AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1205520


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1205520 MtrunA17_Chr4g0054781 100.000 89 0 0 12 100 141 229 3.75e-59 181
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1205520 AT1G32520.1 86.517 89 12 0 12 100 151 239 1.94e-50 159

Find 32 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTCGTGGTGGGCCGCAATT+TGG 0.091289 8_1:-61870756 Msa1205520:CDS
CTAGTATAAGCTTGCAATTT+TGG 0.186690 8_1:+61870530 None:intergenic
CTCGTGGTGGGCCGCAATTT+GGG 0.206328 8_1:-61870755 Msa1205520:CDS
GCTGGGCCTGATACTAATTC+TGG 0.242393 8_1:-61870681 Msa1205520:CDS
CTCCTTGCCATCTTCCCTTT+TGG 0.242724 8_1:+61870611 None:intergenic
CCAGCAAAACCACCCATAAC+TGG 0.267578 8_1:+61870699 None:intergenic
CACCCATAACTGGGGCTAAT+GGG 0.279555 8_1:+61870709 None:intergenic
GGGCTGATGGGCTTCTCATC+GGG 0.321712 8_1:-61870734 Msa1205520:CDS
CCACCCATAACTGGGGCTAA+TGG 0.338213 8_1:+61870708 None:intergenic
GGGCCGCAATTTGGGGCTGA+TGG 0.348553 8_1:-61870747 Msa1205520:CDS
GGGGCTGATGGGCTTCTCAT+CGG 0.364017 8_1:-61870735 Msa1205520:CDS
GAGACAAGCCAAGTCTAGAT+TGG 0.419344 8_1:-61870646 Msa1205520:CDS
GGCCGCAATTTGGGGCTGAT+GGG 0.455119 8_1:-61870746 Msa1205520:CDS
AGACAAGCCAAGTCTAGATT+GGG 0.460900 8_1:-61870645 Msa1205520:CDS
TGGGATTGTCTTATGCCAAA+AGG 0.463760 8_1:-61870626 Msa1205520:CDS
CAGCAAAACCACCCATAACT+GGG 0.479885 8_1:+61870700 None:intergenic
CCAACACCAGAATTAGTATC+AGG 0.485918 8_1:+61870675 None:intergenic
GGGATTGTCTTATGCCAAAA+GGG 0.500151 8_1:-61870625 Msa1205520:CDS
ACCCATAACTGGGGCTAATG+GGG 0.505857 8_1:+61870710 None:intergenic
TCGTGGTGGGCCGCAATTTG+GGG 0.534768 8_1:-61870754 Msa1205520:CDS
TCTTATGCCAAAAGGGAAGA+TGG 0.539221 8_1:-61870618 Msa1205520:CDS
CTGTTTGATTATGCTCGTGG+TGG 0.546126 8_1:-61870768 Msa1205520:CDS
CCTGATACTAATTCTGGTGT+TGG 0.548121 8_1:-61870675 Msa1205520:CDS
TGCCAAAAGGGAAGATGGCA+AGG 0.559565 8_1:-61870613 Msa1205520:CDS
TAGGGCAACTATTCAAGAAG+TGG 0.560250 8_1:-61870568 Msa1205520:CDS
CCATTAGCCCCAGTTATGGG+TGG 0.560552 8_1:-61870708 Msa1205520:CDS
AGCCCATCAGCCCCAAATTG+CGG 0.561376 8_1:+61870744 None:intergenic
TGTTTGATTATGCTCGTGGT+GGG 0.570159 8_1:-61870767 Msa1205520:CDS
AGACAATCCCAATCTAGACT+TGG 0.587589 8_1:+61870638 None:intergenic
CCCATAACTGGGGCTAATGG+GGG 0.595547 8_1:+61870711 None:intergenic
GCTCTGTTTGATTATGCTCG+TGG 0.617447 8_1:-61870771 Msa1205520:CDS
