AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0797120


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0797120 MtrunA17_Chr5g0400191 98.095 105 2 0 1 105 1 105 7.83e-72 208
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0797120 AT3G59840.1 58.095 105 36 2 1 105 1 97 1.65e-34 114

Find 35 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACGATAAAGTTACTCTTGC+CGG 0.302379 5_3:+9201680 Msa0797120:CDS
GTCGTCGATGACTTCGCTTC+AGG 0.338584 5_3:-9201518 None:intergenic
GGTTCAAGATCTTCAGAAAC+TGG 0.373697 5_3:-9201710 None:intergenic
TTCAGAAACTGGACAATAAC+CGG 0.394776 5_3:-9201699 None:intergenic
ATCCCTGGCGCCTCCGTGGT+TGG 0.398567 5_3:-9201581 None:intergenic
AAACCAACCACGGAGGCGCC+AGG 0.442569 5_3:+9201578 Msa0797120:CDS
GTTTACTGTGGTGGCGGAAG+GGG 0.469288 5_3:+9201483 Msa0797120:CDS
AGATCTTGAACCTTGTCGTT+GGG 0.475907 5_3:+9201721 Msa0797120:CDS
AGCAAAGAATGGCGGTGCCT+CGG 0.478420 5_3:+9201550 Msa0797120:CDS
TCCACTGCACCGTTCATCCC+TGG 0.487594 5_3:-9201596 None:intergenic
GGGTTTACTGTGGTGGCGGA+AGG 0.492850 5_3:+9201481 Msa0797120:CDS
ACTGAAACACTCGCGTTCAA+AGG 0.493969 5_3:-9201629 None:intergenic
AAGATCTTGAACCTTGTCGT+TGG 0.501854 5_3:+9201720 Msa0797120:CDS
ACGGTGCAGTGGAGGTTAAA+CGG 0.502142 5_3:+9201606 Msa0797120:CDS
GGTTTACTGTGGTGGCGGAA+GGG 0.516623 5_3:+9201482 Msa0797120:CDS
ACGGAGAACGCAGCAAAGAA+TGG 0.516724 5_3:+9201539 Msa0797120:CDS
TTGTCGTTGGGAAATTCTGC+CGG 0.548386 5_3:+9201733 Msa0797120:CDS
GGCGCGTTTGACTCAACCGC+CGG 0.563952 5_3:-9201752 None:intergenic
GAATGGGTTTACTGTGGTGG+CGG 0.565035 5_3:+9201477 None:intergenic
ACGGAGGCGCCAGGGATGAA+CGG 0.590223 5_3:+9201587 Msa0797120:CDS
AGGGATGAACGGTGCAGTGG+AGG 0.592078 5_3:+9201598 Msa0797120:CDS
TAAGAATGGGTTTACTGTGG+TGG 0.597545 5_3:+9201474 None:intergenic
GGCAGAATTTCCCAACGACA+AGG 0.605086 5_3:-9201731 None:intergenic
GTTCATCCCTGGCGCCTCCG+TGG 0.608954 5_3:-9201585 None:intergenic
AACCAACCACGGAGGCGCCA+GGG 0.609462 5_3:+9201579 Msa0797120:CDS
GCCAGGGATGAACGGTGCAG+TGG 0.624288 5_3:+9201595 Msa0797120:CDS
CGTGGTTGGTTTCACCGCCG+AGG 0.625680 5_3:-9201567 None:intergenic
CAGAAAACAACGCGAAACTG+CGG 0.626649 5_3:-9201773 None:intergenic
AAAGAATGGCGGTGCCTCGG+CGG 0.629398 5_3:+9201553 Msa0797120:CDS
GCATAAGAATGGGTTTACTG+TGG 0.664009 5_3:+9201471 None:intergenic
TCGTTGGGAAATTCTGCCGG+CGG 0.672246 5_3:+9201736 Msa0797120:CDS
TGAAGCGAAGTCATCGACGA+CGG 0.700439 5_3:+9201520 Msa0797120:CDS
GAGAACGCAGCAAAGAATGG+CGG 0.729371 5_3:+9201542 Msa0797120:CDS
CTCGGCGGTGAAACCAACCA+CGG 0.734856 5_3:+9201568 Msa0797120:CDS
GGCGGTGAAACCAACCACGG+AGG 0.756389 5_3:+9201571 Msa0797120:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTGTTTCAGTTTTCGAGTT+TGG + chr5_3:9201641-9201660 Msa0797120:CDS 35.0%
!!! TTCAGTTTTCGAGTTTGGTT+CGG + chr5_3:9201646-9201665 Msa0797120:CDS 35.0%
AACGATAAAGTTACTCTTGC+CGG + chr5_3:9201680-9201699 Msa0797120:CDS 35.0%
TTCAGAAACTGGACAATAAC+CGG - chr5_3:9201702-9201721 None:intergenic 35.0%
GGTTCAAGATCTTCAGAAAC+TGG - chr5_3:9201713-9201732 None:intergenic 40.0%
