AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0130620


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0130620 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_3:-61033352 None:intergenic
ACTTACACACTACTCTTCTA+AGG 0.295265 1_3:-61032963 None:intergenic
TATTTATGTACCTTCCTCTT+AGG 0.298377 1_3:-61033147 None:intergenic
ACCTTGGAGGCTCTAGCTTT+AGG 0.324474 1_3:-61033093 None:intergenic
AGTAGTGTGTAAGTGTAAAA+TGG 0.327048 1_3:+61032972 Msa0130620:exon
AATATGAAGAATCCATAATA+TGG 0.340279 1_3:+61033340 Msa0130620:three_prime_UTR
AGGAGTAGTCCCACTAGTTT+TGG 0.346620 1_3:-61033073 None:intergenic
CATGTAAATCCTTGCCAGTT+TGG 0.348500 1_3:+61033436 Msa0130620:three_prime_UTR
TCTTTCTTGACTTGCCCTGA+TGG 0.433141 1_3:-61033042 None:intergenic
TCTGGTAGCTCTCAACCATC+AGG 0.435394 1_3:+61033027 Msa0130620:CDS
TTTCTTTGGTGCTACCTTGG+AGG 0.439933 1_3:-61033106 None:intergenic
TATCAGTAGTACTATCTGTA+TGG 0.447641 1_3:+61033381 Msa0130620:three_prime_UTR
GAGAAACCAACTGAGAAATC+TGG 0.453123 1_3:+61033009 Msa0130620:CDS
GAGCTACCAGATTTCTCAGT+TGG 0.466377 1_3:-61033015 None:intergenic
AGCAGAAATCTCAGCCTAAG+AGG 0.534590 1_3:+61033133 Msa0130620:CDS
TCCTAAAGCTAGAGCCTCCA+AGG 0.550929 1_3:+61033092 Msa0130620:CDS
TTTAAAAGGCCAAACTGGCA+AGG 0.553496 1_3:-61033445 None:intergenic
GAAATCTCAGCCTAAGAGGA+AGG 0.560994 1_3:+61033137 Msa0130620:CDS
CAAACTGGCAAGGATTTACA+TGG 0.573072 1_3:-61033435 None:intergenic
GAGCCTGCTGCCAAAACTAG+TGG 0.582011 1_3:+61033063 Msa0130620:CDS
AGCCTGCTGCCAAAACTAGT+GGG 0.610029 1_3:+61033064 Msa0130620:CDS
AATGAGACAACATAAGCAAG+TGG 0.629024 1_3:-61033406 None:intergenic
CTGGTAGCTCTCAACCATCA+GGG 0.637266 1_3:+61033028 Msa0130620:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTACTTGAAAAAATAATTGT+TGG + chr1_3:61033295-61033314 Msa0130620:three_prime_UTR 15.0%
!! AATATGAAGAATCCATAATA+TGG + chr1_3:61033340-61033359 Msa0130620:three_prime_UTR 20.0%
!!! ATCTTTTGATTACTTGTTTC+AGG + chr1_3:61033233-61033252 Msa0130620:intron 25.0%
!!! TTTTATTTAAAAGGCCAAAC+TGG - chr1_3:61033453-61033472 None:intergenic 25.0%
AGTAGTGTGTAAGTGTAAAA+TGG + chr1_3:61032972-61032991 Msa0130620:exon 30.0%
TATTTATGTACCTTCCTCTT+AGG - chr1_3:61033150-61033169 None:intergenic 30.0%
ATGAAACATGCACCATATTA+TGG - chr1_3:61033355-61033374 None:intergenic 30.0%
TATCAGTAGTACTATCTGTA+TGG + chr1_3:61033381-61033400 Msa0130620:three_prime_UTR 30.0%
ACTTACACACTACTCTTCTA+AGG - chr1_3:61032966-61032985 None:intergenic 35.0%
! GATTTCTGCTCAGTTTTCTT+TGG - chr1_3:61033123-61033142 None:intergenic 35.0%
AATGAGACAACATAAGCAAG+TGG - chr1_3:61033409-61033428 None:intergenic 35.0%
