AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0473530


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0473530 MtrunA17_Chr3g0129411 98.824 85 1 0 1 85 35 119 1.31e-58 175
Msa0473530 MtrunA17_Chr8g0383481 52.941 85 32 4 1 85 36 112 1.41e-20 78.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 27 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTAAATAGTGCACAAATTT+TGG 0.112038 3_3:+76221888 Msa0473530:exon
TCCATCCATATTCAAGTTAA+AGG 0.155938 3_3:+76221578 Msa0473530:CDS
CCATATGGATATGTTAATTT+AGG 0.228692 3_3:-76221435 None:intergenic
AGGTACCTTTAACTTGAATA+TGG 0.246398 3_3:-76221583 None:intergenic
TCCTATATATAGACACATTT+TGG 0.251593 3_3:-76221412 None:intergenic
CAATTAACCATGTTAGTATC+TGG 0.347082 3_3:+76222077 Msa0473530:three_prime_UTR
ATAAGGTGGTGATAATGTTT+TGG 0.354103 3_3:+76222109 Msa0473530:three_prime_UTR
TGCACTATTTAATTGTGAAT+TGG 0.396593 3_3:-76221878 None:intergenic
GTATCTGGATCTAGAATATA+AGG 0.397126 3_3:+76222092 Msa0473530:three_prime_UTR
GCCAAAATGTGTCTATATAT+AGG 0.397555 3_3:+76221411 Msa0473530:five_prime_UTR
ATTGGTGGTTTCCTTGATGC+TGG 0.439868 3_3:-76221860 None:intergenic
TGTTGACATCCTCACTACTT+TGG 0.458998 3_3:-76221742 None:intergenic
CAACAAAGCTCAACAACATA+AGG 0.461599 3_3:+76221760 Msa0473530:CDS
ACCTTTAACTTGAATATGGA+TGG 0.490545 3_3:-76221579 None:intergenic
ACTATTTAATTGTGAATTGG+TGG 0.515565 3_3:-76221875 None:intergenic
CCTAAATTAACATATCCATA+TGG 0.523592 3_3:+76221435 Msa0473530:five_prime_UTR
GACATGTTTAAGCTAAAAGA+AGG 0.527331 3_3:+76221794 Msa0473530:CDS
AAATAGCTATTCTATAGCTA+TGG 0.532562 3_3:+76221954 Msa0473530:three_prime_UTR
TATGGATGGAGAAGAAGCAA+AGG 0.568511 3_3:-76221565 None:intergenic
TGGATTATACTCCAGCATCA+AGG 0.596772 3_3:+76221849 Msa0473530:CDS
AATAAACAACCAAAGTAGTG+AGG 0.645718 3_3:+76221733 Msa0473530:CDS
CAAAGCTCAACAACATAAGG+AGG 0.647677 3_3:+76221763 Msa0473530:CDS
ATGTTTAAGCTAAAAGAAGG+AGG 0.667536 3_3:+76221797 Msa0473530:CDS
AAAGAAGGAGGAGATAACGT+TGG 0.669136 3_3:+76221809 Msa0473530:CDS
TCTAGATCCAGATACTAACA+TGG 0.690048 3_3:-76222084 None:intergenic
TCTGGATCTAGAATATAAGG+TGG 0.701138 3_3:+76222095 Msa0473530:three_prime_UTR
TGATGCTGGAGTATAATCCA+TGG 0.719915 3_3:-76221846 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAAAAAATATTACAACAT+TGG + chr3_3:76221627-76221646 Msa0473530:intron 10.0%
!! AATTAAACAGAAAATAAAAA+TGG - chr3_3:76221666-76221685 None:intergenic 10.0%
!!! AATTTTTCTTACATTTTTTT+TGG + chr3_3:76221686-76221705 Msa0473530:intron 10.0%
!!! TGTAATATTTTTTTTAGCTA+TGG - chr3_3:76221623-76221642 None:intergenic 15.0%
!!! AATTGCTTTTAACTTTAAGA+TGG + chr3_3:76221499-76221518 Msa0473530:exon 20.0%
!!! ATTAAATAGTGCACAAATTT+TGG + chr3_3:76221888-76221907 Msa0473530:exon 20.0%
!! TCCTATATATAGACACATTT+TGG - chr3_3:76221415-76221434 None:intergenic 25.0%
! CCATATGGATATGTTAATTT+AGG - chr3_3:76221438-76221457 None:intergenic 25.0%
! CCTAAATTAACATATCCATA+TGG + chr3_3:76221435-76221454 Msa0473530:five_prime_UTR 25.0%
!! CTTTTTCTGAATATACCATA+TGG - chr3_3:76221453-76221472 None:intergenic 25.0%
! ACTATTTAATTGTGAATTGG+TGG - chr3_3:76221878-76221897 None:intergenic 25.0%
