AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0176530


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0176530 MtrunA17_Chr1g0198941 97.059 68 1 1 1 68 1 67 7.74e-36 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAAACATGCACCATATTA+TGG 0.203774 1_4:-62974703 Msa0176520:intron
ACTTACACACTACTCTTCTA+AGG 0.295265 1_4:-62974314 Msa0176520:intron
TATTTATGTACCTTCCTCTT+AGG 0.298377 1_4:-62974498 Msa0176520:intron
ACCTTGGAGGCTCTAGCTTT+AGG 0.324474 1_4:-62974444 Msa0176520:intron
AGTAGTGTGTAAGTGTAAAA+TGG 0.327048 1_4:+62974323 Msa0176530:exon
AATATGAAGAATCCATAATA+TGG 0.340279 1_4:+62974691 Msa0176530:three_prime_UTR
AGGAGTAGTCCCACTAGTTT+TGG 0.346620 1_4:-62974424 Msa0176520:intron
CATGTAAATCCTTGCCAGTT+TGG 0.348500 1_4:+62974787 Msa0176530:three_prime_UTR
TCTTTCTTGACTTGCCCTGA+TGG 0.433141 1_4:-62974393 Msa0176520:intron
TCTGGTAGCTCTCAACCATC+AGG 0.435394 1_4:+62974378 Msa0176530:CDS
TTTCTTTGGTGCTACCTTGG+AGG 0.439933 1_4:-62974457 Msa0176520:intron
TATCAGTAGTACTATCTGTA+TGG 0.447641 1_4:+62974732 Msa0176530:three_prime_UTR
GAGAAACCAACTGAGAAATC+TGG 0.453123 1_4:+62974360 Msa0176530:CDS
GAGCTACCAGATTTCTCAGT+TGG 0.466377 1_4:-62974366 Msa0176520:intron
AGCAGAAATCTCAGCCTAAG+AGG 0.534590 1_4:+62974484 Msa0176530:CDS
TCCTAAAGCTAGAGCCTCCA+AGG 0.550929 1_4:+62974443 Msa0176530:CDS
TTTAAAAGGCCAAACTGGCA+AGG 0.553496 1_4:-62974796 Msa0176520:intron
GAAATCTCAGCCTAAGAGGA+AGG 0.560994 1_4:+62974488 Msa0176530:CDS
CAAACTGGCAAGGATTTACA+TGG 0.573072 1_4:-62974786 Msa0176520:intron
GAGCCTGCTGCCAAAACTAG+TGG 0.582011 1_4:+62974414 Msa0176530:CDS
AGCCTGCTGCCAAAACTAGT+GGG 0.610029 1_4:+62974415 Msa0176530:CDS
AATGAGACAACATAAGCAAG+TGG 0.629024 1_4:-62974757 Msa0176520:intron
CTGGTAGCTCTCAACCATCA+GGG 0.637266 1_4:+62974379 Msa0176530:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTACTTGAAAAAATAATTGT+TGG + chr1_4:62974646-62974665 Msa0176530:three_prime_UTR 15.0%
!! AATATGAAGAATCCATAATA+TGG + chr1_4:62974691-62974710 Msa0176530:three_prime_UTR 20.0%
!!! ATCTTTTGATTACTTGTTTC+AGG + chr1_4:62974584-62974603 Msa0176530:intron 25.0%
!!! TTTTATTTAAAAGGCCAAAC+TGG - chr1_4:62974804-62974823 Msa0176520:intron 25.0%
AGTAGTGTGTAAGTGTAAAA+TGG + chr1_4:62974323-62974342 Msa0176530:exon 30.0%
TATTTATGTACCTTCCTCTT+AGG - chr1_4:62974501-62974520 Msa0176520:intron 30.0%
ATGAAACATGCACCATATTA+TGG - chr1_4:62974706-62974725 Msa0176520:intron 30.0%
TATCAGTAGTACTATCTGTA+TGG + chr1_4:62974732-62974751 Msa0176530:three_prime_UTR 30.0%
ACTTACACACTACTCTTCTA+AGG - chr1_4:62974317-62974336 Msa0176520:intron 35.0%
! GATTTCTGCTCAGTTTTCTT+TGG - chr1_4:62974474-62974493 Msa0176520:intron 35.0%
AATGAGACAACATAAGCAAG+TGG - chr1_4:62974760-62974779 Msa0176520:intron 35.0%
