AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0924730

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0924730 MtrunA17_Chr8g0339041 72.581 124 29 1 1 119 139 262 5.74e-58 182
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0924730 AT1G79220.1 44.000 125 64 2 1 119 165 289 1.60e-26 101

Find 20 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTCGTTGCTATGTGAAAA+TGG 0.268635 6_2:-67197654 Msa0924730:CDS
TCTTACAAAGTTTGGTTTAT+CGG 0.270206 6_2:-67197411 Msa0924730:CDS
GTTGACAATGTCATAATATT+AGG 0.285517 6_2:+67197356 None:intergenic
GTGTTAAATCTTACAAAGTT+TGG 0.362500 6_2:-67197419 Msa0924730:CDS
AAATATGTGGTGACGTCAAT+AGG 0.373849 6_2:-67197473 Msa0924730:CDS
GAAGTCCTTGTAATAATTGC+CGG 0.407956 6_2:+67197549 None:intergenic
CGGCGTATTGAAAAGGGACT+TGG 0.410408 6_2:-67197592 Msa0924730:CDS
AAGAGTTCGGCGTATTGAAA+AGG 0.453219 6_2:-67197599 Msa0924730:CDS
TATGACATTGTCAACTGATA+AGG 0.455700 6_2:-67197348 Msa0924730:CDS
GTTGCACAATATGAAGAGTT+CGG 0.489950 6_2:-67197612 Msa0924730:CDS
TTATCGGATGATGAGATACT+TGG 0.497585 6_2:-67197395 Msa0924730:CDS
TGCAGCCGGCAATTATTACA+AGG 0.522002 6_2:-67197554 Msa0924730:CDS
CAACGAAGGGTTTCTTGCAA+TGG 0.530280 6_2:+67197668 None:intergenic
AGAGTTCGGCGTATTGAAAA+GGG 0.547523 6_2:-67197598 Msa0924730:CDS
TGCAAAATTGTACAAATATG+TGG 0.567808 6_2:-67197486 Msa0924730:CDS
CTACTTGTATATATCATCAA+AGG 0.574978 6_2:+67197527 None:intergenic
GAAAATGGCTATGACATTGA+AGG 0.583187 6_2:-67197639 Msa0924730:CDS
GTCAATAGGCATCTCTCGCG+TGG 0.592493 6_2:-67197459 Msa0924730:CDS
CGTGGAAATGATTCACGCAA+AGG 0.597282 6_2:-67197441 Msa0924730:CDS
GATATATACAAGTAGGACTG+GGG 0.707615 6_2:-67197519 Msa0924730:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CTACTTGTATATATCATCAA+AGG + chr6_2:67197497-67197516 None:intergenic 25.0%
!! CTTTGATGATATATACAAGT+AGG - chr6_2:67197495-67197514 Msa0924730:CDS 25.0%
! TGCAAAATTGTACAAATATG+TGG - chr6_2:67197535-67197554 Msa0924730:CDS 25.0%
! GTGTTAAATCTTACAAAGTT+TGG - chr6_2:67197602-67197621 Msa0924730:CDS 25.0%
!! TCTTACAAAGTTTGGTTTAT+CGG - chr6_2:67197610-67197629 Msa0924730:CDS 25.0%
! GTTGACAATGTCATAATATT+AGG + chr6_2:67197668-67197687 None:intergenic 25.0%
ATGATATATACAAGTAGGAC+TGG - chr6_2:67197500-67197519 Msa0924730:CDS 30.0%
TGATATATACAAGTAGGACT+GGG - chr6_2:67197501-67197520 Msa0924730:CDS 30.0%
TATGACATTGTCAACTGATA+AGG - chr6_2:67197673-67197692 Msa0924730:CDS 30.0%
! CATTTTCACATAGCAACGAA+GGG + chr6_2:67197369-67197388 None:intergenic 35.0%
