AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0230100

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0230100 MtrunA17_Chr4g0064711 59.574 47 19 0 17 63 215 261 2.34e-12 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTAACAAGAGGGTCAATT+TGG 0.192572 2_2:-1965395 Msa0230100:CDS
TTTGGAGACAAAATTATATA+TGG 0.209786 2_2:-1965974 Msa0230100:five_prime_UTR
GACAAGAATAAGGATGAATT+TGG 0.329771 2_2:-1965992 Msa0230100:five_prime_UTR
GGGTCAATTTGGGACTAAAT+AGG 0.371012 2_2:-1965384 Msa0230100:exon
TTTGGGACTAAATAGGTGTT+TGG 0.379595 2_2:-1965377 Msa0230100:exon
GTTTAAAATTACACATTTGT+TGG 0.414296 2_2:-1965701 Msa0230100:five_prime_UTR
TTTATGTCTAAGAAAGGTCT+AGG 0.418606 2_2:+1965303 None:intergenic
ACAGGGGTGAGACAAGAATA+AGG 0.429745 2_2:-1966002 Msa0230100:five_prime_UTR
TTAAAATTTATGTCTAAGAA+AGG 0.433401 2_2:+1965297 None:intergenic
GTTGTAGTAAATTGAGGAGA+AGG 0.436524 2_2:-1965726 Msa0230100:five_prime_UTR
CTTATTCCAGGTTTCATCCA+TGG 0.439084 2_2:-1965536 Msa0230100:intron
GCTAACAAGAGGGTCAATTT+GGG 0.442891 2_2:-1965394 Msa0230100:CDS
TTGGAGACAAAATTATATAT+GGG 0.456932 2_2:-1965973 Msa0230100:five_prime_UTR
TTATTGCTCTTTACATGAAG+TGG 0.459678 2_2:-1965502 Msa0230100:CDS
TTGTAGTAAATTGAGGAGAA+GGG 0.474580 2_2:-1965725 Msa0230100:five_prime_UTR
AGACTGATATCAACTGAGAA+AGG 0.475808 2_2:+1965854 None:intergenic
TTATTCCAGGTTTCATCCAT+GGG 0.496206 2_2:-1965535 Msa0230100:intron
GACTGATATCAACTGAGAAA+GGG 0.535636 2_2:+1965855 None:intergenic
TAGTTTCATCTCCAGTGCAA+AGG 0.555004 2_2:-1965668 Msa0230100:CDS
TTCTTCAAGTCCCACTTGTG+AGG 0.564284 2_2:+1965470 None:intergenic
GTTAGAAATGAAATCAAATG+TGG 0.587580 2_2:+1965772 None:intergenic
TTATAGGCAAGTCATAAACT+CGG 0.589810 2_2:+1965439 None:intergenic
GAAATGAAATCAAATGTGGA+AGG 0.591606 2_2:+1965776 None:intergenic
TATAGGCAAGTCATAAACTC+GGG 0.597655 2_2:+1965440 None:intergenic
TTATGTCTAAGAAAGGTCTA+GGG 0.603744 2_2:+1965304 None:intergenic
GAGACAAAATTATATATGGG+TGG 0.604560 2_2:-1965970 Msa0230100:five_prime_UTR
TGTTGAAGCAAAGAAATCAG+TGG 0.631702 2_2:+1965946 None:intergenic
CAATAACATCTATTCACCCA+TGG 0.638860 2_2:+1965519 None:intergenic
GGAGAACAAAGCCTCACAAG+TGG 0.638950 2_2:-1965481 Msa0230100:CDS
GAGAACAAAGCCTCACAAGT+GGG 0.677160 2_2:-1965480 Msa0230100:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAACAATTCTTCTATTAT+AGG + chr2_2:1965836-1965855 None:intergenic 15.0%
!!! AATAGAAGAATTGTTTTTAT+TGG - chr2_2:1965838-1965857 Msa0230100:five_prime_UTR 15.0%
!! TTAAAATTTATGTCTAAGAA+AGG + chr2_2:1965962-1965981 None:intergenic 15.0%
!!! TTCTTAGACATAAATTTTAA+TGG - chr2_2:1965962-1965981 Msa0230100:five_prime_UTR 15.0%
!! AAAAACAATTCTTCTATTAT+AGG + chr2_2:1965836-1965855 None:intergenic 15.0%