! TGCACTATTTAATTGTGAAT+TGG - chr3_3:76221881-76221900 None:intergenic 25.0%
! AAATAGCTATTCTATAGCTA+TGG + chr3_3:76221954-76221973 Msa0473530:three_prime_UTR 25.0%
GCCAAAATGTGTCTATATAT+AGG + chr3_3:76221411-76221430 Msa0473530:five_prime_UTR 30.0%
! TCCATCCATATTCAAGTTAA+AGG + chr3_3:76221578-76221597 Msa0473530:CDS 30.0%
!! ACCTTTAACTTGAATATGGA+TGG - chr3_3:76221582-76221601 None:intergenic 30.0%
!! AGGTACCTTTAACTTGAATA+TGG - chr3_3:76221586-76221605 None:intergenic 30.0%
! CTATGGATATTTGAAGCAAA+AGG - chr3_3:76221606-76221625 None:intergenic 30.0%
AATAAACAACCAAAGTAGTG+AGG + chr3_3:76221733-76221752 Msa0473530:CDS 30.0%
GACATGTTTAAGCTAAAAGA+AGG + chr3_3:76221794-76221813 Msa0473530:CDS 30.0%
ATGTTTAAGCTAAAAGAAGG+AGG + chr3_3:76221797-76221816 Msa0473530:CDS 30.0%
CAATTAACCATGTTAGTATC+TGG + chr3_3:76222077-76222096 Msa0473530:three_prime_UTR 30.0%
! GTATCTGGATCTAGAATATA+AGG + chr3_3:76222092-76222111 Msa0473530:three_prime_UTR 30.0%
!! ATAAGGTGGTGATAATGTTT+TGG + chr3_3:76222109-76222128 Msa0473530:three_prime_UTR 30.0%
CAACAAAGCTCAACAACATA+AGG + chr3_3:76221760-76221779 Msa0473530:CDS 35.0%
TCTAGATCCAGATACTAACA+TGG - chr3_3:76222087-76222106 None:intergenic 35.0%
! TCTGGATCTAGAATATAAGG+TGG + chr3_3:76222095-76222114 Msa0473530:three_prime_UTR 35.0%
TATGGATGGAGAAGAAGCAA+AGG - chr3_3:76221568-76221587 None:intergenic 40.0%
TGTTGACATCCTCACTACTT+TGG - chr3_3:76221745-76221764 None:intergenic 40.0%
CAAAGCTCAACAACATAAGG+AGG + chr3_3:76221763-76221782 Msa0473530:CDS 40.0%
AAAGAAGGAGGAGATAACGT+TGG + chr3_3:76221809-76221828 Msa0473530:CDS 40.0%
!!! TGGTTCTGATGTTTTCACCA+TGG + chr3_3:76221829-76221848 Msa0473530:CDS 40.0%
TGATGCTGGAGTATAATCCA+TGG - chr3_3:76221849-76221868 None:intergenic 40.0%
TGGATTATACTCCAGCATCA+AGG + chr3_3:76221849-76221868 Msa0473530:CDS 40.0%
! ATTGGTGGTTTCCTTGATGC+TGG - chr3_3:76221863-76221882 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 76221404 76222147 76221404 ID=Msa0473530;Name=Msa0473530
chr3_3 mRNA 76221404 76222147 76221404 ID=Msa0473530-mRNA-1;Parent=Msa0473530;Name=Msa0473530-mRNA-1;_AED=0.08;_eAED=0.08;_QI=114|1|1|1|1|1|2|255|85
chr3_3 exon 76221404 76221599 76221404 ID=Msa0473530-mRNA-1:exon:19891;Parent=Msa0473530-mRNA-1
chr3_3 exon 76221717 76222147 76221717 ID=Msa0473530-mRNA-1:exon:19892;Parent=Msa0473530-mRNA-1
chr3_3 five_prime_UTR 76221404 76221517 76221404 ID=Msa0473530-mRNA-1:five_prime_utr;Parent=Msa0473530-mRNA-1
chr3_3 CDS 76221518 76221599 76221518 ID=Msa0473530-mRNA-1:cds;Parent=Msa0473530-mRNA-1
chr3_3 CDS 76221717 76221892 76221717 ID=Msa0473530-mRNA-1:cds;Parent=Msa0473530-mRNA-1
chr3_3 three_prime_UTR 76221893 76222147 76221893 ID=Msa0473530-mRNA-1:three_prime_utr;Parent=Msa0473530-mRNA-1
Gene Sequence

>Msa0473530

ATGGTTGCTTCACAAAACAAACGCATTCTACAAGTGATTTTTGTTCTCCTTTGCTTCTTCTCCATCCATATTCAAGTTAAAGCAAGAGTATTGAAAGAAATAAACAACCAAAGTAGTGAGGATGTCAACAAAGCTCAACAACATAAGGAGGTACATGCTGACATGTTTAAGCTAAAAGAAGGAGGAGATAACGTTGGTTCTGATGTTTTCACCATGGATTATACTCCAGCATCAAGGAAACCACCAATTCACAATTAA

Protein sequence

>Msa0473530

MVASQNKRILQVIFVLLCFFSIHIQVKARVLKEINNQSSEDVNKAQQHKEVHADMFKLKEGGDNVGSDVFTMDYTPASRKPPIHN*