AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0610370

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0610370 MtrunA17_Chr4g0043191 96.629 89 3 0 1 89 1 89 9.42e-58 172
Msa0610370 MtrunA17_Chr4g0043181 80.899 89 13 1 1 89 1 85 5.05e-40 127
Msa0610370 MtrunA17_Chr8g0376661 79.545 88 18 0 1 88 1 88 1.65e-36 118
Msa0610370 MtrunA17_Chr5g0434291 77.528 89 20 0 1 89 1 89 2.91e-36 117
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0610370 AT1G30260.1 60.417 48 18 1 1 48 1 47 3.72e-15 65.1

Find 12 sgRNAs with CRISPR-Local

Find 18 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAATGCAGTTGTTAATTCT+AGG 0.257861 4_2:-58070873 Msa0610370:CDS
AACAATCACTGAAGAGGATA+TGG 0.331678 4_2:-58070980 Msa0610370:CDS
GTGTTCTATGAACTTCCTTC+AGG 0.381163 4_2:+58070845 None:intergenic
GCGTAGAACATCAAAGATGA+TGG 0.510830 4_2:-58071004 Msa0610370:CDS
CCTAGAATTAACAACTGCAT+TGG 0.551602 4_2:+58070873 None:intergenic
AACAACTGCATTGGTAGAAG+AGG 0.557920 4_2:+58070882 None:intergenic
TGGCGAATTCTCGCATTGCA+AGG 0.566271 4_2:-58071071 Msa0610370:CDS
CACAGTATGTTAGCGTGATG+AGG 0.569645 4_2:-58071026 Msa0610370:CDS
TAATTCTAGGTACTTCCTGA+AGG 0.589595 4_2:-58070860 Msa0610370:CDS
GATGGAAACAATCACTGAAG+AGG 0.591147 4_2:-58070986 Msa0610370:CDS
CTCATCACGCTAACATACTG+TGG 0.654266 4_2:+58071027 None:intergenic
ATCACGCTAACATACTGTGG+TGG 0.690677 4_2:+58071030 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATGAAGTTGATGAACTTTT+AGG + chr4_2:58070975-58070994 None:intergenic 30.0%
AACAATCACTGAAGAGGATA+TGG - chr4_2:58070917-58070936 Msa0610370:CDS 35.0%
!!! GAAGTTGATGAACTTTTAGG+TGG + chr4_2:58070972-58070991 None:intergenic 35.0%
CCTAGAATTAACAACTGCAT+TGG + chr4_2:58071027-58071046 None:intergenic 35.0%
CCAATGCAGTTGTTAATTCT+AGG - chr4_2:58071024-58071043 Msa0610370:CDS 35.0%
TAATTCTAGGTACTTCCTGA+AGG - chr4_2:58071037-58071056 Msa0610370:CDS 35.0%
! TCGCATTGCAAGGTTTTTCA+TGG - chr4_2:58070836-58070855 Msa0610370:CDS 40.0%
! CATTGCAAGGTTTTTCATGG+AGG - chr4_2:58070839-58070858 Msa0610370:CDS 40.0%
GCGTAGAACATCAAAGATGA+TGG - chr4_2:58070893-58070912 Msa0610370:CDS 40.0%
GATGGAAACAATCACTGAAG+AGG - chr4_2:58070911-58070930 Msa0610370:CDS 40.0%
!! GTTGATGAACTTTTAGGTGG+TGG + chr4_2:58070969-58070988 None:intergenic 40.0%
! AACAACTGCATTGGTAGAAG+AGG + chr4_2:58071018-58071037 None:intergenic 40.0%
GTGTTCTATGAACTTCCTTC+AGG + chr4_2:58071055-58071074 None:intergenic 40.0%
! TGCAAGGTTTTTCATGGAGG+TGG - chr4_2:58070842-58070861 Msa0610370:CDS 45.0%
ATCACGCTAACATACTGTGG+TGG + chr4_2:58070870-58070889 None:intergenic 45.0%
CTCATCACGCTAACATACTG+TGG + chr4_2:58070873-58070892 None:intergenic 45.0%
CACAGTATGTTAGCGTGATG+AGG - chr4_2:58070871-58070890 Msa0610370:CDS 45.0%
TGGCGAATTCTCGCATTGCA+AGG - chr4_2:58070826-58070845 Msa0610370:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 58070825 58071094 58070825 ID=Msa0610370;Name=Msa0610370
chr4_2 mRNA 58070825 58071094 58070825 ID=Msa0610370-mRNA-1;Parent=Msa0610370;Name=Msa0610370-mRNA-1;_AED=0.27;_eAED=0.27;_QI=0|-1|0|1|-1|1|1|0|89
chr4_2 exon 58070825 58071094 58070825 ID=Msa0610370-mRNA-1:exon:15226;Parent=Msa0610370-mRNA-1
chr4_2 CDS 58070825 58071094 58070825 ID=Msa0610370-mRNA-1:cds;Parent=Msa0610370-mRNA-1
Gene Sequence

>Msa0610370

ATGGCGAATTCTCGCATTGCAAGGTTTTTCATGGAGGTGGCACCACCACAGTATGTTAGCGTGATGAGGCGTAGAACATCAAAGATGATGGAAACAATCACTGAAGAGGATATGGAAATGAGTTCAAATGATAGTGTAATTCCACCACCTAAAAGTTCATCAACTTCATCACTTGCTGCTTCTGCATGTGCCTCTTCTACCAATGCAGTTGTTAATTCTAGGTACTTCCTGAAGGAAGTTCATAGAACACTCTCAAGTTTGAATCACTGA
Protein sequence

>Msa0610370

MANSRIARFFMEVAPPQYVSVMRRRTSKMMETITEEDMEMSSNDSVIPPPKSSSTSSLAASACASSTNAVVNSRYFLKEVHRTLSSLNH*