!!! AATAGAAGAATTGTTTTTAT+TGG - chr2_2:1965838-1965857 Msa0230100:five_prime_UTR 15.0%
!! TTAAAATTTATGTCTAAGAA+AGG + chr2_2:1965962-1965981 None:intergenic 15.0%
!!! TTCTTAGACATAAATTTTAA+TGG - chr2_2:1965962-1965981 Msa0230100:five_prime_UTR 15.0%
!! TTTGGAGACAAAATTATATA+TGG - chr2_2:1965282-1965301 Msa0230100:three_prime_UTR 20.0%
!! TTGGAGACAAAATTATATAT+GGG - chr2_2:1965283-1965302 Msa0230100:three_prime_UTR 20.0%
!!! TGAAAACGAAAAACAAATTT+TGG + chr2_2:1965450-1965469 None:intergenic 20.0%
!!! TTTTTTGTTGTAGTAAATTG+AGG - chr2_2:1965524-1965543 Msa0230100:CDS 20.0%
!!! GTTTAAAATTACACATTTGT+TGG - chr2_2:1965555-1965574 Msa0230100:intron 20.0%
!! CATAGCAATAAAAAATAACA+TGG + chr2_2:1965679-1965698 None:intergenic 20.0%
!!! TAGTATTTTAAACTTATTCC+AGG - chr2_2:1965708-1965727 Msa0230100:five_prime_UTR 20.0%
!! TTTGGAGACAAAATTATATA+TGG - chr2_2:1965282-1965301 Msa0230100:three_prime_UTR 20.0%
!! TTGGAGACAAAATTATATAT+GGG - chr2_2:1965283-1965302 Msa0230100:three_prime_UTR 20.0%
!!! TGAAAACGAAAAACAAATTT+TGG + chr2_2:1965450-1965469 None:intergenic 20.0%
!!! TTTTTTGTTGTAGTAAATTG+AGG - chr2_2:1965524-1965543 Msa0230100:CDS 20.0%
!!! GTTTAAAATTACACATTTGT+TGG - chr2_2:1965555-1965574 Msa0230100:intron 20.0%
!! CATAGCAATAAAAAATAACA+TGG + chr2_2:1965679-1965698 None:intergenic 20.0%
!!! TAGTATTTTAAACTTATTCC+AGG - chr2_2:1965708-1965727 Msa0230100:five_prime_UTR 20.0%
! GTTAGAAATGAAATCAAATG+TGG + chr2_2:1965487-1965506 None:intergenic 25.0%
! AATAACATGGCATTATTTGA+AGG + chr2_2:1965666-1965685 None:intergenic 25.0%
! GTTAGAAATGAAATCAAATG+TGG + chr2_2:1965487-1965506 None:intergenic 25.0%
! AATAACATGGCATTATTTGA+AGG + chr2_2:1965666-1965685 None:intergenic 25.0%
GACAAGAATAAGGATGAATT+TGG - chr2_2:1965264-1965283 Msa0230100:three_prime_UTR 30.0%
GAGACAAAATTATATATGGG+TGG - chr2_2:1965286-1965305 Msa0230100:three_prime_UTR 30.0%
GAAATGAAATCAAATGTGGA+AGG + chr2_2:1965483-1965502 None:intergenic 30.0%
TTGTAGTAAATTGAGGAGAA+GGG - chr2_2:1965531-1965550 Msa0230100:intron 30.0%
!! ATATTTTTCAACCTTTGCAC+TGG + chr2_2:1965602-1965621 None:intergenic 30.0%
TTATTGCTCTTTACATGAAG+TGG - chr2_2:1965754-1965773 Msa0230100:five_prime_UTR 30.0%
TTATAGGCAAGTCATAAACT+CGG + chr2_2:1965820-1965839 None:intergenic 30.0%
!!! TTTTTATTGGTGCTAACAAG+AGG - chr2_2:1965851-1965870 Msa0230100:five_prime_UTR 30.0%
!!! TTTTATTGGTGCTAACAAGA+GGG - chr2_2:1965852-1965871 Msa0230100:five_prime_UTR 30.0%
! TTTTATAGTGCGTAATCACA+AGG - chr2_2:1965918-1965937 Msa0230100:five_prime_UTR 30.0%
TTATGTCTAAGAAAGGTCTA+GGG + chr2_2:1965955-1965974 None:intergenic 30.0%
TTTATGTCTAAGAAAGGTCT+AGG + chr2_2:1965956-1965975 None:intergenic 30.0%
