AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0584810

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0584810 MtrunA17_Chr4g0019481 83.761 117 18 1 1 116 1 117 5.95e-61 182
Msa0584810 MtrunA17_Chr4g0019471 74.809 131 18 2 1 116 1 131 1.85e-56 171
Msa0584810 MtrunA17_Chr4g0019551 76.068 117 27 1 1 116 1 117 8.18e-46 144
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 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGGTTCAGGCTGGTTATT+TGG 0.175696 4_2:-4883062 None:intergenic
TCTCATTCATCTGGTGTATA+AGG 0.203991 4_2:-4883263 None:intergenic
CTTGATTCTAATATATAATC+TGG 0.305373 4_2:-4883023 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.375685 4_2:-4883262 None:intergenic
TCAGGCTGGTTATTTGGTGG+TGG 0.452210 4_2:-4883056 None:intergenic
TTGAGGTCGAAAGCTTGAAC+AGG 0.493044 4_2:-4883236 None:intergenic
GGAGGCTGGTTCAAGTCAAA+TGG 0.506887 4_2:-4883215 None:intergenic
GGTTCAGGCTGGTTATTTGG+TGG 0.509510 4_2:-4883059 None:intergenic
CGAAAGCTTGAACAGGAGGC+TGG 0.520977 4_2:-4883229 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4_2:-4883203 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4_2:-4883197 None:intergenic
ACTGTTAAAGCTTCTCGAGA+TGG 0.587984 4_2:-4882978 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4_2:-4883253 None:intergenic
AGGTCGAAAGCTTGAACAGG+AGG 0.614849 4_2:-4883233 None:intergenic
ATATTAGAATCAAGTAAACA+AGG 0.665430 4_2:+4883032 Msa0584810:CDS
TCAAATGGTTGCACATGTGG+AGG 0.671560 4_2:-4883200 None:intergenic
TCAAAGCTAGAATTCTTATG+CGG 0.715209 4_2:+4882936 Msa0584810:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTTGATTCTAATATATAATC+TGG - chr4_2:4883026-4883045 None:intergenic 20.0%
!! ATATTAGAATCAAGTAAACA+AGG + chr4_2:4883032-4883051 Msa0584810:CDS 20.0%
TCAAAGCTAGAATTCTTATG+CGG + chr4_2:4882936-4882955 Msa0584810:CDS 30.0%
! TGTTCAACATTTTGTGGTTG+AGG - chr4_2:4883098-4883117 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG - chr4_2:4883104-4883123 None:intergenic 35.0%
! TGATGTTCAACATTTTGTGG+TGG - chr4_2:4883101-4883120 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG - chr4_2:4883104-4883123 None:intergenic 35.0%
ACTGTTAAAGCTTCTCGAGA+TGG - chr4_2:4882981-4883000 None:intergenic 40.0%
AAGTCAAATGGTTGCACATG+TGG - chr4_2:4883206-4883225 None:intergenic 40.0%
! TCTGGTTCAGGCTGGTTATT+TGG - chr4_2:4883065-4883084 None:intergenic 45.0%
!! TCAACATTTTGTGGTGGAGC+TGG - chr4_2:4883137-4883156 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG - chr4_2:4883203-4883222 None:intergenic 45.0%
TTGAGGTCGAAAGCTTGAAC+AGG - chr4_2:4883239-4883258 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG - chr4_2:4883256-4883275 None:intergenic 45.0%
! TCAGGCTGGTTATTTGGTGG+TGG - chr4_2:4883059-4883078 None:intergenic 50.0%
! GGTTCAGGCTGGTTATTTGG+TGG - chr4_2:4883062-4883081 None:intergenic 50.0%
!!! GAGCATTTTCTGGTTCAGGC+TGG - chr4_2:4883073-4883092 None:intergenic 50.0%
!!! GGCTGAGCATTTTCTGGTTC+AGG - chr4_2:4883077-4883096 None:intergenic 50.0%
! GGTTGAGGCTGAGCATTTTC+TGG - chr4_2:4883083-4883102 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG - chr4_2:4883188-4883207 None:intergenic 50.0%
AATGGTTGCACATGTGGAGG+TGG - chr4_2:4883200-4883219 None:intergenic 50.0%
! GGAGGCTGGTTCAAGTCAAA+TGG - chr4_2:4883218-4883237 None:intergenic 50.0%
AGGTCGAAAGCTTGAACAGG+AGG - chr4_2:4883236-4883255 None:intergenic 50.0%
! GGTGGAGCTGGTGCATTTTG+TGG - chr4_2:4883125-4883144 None:intergenic 55.0%
! GGTGGAGCTGGTGCATTTTG+TGG - chr4_2:4883125-4883144 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG - chr4_2:4883179-4883198 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG - chr4_2:4883185-4883204 None:intergenic 55.0%
CGAAAGCTTGAACAGGAGGC+TGG - chr4_2:4883232-4883251 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 4882933 4883283 4882933 ID=Msa0584810;Name=Msa0584810
chr4_2 mRNA 4882933 4883283 4882933 ID=Msa0584810-mRNA-1;Parent=Msa0584810;Name=Msa0584810-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|116
chr4_2 exon 4882933 4883283 4882933 ID=Msa0584810-mRNA-1:exon:1217;Parent=Msa0584810-mRNA-1
chr4_2 CDS 4882933 4883283 4882933 ID=Msa0584810-mRNA-1:cds;Parent=Msa0584810-mRNA-1
Gene Sequence

>Msa0584810

ATGTCAAAGCTAGAATTCTTATGCGGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAACAGTGCATGTTATCGAAGAACATCATCCAGATTATATATTAGAATCAAGTAAACAAGGTCCACCACCAAATAACCAGCCTGAACCAGAAAATGCTCAGCCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAGCCTCCTGTTCAAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>Msa0584810

MSKLEFLCGECDTMFPSREALTVHVIEEHHPDYILESSKQGPPPNNQPEPENAQPQPQNVEHQPQNAPAPPQNVEHQPQNAPAPPQNAPPPHVQPFDLNQPPVQAFDLNLPYTPDE*