AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0582850


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582850 MtrunA17_CPg0492821 100.000 83 0 0 1 83 1 83 5.28e-56 167
Msa0582850 MtrunA17_Chr4g0016851 100.000 83 0 0 1 83 1 83 5.28e-56 167
Msa0582850 MtrunA17_Chr4g0015751 100.000 83 0 0 1 83 1 83 5.28e-56 167
Msa0582850 MtrunA17_Chr4g0017011 97.468 79 2 0 1 79 1 79 4.69e-52 157
Msa0582850 MtrunA17_Chr5g0423051 98.684 76 1 0 1 76 1 76 1.14e-49 151
Msa0582850 MtrunA17_Chr6g0451331 94.737 38 2 0 24 61 41 78 2.48e-20 77.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582850 ATCG00580.1 97.590 83 2 0 1 83 1 83 6.85e-55 164

Find 22 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTAGCTTACGATGTATT+TGG 0.244623 4_2:-1264106 Msa0582850:CDS
TCAAAACGGCCAGTTATTAA+TGG 0.307608 4_2:+1264037 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 4_2:+1264140 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 4_2:-1264189 Msa0582850:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 4_2:-1264241 None:intergenic
ATACCCTCCCTATTCATTGC+GGG 0.391873 4_2:-1264148 Msa0582850:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 4_2:+1264141 None:intergenic
CTTTCTGTAAAATACTCGTT+TGG 0.412027 4_2:+1264073 None:intergenic
CAAGGAATTCCATTAATAAC+TGG 0.412082 4_2:-1264046 Msa0582850:CDS
AATAATCCAGTATCGAATAC+TGG 0.423687 4_2:+1264183 None:intergenic
TTATTAATGGAATTCCTTGT+CGG 0.434610 4_2:+1264050 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 4_2:-1264232 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 4_2:-1264127 Msa0582850:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 4_2:+1264078 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 4_2:+1264079 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 4_2:-1264128 Msa0582850:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 4_2:-1264144 Msa0582850:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 4_2:+1264077 None:intergenic
GTTGTTCCAAAGAATCAAAA+CGG 0.551629 4_2:+1264023 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 4_2:-1264149 Msa0582850:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 4_2:+1264145 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 4_2:+1264144 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTATTAATGGAATTCCTTGT+CGG + chr4_2:1264176-1264195 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - chr4_2:1264034-1264053 Msa0582850:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + chr4_2:1264043-1264062 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + chr4_2:1264153-1264172 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - chr4_2:1264177-1264196 Msa0582850:CDS 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + chr4_2:1264203-1264222 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - chr4_2:1264117-1264136 Msa0582850:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG + chr4_2:1264148-1264167 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + chr4_2:1264149-1264168 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - chr4_2:1264159-1264178 Msa0582850:CDS 35.0%
TCAAAACGGCCAGTTATTAA+TGG + chr4_2:1264189-1264208 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - chr4_2:1264074-1264093 Msa0582850:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + chr4_2:1264085-1264104 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + chr4_2:1264086-1264105 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + chr4_2:1264147-1264166 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - chr4_2:1264194-1264213 Msa0582850:CDS 40.0%
ATACCCTCCCTATTCATTGC+GGG - chr4_2:1264075-1264094 Msa0582850:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - chr4_2:1264095-1264114 Msa0582850:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - chr4_2:1264096-1264115 Msa0582850:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + chr4_2:1264081-1264100 None:intergenic 50.0%
CCAACCCGCAATGAATAGGG+AGG + chr4_2:1264082-1264101 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - chr4_2:1264079-1264098 Msa0582850:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 1263997 1264248 1263997 ID=Msa0582850;Name=Msa0582850
chr4_2 mRNA 1263997 1264248 1263997 ID=Msa0582850-mRNA-1;Parent=Msa0582850;Name=Msa0582850-mRNA-1;_AED=0.26;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|83
chr4_2 exon 1263997 1264248 1263997 ID=Msa0582850-mRNA-1:exon:281;Parent=Msa0582850-mRNA-1
chr4_2 CDS 1263997 1264248 1263997 ID=Msa0582850-mRNA-1:cds;Parent=Msa0582850-mRNA-1
Gene Sequence

>Msa0582850

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGAGTATTTTACAGAAAGCCGACAAGGAATTCCATTAATAACTGGCCGTTTTGATTCTTTGGAACAACTCGATGAATTTAGTAGATCTTTTTAG

Protein sequence

>Msa0582850

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNEYFTESRQGIPLITGRFDSLEQLDEFSRSF*