AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0584760

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0584760 MtrunA17_Chr4g0019481 82.906 117 19 1 1 116 1 117 3.88e-60 180
Msa0584760 MtrunA17_Chr4g0019471 74.046 131 19 2 1 116 1 131 1.54e-55 169
Msa0584760 MtrunA17_Chr4g0019551 78.632 117 24 1 1 116 1 117 1.91e-48 150
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGGTTCAGGCTGATTATT+TGG 0.174092 4_2:-4745661 None:intergenic
TCTCATTCATCTGGTGTATA+AGG 0.203991 4_2:-4745862 None:intergenic
ACTCGATTCTAATATAAAAT+CGG 0.323743 4_2:-4745623 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.375685 4_2:-4745861 None:intergenic
CTCGATTCTAATATAAAATC+GGG 0.421980 4_2:-4745622 None:intergenic
GGAGGTTGGTTCAAGTCAAA+TGG 0.461699 4_2:-4745814 None:intergenic
TTGAGGTCGAAAGCTCGAAC+AGG 0.496472 4_2:-4745835 None:intergenic
TCAGGCTGATTATTTGGTGG+TGG 0.505165 4_2:-4745655 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4_2:-4745802 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4_2:-4745796 None:intergenic
GGTTCAGGCTGATTATTTGG+TGG 0.558373 4_2:-4745658 None:intergenic
CGAAAGCTCGAACAGGAGGT+TGG 0.564077 4_2:-4745828 None:intergenic
ACTGCTAAAGCTTCTCGAGA+TGG 0.596385 4_2:-4745577 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4_2:-4745852 None:intergenic
ATATTAGAATCGAGTAAACA+AGG 0.624706 4_2:+4745631 Msa0584760:CDS
AGGTCGAAAGCTCGAACAGG+AGG 0.636300 4_2:-4745832 None:intergenic
TCAAATGGTTGCACATGTGG+AGG 0.671560 4_2:-4745799 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTCGATTCTAATATAAAAT+CGG - chr4_2:4745626-4745645 None:intergenic 20.0%
! CTCGATTCTAATATAAAATC+GGG - chr4_2:4745625-4745644 None:intergenic 25.0%
! ATATTAGAATCGAGTAAACA+AGG + chr4_2:4745631-4745650 Msa0584760:CDS 25.0%
! TGTTCAACATTTTGTGGTTG+AGG - chr4_2:4745697-4745716 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG - chr4_2:4745703-4745722 None:intergenic 35.0%
! TGTTGTTCAACATTTTGTGG+TGG - chr4_2:4745742-4745761 None:intergenic 35.0%
!! GGTTGTTGTTCAACATTTTG+TGG - chr4_2:4745745-4745764 None:intergenic 35.0%
! TCTGGTTCAGGCTGATTATT+TGG - chr4_2:4745664-4745683 None:intergenic 40.0%
AAGTCAAATGGTTGCACATG+TGG - chr4_2:4745805-4745824 None:intergenic 40.0%
ACTGCTAAAGCTTCTCGAGA+TGG - chr4_2:4745580-4745599 None:intergenic 45.0%
! TCAGGCTGATTATTTGGTGG+TGG - chr4_2:4745658-4745677 None:intergenic 45.0%
GGTTCAGGCTGATTATTTGG+TGG - chr4_2:4745661-4745680 None:intergenic 45.0%
!!! GGTTGAGCATTTTCTGGTTC+AGG - chr4_2:4745676-4745695 None:intergenic 45.0%
! GGTTGAGGTTGAGCATTTTC+TGG - chr4_2:4745682-4745701 None:intergenic 45.0%
!! TCAACATTTTGTGGTGGAGC+TGG - chr4_2:4745736-4745755 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG - chr4_2:4745802-4745821 None:intergenic 45.0%
! GGAGGTTGGTTCAAGTCAAA+TGG - chr4_2:4745817-4745836 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG - chr4_2:4745855-4745874 None:intergenic 45.0%
! TGTGGAGGTGGTGCATTTTG+TGG - chr4_2:4745787-4745806 None:intergenic 50.0%
AATGGTTGCACATGTGGAGG+TGG - chr4_2:4745799-4745818 None:intergenic 50.0%
TTGAGGTCGAAAGCTCGAAC+AGG - chr4_2:4745838-4745857 None:intergenic 50.0%
! GGTGGAGCTGGTGCATTTTG+TGG - chr4_2:4745724-4745743 None:intergenic 55.0%
! GGTGGAGCTGGTGCATTTTG+TGG - chr4_2:4745724-4745743 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG - chr4_2:4745778-4745797 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG - chr4_2:4745784-4745803 None:intergenic 55.0%
CGAAAGCTCGAACAGGAGGT+TGG - chr4_2:4745831-4745850 None:intergenic 55.0%
AGGTCGAAAGCTCGAACAGG+AGG - chr4_2:4745835-4745854 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 4745532 4745882 4745532 ID=Msa0584760;Name=Msa0584760
chr4_2 mRNA 4745532 4745882 4745532 ID=Msa0584760-mRNA-1;Parent=Msa0584760;Name=Msa0584760-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|116
chr4_2 exon 4745532 4745882 4745532 ID=Msa0584760-mRNA-1:exon:1195;Parent=Msa0584760-mRNA-1
chr4_2 CDS 4745532 4745882 4745532 ID=Msa0584760-mRNA-1:cds;Parent=Msa0584760-mRNA-1
Gene Sequence

>Msa0584760

ATGTCAAAGCTAGAATTCTTATGCAGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCCGATTTTATATTAGAATCGAGTAAACAAGGTCCACCACCAAATAATCAGCCTGAACCAGAAAATGCTCAACCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGTTGAACAACAACCACAAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAACCTCCTGTTCGAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>Msa0584760

MSKLEFLCSECDTMFPSREALAVHVIEEHHPDFILESSKQGPPPNNQPEPENAQPQPQNVEHQPQNAPAPPQNVEQQPQNAPAPPQNAPPPHVQPFDLNQPPVRAFDLNLPYTPDE*