AAGATCTTGAACCTTGTCGT+TGG + chr5_3:9201720-9201739 Msa0797120:CDS 40.0%
AGATCTTGAACCTTGTCGTT+GGG + chr5_3:9201721-9201740 Msa0797120:CDS 40.0%
ACTGAAACACTCGCGTTCAA+AGG - chr5_3:9201632-9201651 None:intergenic 45.0%
TTGTCGTTGGGAAATTCTGC+CGG + chr5_3:9201733-9201752 Msa0797120:CDS 45.0%
CAGAAAACAACGCGAAACTG+CGG - chr5_3:9201776-9201795 None:intergenic 45.0%
TGAAGCGAAGTCATCGACGA+CGG + chr5_3:9201520-9201539 Msa0797120:CDS 50.0%
ACGGAGAACGCAGCAAAGAA+TGG + chr5_3:9201539-9201558 Msa0797120:CDS 50.0%
GAGAACGCAGCAAAGAATGG+CGG + chr5_3:9201542-9201561 Msa0797120:CDS 50.0%
ACGGTGCAGTGGAGGTTAAA+CGG + chr5_3:9201606-9201625 Msa0797120:CDS 50.0%
GGCAGAATTTCCCAACGACA+AGG - chr5_3:9201734-9201753 None:intergenic 50.0%
!! GGTTTACTGTGGTGGCGGAA+GGG + chr5_3:9201482-9201501 Msa0797120:CDS 55.0%
!! GTTTACTGTGGTGGCGGAAG+GGG + chr5_3:9201483-9201502 Msa0797120:CDS 55.0%
GTCGTCGATGACTTCGCTTC+AGG - chr5_3:9201521-9201540 None:intergenic 55.0%
AGCAAAGAATGGCGGTGCCT+CGG + chr5_3:9201550-9201569 Msa0797120:CDS 55.0%
TCGTTGGGAAATTCTGCCGG+CGG + chr5_3:9201736-9201755 Msa0797120:CDS 55.0%
!! GGGTTTACTGTGGTGGCGGA+AGG + chr5_3:9201481-9201500 Msa0797120:CDS 60.0%
AAAGAATGGCGGTGCCTCGG+CGG + chr5_3:9201553-9201572 Msa0797120:CDS 60.0%
CTCGGCGGTGAAACCAACCA+CGG + chr5_3:9201568-9201587 Msa0797120:CDS 60.0%
TCCACTGCACCGTTCATCCC+TGG - chr5_3:9201599-9201618 None:intergenic 60.0%
AGGGATGAACGGTGCAGTGG+AGG + chr5_3:9201598-9201617 Msa0797120:CDS 60.0%
!! CGTGGTTGGTTTCACCGCCG+AGG - chr5_3:9201570-9201589 None:intergenic 65.0%
GGCGGTGAAACCAACCACGG+AGG + chr5_3:9201571-9201590 Msa0797120:CDS 65.0%
!! AAACCAACCACGGAGGCGCC+AGG + chr5_3:9201578-9201597 Msa0797120:CDS 65.0%
!! AACCAACCACGGAGGCGCCA+GGG + chr5_3:9201579-9201598 Msa0797120:CDS 65.0%
!! ACGGAGGCGCCAGGGATGAA+CGG + chr5_3:9201587-9201606 Msa0797120:CDS 65.0%
GCCAGGGATGAACGGTGCAG+TGG + chr5_3:9201595-9201614 Msa0797120:CDS 65.0%
GGCGCGTTTGACTCAACCGC+CGG - chr5_3:9201755-9201774 None:intergenic 65.0%
ATCCCTGGCGCCTCCGTGGT+TGG - chr5_3:9201584-9201603 None:intergenic 70.0%
GTTCATCCCTGGCGCCTCCG+TGG - chr5_3:9201588-9201607 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 9201479 9201796 9201479 ID=Msa0797120;Name=Msa0797120
chr5_3 mRNA 9201479 9201796 9201479 ID=Msa0797120-mRNA-1;Parent=Msa0797120;Name=Msa0797120-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|105
chr5_3 exon 9201479 9201796 9201479 ID=Msa0797120-mRNA-1:exon:3970;Parent=Msa0797120-mRNA-1
chr5_3 CDS 9201479 9201796 9201479 ID=Msa0797120-mRNA-1:cds;Parent=Msa0797120-mRNA-1
Gene Sequence

>Msa0797120

ATGGGTTTACTGTGGTGGCGGAAGGGGAAGAATTCACAACCTGAAGCGAAGTCATCGACGACGGAGAACGCAGCAAAGAATGGCGGTGCCTCGGCGGTGAAACCAACCACGGAGGCGCCAGGGATGAACGGTGCAGTGGAGGTTAAACGGCCTTTGAACGCGAGTGTTTCAGTTTTCGAGTTTGGTTCGGTTGCTGCGAGCAACGATAAAGTTACTCTTGCCGGTTATTGTCCAGTTTCTGAAGATCTTGAACCTTGTCGTTGGGAAATTCTGCCGGCGGTTGAGTCAAACGCGCCGCAGTTTCGCGTTGTTTTCTGA

Protein sequence

>Msa0797120

MGLLWWRKGKNSQPEAKSSTTENAAKNGGASAVKPTTEAPGMNGAVEVKRPLNASVSVFEFGSVAASNDKVTLAGYCPVSEDLEPCRWEILPAVESNAPQFRVVF*