AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0796700


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0796700 MtrunA17_Chr5g0399601 80.822 73 14 0 1 73 338 410 1.58e-36 126
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATATTTGACTGTTGAAAAT+TGG 0.316067 5_3:+8692385 None:intergenic
TCAAATATCACGGAGATTAC+AGG 0.343830 5_3:-8692371 Msa0796700:CDS
TTGTAGTGTTCAACAAGTAT+AGG 0.428975 5_3:-8692470 Msa0796700:intron
TCACGGAGATTACAGGGAAA+TGG 0.459332 5_3:-8692364 Msa0796700:CDS
GCTTAAGAGATGGGTTCATA+AGG 0.466191 5_3:-8692288 Msa0796700:CDS
TTCAAAGCAGGCCTACGGTC+AGG 0.467928 5_3:+8692320 None:intergenic
AAGAGATGGGTTCATAAGGT+TGG 0.479955 5_3:-8692284 Msa0796700:CDS
CGGTCAGGTTTACGTTTCTG+TGG 0.490934 5_3:+8692335 None:intergenic
AGCCTAGGTTGCTTCAAAGC+AGG 0.506799 5_3:+8692308 None:intergenic
AGCAACCTAGGCTTAAGAGA+TGG 0.510316 5_3:-8692298 Msa0796700:CDS
GAATGGTGTTGCAAAGAGAA+AGG 0.528695 5_3:-8692423 Msa0796700:CDS
GCAACCTAGGCTTAAGAGAT+GGG 0.542462 5_3:-8692297 Msa0796700:CDS
CAAATATCACGGAGATTACA+GGG 0.544371 5_3:-8692370 Msa0796700:CDS
GGTCAGGTTTACGTTTCTGT+GGG 0.548383 5_3:+8692336 None:intergenic
TGAACCCATCTCTTAAGCCT+AGG 0.559582 5_3:+8692293 None:intergenic
AAGTATAGGAACAGTTCCAT+TGG 0.591926 5_3:-8692456 Msa0796700:CDS
GTTGCTTCAAAGCAGGCCTA+CGG 0.594096 5_3:+8692315 None:intergenic
GGCCTGCTTTGAAGCAACCT+AGG 0.627807 5_3:-8692310 Msa0796700:CDS
CCATTGGCATGTGAAAAGAA+TGG 0.681612 5_3:-8692440 Msa0796700:CDS
AGAAACGTAAACCTGACCGT+AGG 0.705065 5_3:-8692331 Msa0796700:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GATATTTGACTGTTGAAAAT+TGG + chr5_3:8692414-8692433 None:intergenic 25.0%
!! TTTTCAACAGTCAAATATCA+CGG - chr5_3:8692415-8692434 Msa0796700:CDS 25.0%
TTGTAGTGTTCAACAAGTAT+AGG - chr5_3:8692326-8692345 Msa0796700:CDS 30.0%
ACAACGACGAAGAAAATTCT+TGG - chr5_3:8692282-8692301 Msa0796700:CDS 35.0%
GAAAATTCTTGGAAGAAACC+AGG - chr5_3:8692293-8692312 Msa0796700:CDS 35.0%
CACTACAATAATGTCTTTCC+TGG + chr5_3:8692314-8692333 None:intergenic 35.0%
AAGTATAGGAACAGTTCCAT+TGG - chr5_3:8692340-8692359 Msa0796700:CDS 35.0%
TCAAATATCACGGAGATTAC+AGG - chr5_3:8692425-8692444 Msa0796700:CDS 35.0%
CAAATATCACGGAGATTACA+GGG - chr5_3:8692426-8692445 Msa0796700:CDS 35.0%
! CCATTCTTTTCACATGCCAA+TGG + chr5_3:8692359-8692378 None:intergenic 40.0%
CCATTGGCATGTGAAAAGAA+TGG - chr5_3:8692356-8692375 Msa0796700:CDS 40.0%
!! GAATGGTGTTGCAAAGAGAA+AGG - chr5_3:8692373-8692392 Msa0796700:CDS 40.0%
! GCTTAAGAGATGGGTTCATA+AGG - chr5_3:8692508-8692527 Msa0796700:intron 40.0%
! AAGAGATGGGTTCATAAGGT+TGG - chr5_3:8692512-8692531 Msa0796700:intron 40.0%
TCACGGAGATTACAGGGAAA+TGG - chr5_3:8692432-8692451 Msa0796700:CDS 45.0%
GGTCAGGTTTACGTTTCTGT+GGG + chr5_3:8692463-8692482 None:intergenic 45.0%
AGAAACGTAAACCTGACCGT+AGG - chr5_3:8692465-8692484 Msa0796700:CDS 45.0%
AGCAACCTAGGCTTAAGAGA+TGG - chr5_3:8692498-8692517 Msa0796700:intron 45.0%
GCAACCTAGGCTTAAGAGAT+GGG - chr5_3:8692499-8692518 Msa0796700:intron 45.0%
TGAACCCATCTCTTAAGCCT+AGG + chr5_3:8692506-8692525 None:intergenic 45.0%
CGGTCAGGTTTACGTTTCTG+TGG + chr5_3:8692464-8692483 None:intergenic 50.0%
GTTGCTTCAAAGCAGGCCTA+CGG + chr5_3:8692484-8692503 None:intergenic 50.0%
AGCCTAGGTTGCTTCAAAGC+AGG + chr5_3:8692491-8692510 None:intergenic 50.0%
TTCAAAGCAGGCCTACGGTC+AGG + chr5_3:8692479-8692498 None:intergenic 55.0%
!! GGCCTGCTTTGAAGCAACCT+AGG - chr5_3:8692486-8692505 Msa0796700:intron 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 8692268 8692550 8692268 ID=Msa0796700;Name=Msa0796700
chr5_3 mRNA 8692268 8692550 8692268 ID=Msa0796700-mRNA-1;Parent=Msa0796700;Name=Msa0796700-mRNA-1;_AED=0.49;_eAED=0.51;_QI=0|0|0|1|1|1|2|0|74
chr5_3 exon 8692545 8692550 8692545 ID=Msa0796700-mRNA-1:exon:3719;Parent=Msa0796700-mRNA-1
chr5_3 exon 8692268 8692486 8692268 ID=Msa0796700-mRNA-1:exon:3718;Parent=Msa0796700-mRNA-1
chr5_3 CDS 8692545 8692550 8692545 ID=Msa0796700-mRNA-1:cds;Parent=Msa0796700-mRNA-1
chr5_3 CDS 8692268 8692486 8692268 ID=Msa0796700-mRNA-1:cds;Parent=Msa0796700-mRNA-1
Gene Sequence

>Msa0796700

ATGATGTGTTCAACAAGTATAGGAACAGTTCCATTGGCATGTGAAAAGAATGGTGTTGCAAAGAGAAAGGCATTGACAGAAGCAACCAATTTTCAACAGTCAAATATCACGGAGATTACAGGGAAATGGCAATGCCCACAGAAACGTAAACCTGACCGTAGGCCTGCTTTGAAGCAACCTAGGCTTAAGAGATGGGTTCATAAGGTTGGAAAGATCTCTCAGTGA

Protein sequence

>Msa0796700

MMCSTSIGTVPLACEKNGVAKRKALTEATNFQQSNITEITGKWQCPQKRKPDRRPALKQPRLKRWVHKVGKISQ*