AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0140820


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 15 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTCCTGAATTTCTGAATT+TGG 0.202611 1_3:-75151769 Msa0140820:three_prime_UTR
TCTCTCTCGTATTGATGTTT+TGG 0.256448 1_3:-75151884 Msa0140820:three_prime_UTR
TGGATCTCTGTCTCATCTTT+CGG 0.332419 1_3:+75152018 None:intergenic
TGCGCCAAATTCAGAAATTC+AGG 0.357947 1_3:+75151765 None:intergenic
TGCTTCTGCGCAGTCTCATT+AGG 0.363924 1_3:-75152216 Msa0140820:five_prime_UTR
GCGCAGAAGCAACTGCGATT+AGG 0.428523 1_3:+75152228 None:intergenic
AGCGTATGAGGAGGTTGAAG+AGG 0.488055 1_3:-75152046 Msa0140820:CDS
AAGAACACCAACATACTACT+TGG 0.523061 1_3:+75151998 None:intergenic
AGTGGAAGAAGAAGCGTATG+AGG 0.538884 1_3:-75152058 Msa0140820:CDS
TTCAACAATCATGCGTGCCA+AGG 0.540770 1_3:-75152166 Msa0140820:intron
GCACGCATGATTGTTGAAAA+CGG 0.548829 1_3:+75152171 None:intergenic
ATATGTTAAGAGAGTAGTAT+CGG 0.555824 1_3:-75151913 Msa0140820:three_prime_UTR
CAGAGATCCAAGTAGTATGT+TGG 0.564238 1_3:-75152005 Msa0140820:exon
GGAAGAAGAAGCGTATGAGG+AGG 0.665498 1_3:-75152055 Msa0140820:CDS
ATAAGTCTGATTAAACAACA+CGG 0.774353 1_3:+75151937 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGTTATAGTTATAATAA+TGG - chr1_3:75151841-75151860 Msa0140820:three_prime_UTR 10.0%
!! AAAACAAAAATTAATTGCAA+TGG + chr1_3:75151825-75151844 None:intergenic 15.0%
!!! TATAGTTATAATAATGGTTT+TGG - chr1_3:75151847-75151866 Msa0140820:three_prime_UTR 15.0%
!!! TTTGATTTTGATTTTGATTT+TGG - chr1_3:75151870-75151889 Msa0140820:three_prime_UTR 15.0%
!!! TGTTTATTTTTTTGTTTTTG+CGG - chr1_3:75152169-75152188 Msa0140820:exon 15.0%
! ATAAGTCTGATTAAACAACA+CGG + chr1_3:75152025-75152044 None:intergenic 25.0%
! ATATGTTAAGAGAGTAGTAT+CGG - chr1_3:75152046-75152065 Msa0140820:CDS 25.0%
!! GCTCAAAGATATTTTCTTTA+TGG - chr1_3:75152108-75152127 Msa0140820:intron 25.0%
!! AATATCAAAGATGAAAGCAT+AGG + chr1_3:75152226-75152245 None:intergenic 25.0%
AATTGCAATGGATCTAACCT+TGG + chr1_3:75151813-75151832 None:intergenic 35.0%
! TTGATTTTGGATTTGTGCAG+TGG - chr1_3:75151883-75151902 Msa0140820:three_prime_UTR 35.0%
AAGAACACCAACATACTACT+TGG + chr1_3:75151964-75151983 None:intergenic 35.0%
!! TCTCTCTCGTATTGATGTTT+TGG - chr1_3:75152075-75152094 Msa0140820:intron 35.0%
GGTTCCTGAATTTCTGAATT+TGG - chr1_3:75152190-75152209 Msa0140820:five_prime_UTR 35.0%
GCACGCATGATTGTTGAAAA+CGG + chr1_3:75151791-75151810 None:intergenic 40.0%
TGGATCTCTGTCTCATCTTT+CGG + chr1_3:75151944-75151963 None:intergenic 40.0%
CAGAGATCCAAGTAGTATGT+TGG - chr1_3:75151954-75151973 Msa0140820:three_prime_UTR 40.0%
TGCGCCAAATTCAGAAATTC+AGG + chr1_3:75152197-75152216 None:intergenic 40.0%
TTCAACAATCATGCGTGCCA+AGG - chr1_3:75151793-75151812 Msa0140820:three_prime_UTR 45.0%
! AGTGGAAGAAGAAGCGTATG+AGG - chr1_3:75151901-75151920 Msa0140820:three_prime_UTR 45.0%
TGCTTCTGCGCAGTCTCATT+AGG - chr1_3:75151743-75151762 Msa0140820:three_prime_UTR 50.0%
! GGAAGAAGAAGCGTATGAGG+AGG - chr1_3:75151904-75151923 Msa0140820:three_prime_UTR 50.0%
AGCGTATGAGGAGGTTGAAG+AGG - chr1_3:75151913-75151932 Msa0140820:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 75151734 75152247 75151734 ID=Msa0140820;Name=Msa0140820
chr1_3 mRNA 75151734 75152247 75151734 ID=Msa0140820-mRNA-1;Parent=Msa0140820;Name=Msa0140820-mRNA-1;_AED=0.00;_eAED=0.00;_QI=69|1|1|1|1|1|2|279|25
chr1_3 exon 75151734 75152078 75151734 ID=Msa0140820-mRNA-1:exon:26286;Parent=Msa0140820-mRNA-1
chr1_3 exon 75152167 75152247 75152167 ID=Msa0140820-mRNA-1:exon:26285;Parent=Msa0140820-mRNA-1
chr1_3 five_prime_UTR 75152179 75152247 75152179 ID=Msa0140820-mRNA-1:five_prime_utr;Parent=Msa0140820-mRNA-1
chr1_3 CDS 75152167 75152178 75152167 ID=Msa0140820-mRNA-1:cds;Parent=Msa0140820-mRNA-1
chr1_3 CDS 75152013 75152078 75152013 ID=Msa0140820-mRNA-1:cds;Parent=Msa0140820-mRNA-1
chr1_3 three_prime_UTR 75151734 75152012 75151734 ID=Msa0140820-mRNA-1:three_prime_utr;Parent=Msa0140820-mRNA-1
Gene Sequence

>Msa0140820

ATGCGTGCCAAGTGGAAGAAGAAGCGTATGAGGAGGTTGAAGAGGAAGCGCCGAAAGATGAGACAGAGATCCAAGTAG

Protein sequence

>Msa0140820

MRAKWKKKRMRRLKRKRRKMRQRSK*