AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene25663

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25663.t1 MTR_4g124920 76.190 105 22 1 8 112 3 104 1.23e-50 155
MS.gene25663.t1 MTR_4g124920 75.000 72 15 1 8 79 3 71 2.58e-30 103
MS.gene25663.t1 MTR_2g084985 36.893 103 60 2 9 111 8 105 1.77e-14 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25663.t1 AT3G17210 62.500 112 39 1 1 112 1 109 2.50e-45 142
MS.gene25663.t1 AT3G17210 62.500 112 39 1 1 112 1 109 2.50e-45 142
MS.gene25663.t1 AT5G22580 34.021 97 59 2 9 105 7 98 8.25e-15 65.5

Find 25 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAGTTCCTCAATCTTCTCT+TGG 0.329948 8.2:-7998877 None:intergenic
GATTCAGGTAACAAATAATA+AGG 0.348275 8.2:-7999195 None:intergenic
AATGAGTAAATCCTTGATTC+AGG 0.352373 8.2:-7999210 None:intergenic
TTACCAATGGAATGACTTCA+TGG 0.420824 8.2:-7998936 None:intergenic
ATTATTTGTTACCTGAATCA+AGG 0.432767 8.2:+7999199 MS.gene25663:CDS
AAAGTTGCTCGTTCCTTGCT+TGG 0.439365 8.2:+7999306 MS.gene25663:CDS
GAGTTCCTCAATCTTCTCTT+GGG 0.443255 8.2:-7998876 None:intergenic
GTAGTGAAGAACATAGTGAT+TGG 0.457715 8.2:+7998833 MS.gene25663:CDS
GAGGAAATGGAGGAAGCAAA+AGG 0.502851 8.2:+7998809 None:intergenic
TGGGATGAGATTGACGAGAT+TGG 0.516286 8.2:-7998912 None:intergenic
ATTCAAAGGTTAACGATGGT+GGG 0.545431 8.2:-7999355 None:intergenic
TCCTTGCTTGGAGAAAGTGC+TGG 0.548785 8.2:+7999318 MS.gene25663:CDS
CACCCATGAAGTCATTCCAT+TGG 0.553232 8.2:+7998933 MS.gene25663:CDS
TGAATCAACATTTGAGAGTG+TGG 0.555452 8.2:+7999237 MS.gene25663:CDS
TTTGCATACTCAACATGAGC+AGG 0.558557 8.2:-7999286 None:intergenic
GAAGATTGAGGAACTCATCA+AGG 0.571882 8.2:+7998883 MS.gene25663:CDS
GCCAGCACTTTCTCCAAGCA+AGG 0.576667 8.2:-7999319 None:intergenic
GATTCAAAGGTTAACGATGG+TGG 0.578082 8.2:-7999356 None:intergenic
GAGATTGACGAGATTGGCAA+AGG 0.580515 8.2:-7998906 None:intergenic
CAATGGAATGACTTCATGGG+TGG 0.583790 8.2:-7998932 None:intergenic
AATCTCCCAAGAGAAGATTG+AGG 0.597731 8.2:+7998871 MS.gene25663:CDS
ATGAGCTACATACTCTGCAA+TGG 0.614733 8.2:-7999263 None:intergenic
TACCAATGGAATGACTTCAT+GGG 0.631729 8.2:-7998935 None:intergenic
AATGGAATGACTTCATGGGT+GGG 0.706119 8.2:-7998931 None:intergenic
ACGGATTCAAAGGTTAACGA+TGG 0.711712 8.2:-7999359 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTAAGTTTTTTAAGTTT+TGG - chr8.2:7999038-7999057 None:intergenic 10.0%
!!! TATACATGTCTTATTTTTTT+AGG + chr8.2:7999155-7999174 MS.gene25663:intron 15.0%
! GATTCAGGTAACAAATAATA+AGG - chr8.2:7999198-7999217 None:intergenic 25.0%
!! ATTATTTGTTACCTGAATCA+AGG + chr8.2:7999199-7999218 MS.gene25663:CDS 25.0%
!! TTTAAGTTTCATCTTACCAA+TGG - chr8.2:7998952-7998971 None:intergenic 25.0%
AATGAGTAAATCCTTGATTC+AGG - chr8.2:7999213-7999232 None:intergenic 30.0%
GTAGTGAAGAACATAGTGAT+TGG + chr8.2:7998833-7998852 MS.gene25663:CDS 35.0%
TACCAATGGAATGACTTCAT+GGG - chr8.2:7998938-7998957 None:intergenic 35.0%
TGAATCAACATTTGAGAGTG+TGG + chr8.2:7999237-7999256 MS.gene25663:CDS 35.0%
TTACCAATGGAATGACTTCA+TGG - chr8.2:7998939-7998958 None:intergenic 35.0%
!! ATAGTCTAGACTGCTTTTGT+CGG - chr8.2:7998988-7999007 None:intergenic 35.0%
AATCTCCCAAGAGAAGATTG+AGG + chr8.2:7998871-7998890 MS.gene25663:CDS 40.0%
AATGGAATGACTTCATGGGT+GGG - chr8.2:7998934-7998953 None:intergenic 40.0%
ATGAGCTACATACTCTGCAA+TGG - chr8.2:7999266-7999285 None:intergenic 40.0%
GAAGATTGAGGAACTCATCA+AGG + chr8.2:7998883-7998902 MS.gene25663:CDS 40.0%
GAGTTCCTCAATCTTCTCTT+GGG - chr8.2:7998879-7998898 None:intergenic 40.0%
TGAGTTCCTCAATCTTCTCT+TGG - chr8.2:7998880-7998899 None:intergenic 40.0%
TTTGCATACTCAACATGAGC+AGG - chr8.2:7999289-7999308 None:intergenic 40.0%
AAAGTTGCTCGTTCCTTGCT+TGG + chr8.2:7999306-7999325 MS.gene25663:CDS 45.0%
CAATGGAATGACTTCATGGG+TGG - chr8.2:7998935-7998954 None:intergenic 45.0%
CACCCATGAAGTCATTCCAT+TGG + chr8.2:7998933-7998952 MS.gene25663:CDS 45.0%
GAGATTGACGAGATTGGCAA+AGG - chr8.2:7998909-7998928 None:intergenic 45.0%
TGGGATGAGATTGACGAGAT+TGG - chr8.2:7998915-7998934 None:intergenic 45.0%
! GATTTTCGCTAAGTGGACGA+GGG - chr8.2:7999074-7999093 None:intergenic 45.0%
! TACCAGCGATTTTCGCTAAG+TGG - chr8.2:7999081-7999100 None:intergenic 45.0%
GTCCACTTAGCGAAAATCGC+TGG + chr8.2:7999076-7999095 MS.gene25663:intron 50.0%
! CGATTTTCGCTAAGTGGACG+AGG - chr8.2:7999075-7999094 None:intergenic 50.0%
! TCCTTGCTTGGAGAAAGTGC+TGG + chr8.2:7999318-7999337 MS.gene25663:CDS 50.0%
GCCAGCACTTTCTCCAAGCA+AGG - chr8.2:7999322-7999341 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 7998815 7999375 7998815 ID=MS.gene25663
chr8.2 mRNA 7998815 7999375 7998815 ID=MS.gene25663.t1;Parent=MS.gene25663
chr8.2 exon 7998815 7998954 7998815 ID=MS.gene25663.t1.exon1;Parent=MS.gene25663.t1
chr8.2 CDS 7998815 7998954 7998815 ID=cds.MS.gene25663.t1;Parent=MS.gene25663.t1
chr8.2 exon 7999177 7999375 7999177 ID=MS.gene25663.t1.exon2;Parent=MS.gene25663.t1
chr8.2 CDS 7999177 7999375 7999177 ID=cds.MS.gene25663.t1;Parent=MS.gene25663.t1
Gene Sequence