GACAAGAATAAGGATGAATT+TGG - chr2_2:1965264-1965283 Msa0230100:three_prime_UTR 30.0%
GAGACAAAATTATATATGGG+TGG - chr2_2:1965286-1965305 Msa0230100:three_prime_UTR 30.0%
GAAATGAAATCAAATGTGGA+AGG + chr2_2:1965483-1965502 None:intergenic 30.0%
TTGTAGTAAATTGAGGAGAA+GGG - chr2_2:1965531-1965550 Msa0230100:intron 30.0%
!! ATATTTTTCAACCTTTGCAC+TGG + chr2_2:1965602-1965621 None:intergenic 30.0%
TTATTGCTCTTTACATGAAG+TGG - chr2_2:1965754-1965773 Msa0230100:five_prime_UTR 30.0%
TTATAGGCAAGTCATAAACT+CGG + chr2_2:1965820-1965839 None:intergenic 30.0%
!!! TTTTTATTGGTGCTAACAAG+AGG - chr2_2:1965851-1965870 Msa0230100:five_prime_UTR 30.0%
!!! TTTTATTGGTGCTAACAAGA+GGG - chr2_2:1965852-1965871 Msa0230100:five_prime_UTR 30.0%
! TTTTATAGTGCGTAATCACA+AGG - chr2_2:1965918-1965937 Msa0230100:five_prime_UTR 30.0%
TTATGTCTAAGAAAGGTCTA+GGG + chr2_2:1965955-1965974 None:intergenic 30.0%
TTTATGTCTAAGAAAGGTCT+AGG + chr2_2:1965956-1965975 None:intergenic 30.0%
TGTTGAAGCAAAGAAATCAG+TGG + chr2_2:1965313-1965332 None:intergenic 35.0%
GACTGATATCAACTGAGAAA+GGG + chr2_2:1965404-1965423 None:intergenic 35.0%
AGACTGATATCAACTGAGAA+AGG + chr2_2:1965405-1965424 None:intergenic 35.0%
GTTGTAGTAAATTGAGGAGA+AGG - chr2_2:1965530-1965549 Msa0230100:intron 35.0%
GGCATTATTTGAAGGATTTG+AGG + chr2_2:1965658-1965677 None:intergenic 35.0%
TTATTCCAGGTTTCATCCAT+GGG - chr2_2:1965721-1965740 Msa0230100:five_prime_UTR 35.0%
CAATAACATCTATTCACCCA+TGG + chr2_2:1965740-1965759 None:intergenic 35.0%
TATAGGCAAGTCATAAACTC+GGG + chr2_2:1965819-1965838 None:intergenic 35.0%
! TTTGGGACTAAATAGGTGTT+TGG - chr2_2:1965879-1965898 Msa0230100:five_prime_UTR 35.0%
TGTTGAAGCAAAGAAATCAG+TGG + chr2_2:1965313-1965332 None:intergenic 35.0%
GACTGATATCAACTGAGAAA+GGG + chr2_2:1965404-1965423 None:intergenic 35.0%
AGACTGATATCAACTGAGAA+AGG + chr2_2:1965405-1965424 None:intergenic 35.0%
GTTGTAGTAAATTGAGGAGA+AGG - chr2_2:1965530-1965549 Msa0230100:intron 35.0%
GGCATTATTTGAAGGATTTG+AGG + chr2_2:1965658-1965677 None:intergenic 35.0%
TTATTCCAGGTTTCATCCAT+GGG - chr2_2:1965721-1965740 Msa0230100:five_prime_UTR 35.0%
CAATAACATCTATTCACCCA+TGG + chr2_2:1965740-1965759 None:intergenic 35.0%
TATAGGCAAGTCATAAACTC+GGG + chr2_2:1965819-1965838 None:intergenic 35.0%
! TTTGGGACTAAATAGGTGTT+TGG - chr2_2:1965879-1965898 Msa0230100:five_prime_UTR 35.0%
GGGAAAAAACACAGTGCAAA+AGG + chr2_2:1965384-1965403 None:intergenic 40.0%
TAGTTTCATCTCCAGTGCAA+AGG - chr2_2:1965588-1965607 Msa0230100:intron 40.0%
CTTATTCCAGGTTTCATCCA+TGG - chr2_2:1965720-1965739 Msa0230100:five_prime_UTR 40.0%
TGCTAACAAGAGGGTCAATT+TGG - chr2_2:1965861-1965880 Msa0230100:five_prime_UTR 40.0%