GAAAATGGCTATGACATTGA+AGG - chr6_2:67197382-67197401 Msa0924730:CDS 35.0%
GTTGCACAATATGAAGAGTT+CGG - chr6_2:67197409-67197428 Msa0924730:CDS 35.0%
GAAGTCCTTGTAATAATTGC+CGG + chr6_2:67197475-67197494 None:intergenic 35.0%
GATATATACAAGTAGGACTG+GGG - chr6_2:67197502-67197521 Msa0924730:CDS 35.0%
! AAATATGTGGTGACGTCAAT+AGG - chr6_2:67197548-67197567 Msa0924730:CDS 35.0%
TTATCGGATGATGAGATACT+TGG - chr6_2:67197626-67197645 Msa0924730:CDS 35.0%
!! GATGAGATACTTGGTCTTTT+TGG - chr6_2:67197635-67197654 Msa0924730:CDS 35.0%
! CCATTTTCACATAGCAACGA+AGG + chr6_2:67197370-67197389 None:intergenic 40.0%
CCTTCGTTGCTATGTGAAAA+TGG - chr6_2:67197367-67197386 Msa0924730:CDS 40.0%
AAGAGTTCGGCGTATTGAAA+AGG - chr6_2:67197422-67197441 Msa0924730:CDS 40.0%
AGAGTTCGGCGTATTGAAAA+GGG - chr6_2:67197423-67197442 Msa0924730:CDS 40.0%
!!! TCAAATGCTGATTTTGCAGC+CGG - chr6_2:67197453-67197472 Msa0924730:CDS 40.0%
CAACGAAGGGTTTCTTGCAA+TGG + chr6_2:67197356-67197375 None:intergenic 45.0%
TGCAGCCGGCAATTATTACA+AGG - chr6_2:67197467-67197486 Msa0924730:CDS 45.0%
!! AAGTAGGACTGGGGTTTTGA+AGG - chr6_2:67197511-67197530 Msa0924730:intron 45.0%
CGTGGAAATGATTCACGCAA+AGG - chr6_2:67197580-67197599 Msa0924730:CDS 45.0%
CGGCGTATTGAAAAGGGACT+TGG - chr6_2:67197429-67197448 Msa0924730:CDS 50.0%
GTCAATAGGCATCTCTCGCG+TGG - chr6_2:67197562-67197581 Msa0924730:CDS 55.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 67197340 67197703 67197340 ID=Msa0924730;Name=Msa0924730
chr6_2 mRNA 67197340 67197703 67197340 ID=Msa0924730-mRNA-1;Parent=Msa0924730;Name=Msa0924730-mRNA-1;_AED=0.41;_eAED=0.43;_QI=0|0|0|1|0|0|2|0|119
chr6_2 exon 67197531 67197703 67197531 ID=Msa0924730-mRNA-1:exon:10623;Parent=Msa0924730-mRNA-1
chr6_2 exon 67197340 67197526 67197340 ID=Msa0924730-mRNA-1:exon:10622;Parent=Msa0924730-mRNA-1
chr6_2 CDS 67197531 67197703 67197531 ID=Msa0924730-mRNA-1:cds;Parent=Msa0924730-mRNA-1
chr6_2 CDS 67197340 67197526 67197340 ID=Msa0924730-mRNA-1:cds;Parent=Msa0924730-mRNA-1
Gene Sequence

>Msa0924730

ATGCTTCATAAGACCATTGCAAGAAACCCTTCGTTGCTATGTGAAAATGGCTATGACATTGAAGGTATTGTTGCACAATATGAAGAGTTCGGCGTATTGAAAAGGGACTTGGTTCAAATGCTGATTTTGCAGCCGGCAATTATTACAAGGACTTCCTTTGATGATATATACAAGACTGGGGTTTTGAAGGATGCAAAATTGTACAAATATGTGGTGACGTCAATAGGCATCTCTCGCGTGGAAATGATTCACGCAAAGGTGTTAAATCTTACAAAGTTTGGTTTATCGGATGATGAGATACTTGGTCTTTTTGGTAAGTCTCCTAATATTATGACATTGTCAACTGATAAGGCACAATGA
Protein sequence

>Msa0924730

MLHKTIARNPSLLCENGYDIEGIVAQYEEFGVLKRDLVQMLILQPAIITRTSFDDIYKTGVLKDAKLYKYVVTSIGISRVEMIHAKVLNLTKFGLSDDEILGLFGKSPNIMTLSTDKAQ*