AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene056448


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATTACCTGATAAATTATT+TGG 0.148310 8.3:-32985718 None:intergenic
CTTTGGTCACTATTTACTTT+GGG 0.231865 8.3:+32985201 MS.gene056448:CDS
TCCATGCTTGTGTTTCAATT+TGG 0.238612 8.3:+32986444 MS.gene056448:CDS
GCATCATGTTTCTCACTATA+TGG 0.243670 8.3:+32985518 MS.gene056448:CDS
AGATGCAGTAAGCAATTATA+TGG 0.327192 8.3:+32985595 MS.gene056448:CDS
CATCTTCATATGCTCCCTTA+TGG 0.334725 8.3:+32986601 MS.gene056448:CDS
ACTTTGGTCACTATTTACTT+TGG 0.380949 8.3:+32985200 MS.gene056448:CDS
TGGATGTTCTCACTGGATAA+AGG 0.409512 8.3:-32986045 None:intergenic
CTGGTATGAAATTCCTGATC+AGG 0.431887 8.3:-32985665 None:intergenic
AAAATCAAGACTGTAATGAT+TGG 0.445159 8.3:-32986065 None:intergenic
ACTGACTAAAAGTCCTGATC+AGG 0.477095 8.3:+32985652 MS.gene056448:CDS
TTTCATACCAGGGAAATTGC+TGG 0.477383 8.3:+32985677 MS.gene056448:CDS
ATATGGCTCCAGGTCTTGAA+AGG 0.492151 8.3:+32985612 MS.gene056448:CDS
TGACACATCATTGAATTGTA+TGG 0.503761 8.3:+32986239 MS.gene056448:CDS
GAACAGATTGACCTTCACTT+TGG 0.506577 8.3:+32985184 None:intergenic
CTGATCAGGAATTTCATACC+AGG 0.518748 8.3:+32985666 MS.gene056448:CDS
AAGATGACAAGTCAAGGAAA+GGG 0.529829 8.3:-32986584 None:intergenic
TAATGATTGGATGTTCTCAC+TGG 0.531785 8.3:-32986052 None:intergenic
GTAAGCAATTATATGGCTCC+AGG 0.541746 8.3:+32985602 MS.gene056448:CDS
TATGGCTCCAGGTCTTGAAA+GGG 0.542384 8.3:+32985613 MS.gene056448:CDS
GAAGATGACAAGTCAAGGAA+AGG 0.548910 8.3:-32986585 None:intergenic
ACCAAATTGAAACACAAGCA+TGG 0.552719 8.3:-32986445 None:intergenic
AAATATGCAAATCTAAACAC+TGG 0.556712 8.3:-32986380 None:intergenic
GACAAGTCAAGGAAAGGGTA+AGG 0.557794 8.3:-32986579 None:intergenic
TTTGGTGGAAGAACAGTCAA+TGG 0.558349 8.3:+32985563 MS.gene056448:CDS
TTTGGTCACTATTTACTTTG+GGG 0.562730 8.3:+32985202 MS.gene056448:CDS
CTGCATTTGTGATTATTCAG+TGG 0.563990 8.3:+32986417 MS.gene056448:CDS
AGGGAAATTGCTGGTGTATG+TGG 0.569209 8.3:+32985686 MS.gene056448:CDS
TCTAAAACCCTTTCAAGACC+TGG 0.572549 8.3:-32985620 None:intergenic
CATATGAAGATGACAAGTCA+AGG 0.594852 8.3:-32986590 None:intergenic
AAATTGAGAACATACCATAA+GGG 0.597196 8.3:-32986615 None:intergenic
ACATACACCAGCAATTTCCC+TGG 0.622121 8.3:-32985684 None:intergenic
GTAAATAGTGACCAAAGTGA+AGG 0.623574 8.3:-32985195 None:intergenic
TGATCAGGAATTTCATACCA+GGG 0.670283 8.3:+32985667 MS.gene056448:CDS
AATTCAATGATGTGTCACCA+AGG 0.698539 8.3:-32986233 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAAAATGTTAAATTATTG+AGG + chr8.3:32985299-32985318 MS.gene056448:intron 10.0%
!! TAAAAATGTTAAATTATTGA+GGG + chr8.3:32985300-32985319 MS.gene056448:intron 10.0%
