AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1435820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1435820 MtrunA17_Chr3g0141141 85.057 87 7 1 4 90 1 81 4.22e-47 145
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGGGTTGCTTTCATGCTT+TGG 0.283837 tig0027777:+24405 Msa1435820:CDS
TTAGCTAGCAATGGAAAGTT+TGG 0.296785 tig0027777:+24341 None:intergenic
GAGGGTTGCTTTCATGCTTT+GGG 0.333399 tig0027777:+24406 Msa1435820:CDS
TTGTTTGTTCTCCTCTTCCA+TGG 0.436490 tig0027777:-24447 None:intergenic
GAGGACGACGAAGAATCTTT+AGG 0.441691 tig0027777:+24546 Msa1435820:CDS
TCTCCTATAAGAAGCAAAAC+AGG 0.462208 tig0027777:+24378 Msa1435820:CDS
AGAAGCAAAACAGGTGGAGG+AGG 0.521376 tig0027777:+24387 Msa1435820:CDS
TGATGATGGTAATTTGGAGG+AGG 0.522189 tig0027777:+24527 Msa1435820:CDS
AACACTTATAGAACCGTTGG+TGG 0.530511 tig0027777:+24468 Msa1435820:CDS
AATTGAAGCTTCCATGGAAG+AGG 0.536567 tig0027777:+24436 Msa1435820:CDS
AACAACACTTATAGAACCGT+TGG 0.561342 tig0027777:+24465 Msa1435820:CDS
GTCTCAAATTGAAGCTTCCA+TGG 0.569556 tig0027777:+24430 Msa1435820:CDS
ATAAGAAGCAAAACAGGTGG+AGG 0.576069 tig0027777:+24384 Msa1435820:CDS
GACGAAGAATCTTTAGGTCG+CGG 0.579606 tig0027777:+24552 Msa1435820:CDS
ATCATACCTAAAACCACCAA+CGG 0.621720 tig0027777:-24481 None:intergenic
TTGCTTCTTATAGGAGACGA+TGG 0.630393 tig0027777:-24372 None:intergenic
GAAGCAAAACAGGTGGAGGA+GGG 0.645020 tig0027777:+24388 Msa1435820:CDS
CCTATAAGAAGCAAAACAGG+TGG 0.657762 tig0027777:+24381 Msa1435820:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTTGATGATGGTAATT+TGG + tig0027777:24521-24540 Msa1435820:CDS 20.0%
!! AAATTTTGAGCATAGCTTAA+AGG - tig0027777:24507-24526 None:intergenic 25.0%
!!! TATGCTCAAAATTTTGATGA+TGG + tig0027777:24513-24532 Msa1435820:CDS 25.0%
!!! TTTTGATGATGGTAATTTGG+AGG + tig0027777:24524-24543 Msa1435820:CDS 30.0%
TCTCCTATAAGAAGCAAAAC+AGG + tig0027777:24378-24397 Msa1435820:CDS 35.0%
AACAACACTTATAGAACCGT+TGG + tig0027777:24465-24484 Msa1435820:CDS 35.0%
ATCATACCTAAAACCACCAA+CGG - tig0027777:24484-24503 None:intergenic 35.0%
TTGCTTCTTATAGGAGACGA+TGG - tig0027777:24375-24394 None:intergenic 40.0%
! CCACCTGTTTTGCTTCTTAT+AGG - tig0027777:24384-24403 None:intergenic 40.0%
CCTATAAGAAGCAAAACAGG+TGG + tig0027777:24381-24400 Msa1435820:CDS 40.0%
ATAAGAAGCAAAACAGGTGG+AGG + tig0027777:24384-24403 Msa1435820:CDS 40.0%
GTCTCAAATTGAAGCTTCCA+TGG + tig0027777:24430-24449 Msa1435820:CDS 40.0%
AATTGAAGCTTCCATGGAAG+AGG + tig0027777:24436-24455 Msa1435820:CDS 40.0%
TTGTTTGTTCTCCTCTTCCA+TGG - tig0027777:24450-24469 None:intergenic 40.0%
AACACTTATAGAACCGTTGG+TGG + tig0027777:24468-24487 Msa1435820:CDS 40.0%
!!! ATAGAACCGTTGGTGGTTTT+AGG + tig0027777:24475-24494 Msa1435820:CDS 40.0%
!! TGATGATGGTAATTTGGAGG+AGG + tig0027777:24527-24546 Msa1435820:CDS 40.0%
!!! TGCTTGAGTGTTTTAGCTGA+AGG - tig0027777:24600-24619 None:intergenic 40.0%
! GAGGGTTGCTTTCATGCTTT+GGG + tig0027777:24406-24425 Msa1435820:CDS 45.0%
GAGGACGACGAAGAATCTTT+AGG + tig0027777:24546-24565 Msa1435820:CDS 45.0%
GACGAAGAATCTTTAGGTCG+CGG + tig0027777:24552-24571 Msa1435820:CDS 45.0%
AGAAGCAAAACAGGTGGAGG+AGG + tig0027777:24387-24406 Msa1435820:CDS 50.0%
GAAGCAAAACAGGTGGAGGA+GGG + tig0027777:24388-24407 Msa1435820:CDS 50.0%
! GGAGGGTTGCTTTCATGCTT+TGG + tig0027777:24405-24424 Msa1435820:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0027777 gene 24351 24623 24351 ID=Msa1435820;Name=Msa1435820
tig0027777 mRNA 24351 24623 24351 ID=Msa1435820-mRNA-1;Parent=Msa1435820;Name=Msa1435820-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|90
tig0027777 exon 24351 24623 24351 ID=Msa1435820-mRNA-1:exon:9904;Parent=Msa1435820-mRNA-1
tig0027777 CDS 24351 24623 24351 ID=Msa1435820-mRNA-1:cds;Parent=Msa1435820-mRNA-1
Gene Sequence

>Msa1435820

ATGGAAAGTTTGGAAACAAGTCCATCGTCTCCTATAAGAAGCAAAACAGGTGGAGGAGGGTTGCTTTCATGCTTTGGGCGTCTCAAATTGAAGCTTCCATGGAAGAGGAGAACAAACAACACTTATAGAACCGTTGGTGGTTTTAGGTATGATCCTTTAAGCTATGCTCAAAATTTTGATGATGGTAATTTGGAGGAGGACGACGAAGAATCTTTAGGTCGCGGTTTCTCTGCTAGATATGCTGCACCTTCAGCTAAAACACTCAAGCAATGA

Protein sequence

>Msa1435820

MESLETSPSSPIRSKTGGGGLLSCFGRLKLKLPWKRRTNNTYRTVGGFRYDPLSYAQNFDDGNLEEDDEESLGRGFSARYAAPSAKTLKQ*