AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65503

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65503.t1 MTR_1g043320 96.078 102 4 0 1 102 1 102 8.79e-67 196
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTCACTGTGTCTTCTATT+AGG 0.227341 1.4:-27974847 MS.gene65503:CDS
AAGACACAGTGAGATGTATT+TGG 0.235014 1.4:+27974855 None:intergenic
TTTGGTGGCCAGTGTTTCTT+AGG 0.235134 1.4:+27974739 None:intergenic
GGGATTGTTTGGTCCACTTT+TGG 0.317502 1.4:+27974676 None:intergenic
GTAGGAGGCCAGTGTTTCTT+TGG 0.327069 1.4:+27974721 None:intergenic
TGGAAGAAGCATCCTCCTTC+AGG 0.366754 1.4:-27974583 MS.gene65503:CDS
TCTCACTGTGTCTTCTATTA+GGG 0.371015 1.4:-27974846 MS.gene65503:CDS
AGACACAGTGAGATGTATTT+GGG 0.409412 1.4:+27974856 None:intergenic
GAAGGAGGATGCTTCTTCCA+TGG 0.436291 1.4:+27974586 None:intergenic
GGAGGCCAGTGTTTCTTTGG+TGG 0.468858 1.4:+27974724 None:intergenic
CTTGTGACTATCCTCAACTA+TGG 0.473523 1.4:+27974624 None:intergenic
ACAAAATGATCTTCCAAAAG+TGG 0.476864 1.4:-27974689 MS.gene65503:CDS
AAGGAGGATGCTTCTTCCAT+GGG 0.483462 1.4:+27974587 None:intergenic
GCTTCTTCCATGGGTGCTTG+TGG 0.496634 1.4:+27974596 None:intergenic
GACTATCCTCAACTATGGTA+TGG 0.539163 1.4:+27974629 None:intergenic
AGCATCACCACAAGCACCCA+TGG 0.549276 1.4:-27974603 MS.gene65503:CDS
CCTCTGTGAGTGTTAATGCT+TGG 0.552898 1.4:-27974774 MS.gene65503:CDS
ATTAATCAATTTCCTGAAGG+AGG 0.566620 1.4:+27974571 None:intergenic
ATGATTAATCAATTTCCTGA+AGG 0.570240 1.4:+27974568 None:intergenic
ACTGGCCACCAAAGAAACAC+TGG 0.593745 1.4:-27974729 MS.gene65503:CDS
TTCTCTAGCAGATCTTTCAG+AGG 0.609208 1.4:-27974803 MS.gene65503:CDS
ATAAGCAACCTAAGAAACAC+TGG 0.614646 1.4:-27974747 MS.gene65503:CDS
AGAAGACCATACCATAGTTG+AGG 0.630682 1.4:-27974635 MS.gene65503:CDS
TGAAAGATCTGCTAGAGAAG+TGG 0.631719 1.4:+27974807 None:intergenic
AAGATCTGCTAGAGAAGTGG+TGG 0.634386 1.4:+27974810 None:intergenic
CCAAGCATTAACACTCACAG+AGG 0.666199 1.4:+27974774 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ACAAAATGATCTTCCAAAAG+TGG - chr1.4:27974749-27974768 MS.gene65503:CDS 30.0%
! AAGATCATTTTGTGTAGTTG+TGG + chr1.4:27974742-27974761 None:intergenic 30.0%
AAGACACAGTGAGATGTATT+TGG + chr1.4:27974586-27974605 None:intergenic 35.0%
AGACACAGTGAGATGTATTT+GGG + chr1.4:27974585-27974604 None:intergenic 35.0%
ATAAGCAACCTAAGAAACAC+TGG - chr1.4:27974691-27974710 MS.gene65503:CDS 35.0%
ATCTCACTGTGTCTTCTATT+AGG - chr1.4:27974591-27974610 MS.gene65503:CDS 35.0%
TCTCACTGTGTCTTCTATTA+GGG - chr1.4:27974592-27974611 MS.gene65503:CDS 35.0%
