AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene93489

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene93489.t1 MTR_3g025510 50.943 159 64 6 1 151 1 153 4.49e-39 130
MS.gene93489.t1 MTR_3g025380 46.753 154 65 5 1 150 1 141 4.45e-29 103
MS.gene93489.t1 MTR_3g025620 84.211 57 6 1 99 152 1 57 1.47e-26 95.1
MS.gene93489.t1 MTR_3g025550 54.688 64 26 1 90 150 1 64 1.17e-18 75.1
MS.gene93489.t1 MTR_2g058360 46.512 86 42 3 67 148 56 141 6.38e-16 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACCGCATGAACGAGATTT+TGG 0.149717 3.4:+17946053 MS.gene93489:CDS
ATGAAGGGTGTATTGTAAAA+TGG 0.296379 3.4:+17946232 MS.gene93489:CDS
GATTGCGACCAAGATGTCTT+TGG 0.360779 3.4:-17946101 None:intergenic
ATAAGCACGTAAGACATTAT+AGG 0.361737 3.4:-17946019 None:intergenic
GTCCGAAGCTTCTATATGTT+TGG 0.391153 3.4:+17946155 MS.gene93489:CDS
TCGGTTGCAACACTTCTTGT+AGG 0.395824 3.4:-17945874 None:intergenic
CATAATTGAATTGTTGTCTT+CGG 0.406577 3.4:-17945893 None:intergenic
TTCTGAACCTTCTTGATGAC+GGG 0.406773 3.4:-17945969 None:intergenic
CGCCAAACATATAGAAGCTT+CGG 0.444454 3.4:-17946157 None:intergenic
TGTTTGGCGGATCTCTCGGT+TGG 0.445635 3.4:+17946171 MS.gene93489:CDS
TATATGTTTGGCGGATCTCT+CGG 0.463458 3.4:+17946167 MS.gene93489:CDS
CTTCTGAACCTTCTTGATGA+CGG 0.466963 3.4:-17945970 None:intergenic
GTTTGGCGGATCTCTCGGTT+GGG 0.472937 3.4:+17946172 MS.gene93489:CDS
GAAACAAACCAAAGACATCT+TGG 0.499768 3.4:+17946093 MS.gene93489:CDS
CTTCTACAAATAATGCGATA+GGG 0.511833 3.4:-17945940 None:intergenic
TCTTCTACAAATAATGCGAT+AGG 0.512827 3.4:-17945941 None:intergenic
TGTTCGCATTTGTACCATGA+AGG 0.519031 3.4:+17946216 MS.gene93489:CDS
CGAAGCTTCTATATGTTTGG+CGG 0.523704 3.4:+17946158 MS.gene93489:CDS
TTCTACAAATAATGCGATAG+GGG 0.558963 3.4:-17945939 None:intergenic
TGAACCTTCTTGATGACGGG+TGG 0.560392 3.4:-17945966 None:intergenic
AAACAATACGACGACACAAA+GGG 0.563961 3.4:-17946275 None:intergenic
GATTCCACCCGTCATCAAGA+AGG 0.580470 3.4:+17945962 MS.gene93489:CDS
GTTCGCATTTGTACCATGAA+GGG 0.612669 3.4:+17946217 MS.gene93489:CDS
GAAACAATACGACGACACAA+AGG 0.619273 3.4:-17946276 None:intergenic
TCGCCAAAATCTCGTTCATG+CGG 0.665960 3.4:-17946056 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCAAAAATCAAAATTGATGA+AGG + chr3.4:17946126-17946145 MS.gene93489:CDS 20.0%
! CATAATTGAATTGTTGTCTT+CGG - chr3.4:17945896-17945915 None:intergenic 25.0%
ATAAGCACGTAAGACATTAT+AGG - chr3.4:17946022-17946041 None:intergenic 30.0%
CTTCTACAAATAATGCGATA+GGG - chr3.4:17945943-17945962 None:intergenic 30.0%
TCTTCTACAAATAATGCGAT+AGG - chr3.4:17945944-17945963 None:intergenic 30.0%
TTCTACAAATAATGCGATAG+GGG - chr3.4:17945942-17945961 None:intergenic 30.0%
! ATGAAGGGTGTATTGTAAAA+TGG + chr3.4:17946232-17946251 MS.gene93489:CDS 30.0%
! ATTTTACAATACACCCTTCA+TGG - chr3.4:17946233-17946252 None:intergenic 30.0%
AAACAATACGACGACACAAA+GGG - chr3.4:17946278-17946297 None:intergenic 35.0%
GAAACAAACCAAAGACATCT+TGG + chr3.4:17946093-17946112 MS.gene93489:CDS 35.0%
CGAAGCTTCTATATGTTTGG+CGG + chr3.4:17946158-17946177 MS.gene93489:CDS 40.0%
CGCCAAACATATAGAAGCTT+CGG - chr3.4:17946160-17946179 None:intergenic 40.0%
CTTCTGAACCTTCTTGATGA+CGG - chr3.4:17945973-17945992 None:intergenic 40.0%
GAAACAATACGACGACACAA+AGG - chr3.4:17946279-17946298 None:intergenic 40.0%
GTCCGAAGCTTCTATATGTT+TGG + chr3.4:17946155-17946174 MS.gene93489:CDS 40.0%
GTTCGCATTTGTACCATGAA+GGG + chr3.4:17946217-17946236 MS.gene93489:CDS 40.0%
TGTTCGCATTTGTACCATGA+AGG + chr3.4:17946216-17946235 MS.gene93489:CDS 40.0%
! TATATGTTTGGCGGATCTCT+CGG + chr3.4:17946167-17946186 MS.gene93489:CDS 40.0%
! TTCTGAACCTTCTTGATGAC+GGG - chr3.4:17945972-17945991 None:intergenic 40.0%
GATTGCGACCAAGATGTCTT+TGG - chr3.4:17946104-17946123 None:intergenic 45.0%
TCGCCAAAATCTCGTTCATG+CGG - chr3.4:17946059-17946078 None:intergenic 45.0%
TCGGTTGCAACACTTCTTGT+AGG - chr3.4:17945877-17945896 None:intergenic 45.0%
! CAACCGCATGAACGAGATTT+TGG + chr3.4:17946053-17946072 MS.gene93489:CDS 45.0%
GATTCCACCCGTCATCAAGA+AGG + chr3.4:17945962-17945981 MS.gene93489:CDS 50.0%
!! TGAACCTTCTTGATGACGGG+TGG - chr3.4:17945969-17945988 None:intergenic 50.0%
! GTTTGGCGGATCTCTCGGTT+GGG + chr3.4:17946172-17946191 MS.gene93489:CDS 55.0%
! TGTTTGGCGGATCTCTCGGT+TGG + chr3.4:17946171-17946190 MS.gene93489:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 17945856 17946314 17945856 ID=MS.gene93489
chr3.4 mRNA 17945856 17946314 17945856 ID=MS.gene93489.t1;Parent=MS.gene93489
chr3.4 exon 17945856 17946314 17945856 ID=MS.gene93489.t1.exon1;Parent=MS.gene93489.t1
chr3.4 CDS 17945856 17946314 17945856 ID=cds.MS.gene93489.t1;Parent=MS.gene93489.t1
Gene Sequence