AGCAAAACCACCCATAACTG+GGG 0.696608 8_1:+61870701 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGATGCATTTCTATTTTAT+TGG - chr8_1:61870539-61870558 Msa1205520:CDS 20.0%
!!! TGATGCATTTCTATTTTATT+GGG - chr8_1:61870540-61870559 Msa1205520:CDS 20.0%
!! TAGTATAAGCTTGCAATTTT+GGG + chr8_1:61870859-61870878 None:intergenic 25.0%
! TGAACCAATAATTTTGCCTA+AGG - chr8_1:61870576-61870595 Msa1205520:CDS 30.0%
!!! TATTTTTGGTGATGAGTCTA+GGG - chr8_1:61870801-61870820 Msa1205520:intron 30.0%
! AGTATAAGCTTGCAATTTTG+GGG + chr8_1:61870858-61870877 None:intergenic 30.0%
! CTAGTATAAGCTTGCAATTT+TGG + chr8_1:61870860-61870879 None:intergenic 30.0%
CCAACCTTAGGCAAAATTAT+TGG + chr8_1:61870583-61870602 None:intergenic 35.0%
! CCAATAATTTTGCCTAAGGT+TGG - chr8_1:61870580-61870599 Msa1205520:CDS 35.0%
! ATAATTTTGCCTAAGGTTGG+TGG - chr8_1:61870583-61870602 Msa1205520:CDS 35.0%
!!! CTATTTTTGGTGATGAGTCT+AGG - chr8_1:61870800-61870819 Msa1205520:intron 35.0%
TGTTTGATTATGCTCGTGGT+GGG - chr8_1:61870620-61870639 Msa1205520:CDS 40.0%
CCAACACCAGAATTAGTATC+AGG + chr8_1:61870715-61870734 None:intergenic 40.0%
CCTGATACTAATTCTGGTGT+TGG - chr8_1:61870712-61870731 Msa1205520:CDS 40.0%
AGACAAGCCAAGTCTAGATT+GGG - chr8_1:61870742-61870761 Msa1205520:CDS 40.0%
AGACAATCCCAATCTAGACT+TGG + chr8_1:61870752-61870771 None:intergenic 40.0%
TGGGATTGTCTTATGCCAAA+AGG - chr8_1:61870761-61870780 Msa1205520:CDS 40.0%
GGGATTGTCTTATGCCAAAA+GGG - chr8_1:61870762-61870781 Msa1205520:CDS 40.0%
TCTTATGCCAAAAGGGAAGA+TGG - chr8_1:61870769-61870788 Msa1205520:CDS 40.0%
! GATGGCAAGGAGTCTATTTT+TGG - chr8_1:61870787-61870806 Msa1205520:intron 40.0%
TAGGGCAACTATTCAAGAAG+TGG - chr8_1:61870819-61870838 Msa1205520:intron 40.0%
GCTCTGTTTGATTATGCTCG+TGG - chr8_1:61870616-61870635 Msa1205520:CDS 45.0%
CTGTTTGATTATGCTCGTGG+TGG - chr8_1:61870619-61870638 Msa1205520:CDS 45.0%
AGCAAAACCACCCATAACTG+GGG + chr8_1:61870689-61870708 None:intergenic 45.0%
CAGCAAAACCACCCATAACT+GGG + chr8_1:61870690-61870709 None:intergenic 45.0%
!! CAGTTATGGGTGGTTTTGCT+GGG - chr8_1:61870689-61870708 Msa1205520:CDS 45.0%
GAGACAAGCCAAGTCTAGAT+TGG - chr8_1:61870741-61870760 Msa1205520:CDS 45.0%
ACCCATAACTGGGGCTAATG+GGG + chr8_1:61870680-61870699 None:intergenic 50.0%
CACCCATAACTGGGGCTAAT+GGG + chr8_1:61870681-61870700 None:intergenic 50.0%
CCAGCAAAACCACCCATAAC+TGG + chr8_1:61870691-61870710 None:intergenic 50.0%
!! CCAGTTATGGGTGGTTTTGC+TGG - chr8_1:61870688-61870707 Msa1205520:CDS 50.0%
GCTGGGCCTGATACTAATTC+TGG - chr8_1:61870706-61870725 Msa1205520:CDS 50.0%