!! AAATTACCTGATAAATTATT+TGG - chr8.3:32985721-32985740 None:intergenic 15.0%
!! ACAGTAATAATAAAAAAAAG+TGG - chr8.3:32986483-32986502 None:intergenic 15.0%
!! TTATTTAAGCACAAAAAATT+TGG + chr8.3:32985545-32985564 MS.gene056448:CDS 15.0%
!! AATAAAAAAAAGTGGATGTT+AGG - chr8.3:32986475-32986494 None:intergenic 20.0%
!! AGAAAAACAAAAATTAGTTG+CGG - chr8.3:32985413-32985432 None:intergenic 20.0%
!!! AATTGTTTCTTATCAAATTC+AGG + chr8.3:32985931-32985950 MS.gene056448:intron 20.0%
!!! CATTTTCCAAATAATTTATC+AGG + chr8.3:32985712-32985731 MS.gene056448:CDS 20.0%
! AAAATCAAGACTGTAATGAT+TGG - chr8.3:32986068-32986087 None:intergenic 25.0%
! AAATATGCAAATCTAAACAC+TGG - chr8.3:32986383-32986402 None:intergenic 25.0%
! ATCTCTTGAGAAATTATCTT+CGG + chr8.3:32985769-32985788 MS.gene056448:intron 25.0%
! TATTGAGGGAAATATAGAAA+GGG + chr8.3:32985314-32985333 MS.gene056448:intron 25.0%
! TTATTGAGGGAAATATAGAA+AGG + chr8.3:32985313-32985332 MS.gene056448:intron 25.0%
! TTTAAGCACAAAAAATTTGG+TGG + chr8.3:32985548-32985567 MS.gene056448:CDS 25.0%
!!! TTCTCACTGATTTTGTATTT+TGG + chr8.3:32986017-32986036 MS.gene056448:CDS 25.0%
AAGGAGAAAAACAGCATTAA+TGG - chr8.3:32986217-32986236 None:intergenic 30.0%
ACTTTGGTCACTATTTACTT+TGG + chr8.3:32985200-32985219 MS.gene056448:CDS 30.0%
AGATGCAGTAAGCAATTATA+TGG + chr8.3:32985595-32985614 MS.gene056448:CDS 30.0%
CTTTGGTCACTATTTACTTT+GGG + chr8.3:32985201-32985220 MS.gene056448:CDS 30.0%
TCTCTTGAGAAATTATCTTC+GGG + chr8.3:32985770-32985789 MS.gene056448:intron 30.0%
TGACACATCATTGAATTGTA+TGG + chr8.3:32986239-32986258 MS.gene056448:CDS 30.0%
TTTGGTCACTATTTACTTTG+GGG + chr8.3:32985202-32985221 MS.gene056448:CDS 30.0%
! GATTTGCATATTTTGTCTTG+TGG + chr8.3:32986390-32986409 MS.gene056448:CDS 30.0%
! TTTTCATTATAGACTTGTGC+AGG + chr8.3:32985986-32986005 MS.gene056448:intron 30.0%
!!! ATTAATGCTGTTTTTCTCCT+TGG + chr8.3:32986216-32986235 MS.gene056448:CDS 30.0%
AAGATGACAAGTCAAGGAAA+GGG - chr8.3:32986587-32986606 None:intergenic 35.0%
AATTCAATGATGTGTCACCA+AGG - chr8.3:32986236-32986255 None:intergenic 35.0%
ACCAAATTGAAACACAAGCA+TGG - chr8.3:32986448-32986467 None:intergenic 35.0%
CATATGAAGATGACAAGTCA+AGG - chr8.3:32986593-32986612 None:intergenic 35.0%
CGTGTCACAAAATTTAGTGA+CGG - chr8.3:32985364-32985383 None:intergenic 35.0%
CTGCATTTGTGATTATTCAG+TGG + chr8.3:32986417-32986436 MS.gene056448:CDS 35.0%
GCATCATGTTTCTCACTATA+TGG + chr8.3:32985518-32985537 MS.gene056448:CDS 35.0%
GGTATTCAGTGTTTCCAAAA+TGG + chr8.3:32985828-32985847 MS.gene056448:intron 35.0%
GTAAATAGTGACCAAAGTGA+AGG - chr8.3:32985198-32985217 None:intergenic 35.0%
TAATGATTGGATGTTCTCAC+TGG - chr8.3:32986055-32986074 None:intergenic 35.0%
TCCATGCTTGTGTTTCAATT+TGG + chr8.3:32986444-32986463 MS.gene056448:CDS 35.0%
TGATCAGGAATTTCATACCA+GGG + chr8.3:32985667-32985686 MS.gene056448:CDS 35.0%
! CGTCACTAAATTTTGTGACA+CGG + chr8.3:32985362-32985381 MS.gene056448:intron 35.0%
!! TCACTATTTACTTTGGGGTA+AGG + chr8.3:32985207-32985226 MS.gene056448:intron 35.0%
ACTGACTAAAAGTCCTGATC+AGG + chr8.3:32985652-32985671 MS.gene056448:CDS 40.0%
CTGATCAGGAATTTCATACC+AGG + chr8.3:32985666-32985685 MS.gene056448:CDS 40.0%
CTGGAAATCTCTGCATGTTT+AGG - chr8.3:32986364-32986383 None:intergenic 40.0%
CTGGTATGAAATTCCTGATC+AGG - chr8.3:32985668-32985687 None:intergenic 40.0%
GAAGATGACAAGTCAAGGAA+AGG - chr8.3:32986588-32986607 None:intergenic 40.0%
GTAAGCAATTATATGGCTCC+AGG + chr8.3:32985602-32985621 MS.gene056448:CDS 40.0%
TAACCTTCATTTGTCACAGG+TGG + chr8.3:32986556-32986575 MS.gene056448:intron 40.0%
TCTGTGATCACGATCTGTAA+CGG + chr8.3:32985807-32985826 MS.gene056448:intron 40.0%
TGCTAACCTTCATTTGTCAC+AGG + chr8.3:32986553-32986572 MS.gene056448:intron 40.0%
TGGATGTTCTCACTGGATAA+AGG - chr8.3:32986048-32986067 None:intergenic 40.0%
TTGTGACACGGAAATTAGAG+AGG + chr8.3:32985374-32985393 MS.gene056448:intron 40.0%
TTTCATACCAGGGAAATTGC+TGG + chr8.3:32985677-32985696 MS.gene056448:CDS 40.0%
TTTGGTGGAAGAACAGTCAA+TGG + chr8.3:32985563-32985582 MS.gene056448:CDS 40.0%
! TCAGGACTTTTAGTCAGTTC+AGG - chr8.3:32985650-32985669 None:intergenic 40.0%
! TCTAAAACCCTTTCAAGACC+TGG - chr8.3:32985623-32985642 None:intergenic 40.0%
ACATACACCAGCAATTTCCC+TGG - chr8.3:32985687-32985706 None:intergenic 45.0%
AGGGAAATTGCTGGTGTATG+TGG + chr8.3:32985686-32985705 MS.gene056448:CDS 45.0%
ATATGGCTCCAGGTCTTGAA+AGG + chr8.3:32985612-32985631 MS.gene056448:CDS 45.0%
GACAAGTCAAGGAAAGGGTA+AGG - chr8.3:32986582-32986601 None:intergenic 45.0%
GATTGACGCGACCTCAATAT+CGG - chr8.3:32985862-32985881 None:intergenic 45.0%
TATGGCTCCAGGTCTTGAAA+GGG + chr8.3:32985613-32985632 MS.gene056448:CDS 45.0%
!! TATCGGTCACGTTGCCATTT+TGG - chr8.3:32985845-32985864 None:intergenic 45.0%
AGGCCACCTGTGACAAATGA+AGG - chr8.3:32986562-32986581 None:intergenic 50.0%
TGGCAACGTGACCGATATTG+AGG + chr8.3:32985848-32985867 MS.gene056448:intron 50.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 32985190 32986622 32985190 ID=MS.gene056448
chr8.3 mRNA 32985190 32986622 32985190 ID=MS.gene056448.t1;Parent=MS.gene056448
chr8.3 exon 32985190 32985223 32985190 ID=MS.gene056448.t1.exon1;Parent=MS.gene056448.t1
chr8.3 CDS 32985190 32985223 32985190 ID=cds.MS.gene056448.t1;Parent=MS.gene056448.t1