! TCATTTTGTGTAGTTGTGGT+AGG + chr1.4:27974738-27974757 None:intergenic 35.0%
!!! CTTGTGCTTGTTTGTTTTGT+GGG + chr1.4:27974785-27974804 None:intergenic 35.0%
!!! GTTTGTTTTGTGGGATTGTT+TGG + chr1.4:27974776-27974795 None:intergenic 35.0%
!!! TCTTGTGCTTGTTTGTTTTG+TGG + chr1.4:27974786-27974805 None:intergenic 35.0%
AGAAGACCATACCATAGTTG+AGG - chr1.4:27974803-27974822 MS.gene65503:CDS 40.0%
CTTGTGACTATCCTCAACTA+TGG + chr1.4:27974817-27974836 None:intergenic 40.0%
GACTATCCTCAACTATGGTA+TGG + chr1.4:27974812-27974831 None:intergenic 40.0%
TGAAAGATCTGCTAGAGAAG+TGG + chr1.4:27974634-27974653 None:intergenic 40.0%
TTCTCTAGCAGATCTTTCAG+AGG - chr1.4:27974635-27974654 MS.gene65503:CDS 40.0%
! TTTTGTGTAGTTGTGGTAGG+AGG + chr1.4:27974735-27974754 None:intergenic 40.0%
AAGATCTGCTAGAGAAGTGG+TGG + chr1.4:27974631-27974650 None:intergenic 45.0%
AAGGAGGATGCTTCTTCCAT+GGG + chr1.4:27974854-27974873 None:intergenic 45.0%
CCAAGCATTAACACTCACAG+AGG + chr1.4:27974667-27974686 None:intergenic 45.0%
CCTCTGTGAGTGTTAATGCT+TGG - chr1.4:27974664-27974683 MS.gene65503:CDS 45.0%
! GGGATTGTTTGGTCCACTTT+TGG + chr1.4:27974765-27974784 None:intergenic 45.0%
! TTTGGTGGCCAGTGTTTCTT+AGG + chr1.4:27974702-27974721 None:intergenic 45.0%
ACTGGCCACCAAAGAAACAC+TGG - chr1.4:27974709-27974728 MS.gene65503:CDS 50.0%
GAAGGAGGATGCTTCTTCCA+TGG + chr1.4:27974855-27974874 None:intergenic 50.0%
GTAGGAGGCCAGTGTTTCTT+TGG + chr1.4:27974720-27974739 None:intergenic 50.0%
!! TGGAAGAAGCATCCTCCTTC+AGG - chr1.4:27974855-27974874 MS.gene65503:CDS 50.0%
AGCATCACCACAAGCACCCA+TGG - chr1.4:27974835-27974854 MS.gene65503:CDS 55.0%
GCTTCTTCCATGGGTGCTTG+TGG + chr1.4:27974845-27974864 None:intergenic 55.0%
GGAGGCCAGTGTTTCTTTGG+TGG + chr1.4:27974717-27974736 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 27974576 27974884 27974576 ID=MS.gene65503
chr1.4 mRNA 27974576 27974884 27974576 ID=MS.gene65503.t1;Parent=MS.gene65503
chr1.4 exon 27974576 27974884 27974576 ID=MS.gene65503.t1.exon1;Parent=MS.gene65503.t1
chr1.4 CDS 27974576 27974884 27974576 ID=cds.MS.gene65503.t1;Parent=MS.gene65503.t1
Gene Sequence

>MS.gene65503

ATGTCTCCCAAATACATCTCACTGTGTCTTCTATTAGGGATAGTACTTCTTGCCACCACTTCTCTAGCAGATCTTTCAGAGGATGAATCCTCTGTGAGTGTTAATGCTTGGAAACATAAGCAACCTAAGAAACACTGGCCACCAAAGAAACACTGGCCTCCTACCACAACTACACAAAATGATCTTCCAAAAGTGGACCAAACAATCCCACAAAACAAACAAGCACAAGAAGACCATACCATAGTTGAGGATAGTCACAAGCATCACCACAAGCACCCATGGAAGAAGCATCCTCCTTCAGGAAATTGA
Protein sequence

>MS.gene65503.t1

MSPKYISLCLLLGIVLLATTSLADLSEDESSVSVNAWKHKQPKKHWPPKKHWPPTTTTQNDLPKVDQTIPQNKQAQEDHTIVEDSHKHHHKHPWKKHPPSGN