AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene066071

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066071.t1 MTR_1g111300 93.893 131 7 1 1 130 1 131 1.15e-87 251
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 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAAATTTGTTAGCCAAAT+AGG 0.230270 1.4:-84947884 None:intergenic
ATCAATGTGTTTGAAACTAT+TGG 0.284145 1.4:-84947759 None:intergenic
GCTCTGGTTCGCCACCTATT+TGG 0.320551 1.4:+84947870 MS.gene066071:CDS
TGGTTTCAACTAAATCTTCA+TGG 0.350113 1.4:-84947739 None:intergenic
CACATTGATGTTACAAATGA+TGG 0.350128 1.4:+84947773 MS.gene066071:CDS
TGAATTCAAATCCTAGTGTT+TGG 0.353031 1.4:+84947642 MS.gene066071:CDS
TTGCAGCAAGAATGAACAAT+AGG 0.400328 1.4:+84948101 MS.gene066071:intron
CTTCATTTCTTATTCACCAC+TGG 0.403164 1.4:-84948142 None:intergenic
CTTTCTATGCTGAGATTAAG+AGG 0.404596 1.4:+84947690 MS.gene066071:CDS
CTATTTGGCTAACAAATTTG+TGG 0.413481 1.4:+84947885 MS.gene066071:CDS
TACAAGAAAATTCTATTTGT+GGG 0.427304 1.4:+84947838 MS.gene066071:CDS
TGGAGGAATGGTAAAGGTAC+TGG 0.427886 1.4:+84947905 MS.gene066071:CDS
TTGTGGGAAACAGATAGCTC+TGG 0.484793 1.4:+84947854 MS.gene066071:CDS
CTACAAGAAAATTCTATTTG+TGG 0.487604 1.4:+84947837 MS.gene066071:CDS
CTAACAAATTTGTGGAGGAA+TGG 0.499619 1.4:+84947893 MS.gene066071:CDS
TTACAAATGATGGTTCAAAC+AGG 0.502417 1.4:+84947783 MS.gene066071:CDS
CATTCCTCAAGTTTCATGCA+AGG 0.516692 1.4:+84947934 MS.gene066071:CDS
TCTGTCTCAAACCAAACACT+AGG 0.561762 1.4:-84947653 None:intergenic
GGTCTTCAGATGTTAACTGC+AGG 0.570063 1.4:-84947718 None:intergenic
TTTGGCTAACAAATTTGTGG+AGG 0.590197 1.4:+84947888 MS.gene066071:CDS
CAAGAATGAACAATAGGACG+AGG 0.601849 1.4:+84948107 MS.gene066071:CDS
AATTTGTGGAGGAATGGTAA+AGG 0.605795 1.4:+84947899 MS.gene066071:CDS
TGCAAGGAAAATCAAAGACC+AGG 0.622181 1.4:+84947950 MS.gene066071:CDS
AAATTTGTTAGCCAAATAGG+TGG 0.659873 1.4:-84947881 None:intergenic
GAGGAAAATATATAGACCAG+TGG 0.692967 1.4:+84948126 MS.gene066071:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TACAAGAAAATTCTATTTGT+GGG + chr1.4:84947838-84947857 MS.gene066071:CDS 20.0%
!! TTCACAAATTTGTAAATTAG+TGG + chr1.4:84948012-84948031 MS.gene066071:intron 20.0%
! CTACAAGAAAATTCTATTTG+TGG + chr1.4:84947837-84947856 MS.gene066071:CDS 25.0%
!! ATCAATGTGTTTGAAACTAT+TGG - chr1.4:84947762-84947781 None:intergenic 25.0%
!! CACAAATAGAATTTTCTTGT+AGG - chr1.4:84947839-84947858 None:intergenic 25.0%
CACATTGATGTTACAAATGA+TGG + chr1.4:84947773-84947792 MS.gene066071:CDS 30.0%
CTATTTGGCTAACAAATTTG+TGG + chr1.4:84947885-84947904 MS.gene066071:CDS 30.0%
TAAGAGATCAAAATTGTACC+TGG - chr1.4:84947971-84947990 None:intergenic 30.0%
TGAATTCAAATCCTAGTGTT+TGG + chr1.4:84947642-84947661 MS.gene066071:CDS 30.0%
TGGTTTCAACTAAATCTTCA+TGG - chr1.4:84947742-84947761 None:intergenic 30.0%
TTACAAATGATGGTTCAAAC+AGG + chr1.4:84947783-84947802 MS.gene066071:CDS 30.0%
!! AAATTTGTTAGCCAAATAGG+TGG - chr1.4:84947884-84947903 None:intergenic 30.0%
!! CACAAATTTGTTAGCCAAAT+AGG - chr1.4:84947887-84947906 None:intergenic 30.0%
AATTTGTGGAGGAATGGTAA+AGG + chr1.4:84947899-84947918 MS.gene066071:CDS 35.0%
CTAACAAATTTGTGGAGGAA+TGG + chr1.4:84947893-84947912 MS.gene066071:CDS 35.0%
CTTTCTATGCTGAGATTAAG+AGG + chr1.4:84947690-84947709 MS.gene066071:CDS 35.0%
GAGGAAAATATATAGACCAG+TGG + chr1.4:84948126-84948145 MS.gene066071:CDS 35.0%
TTGCAGCAAGAATGAACAAT+AGG + chr1.4:84948101-84948120 MS.gene066071:intron 35.0%
TTTGGCTAACAAATTTGTGG+AGG + chr1.4:84947888-84947907 MS.gene066071:CDS 35.0%
! TTTTCCTTGCATGAAACTTG+AGG - chr1.4:84947941-84947960 None:intergenic 35.0%
CAAGAATGAACAATAGGACG+AGG + chr1.4:84948107-84948126 MS.gene066071:CDS 40.0%
CATTCCTCAAGTTTCATGCA+AGG + chr1.4:84947934-84947953 MS.gene066071:CDS 40.0%
TCTGTCTCAAACCAAACACT+AGG - chr1.4:84947656-84947675 None:intergenic 40.0%
TGCAAGGAAAATCAAAGACC+AGG + chr1.4:84947950-84947969 MS.gene066071:CDS 40.0%
GGTCTTCAGATGTTAACTGC+AGG - chr1.4:84947721-84947740 None:intergenic 45.0%
TTGTGGGAAACAGATAGCTC+TGG + chr1.4:84947854-84947873 MS.gene066071:CDS 45.0%
! TGGAGGAATGGTAAAGGTAC+TGG + chr1.4:84947905-84947924 MS.gene066071:CDS 45.0%
! GCTCTGGTTCGCCACCTATT+TGG + chr1.4:84947870-84947889 MS.gene066071:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 84947635 84948162 84947635 ID=MS.gene066071
chr1.4 mRNA 84947635 84948162 84947635 ID=MS.gene066071.t1;Parent=MS.gene066071
chr1.4 exon 84947635 84947971 84947635 ID=MS.gene066071.t1.exon1;Parent=MS.gene066071.t1
chr1.4 CDS 84947635 84947971 84947635 ID=cds.MS.gene066071.t1;Parent=MS.gene066071.t1
chr1.4 exon 84948107 84948162 84948107 ID=MS.gene066071.t1.exon2;Parent=MS.gene066071.t1
chr1.4 CDS 84948107 84948162 84948107 ID=cds.MS.gene066071.t1;Parent=MS.gene066071.t1
Gene Sequence

