AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0489790


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0489790 MtrunA17_Chr1g0175161 91.304 46 4 0 1 46 269 314 1.86e-22 87.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAATTTCTAGTGTCAGTTT+TGG 0.313511 3_4:-10487470 Msa0489790:intron
GGAGGAGGGAAAAGCTTTGA+GGG 0.400312 3_4:-10487776 Msa0489790:CDS
TGGAGGAGGGAAAAGCTTTG+AGG 0.441086 3_4:-10487777 Msa0489790:CDS
AGAAAGAATGAGAAGAAAAC+CGG 0.442575 3_4:-10487752 Msa0489790:CDS
GGAATGATGTGGAGGATCTT+CGG 0.463224 3_4:-10487823 Msa0489790:CDS
GGAGAGAATTCACTAGTGTA+AGG 0.470518 3_4:-10487802 Msa0489790:CDS
GAGGCAAATGGAGGTTCTGC+AGG 0.475327 3_4:-10487864 None:intergenic
GAGGTTCTGCAGGCGGAGAA+TGG 0.475648 3_4:-10487854 Msa0489790:CDS
TTCACTAGTGTAAGGATTGG+AGG 0.529400 3_4:-10487794 Msa0489790:CDS
GAATTCACTAGTGTAAGGAT+TGG 0.533076 3_4:-10487797 Msa0489790:CDS
ACTAGTGTAAGGATTGGAGG+AGG 0.570999 3_4:-10487791 Msa0489790:CDS
GAGGAGGGAAAAGCTTTGAG+GGG 0.601233 3_4:-10487775 Msa0489790:CDS
TGGATTGCTGAGGAATGATG+TGG 0.628104 3_4:-10487834 Msa0489790:CDS
GCAAATGGAGGTTCTGCAGG+CGG 0.640904 3_4:-10487861 None:intergenic
GAAAGAATGAGAAGAAAACC+GGG 0.648044 3_4:-10487751 Msa0489790:intron
AGGCGGAGAATGGATTGCTG+AGG 0.664151 3_4:-10487844 Msa0489790:CDS
CTAGTGTAAGGATTGGAGGA+GGG 0.671920 3_4:-10487790 Msa0489790:CDS
ATTGCTGAGGAATGATGTGG+AGG 0.720743 3_4:-10487831 Msa0489790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTGTTTATAATATATC+TGG - chr3_4:10487740-10487759 Msa0489790:intron 10.0%
!! TTTGTTTATAATATATCTGG+TGG - chr3_4:10487743-10487762 Msa0489790:intron 20.0%
! GAATTCAAAATAGATGTAGT+CGG - chr3_4:10487626-10487645 Msa0489790:intron 25.0%
AGAAAGAATGAGAAGAAAAC+CGG - chr3_4:10487508-10487527 Msa0489790:intron 30.0%
!!! CAAATTTCTAGTGTCAGTTT+TGG - chr3_4:10487790-10487809 Msa0489790:CDS 30.0%
GAATTCACTAGTGTAAGGAT+TGG - chr3_4:10487463-10487482 Msa0489790:intron 35.0%
GAAAGAATGAGAAGAAAACC+GGG - chr3_4:10487509-10487528 Msa0489790:intron 35.0%
ATAACCACTAAAATCTGACC+CGG + chr3_4:10487530-10487549 None:intergenic 35.0%
!! TCAGATTTTAGTGGTTATCC+TGG - chr3_4:10487532-10487551 Msa0489790:intron 35.0%
!! CAGATTTTAGTGGTTATCCT+GGG - chr3_4:10487533-10487552 Msa0489790:intron 35.0%
! AATAGATGTAGTCGGCTTTA+TGG - chr3_4:10487634-10487653 Msa0489790:intron 35.0%
TCCTATCTTTCGTAACCTAA+CGG + chr3_4:10487676-10487695 None:intergenic 35.0%
CAGTTCGACAAGAATTCAAA+CGG + chr3_4:10487706-10487725 None:intergenic 35.0%
GGAGAGAATTCACTAGTGTA+AGG - chr3_4:10487458-10487477 Msa0489790:CDS 40.0%
TTCACTAGTGTAAGGATTGG+AGG - chr3_4:10487466-10487485 Msa0489790:intron 40.0%
! AAAACCGGGTCAGATTTTAG+TGG - chr3_4:10487523-10487542 Msa0489790:intron 40.0%
TTGAATTCAAGCTCCAACAG+TGG + chr3_4:10487614-10487633 None:intergenic 40.0%