GAGAAACCAACTGAGAAATC+TGG + chr1_3:61033009-61033028 Msa0130620:CDS 40.0%
!!! AGTTTTCTTTGGTGCTACCT+TGG - chr1_3:61033112-61033131 None:intergenic 40.0%
CAAACTGGCAAGGATTTACA+TGG - chr1_3:61033438-61033457 None:intergenic 40.0%
CATGTAAATCCTTGCCAGTT+TGG + chr1_3:61033436-61033455 Msa0130620:three_prime_UTR 40.0%
TTTAAAAGGCCAAACTGGCA+AGG - chr1_3:61033448-61033467 None:intergenic 40.0%
GAGCTACCAGATTTCTCAGT+TGG - chr1_3:61033018-61033037 None:intergenic 45.0%
!! TCTTTCTTGACTTGCCCTGA+TGG - chr1_3:61033045-61033064 None:intergenic 45.0%
!! AGGAGTAGTCCCACTAGTTT+TGG - chr1_3:61033076-61033095 None:intergenic 45.0%
!! TTTCTTTGGTGCTACCTTGG+AGG - chr1_3:61033109-61033128 None:intergenic 45.0%
AGCAGAAATCTCAGCCTAAG+AGG + chr1_3:61033133-61033152 Msa0130620:CDS 45.0%
GAAATCTCAGCCTAAGAGGA+AGG + chr1_3:61033137-61033156 Msa0130620:CDS 45.0%
!!! ATAAGTATATTTTATTTAAA+AGG - chr1_3:61033462-61033481 None:intergenic 5.0%
TCTGGTAGCTCTCAACCATC+AGG + chr1_3:61033027-61033046 Msa0130620:CDS 50.0%
CTGGTAGCTCTCAACCATCA+GGG + chr1_3:61033028-61033047 Msa0130620:CDS 50.0%
AGCCTGCTGCCAAAACTAGT+GGG + chr1_3:61033064-61033083 Msa0130620:CDS 50.0%
TCCTAAAGCTAGAGCCTCCA+AGG + chr1_3:61033092-61033111 Msa0130620:CDS 50.0%
!! ACCTTGGAGGCTCTAGCTTT+AGG - chr1_3:61033096-61033115 None:intergenic 50.0%
GAGCCTGCTGCCAAAACTAG+TGG + chr1_3:61033063-61033082 Msa0130620:CDS 55.0%
!!! GTCCCACTAGTTTTGGCAGC+AGG - chr1_3:61033069-61033088 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 61032944 61033496 61032944 ID=Msa0130620;Name=Msa0130620
chr1_3 mRNA 61032944 61033496 61032944 ID=Msa0130620-mRNA-1;Parent=Msa0130620;Name=Msa0130620-mRNA-1;_AED=0.00;_eAED=0.00;_QI=47|1|1|1|1|1|2|203|68
chr1_3 exon 61032944 61033158 61032944 ID=Msa0130620-mRNA-1:exon:20135;Parent=Msa0130620-mRNA-1
chr1_3 exon 61033255 61033496 61033255 ID=Msa0130620-mRNA-1:exon:20136;Parent=Msa0130620-mRNA-1
chr1_3 five_prime_UTR 61032944 61032990 61032944 ID=Msa0130620-mRNA-1:five_prime_utr;Parent=Msa0130620-mRNA-1
chr1_3 CDS 61032991 61033158 61032991 ID=Msa0130620-mRNA-1:cds;Parent=Msa0130620-mRNA-1
chr1_3 CDS 61033255 61033293 61033255 ID=Msa0130620-mRNA-1:cds;Parent=Msa0130620-mRNA-1
chr1_3 three_prime_UTR 61033294 61033496 61033294 ID=Msa0130620-mRNA-1:three_prime_utr;Parent=Msa0130620-mRNA-1
Gene Sequence

>Msa0130620

ATGGCATCACTCAAAGCTGAGAAACCAACTGAGAAATCTGGTAGCTCTCAACCATCAGGGCAAGTCAAGAAAGAGCCTGCTGCCAAAACTAGTGGGACTACTCCTAAAGCTAGAGCCTCCAAGGTAGCACCAAAGAAAACTGAGCAGAAATCTCAGCCTAAGAGGAAGGCTAGCAGCATTAAGCAGAAGATAACAAGTGAAACTTAA

Protein sequence

>Msa0130620

MASLKAEKPTEKSGSSQPSGQVKKEPAAKTSGTTPKARASKVAPKKTEQKSQPKRKASSIKQKITSET*