GCTAACAAGAGGGTCAATTT+GGG - chr2_2:1965862-1965881 Msa0230100:five_prime_UTR 40.0%
! GGGTCAATTTGGGACTAAAT+AGG - chr2_2:1965872-1965891 Msa0230100:five_prime_UTR 40.0%
!! GTTTTTCTTCAGGCATTGCA+AGG + chr2_2:1966004-1966023 None:intergenic 40.0%
GGGAAAAAACACAGTGCAAA+AGG + chr2_2:1965384-1965403 None:intergenic 40.0%
TAGTTTCATCTCCAGTGCAA+AGG - chr2_2:1965588-1965607 Msa0230100:intron 40.0%
CTTATTCCAGGTTTCATCCA+TGG - chr2_2:1965720-1965739 Msa0230100:five_prime_UTR 40.0%
TGCTAACAAGAGGGTCAATT+TGG - chr2_2:1965861-1965880 Msa0230100:five_prime_UTR 40.0%
GCTAACAAGAGGGTCAATTT+GGG - chr2_2:1965862-1965881 Msa0230100:five_prime_UTR 40.0%
! GGGTCAATTTGGGACTAAAT+AGG - chr2_2:1965872-1965891 Msa0230100:five_prime_UTR 40.0%
!! GTTTTTCTTCAGGCATTGCA+AGG + chr2_2:1966004-1966023 None:intergenic 40.0%
ATTCACCCATGGATGAAACC+TGG + chr2_2:1965729-1965748 None:intergenic 45.0%
GAGAACAAAGCCTCACAAGT+GGG - chr2_2:1965776-1965795 Msa0230100:five_prime_UTR 45.0%
TTCTTCAAGTCCCACTTGTG+AGG + chr2_2:1965789-1965808 None:intergenic 45.0%
ATTCACCCATGGATGAAACC+TGG + chr2_2:1965729-1965748 None:intergenic 45.0%
GAGAACAAAGCCTCACAAGT+GGG - chr2_2:1965776-1965795 Msa0230100:five_prime_UTR 45.0%
TTCTTCAAGTCCCACTTGTG+AGG + chr2_2:1965789-1965808 None:intergenic 45.0%
GGAGAACAAAGCCTCACAAG+TGG - chr2_2:1965775-1965794 Msa0230100:five_prime_UTR 50.0%
CCTTATTCTTGTCTCACCCC+TGG + chr2_2:1965257-1965276 None:intergenic 50.0%
GGAGAACAAAGCCTCACAAG+TGG - chr2_2:1965775-1965794 Msa0230100:five_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 1965255 1966023 1965255 ID=Msa0230100;Name=Msa0230100
chr2_2 mRNA 1965255 1966023 1965255 ID=Msa0230100-mRNA-1;Parent=Msa0230100;Name=Msa0230100-mRNA-1;_AED=0.00;_eAED=0.00;_QI=325|1|1|1|1|1|2|134|68
chr2_2 exon 1965255 1965548 1965255 ID=Msa0230100-mRNA-1:exon:767;Parent=Msa0230100-mRNA-1
chr2_2 exon 1965652 1966023 1965652 ID=Msa0230100-mRNA-1:exon:766;Parent=Msa0230100-mRNA-1
chr2_2 five_prime_UTR 1965699 1966023 1965699 ID=Msa0230100-mRNA-1:five_prime_utr;Parent=Msa0230100-mRNA-1
chr2_2 CDS 1965652 1965698 1965652 ID=Msa0230100-mRNA-1:cds;Parent=Msa0230100-mRNA-1
chr2_2 CDS 1965389 1965548 1965389 ID=Msa0230100-mRNA-1:cds;Parent=Msa0230100-mRNA-1
chr2_2 three_prime_UTR 1965255 1965388 1965255 ID=Msa0230100-mRNA-1:three_prime_utr;Parent=Msa0230100-mRNA-1
Gene Sequence

>Msa0230100

ATGTTGTTTAGTTTCATCTCCAGTGCAAAGGTTGAAAAATATGCAATGTTTCATCCATGGGTGAATAGATGTTATTGCTCTTTACATGAAGTGGAGAACAAAGCCTCACAAGTGGGACTTGAAGAATTTCAAACCCGAGTTTATGACTTGCCTATAATAGAAGAATTGTTTTTATTGGTGCTAACAAGAGGGTCAATTTGGGACTAA
Protein sequence

>Msa0230100

MLFSFISSAKVEKYAMFHPWVNRCYCSLHEVENKASQVGLEEFQTRVYDLPIIEELFLLVLTRGSIWD*