040567:14921-14940 None:intergenic 50.0%
GCAGTGGTAGCAGTGATTCT+AGG + tig0040567:14932-14951 Msa1459960:CDS 50.0%
TGTAAACCCTGCCTCGAACA+AGG + tig0040567:14977-14996 Msa1459960:CDS 50.0%
AACTGCGTTGTCTTCGTCGT+CGG - tig0040567:15044-15063 None:intergenic 50.0%
!! TGAAACGGTTTTAGCAGCGG+TGG - tig0040567:15110-15129 None:intergenic 50.0%
TGACGACCTTGTTCGAGGCA+GGG - tig0040567:14986-15005 None:intergenic 55.0%
TTGACGACCTTGTTCGAGGC+AGG - tig0040567:14987-15006 None:intergenic 55.0%
TGGCTTGACGACCTTGTTCG+AGG - tig0040567:14991-15010 None:intergenic 55.0%
TCGTCGTCGGGATCGTAATC+AGG - tig0040567:15031-15050 None:intergenic 55.0%
ACTGCGTTGTCTTCGTCGTC+GGG - tig0040567:15043-15062 None:intergenic 55.0%
!! AACGGTTTTAGCAGCGGTGG+TGG - tig0040567:15107-15126 None:intergenic 55.0%
CACCGGTGCAGTGATAGCAG+TGG + tig0040567:14916-14935 Msa1459960:CDS 60.0%
!! GGTTTTAGCAGCGGTGGTGG+AGG - tig0040567:15104-15123 None:intergenic 60.0%
GCGTTAGGGGCGGGGTTGAG+TGG - tig0040567:15073-15092 None:intergenic 70.0%
!! TGGAGGCGACGGGGGCGTTA+GGG - tig0040567:15087-15106 None:intergenic 70.0%
!! AGCAGCGGTGGTGGAGGCGA+CGG - tig0040567:15098-15117 None:intergenic 70.0%
!! GGAGGCGACGGGGGCGTTAG+GGG - tig0040567:15086-15105 None:intergenic 75.0%
!! GTGGAGGCGACGGGGGCGTT+AGG - tig0040567:15088-15107 None:intergenic 75.0%
!! AGCGGTGGTGGAGGCGACGG+GGG - tig0040567:15095-15114 None:intergenic 75.0%
!! CAGCGGTGGTGGAGGCGACG+GGG - tig0040567:15096-15115 None:intergenic 75.0%
!! GCAGCGGTGGTGGAGGCGAC+GGG - tig0040567:15097-15116 None:intergenic 75.0%
!!! CGACGGGGGCGTTAGGGGCG+GGG - tig0040567:15081-15100 None:intergenic 80.0%
!!! GCGACGGGGGCGTTAGGGGC+GGG - tig0040567:15082-15101 None:intergenic 80.0%
!!! GGCGACGGGGGCGTTAGGGG+CGG - tig0040567:15083-15102 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
tig0040567 gene 14905 15132 14905 ID=Msa1459960;Name=Msa1459960
tig0040567 mRNA 14905 15132 14905 ID=Msa1459960-mRNA-1;Parent=Msa1459960;Name=Msa1459960-mRNA-1;_AED=0.01;_eAED=0.07;_QI=0|-1|0|1|-1|1|1|0|75
tig0040567 exon 14905 15132 14905 ID=Msa1459960-mRNA-1:exon:22491;Parent=Msa1459960-mRNA-1
tig0040567 CDS 14905 15132 14905 ID=Msa1459960-mRNA-1:cds;Parent=Msa1459960-mRNA-1
Gene Sequence

>Msa1459960

ATGGGAGCAATCACCGGTGCAGTGATAGCAGTGGTAGCAGTGATTCTAGGTTGGATCACAATAGAGATCGCGTGTAAACCCTGCCTCGAACAAGGTCGTCAAGCCATTGATCGCAATCTCAATCCTGATTACGATCCCGACGACGAAGACAACGCAGTTCGTGCTCCACTCAACCCCGCCCCTAACGCCCCCGTCGCCTCCACCACCGCTGCTAAAACCGTTTCATAA

Protein sequence

>Msa1459960

MGAITGAVIAVVAVILGWITIEIACKPCLEQGRQAIDRNLNPDYDPDDEDNAVRAPLNPAPNAPVASTTAAKTVS*