GAGAAACCAACTGAGAAATC+TGG + chr1_4:62974360-62974379 Msa0176530:CDS 40.0%
!!! AGTTTTCTTTGGTGCTACCT+TGG - chr1_4:62974463-62974482 Msa0176520:intron 40.0%
CAAACTGGCAAGGATTTACA+TGG - chr1_4:62974789-62974808 Msa0176520:intron 40.0%
CATGTAAATCCTTGCCAGTT+TGG + chr1_4:62974787-62974806 Msa0176530:three_prime_UTR 40.0%
TTTAAAAGGCCAAACTGGCA+AGG - chr1_4:62974799-62974818 Msa0176520:intron 40.0%
GAGCTACCAGATTTCTCAGT+TGG - chr1_4:62974369-62974388 Msa0176520:intron 45.0%
!! TCTTTCTTGACTTGCCCTGA+TGG - chr1_4:62974396-62974415 Msa0176520:intron 45.0%
!! AGGAGTAGTCCCACTAGTTT+TGG - chr1_4:62974427-62974446 Msa0176520:intron 45.0%
!! TTTCTTTGGTGCTACCTTGG+AGG - chr1_4:62974460-62974479 Msa0176520:intron 45.0%
AGCAGAAATCTCAGCCTAAG+AGG + chr1_4:62974484-62974503 Msa0176530:CDS 45.0%
GAAATCTCAGCCTAAGAGGA+AGG + chr1_4:62974488-62974507 Msa0176530:CDS 45.0%
!!! ATAAGTATATTTTATTTAAA+AGG - chr1_4:62974813-62974832 Msa0176520:intron 5.0%
TCTGGTAGCTCTCAACCATC+AGG + chr1_4:62974378-62974397 Msa0176530:CDS 50.0%
CTGGTAGCTCTCAACCATCA+GGG + chr1_4:62974379-62974398 Msa0176530:CDS 50.0%
AGCCTGCTGCCAAAACTAGT+GGG + chr1_4:62974415-62974434 Msa0176530:CDS 50.0%
TCCTAAAGCTAGAGCCTCCA+AGG + chr1_4:62974443-62974462 Msa0176530:CDS 50.0%
!! ACCTTGGAGGCTCTAGCTTT+AGG - chr1_4:62974447-62974466 Msa0176520:intron 50.0%
GAGCCTGCTGCCAAAACTAG+TGG + chr1_4:62974414-62974433 Msa0176530:CDS 55.0%
!!! GTCCCACTAGTTTTGGCAGC+AGG - chr1_4:62974420-62974439 Msa0176520:intron 55.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 62974295 62974847 62974295 ID=Msa0176530;Name=Msa0176530
chr1_4 mRNA 62974295 62974847 62974295 ID=Msa0176530-mRNA-1;Parent=Msa0176530;Name=Msa0176530-mRNA-1;_AED=0.00;_eAED=0.00;_QI=47|1|1|1|1|1|2|203|68
chr1_4 exon 62974295 62974509 62974295 ID=Msa0176530-mRNA-1:exon:20267;Parent=Msa0176530-mRNA-1
chr1_4 exon 62974606 62974847 62974606 ID=Msa0176530-mRNA-1:exon:20268;Parent=Msa0176530-mRNA-1
chr1_4 five_prime_UTR 62974295 62974341 62974295 ID=Msa0176530-mRNA-1:five_prime_utr;Parent=Msa0176530-mRNA-1
chr1_4 CDS 62974342 62974509 62974342 ID=Msa0176530-mRNA-1:cds;Parent=Msa0176530-mRNA-1
chr1_4 CDS 62974606 62974644 62974606 ID=Msa0176530-mRNA-1:cds;Parent=Msa0176530-mRNA-1
chr1_4 three_prime_UTR 62974645 62974847 62974645 ID=Msa0176530-mRNA-1:three_prime_utr;Parent=Msa0176530-mRNA-1
Gene Sequence

>Msa0176530

ATGGCATCACTCAAAGCTGAGAAACCAACTGAGAAATCTGGTAGCTCTCAACCATCAGGGCAAGTCAAGAAAGAGCCTGCTGCCAAAACTAGTGGGACTACTCCTAAAGCTAGAGCCTCCAAGGTAGCACCAAAGAAAACTGAGCAGAAATCTCAGCCTAAGAGGAAGGCTAGCAGCATTAAGCAGAAGATAACAAGTGAAACTTAA

Protein sequence

>Msa0176530

MASLKAEKPTEKSGSSQPSGQVKKEPAAKTSGTTPKARASKVAPKKTEQKSQPKRKASSIKQKITSET*