>MS.gene93489

ATGGAGCAACAACAACTTCCTACAAGAAGTGTTGCAACCGAAGACAACAATTCAATTATGAGTCTTGATGATATTGATCTAAACCCCTATCGCATTATTTGTAGAAGATTCCACCCGTCATCAAGAAGGTTCAGAAGAAATCACATTCAAACAAGAATTGCTACCTATAATGTCTTACGTGCTTATGTAAACAACATCAACCGCATGAACGAGATTTTGGCGAGTACAAGAAATGTTGAAACAAACCAAAGACATCTTGGTCGCAATCTTTCAAAAATCAAAATTGATGAAGGAATGAAGTCCGAAGCTTCTATATGTTTGGCGGATCTCTCGGTTGGGTTGATAGCAATTCAGTTGTCATGTTCGCATTTGTACCATGAAGGGTGTATTGTAAAATGGCTAGATAGATCAAACACTTGCCCTTTGTGTCGTCGTATTGTTTCTGATTTTTCTTTGTGA
Protein sequence

>MS.gene93489.t1

MEQQQLPTRSVATEDNNSIMSLDDIDLNPYRIICRRFHPSSRRFRRNHIQTRIATYNVLRAYVNNINRMNEILASTRNVETNQRHLGRNLSKIKIDEGMKSEASICLADLSVGLIAIQLSCSHLYHEGCIVKWLDRSNTCPLCRRIVSDFSL