AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268910


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268910 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268910 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268910 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268910 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0268910 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0268910 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0268910 MtrunA17_Chr6g0451331 90.323 31 3 0 24 54 41 71 5.28e-14 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268910 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0268910 ATCG00560.1 97.297 37 1 0 68 104 2 38 3.75e-19 73.9

Find 27 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTAGCTTACGATGTATT+TGG 0.244623 2_2:+70445750 Msa0268910:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 2_2:-70446012 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 2_2:-70445716 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 2_2:+70445667 Msa0268910:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 2_2:+70445615 Msa0268910:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 2_2:+70445708 Msa0268910:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 2_2:-70445715 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 2_2:+70446070 Msa0268910:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 2_2:-70445783 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 2_2:-70446018 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 2_2:-70445673 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 2_2:+70445624 Msa0268910:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 2_2:-70446001 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 2_2:+70446071 Msa0268910:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 2_2:+70445599 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 2_2:+70445729 Msa0268910:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 2_2:-70445778 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 2_2:-70445777 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 2_2:+70445728 Msa0268910:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 2_2:+70445712 Msa0268910:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 2_2:-70445779 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 2_2:-70446079 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 2_2:+70445606 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 2_2:+70445707 Msa0268910:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 2_2:-70445711 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 2_2:-70445712 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 2_2:+70446072 Msa0268910:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr2_2:70445860-70445879 Msa0268910:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr2_2:70446050-70446069 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr2_2:70446051-70446070 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr2_2:70445809-70445828 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr2_2:70445863-70445882 Msa0268910:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr2_2:70445964-70445983 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr2_2:70445667-70445686 Msa0268910:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr2_2:70445676-70445695 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr2_2:70445786-70445805 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr2_2:70445810-70445829 Msa0268910:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr2_2:70445836-70445855 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr2_2:70445915-70445934 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr2_2:70445750-70445769 Msa0268910:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr2_2:70445781-70445800 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr2_2:70445782-70445801 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr2_2:70445792-70445811 Msa0268910:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr2_2:70445822-70445841 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr2_2:70445910-70445929 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr2_2:70445910-70445929 Msa0268910:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr2_2:70445916-70445935 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr2_2:70445914-70445933 Msa0268910:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr2_2:70446004-70446023 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr2_2:70446015-70446034 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr2_2:70446021-70446040 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr2_2:70445707-70445726 Msa0268910:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr2_2:70445718-70445737 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr2_2:70445719-70445738 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr2_2:70445780-70445799 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr2_2:70445827-70445846 Msa0268910:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr2_2:70445891-70445910 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr2_2:70445898-70445917 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr2_2:70445954-70445973 Msa0268910:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr2_2:70445960-70445979 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr2_2:70445961-70445980 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr2_2:70446082-70446101 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr2_2:70445708-70445727 Msa0268910:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr2_2:70445728-70445747 Msa0268910:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr2_2:70445729-70445748 Msa0268910:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr2_2:70445883-70445902 Msa0268910:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr2_2:70445953-70445972 Msa0268910:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr2_2:70446070-70446089 Msa0268910:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr2_2:70446071-70446090 Msa0268910:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr2_2:70446072-70446091 Msa0268910:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr2_2:70445714-70445733 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr2_2:70445924-70445943 Msa0268910:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr2_2:70445615-70445634 Msa0268910:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr2_2:70445715-70445734 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr2_2:70445712-70445731 Msa0268910:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr2_2:70445932-70445951 Msa0268910:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr2_2:70445624-70445643 Msa0268910:exon 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70445613 70446146 70445613 ID=Msa0268910;Name=Msa0268910
chr2_2 mRNA 70445613 70446146 70445613 ID=Msa0268910-mRNA-1;Parent=Msa0268910;Name=Msa0268910-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr2_2 exon 70445613 70445790 70445613 ID=Msa0268910-mRNA-1:exon:22688;Parent=Msa0268910-mRNA-1
chr2_2 exon 70445996 70446146 70445996 ID=Msa0268910-mRNA-1:exon:22689;Parent=Msa0268910-mRNA-1
chr2_2 five_prime_UTR 70445613 70445629 70445613 ID=Msa0268910-mRNA-1:five_prime_utr;Parent=Msa0268910-mRNA-1
chr2_2 CDS 70445630 70445790 70445630 ID=Msa0268910-mRNA-1:cds;Parent=Msa0268910-mRNA-1
chr2_2 CDS 70445996 70446146 70445996 ID=Msa0268910-mRNA-1:cds;Parent=Msa0268910-mRNA-1
Gene Sequence

>Msa0268910

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0268910

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN