AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1430940


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1430940 MtrunA17_Chr2g0279561 90.000 100 4 1 1 100 1 94 1.26e-39 127
Msa1430940 MtrunA17_Chr3g0087151 38.393 112 55 5 1 100 1 110 4.27e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATGGCTTCCATCAATTTC+TGG 0.176747 tig0026773:+49614 None:intergenic
TGAGGCAAAGTTGGTACATT+AGG 0.250872 tig0026773:-49799 Msa1430940:intergenic
GGCAATTGTGGCTGTGTTAA+TGG 0.262929 tig0026773:-49745 Msa1430940:intergenic
CCTCAGATTCCTACTGTTCC+TGG 0.290936 tig0026773:+49844 Msa1430940:CDS
ACTTTAGGTGCTTATGGTTT+AGG 0.331666 tig0026773:-49907 Msa1430940:intergenic
GTTGGTACATTAGGGATTAC+TGG 0.335295 tig0026773:-49790 Msa1430940:intergenic
GAGGCAAAGTTGGTACATTA+GGG 0.367979 tig0026773:-49798 Msa1430940:intergenic
ATTACTGGAACACCTAAGTT+TGG 0.371975 tig0026773:-49775 Msa1430940:intergenic
CCACAAATTCCTCAGATTCC+TGG 0.389504 tig0026773:+49871 Msa1430940:CDS
AATGAATGACCAGAAATTGA+TGG 0.402882 tig0026773:-49623 Msa1430940:intergenic
ACACCTAAGTTTGGAATTGT+TGG 0.404545 tig0026773:-49766 Msa1430940:intergenic
GGCAATGGCACTGGCAGATT+AGG 0.425870 tig0026773:-49724 Msa1430940:intergenic
TGAGGCACAGTTGGTATTTG+AGG 0.431733 tig0026773:-49817 Msa1430940:intergenic
TCATCAATGACAAGTATTGA+AGG 0.467180 tig0026773:+49670 Msa1430940:CDS
TTGCCAACAATTCCAAACTT+AGG 0.468746 tig0026773:+49763 Msa1430940:CDS
CCAGGAATCTGAGGAATTTG+TGG 0.472835 tig0026773:-49871 Msa1430930:intergenic
TTTGGAATTGTTGGCAATTG+TGG 0.474516 tig0026773:-49757 Msa1430930:intergenic
GTTGGTATTTGAGGCAAAGT+TGG 0.507961 tig0026773:-49808 Msa1430930:intergenic
TGAGGAATTTGAGGCACAGT+TGG 0.533770 tig0026773:-49826 Msa1430930:intergenic
TGTGTTAATGGCAATGGCAC+TGG 0.535953 tig0026773:-49733 Msa1430930:intergenic
GTAGGAATCTGAGGAATTTG+AGG 0.536589 tig0026773:-49835 Msa1430930:intergenic
TGAGGAATTTGTGGCACACC+AGG 0.542628 tig0026773:-49862 Msa1430930:intergenic
GCTTATGGTTTAGGCACACT+AGG 0.569725 tig0026773:-49898 Msa1430930:intergenic
GAAAATGTTATGAGTAGAAG+TGG 0.572387 tig0026773:-49649 Msa1430930:intergenic
TTAGGCACACTAGGCACACC+AGG 0.574512 tig0026773:-49889 Msa1430930:intergenic
CTAGGCACACCAGGAATCTG+AGG 0.592705 tig0026773:-49880 Msa1430930:intergenic
GGCACTGGCAGATTAGGTAG+TGG 0.603557 tig0026773:-49718 Msa1430930:intergenic
TGTGGCACACCAGGAACAGT+AGG 0.606684 tig0026773:-49853 Msa1430930:intergenic
CCAGGAACAGTAGGAATCTG+AGG 0.611409 tig0026773:-49844 Msa1430930:intergenic
TGTGGCTGTGTTAATGGCAA+TGG 0.622083 tig0026773:-49739 Msa1430930:intergenic
ACTGGCAGATTAGGTAGTGG+TGG 0.639353 tig0026773:-49715 Msa1430930:intergenic
GTAGTGGTGGCAACTCAACA+AGG 0.734703 tig0026773:-49702 Msa1430930:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AATGAATGACCAGAAATTGA+TGG - tig0026773:49626-49645 None:intergenic 30.0%
GAAAATGTTATGAGTAGAAG+TGG - tig0026773:49652-49671 None:intergenic 30.0%
!! TCATCAATGACAAGTATTGA+AGG + tig0026773:49670-49689 Msa1430940:CDS 30.0%
! TTTGGAATTGTTGGCAATTG+TGG - tig0026773:49760-49779 Msa1430940:intergenic 35.0%
TTGCCAACAATTCCAAACTT+AGG + tig0026773:49763-49782 Msa1430940:CDS 35.0%
! ACACCTAAGTTTGGAATTGT+TGG - tig0026773:49769-49788 Msa1430940:intergenic 35.0%
ATTACTGGAACACCTAAGTT+TGG - tig0026773:49778-49797 Msa1430940:intergenic 35.0%
GTTGGTACATTAGGGATTAC+TGG - tig0026773:49793-49812 Msa1430940:intergenic 40.0%
!! GAGGCAAAGTTGGTACATTA+GGG - tig0026773:49801-49820 Msa1430940:intergenic 40.0%
!! TGAGGCAAAGTTGGTACATT+AGG - tig0026773:49802-49821 Msa1430940:intergenic 40.0%
! GTTGGTATTTGAGGCAAAGT+TGG - tig0026773:49811-49830 Msa1430940:intergenic 40.0%
GTAGGAATCTGAGGAATTTG+AGG - tig0026773:49838-49857 Msa1430940:intergenic 40.0%
TGTGTTAATGGCAATGGCAC+TGG - tig0026773:49736-49755 Msa1430940:intergenic 45.0%
TGTGGCTGTGTTAATGGCAA+TGG - tig0026773:49742-49761 Msa1430940:intergenic 45.0%
GGCAATTGTGGCTGTGTTAA+TGG - tig0026773:49748-49767 Msa1430940:intergenic 45.0%
! TGAGGCACAGTTGGTATTTG+AGG - tig0026773:49820-49839 Msa1430940:intergenic 45.0%
! TGAGGAATTTGAGGCACAGT+TGG - tig0026773:49829-49848 Msa1430940:intergenic 45.0%
CCAGGAATCTGAGGAATTTG+TGG - tig0026773:49874-49893 Msa1430940:intergenic 45.0%
CCACAAATTCCTCAGATTCC+TGG + tig0026773:49871-49890 Msa1430940:CDS 45.0%
GTAGTGGTGGCAACTCAACA+AGG - tig0026773:49705-49724 Msa1430940:intergenic 50.0%
! ACTGGCAGATTAGGTAGTGG+TGG - tig0026773:49718-49737 Msa1430940:intergenic 50.0%
CCAGGAACAGTAGGAATCTG+AGG - tig0026773:49847-49866 Msa1430940:intergenic 50.0%
CCTCAGATTCCTACTGTTCC+TGG + tig0026773:49844-49863 Msa1430940:CDS 50.0%
TGAGGAATTTGTGGCACACC+AGG - tig0026773:49865-49884 Msa1430940:intergenic 50.0%
!! GGCACTGGCAGATTAGGTAG+TGG - tig0026773:49721-49740 Msa1430940:intergenic 55.0%
!! GGCAATGGCACTGGCAGATT+AGG - tig0026773:49727-49746 Msa1430940:intergenic 55.0%
TGTGGCACACCAGGAACAGT+AGG - tig0026773:49856-49875 Msa1430940:intergenic 55.0%
CTAGGCACACCAGGAATCTG+AGG - tig0026773:49883-49902 Msa1430940:intergenic 55.0%
TTAGGCACACTAGGCACACC+AGG - tig0026773:49892-49911 Msa1430940:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0026773 gene 49616 49918 49616 ID=Msa1430940;Name=Msa1430940
tig0026773 mRNA 49616 49918 49616 ID=Msa1430940-mRNA-1;Parent=Msa1430940;Name=Msa1430940-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|100
tig0026773 exon 49616 49918 49616 ID=Msa1430940-mRNA-1:exon:7289;Parent=Msa1430940-mRNA-1
tig0026773 CDS 49616 49918 49616 ID=Msa1430940-mRNA-1:cds;Parent=Msa1430940-mRNA-1
Gene Sequence

>Msa1430940

ATGGCTTCCATCAATTTCTGGTCATTCATTTTACCACTTCTACTCATAACATTTTCATCAATGACAAGTATTGAAGGAGCACGTAACCTTGTTGAGTTGCCACCACTACCTAATCTGCCAGTGCCATTGCCATTAACACAGCCACAATTGCCAACAATTCCAAACTTAGGTGTTCCAGTAATCCCTAATGTACCAACTTTGCCTCAAATACCAACTGTGCCTCAAATTCCTCAGATTCCTACTGTTCCTGGTGTGCCACAAATTCCTCAGATTCCTGGTGTGCCTAGTGTGCCTAAACCATAA

Protein sequence

>Msa1430940

MASINFWSFILPLLLITFSSMTSIEGARNLVELPPLPNLPVPLPLTQPQLPTIPNLGVPVIPNVPTLPQIPTVPQIPQIPTVPGVPQIPQIPGVPSVPKP*