AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0084550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0084550 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_2:-64093698 None:intergenic
ACTTACACACTACTCTTCTA+AGG 0.295265 1_2:-64093309 None:intergenic
TATTTATGTACCTTCCTCTT+AGG 0.298377 1_2:-64093493 None:intergenic
ACCTTGGAGGCTCTAGCTTT+AGG 0.324474 1_2:-64093439 None:intergenic
AGTAGTGTGTAAGTGTAAAA+TGG 0.327048 1_2:+64093318 Msa0084550:exon
AATATGAAGAATCCATAATA+TGG 0.340279 1_2:+64093686 Msa0084550:three_prime_UTR
AGGAGTAGTCCCACTAGTTT+TGG 0.346620 1_2:-64093419 None:intergenic
CATGTAAATCCTTGCCAGTT+TGG 0.348500 1_2:+64093782 Msa0084550:three_prime_UTR
TCTTTCTTGACTTGCCCTGA+TGG 0.433141 1_2:-64093388 None:intergenic
TCTGGTAGCTCTCAACCATC+AGG 0.435394 1_2:+64093373 Msa0084550:CDS
TTTCTTTGGTGCTACCTTGG+AGG 0.439933 1_2:-64093452 None:intergenic
TATCAGTAGTACTATCTGTA+TGG 0.447641 1_2:+64093727 Msa0084550:three_prime_UTR
GAGAAACCAACTGAGAAATC+TGG 0.453123 1_2:+64093355 Msa0084550:CDS
GAGCTACCAGATTTCTCAGT+TGG 0.466377 1_2:-64093361 None:intergenic
AGCAGAAATCTCAGCCTAAG+AGG 0.534590 1_2:+64093479 Msa0084550:CDS
TCCTAAAGCTAGAGCCTCCA+AGG 0.550929 1_2:+64093438 Msa0084550:CDS
TTTAAAAGGCCAAACTGGCA+AGG 0.553496 1_2:-64093791 None:intergenic
GAAATCTCAGCCTAAGAGGA+AGG 0.560994 1_2:+64093483 Msa0084550:CDS
CAAACTGGCAAGGATTTACA+TGG 0.573072 1_2:-64093781 None:intergenic
GAGCCTGCTGCCAAAACTAG+TGG 0.582011 1_2:+64093409 Msa0084550:CDS
AGCCTGCTGCCAAAACTAGT+GGG 0.610029 1_2:+64093410 Msa0084550:CDS
AATGAGACAACATAAGCAAG+TGG 0.629024 1_2:-64093752 None:intergenic
CTGGTAGCTCTCAACCATCA+GGG 0.637266 1_2:+64093374 Msa0084550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTACTTGAAAAAATAATTGT+TGG + chr1_2:64093641-64093660 Msa0084550:three_prime_UTR 15.0%
!! AATATGAAGAATCCATAATA+TGG + chr1_2:64093686-64093705 Msa0084550:three_prime_UTR 20.0%
!!! ATCTTTTGATTACTTGTTTC+AGG + chr1_2:64093579-64093598 Msa0084550:intron 25.0%
!!! TTTTATTTAAAAGGCCAAAC+TGG - chr1_2:64093799-64093818 None:intergenic 25.0%
AGTAGTGTGTAAGTGTAAAA+TGG + chr1_2:64093318-64093337 Msa0084550:exon 30.0%
TATTTATGTACCTTCCTCTT+AGG - chr1_2:64093496-64093515 None:intergenic 30.0%
ATGAAACATGCACCATATTA+TGG - chr1_2:64093701-64093720 None:intergenic 30.0%
TATCAGTAGTACTATCTGTA+TGG + chr1_2:64093727-64093746 Msa0084550:three_prime_UTR 30.0%
ACTTACACACTACTCTTCTA+AGG - chr1_2:64093312-64093331 None:intergenic 35.0%
! GATTTCTGCTCAGTTTTCTT+TGG - chr1_2:64093469-64093488 None:intergenic 35.0%
AATGAGACAACATAAGCAAG+TGG - chr1_2:64093755-64093774 None:intergenic 35.0%