ACCGTTAGGTTACGAAAGAT+AGG - chr3_4:10487672-10487691 Msa0489790:intron 40.0%
! GACAAGAATTCAAACGGACT+TGG + chr3_4:10487700-10487719 None:intergenic 40.0%
TGGATTGCTGAGGAATGATG+TGG - chr3_4:10487426-10487445 Msa0489790:CDS 45.0%
ATTGCTGAGGAATGATGTGG+AGG - chr3_4:10487429-10487448 Msa0489790:CDS 45.0%
GGAATGATGTGGAGGATCTT+CGG - chr3_4:10487437-10487456 Msa0489790:CDS 45.0%
ACTAGTGTAAGGATTGGAGG+AGG - chr3_4:10487469-10487488 Msa0489790:intron 45.0%
CTAGTGTAAGGATTGGAGGA+GGG - chr3_4:10487470-10487489 Msa0489790:intron 45.0%
TTATCCTGGGAAATCGACTG+AGG - chr3_4:10487546-10487565 Msa0489790:intron 45.0%
AATTCAAGCTCCAACAGTGG+TGG + chr3_4:10487611-10487630 None:intergenic 45.0%
TGGAGGAGGGAAAAGCTTTG+AGG - chr3_4:10487483-10487502 Msa0489790:intron 50.0%
! GGAGGAGGGAAAAGCTTTGA+GGG - chr3_4:10487484-10487503 Msa0489790:intron 50.0%
!! GAGGAGGGAAAAGCTTTGAG+GGG - chr3_4:10487485-10487504 Msa0489790:intron 50.0%
TGCGAGCAAGGAATTGGAGA+AGG - chr3_4:10487573-10487592 Msa0489790:intron 50.0%
!! AGGAATTGGAGAAGGCGTTG+AGG - chr3_4:10487581-10487600 Msa0489790:intron 50.0%
!! GGAATTGGAGAAGGCGTTGA+GGG - chr3_4:10487582-10487601 Msa0489790:intron 50.0%
!! GAATTGGAGAAGGCGTTGAG+GGG - chr3_4:10487583-10487602 Msa0489790:intron 50.0%
GCAGTCAATTGCAGACCGTT+AGG - chr3_4:10487658-10487677 Msa0489790:intron 50.0%
!! AGGCGGAGAATGGATTGCTG+AGG - chr3_4:10487416-10487435 Msa0489790:CDS 55.0%
! TCAGCCTCAGTCGATTTCCC+AGG + chr3_4:10487553-10487572 None:intergenic 55.0%
GGCTGATGCGAGCAAGGAAT+TGG - chr3_4:10487567-10487586 Msa0489790:intron 55.0%
GAGGTTCTGCAGGCGGAGAA+TGG - chr3_4:10487406-10487425 Msa0489790:CDS 60.0%
GACTGAGGCTGATGCGAGCA+AGG - chr3_4:10487561-10487580 Msa0489790:intron 60.0%
TTGAGGGGAGCCACCACTGT+TGG - chr3_4:10487598-10487617 Msa0489790:intron 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 10487403 10487879 10487403 ID=Msa0489790;Name=Msa0489790
chr3_4 mRNA 10487403 10487879 10487403 ID=Msa0489790-mRNA-1;Parent=Msa0489790;Name=Msa0489790-mRNA-1;_AED=0.60;_eAED=0.60;_QI=0|0|0|0.5|1|1|2|0|68
chr3_4 exon 10487752 10487879 10487752 ID=Msa0489790-mRNA-1:exon:3454;Parent=Msa0489790-mRNA-1
chr3_4 exon 10487403 10487481 10487403 ID=Msa0489790-mRNA-1:exon:3453;Parent=Msa0489790-mRNA-1
chr3_4 CDS 10487752 10487879 10487752 ID=Msa0489790-mRNA-1:cds;Parent=Msa0489790-mRNA-1
chr3_4 CDS 10487403 10487481 10487403 ID=Msa0489790-mRNA-1:cds;Parent=Msa0489790-mRNA-1
Gene Sequence

>Msa0489790

ATGGAGGTTCTGCAGGCGGAGAATGGATTGCTGAGGAATGATGTGGAGGATCTTCGGAGAGAATTCACTAGTGTAAGGATTGGAGGAGGGAAAAGCTTTGAGGGGAGAAAGAATGAGAAGAAAACCGGTGTCAGTTTTGGAACTGCAAATTTACTTTATTGTCATATGAATAATGATGATATGAATGATGATGATATAAATATGTGA

Protein sequence

>Msa0489790

MEVLQAENGLLRNDVEDLRREFTSVRIGGGKSFEGRKNEKKTGVSFGTANLLYCHMNNDDMNDDDINM*