>MS.gene066071

ATGGAAATGAATTCAAATCCTAGTGTTTGGTTTGAGACAGAAAATGAAGATGATACTTTCTATGCTGAGATTAAGAGGCAGATCCTGCAGTTAACATCTGAAGACCATGAAGATTTAGTTGAAACCAATAGTTTCAAACACATTGATGTTACAAATGATGGTTCAAACAGGTCAATTTACAATTATAACAATGCAACAAAACCTACAAGAAAATTCTATTTGTGGGAAACAGATAGCTCTGGTTCGCCACCTATTTGGCTAACAAATTTGTGGAGGAATGGTAAAGGTACTGGAGTGTTCATTCCTCAAGTTTCATGCAAGGAAAATCAAAGACCAGGTACAATTTTGATCTCTTATTCATTAGTTTATTTTTTAAATTCACAAATTTGTAAATTAGTGGTTATGTTAGTTTTTGACAGTTCGAACTACTACGATAATTGTTACTTTGCTCACTGTTGTGATTATTTTGCAGCAAGAATGAACAATAGGACGAGGAAAATATATAGACCAGTGGTGAATAAGAAATGA
Protein sequence

>MS.gene066071.t1

MEMNSNPSVWFETENEDDTFYAEIKRQILQLTSEDHEDLVETNSFKHIDVTNDGSNRSIYNYNNATKPTRKFYLWETDSSGSPPIWLTNLWRNGKGTGVFIPQVSCKENQRPARMNNRTRKIYRPVVNKK