>MS.gene25663

ATGGAGGAAGCAAAAGGAGTAGTGAAGAACATAGTGATTGGAAAGTTCAAAGATGAAATCTCCCAAGAGAAGATTGAGGAACTCATCAAGGCCTTTGCCAATCTCGTCAATCTCATCCCACCCATGAAGTCATTCCATTGGTAAGATGAAACTTAAACTTAAATAAGTTACCGACAAAAGCAGTCTAGACTATGATTTTAAGTCTAATTTTTTGTCTAAACCAAAACTTAAAAAACTTAATTTAGTTATAAATACTCCCTCGTCCACTTAGCGAAAATCGCTGGTATTAAAACAAATTATTTGAAAAACAAATTTGTCTGAAATATGTTTCAATTTTATATATACATGTCTTATTTTTTTAGGAATTGTTGTTATACTTTCCTTATTATTTGTTACCTGAATCAAGGATTTACTCATTTCTTTGAATCAACATTTGAGAGTGTGGAAGCCATTGCAGAGTATGTAGCTCATCCTGCTCATGTTGAGTATGCAAAGTTGCTCGTTCCTTGCTTGGAGAAAGTGCTGGCATTTGATTATAAGCCCACCATCGTTAACCTTTGA
Protein sequence

>MS.gene25663.t1

MEEAKGVVKNIVIGKFKDEISQEKIEELIKAFANLVNLIPPMKSFHWNCCYTFLIICYLNQGFTHFFESTFESVEAIAEYVAHPAHVEYAKLLVPCLEKVLAFDYKPTIVNL