GAGAAACCAACTGAGAAATC+TGG + chr1_2:64093355-64093374 Msa0084550:CDS 40.0%
!!! AGTTTTCTTTGGTGCTACCT+TGG - chr1_2:64093458-64093477 None:intergenic 40.0%
CAAACTGGCAAGGATTTACA+TGG - chr1_2:64093784-64093803 None:intergenic 40.0%
CATGTAAATCCTTGCCAGTT+TGG + chr1_2:64093782-64093801 Msa0084550:three_prime_UTR 40.0%
TTTAAAAGGCCAAACTGGCA+AGG - chr1_2:64093794-64093813 None:intergenic 40.0%
GAGCTACCAGATTTCTCAGT+TGG - chr1_2:64093364-64093383 None:intergenic 45.0%
!! TCTTTCTTGACTTGCCCTGA+TGG - chr1_2:64093391-64093410 None:intergenic 45.0%
!! AGGAGTAGTCCCACTAGTTT+TGG - chr1_2:64093422-64093441 None:intergenic 45.0%
!! TTTCTTTGGTGCTACCTTGG+AGG - chr1_2:64093455-64093474 None:intergenic 45.0%
AGCAGAAATCTCAGCCTAAG+AGG + chr1_2:64093479-64093498 Msa0084550:CDS 45.0%
GAAATCTCAGCCTAAGAGGA+AGG + chr1_2:64093483-64093502 Msa0084550:CDS 45.0%
!!! ATAAGTATATTTTATTTAAA+AGG - chr1_2:64093808-64093827 None:intergenic 5.0%
TCTGGTAGCTCTCAACCATC+AGG + chr1_2:64093373-64093392 Msa0084550:CDS 50.0%
CTGGTAGCTCTCAACCATCA+GGG + chr1_2:64093374-64093393 Msa0084550:CDS 50.0%
AGCCTGCTGCCAAAACTAGT+GGG + chr1_2:64093410-64093429 Msa0084550:CDS 50.0%
TCCTAAAGCTAGAGCCTCCA+AGG + chr1_2:64093438-64093457 Msa0084550:CDS 50.0%
!! ACCTTGGAGGCTCTAGCTTT+AGG - chr1_2:64093442-64093461 None:intergenic 50.0%
GAGCCTGCTGCCAAAACTAG+TGG + chr1_2:64093409-64093428 Msa0084550:CDS 55.0%
!!! GTCCCACTAGTTTTGGCAGC+AGG - chr1_2:64093415-64093434 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 64093290 64093842 64093290 ID=Msa0084550;Name=Msa0084550
chr1_2 mRNA 64093290 64093842 64093290 ID=Msa0084550-mRNA-1;Parent=Msa0084550;Name=Msa0084550-mRNA-1;_AED=0.00;_eAED=0.00;_QI=47|1|1|1|1|1|2|203|68
chr1_2 exon 64093290 64093504 64093290 ID=Msa0084550-mRNA-1:exon:21517;Parent=Msa0084550-mRNA-1
chr1_2 exon 64093601 64093842 64093601 ID=Msa0084550-mRNA-1:exon:21518;Parent=Msa0084550-mRNA-1
chr1_2 five_prime_UTR 64093290 64093336 64093290 ID=Msa0084550-mRNA-1:five_prime_utr;Parent=Msa0084550-mRNA-1
chr1_2 CDS 64093337 64093504 64093337 ID=Msa0084550-mRNA-1:cds;Parent=Msa0084550-mRNA-1
chr1_2 CDS 64093601 64093639 64093601 ID=Msa0084550-mRNA-1:cds;Parent=Msa0084550-mRNA-1
chr1_2 three_prime_UTR 64093640 64093842 64093640 ID=Msa0084550-mRNA-1:three_prime_utr;Parent=Msa0084550-mRNA-1
Gene Sequence

>Msa0084550

ATGGCATCACTCAAAGCTGAGAAACCAACTGAGAAATCTGGTAGCTCTCAACCATCAGGGCAAGTCAAGAAAGAGCCTGCTGCCAAAACTAGTGGGACTACTCCTAAAGCTAGAGCCTCCAAGGTAGCACCAAAGAAAACTGAGCAGAAATCTCAGCCTAAGAGGAAGGCTAGCAGCATTAAGCAGAAGATAACAAGTGAAACTTAA

Protein sequence

>Msa0084550

MASLKAEKPTEKSGSSQPSGQVKKEPAAKTSGTTPKARASKVAPKKTEQKSQPKRKASSIKQKITSET*