AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1044040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1044040 MtrunA17_Chr5g0409821 98.693 153 2 0 1 153 1 153 1.27e-108 315
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1044040 AT1G32060.1 69.281 153 32 4 1 153 1 138 1.61e-63 199

Find 18 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGGATGATTACCATTCTT+TGG 0.234705 7_2:+2215743 Msa1044040:CDS
GAATCAGGATTTCCACCTTT+TGG 0.277176 7_2:-2215684 None:intergenic
CTGATAAGTGTGTTTGAATC+AGG 0.321702 7_2:-2215699 None:intergenic
ATTGAGATGTTTGTTCTTAG+AGG 0.359760 7_2:-2215429 None:intergenic
ATTGGTCTAGCAGCTGATTC+AGG 0.370444 7_2:+2215600 Msa1044040:CDS
CACAACCACTGTGATATGTT+TGG 0.440482 7_2:+2215725 Msa1044040:CDS
AGTTAAAGCTATTAAAGCTT+AGG 0.446558 7_2:+2215842 Msa1044040:CDS
TACCATTCTTTGGATAGAAC+TGG 0.449333 7_2:+2215753 Msa1044040:CDS
TACCAGTTCTATCCAAAGAA+TGG 0.458109 7_2:-2215755 None:intergenic
AGATCAAAATCATTAGCTCT+TGG 0.471925 7_2:-2215807 None:intergenic
CTAGCAGCTGATTCAGGATG+TGG 0.497361 7_2:+2215606 Msa1044040:CDS
TACTTGATAACATGTGGAGC+AGG 0.532032 7_2:+2215558 Msa1044040:CDS
GACTCACAGACAATTGTGAT+TGG 0.537034 7_2:+2215582 Msa1044040:CDS
GGTGCAGCAGAGCCACCAAA+AGG 0.546897 7_2:+2215669 Msa1044040:CDS
AGAACTGGTAGAAAAGAGAA+AGG 0.567928 7_2:+2215768 Msa1044040:CDS
GCAGCAGAGCCACCAAAAGG+TGG 0.593621 7_2:+2215672 Msa1044040:CDS
AGAAGATACTTGATAACATG+TGG 0.629598 7_2:+2215552 Msa1044040:CDS
ATCATCCAAACATATCACAG+TGG 0.763501 7_2:-2215730 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTGGTTTTAATCAAAAAC+AGG + chr7_2:2215473-2215492 Msa1044040:CDS 25.0%
ATTGAGATGTTTGTTCTTAG+AGG - chr7_2:2215432-2215451 None:intergenic 30.0%
!!! ACATGTGTTTTTGATGATGT+TGG - chr7_2:2215456-2215475 None:intergenic 30.0%
ACATCATCAAAAACACATGT+TGG + chr7_2:2215456-2215475 Msa1044040:CDS 30.0%
! AGAAGATACTTGATAACATG+TGG + chr7_2:2215552-2215571 Msa1044040:CDS 30.0%
TTTGGATGATTACCATTCTT+TGG + chr7_2:2215743-2215762 Msa1044040:CDS 30.0%
! AGATCAAAATCATTAGCTCT+TGG - chr7_2:2215810-2215829 None:intergenic 30.0%
! TCTTCTGTTGTTGCTCTTTT+TGG - chr7_2:2215517-2215536 None:intergenic 35.0%
! AGAAGACTCACAAGTGTTTT+TGG + chr7_2:2215645-2215664 Msa1044040:CDS 35.0%
CTGATAAGTGTGTTTGAATC+AGG - chr7_2:2215702-2215721 None:intergenic 35.0%
ATCATCCAAACATATCACAG+TGG - chr7_2:2215733-2215752 None:intergenic 35.0%
TACCATTCTTTGGATAGAAC+TGG + chr7_2:2215753-2215772 Msa1044040:CDS 35.0%
TACCAGTTCTATCCAAAGAA+TGG - chr7_2:2215758-2215777 None:intergenic 35.0%
AGAACTGGTAGAAAAGAGAA+AGG + chr7_2:2215768-2215787 Msa1044040:CDS 35.0%
! TACTTGATAACATGTGGAGC+AGG + chr7_2:2215558-2215577 Msa1044040:CDS 40.0%
GACTCACAGACAATTGTGAT+TGG + chr7_2:2215582-2215601 Msa1044040:CDS 40.0%
!!! AGACTCACAAGTGTTTTTGG+AGG + chr7_2:2215648-2215667 Msa1044040:CDS 40.0%
! GAATCAGGATTTCCACCTTT+TGG - chr7_2:2215687-2215706 None:intergenic 40.0%
CACAACCACTGTGATATGTT+TGG + chr7_2:2215725-2215744 Msa1044040:CDS 40.0%
! ATTGGTCTAGCAGCTGATTC+AGG + chr7_2:2215600-2215619 Msa1044040:CDS 45.0%
! TCAGGATTTCCACCTTTTGG+TGG - chr7_2:2215684-2215703 None:intergenic 45.0%
! CTAGCAGCTGATTCAGGATG+TGG + chr7_2:2215606-2215625 Msa1044040:CDS 50.0%
GGTGCAGCAGAGCCACCAAA+AGG + chr7_2:2215669-2215688 Msa1044040:CDS 60.0%
GCAGCAGAGCCACCAAAAGG+TGG + chr7_2:2215672-2215691 Msa1044040:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 2215399 2215863 2215399 ID=Msa1044040;Name=Msa1044040
chr7_2 mRNA 2215399 2215863 2215399 ID=Msa1044040-mRNA-1;Parent=Msa1044040;Name=Msa1044040-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|154
chr7_2 exon 2215399 2215863 2215399 ID=Msa1044040-mRNA-1:exon:541;Parent=Msa1044040-mRNA-1
chr7_2 CDS 2215399 2215863 2215399 ID=Msa1044040-mRNA-1:cds;Parent=Msa1044040-mRNA-1
Gene Sequence

>Msa1044040

ATGGCAGCATGTACTGTCTACTCAACACAACCTCTAAGAACAAACATCTCAATTCCAACATCATCAAAAACACATGTTGGTTTTAATCAAAAACAGGTAGTGTTCTACACAACAACCAAAAAGAGCAACAACAGAAGAACTAACAGTAACAGCAGAAGATACTTGATAACATGTGGAGCAGGTGACTCACAGACAATTGTGATTGGTCTAGCAGCTGATTCAGGATGTGGAAAAAGTACTTTCATGAGAAGACTCACAAGTGTTTTTGGAGGTGCAGCAGAGCCACCAAAAGGTGGAAATCCTGATTCAAACACACTTATCAGTGACACAACCACTGTGATATGTTTGGATGATTACCATTCTTTGGATAGAACTGGTAGAAAAGAGAAAGGTGTTACTGCACTTGATCCAAGAGCTAATGATTTTGATCTTATGTATGAACAAGTTAAAGCTATTAAAGCTTAG

Protein sequence

>Msa1044040

MAACTVYSTQPLRTNISIPTSSKTHVGFNQKQVVFYTTTKKSNNRRTNSNSRRYLITCGAGDSQTIVIGLAADSGCGKSTFMRRLTSVFGGAAEPPKGGNPDSNTLISDTTTVICLDDYHSLDRTGRKEKGVTALDPRANDFDLMYEQVKAIKA*