TGCCAAAAGGGAAGATGGCA+AGG - chr8_1:61870774-61870793 Msa1205520:CDS 50.0%
! CTCCTTGCCATCTTCCCTTT+TGG + chr8_1:61870779-61870798 None:intergenic 50.0%
!! TTGCCTAAGGTTGGTGGCAG+TGG - chr8_1:61870589-61870608 Msa1205520:CDS 55.0%
AGCCCATCAGCCCCAAATTG+CGG + chr8_1:61870646-61870665 None:intergenic 55.0%
CCCATAACTGGGGCTAATGG+GGG + chr8_1:61870679-61870698 None:intergenic 55.0%
CCCCCATTAGCCCCAGTTAT+GGG - chr8_1:61870676-61870695 Msa1205520:CDS 55.0%
CCACCCATAACTGGGGCTAA+TGG + chr8_1:61870682-61870701 None:intergenic 55.0%
CCATTAGCCCCAGTTATGGG+TGG - chr8_1:61870679-61870698 Msa1205520:CDS 55.0%
GCACCACTGCCACCAACCTT+AGG + chr8_1:61870595-61870614 None:intergenic 60.0%
!! CTCGTGGTGGGCCGCAATTT+GGG - chr8_1:61870632-61870651 Msa1205520:CDS 60.0%
!! TCGTGGTGGGCCGCAATTTG+GGG - chr8_1:61870633-61870652 Msa1205520:CDS 60.0%
! GGCCGCAATTTGGGGCTGAT+GGG - chr8_1:61870641-61870660 Msa1205520:CDS 60.0%
!! GGGGCTGATGGGCTTCTCAT+CGG - chr8_1:61870652-61870671 Msa1205520:CDS 60.0%
!! GGGCTGATGGGCTTCTCATC+GGG - chr8_1:61870653-61870672 Msa1205520:CDS 60.0%
GCCCCCATTAGCCCCAGTTA+TGG - chr8_1:61870675-61870694 Msa1205520:CDS 60.0%
!! GCTCGTGGTGGGCCGCAATT+TGG - chr8_1:61870631-61870650 Msa1205520:CDS 65.0%
! GGGCCGCAATTTGGGGCTGA+TGG - chr8_1:61870640-61870659 Msa1205520:CDS 65.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 61870530 61870879 61870530 ID=Msa1205520;Name=Msa1205520
chr8_1 mRNA 61870530 61870879 61870530 ID=Msa1205520-mRNA-1;Parent=Msa1205520;Name=Msa1205520-mRNA-1;_AED=0.25;_eAED=0.33;_QI=0|0|0|1|0|0.5|2|0|100
chr8_1 exon 61870848 61870879 61870848 ID=Msa1205520-mRNA-1:exon:20064;Parent=Msa1205520-mRNA-1
chr8_1 exon 61870530 61870800 61870530 ID=Msa1205520-mRNA-1:exon:20063;Parent=Msa1205520-mRNA-1
chr8_1 CDS 61870848 61870879 61870848 ID=Msa1205520-mRNA-1:cds;Parent=Msa1205520-mRNA-1
chr8_1 CDS 61870530 61870800 61870530 ID=Msa1205520-mRNA-1:cds;Parent=Msa1205520-mRNA-1
Gene Sequence

>Msa1205520

ATGAAACATTTGATGCATTTCTATTTTATTGGTGGTGCAGCTCTGTTTGATTATGCTCGTGGTGGGCCGCAATTTGGGGCTGATGGGCTTCTCATCGGGCCCCCATTAGCCCCAGTTATGGGTGGTTTTGCTGGGCCTGATACTAATTCTGGTGTTGGTGACTTGAGACAAGCCAAGTCTAGATTGGGATTGTCTTATGCCAAAAGGGAAGATGGCAAGGAGTCTATTTTTGGTGATGAGTCTAGGGCAACTATTCAAGAAGTGGAAGTGTTTTGTAGCCCCAAAATTGCAAGCTTATACTAG

Protein sequence

>Msa1205520

MKHLMHFYFIGGAALFDYARGGPQFGADGLLIGPPLAPVMGGFAGPDTNSGVGDLRQAKSRLGLSYAKREDGKESIFGDESRATIQEVEVFCSPKIASLY*