chr8.3 exon 32985515 32985733 32985515 ID=MS.gene056448.t1.exon2;Parent=MS.gene056448.t1
chr8.3 CDS 32985515 32985733 32985515 ID=cds.MS.gene056448.t1;Parent=MS.gene056448.t1
chr8.3 exon 32985998 32986087 32985998 ID=MS.gene056448.t1.exon3;Parent=MS.gene056448.t1
chr8.3 CDS 32985998 32986087 32985998 ID=cds.MS.gene056448.t1;Parent=MS.gene056448.t1
chr8.3 exon 32986195 32986260 32986195 ID=MS.gene056448.t1.exon4;Parent=MS.gene056448.t1
chr8.3 CDS 32986195 32986260 32986195 ID=cds.MS.gene056448.t1;Parent=MS.gene056448.t1
chr8.3 exon 32986374 32986465 32986374 ID=MS.gene056448.t1.exon5;Parent=MS.gene056448.t1
chr8.3 CDS 32986374 32986465 32986374 ID=cds.MS.gene056448.t1;Parent=MS.gene056448.t1
chr8.3 exon 32986575 32986622 32986575 ID=MS.gene056448.t1.exon6;Parent=MS.gene056448.t1
chr8.3 CDS 32986575 32986622 32986575 ID=cds.MS.gene056448.t1;Parent=MS.gene056448.t1
Gene Sequence

>MS.gene056448

ATTGACCTTCACTTTGGTCACTATTTACTTTGGGGTAAGGCTTTCAATTTCAGAATCTTGTACATTATAGAAGATAAATTAACATGAAAATGTGATATATATCTCACTAATAAAAATGTTAAATTATTGAGGGAAATATAGAAAGGGAAAACGTGAAATTCTTCTCTAATTCCGTCACTAAATTTTGTGACACGGAAATTAGAGAGGAGTTTTATTTCTTCCGCAACTAATTTTTGTTTTTCTAGTAGTAGTGTCTATTTTTTTAAAATGTTTTAAGTAGTTCATATATTATTTAAGTGACATATACTCTTAATTTTACTTTCAGCTTGCATCATGTTTCTCACTATATGGATGTTTATTTAAGCACAAAAAATTTGGTGGAAGAACAGTCAATGGTGCTTCTTTAGATGCAGTAAGCAATTATATGGCTCCAGGTCTTGAAAGGGTTTTAGATATTCCTGAACTGACTAAAAGTCCTGATCAGGAATTTCATACCAGGGAAATTGCTGGTGTATGTGGTTACATTTTCCAAATAATTTATCAGGTAATTTAATTTAGTGATTCAATTTGTGTATATGAATCTCTTGAGAAATTATCTTCGGGATTTTAAATAAAGATCTGTGATCACGATCTGTAACGGTATTCAGTGTTTCCAAAATGGCAACGTGACCGATATTGAGGTCGCGTCAATCATATTTGACTACAATTTTCATTATTTGATTAACTTGTTTAACAAGTTTCAATTGTTTCTTATCAAATTCAGGAGACAATCTATTGATATAATTATTTTTTCTCATTTTCATTATAGACTTGTGCAGGTGCTGTATTTCTCACTGATTTTGTATTTTGGTTTGTCCTTTATCCAGTGAGAACATCCAATCATTACAGTCTTGATTTTGTAAGTATCATCAACAAAAGTAATTTGAGATTTGCATTGAATATATATCAATGTCATAAGATGCTTTTCTTTCATTTGAAAGTATTTGCACTTTTCAATTCTTGCAGTTGATTTTTTGTATGCATACCATTAATGCTGTTTTTCTCCTTGGTGACACATCATTGAATTGTATGGTGAGTTTTTTTATAGCAGTTAATAGTTAATAATATTTTTTAATTGAAAAAAATTATGTTAAGAATCTAGTTCAAAACTTTAAATTAACAACTATTTACTCCTAAACATGCAGAGATTTCCAGTGTTTAGATTTGCATATTTTGTCTTGTGGACAGCTGCATTTGTGATTATTCAGTGGATAATCCATGCTTGTGTTTCAATTTGGTAAAGCCTAACATCCACTTTTTTTTATTATTACTGTTTTTTTTAGTAAAATACAATACATGAATATGATTTTCTTCATTTGTAATTTGCTAACCTTCATTTGTCACAGGTGGCCTTACCCTTTCCTTGACTTGTCATCTTCATATGCTCCCTTATG

Protein sequence

>MS.gene056448.t1

IDLHFGHYLLWACIMFLTIWMFIUAQKIWWKNSQWCFFRCSKQLYGSRSUKGFRYSUTDUKSUSGISYQGNCWCMWLHFPNNLSDLCRCCISHUFCILVCPLSSENIQSLQSUFFDFLYAYHUCCFSPWUHIIELYEISSVUICIFCLVDSCICDYSVDNPCLCFNLVALPFPULVIFICSLM