AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0660820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 14 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTAAGAATGGCAAATTCT+CGG 0.400516 4_3:+71939558 None:intergenic
AAATTTGTTCACATTAAGAA+TGG 0.434907 4_3:+71939547 None:intergenic
GCTAATTTCCCTATCCTCTT+CGG 0.455895 4_3:-71939666 Msa0660820:CDS
AACAATTACCGAAGAGGATA+GGG 0.456653 4_3:+71939658 None:intergenic
CCAATGCAAGAGTTAATACT+AGG 0.491575 4_3:+71939765 None:intergenic
AAACAATTACCGAAGAGGAT+AGG 0.497703 4_3:+71939657 None:intergenic
GCATAGAACATCAAAGATGA+TGG 0.512561 4_3:+71939634 None:intergenic
AACTCTTGCATTGGTAGAAG+AGG 0.518867 4_3:-71939756 Msa0660820:CDS
TGGCAAATTCTCGGATTGCA+AGG 0.538859 4_3:+71939567 None:intergenic
CCTAGTATTAACTCTTGCAT+TGG 0.546926 4_3:-71939765 Msa0660820:CDS
CACAATATGTTTCTGTGATG+AGG 0.546938 4_3:+71939612 None:intergenic
CTCATCACAGAAACATATTG+TGG 0.621625 4_3:-71939611 Msa0660820:CDS
GATGGAAACAATTACCGAAG+AGG 0.634042 4_3:+71939652 None:intergenic
ATCACAGAAACATATTGTGG+TGG 0.672845 4_3:-71939608 Msa0660820:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTGTTCACATTAAGAA+TGG + chr4_3:71940043-71940062 None:intergenic 20.0%
! ACATAGCAAAATATATATGC+AGG - chr4_3:71939609-71939628 Msa0660820:CDS 25.0%
!! TTCAACGTTTTATATGAACA+AGG + chr4_3:71939674-71939693 None:intergenic 25.0%
GTTCATATAAAACGTTGAAC+AGG - chr4_3:71939675-71939694 Msa0660820:CDS 30.0%
! GAAATTGCAGATGAACTTTT+AGG - chr4_3:71939874-71939893 Msa0660820:intron 30.0%
CATTAAGAATGGCAAATTCT+CGG + chr4_3:71940032-71940051 None:intergenic 30.0%
GATATGTATGCCAAAACTTG+TGG - chr4_3:71939545-71939564 Msa0660820:CDS 35.0%
! CTCAAATCTACCACAAGTTT+TGG + chr4_3:71939558-71939577 None:intergenic 35.0%
ACAAGGATAGTTAAGACTTG+AGG + chr4_3:71939657-71939676 None:intergenic 35.0%
CAACTTTATATGCCTCAAAG+TGG - chr4_3:71939750-71939769 Msa0660820:CDS 35.0%
TGAACAATTGAACCACTTTG+AGG + chr4_3:71939765-71939784 None:intergenic 35.0%
CCAATGCAAGAGTTAATACT+AGG + chr4_3:71939825-71939844 None:intergenic 35.0%
CCTAGTATTAACTCTTGCAT+TGG - chr4_3:71939822-71939841 Msa0660820:intron 35.0%
AACAATTACCGAAGAGGATA+GGG + chr4_3:71939932-71939951 None:intergenic 35.0%
AAACAATTACCGAAGAGGAT+AGG + chr4_3:71939933-71939952 None:intergenic 35.0%
GCATAGAACATCAAAGATGA+TGG + chr4_3:71939956-71939975 None:intergenic 35.0%
! CACAATATGTTTCTGTGATG+AGG + chr4_3:71939978-71939997 None:intergenic 35.0%
CTCATCACAGAAACATATTG+TGG - chr4_3:71939976-71939995 Msa0660820:intron 35.0%
ATCACAGAAACATATTGTGG+TGG - chr4_3:71939979-71939998 Msa0660820:intron 35.0%
! AACTCTTGCATTGGTAGAAG+AGG - chr4_3:71939831-71939850 Msa0660820:intron 40.0%
GCTAATTTCCCTATCCTCTT+CGG - chr4_3:71939921-71939940 Msa0660820:intron 40.0%
GATGGAAACAATTACCGAAG+AGG + chr4_3:71939938-71939957 None:intergenic 40.0%
! TGCAAGGTTTTTCATGGAAG+TGG + chr4_3:71940007-71940026 None:intergenic 40.0%
! TCGGATTGCAAGGTTTTTCA+TGG + chr4_3:71940013-71940032 None:intergenic 40.0%
TGGCAAATTCTCGGATTGCA+AGG + chr4_3:71940023-71940042 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 71939511 71940098 71939511 ID=Msa0660820;Name=Msa0660820
chr4_3 mRNA 71939511 71940098 71939511 ID=Msa0660820-mRNA-1;Parent=Msa0660820;Name=Msa0660820-mRNA-1;_AED=0.61;_eAED=1.00;_QI=0|0|0|0.5|1|1|2|0|94
chr4_3 exon 71940093 71940098 71940093 ID=Msa0660820-mRNA-1:exon:21557;Parent=Msa0660820-mRNA-1
chr4_3 exon 71939511 71939789 71939511 ID=Msa0660820-mRNA-1:exon:21556;Parent=Msa0660820-mRNA-1
chr4_3 CDS 71940093 71940098 71940093 ID=Msa0660820-mRNA-1:cds;Parent=Msa0660820-mRNA-1
chr4_3 CDS 71939511 71939789 71939511 ID=Msa0660820-mRNA-1:cds;Parent=Msa0660820-mRNA-1
Gene Sequence

>Msa0660820

ATGGATTACCTAGTATTAACTCTTGCATTGGTAGAAGAGGCACATGCTGAAGATGAAGCTGAAATTGCAGATGAACTTTTAGGTAGTGAAATTAGACTATCATGTGAGCTAATTTCCCTATCCTCTTCGGTAATTGTTTCCATCATCTTTGATGTTCTATGCCTCATCACAGAAACATATTGTGGTGGTGCCACTTCCATGAAAAACCTTGCAATCCGAGAATTTGCCATTCTTAATGTGAACAAATTTCAAGTGTTTAATTGTGAAAAAATGTGTAATTGCTAA

Protein sequence

>Msa0660820

MDYLVLTLALVEEAHAEDEAEIADELLGSEIRLSCELISLSSSVIVSIIFDVLCLITETYCGGATSMKNLAIREFAILNVNKFQVFNCEKMCNC*