AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1383770

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1383770 MtrunA17_Chr3g0142831 95.455 110 5 0 1 110 1 110 1.69e-73 213
Msa1383770 MtrunA17_Chr1g0156781 52.294 109 45 1 1 102 1 109 5.77e-33 111
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1383770 AT1G75810.1 56.800 125 36 3 1 110 4 125 4.61e-41 132

Find 35 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGAAAGCGGCGTTGGGAAT+AGG 0.382735 tig0020612:+55614 None:intergenic
CGTCCGATCACCGGCTTCTC+AGG 0.402331 tig0020612:-55666 Msa1383770:CDS
CGTGGTGGGCTTTATCCTAA+TGG 0.420862 tig0020612:-55792 Msa1383770:CDS
ATTGTAAGGGAGGTATTTGT+TGG 0.421438 tig0020612:-55700 Msa1383770:CDS
CCCACGTCAGCGTTGCCATT+AGG 0.438021 tig0020612:+55777 None:intergenic
TCATCCACCGTTGAATTGTA+AGG 0.438749 tig0020612:-55714 Msa1383770:CDS
CTCTGTGCTCGTACCTTCAC+CGG 0.467220 tig0020612:-55842 Msa1383770:CDS
CTATCATTAGAAAGCGGCGT+TGG 0.486546 tig0020612:+55607 None:intergenic
CGGTGTCGCCGTCCGATCAC+CGG 0.487196 tig0020612:-55675 Msa1383770:CDS
TATCATTAGAAAGCGGCGTT+GGG 0.494168 tig0020612:+55608 None:intergenic
CAGCCACGTAGATTGTTGTA+AGG 0.502912 tig0020612:+55894 None:intergenic
TACAATTCAACGGTGGATGA+TGG 0.506956 tig0020612:+55717 None:intergenic
CTGAAACGGACCTGAGAAGC+CGG 0.530738 tig0020612:+55656 None:intergenic
TCCTAATGGCAACGCTGACG+TGG 0.535183 tig0020612:-55778 Msa1383770:CDS
AAAGCCGTAGAGCTTAATAC+AGG 0.546620 tig0020612:+55865 None:intergenic
GGAATAGGAAATATCTGTTG+TGG 0.547341 tig0020612:+55629 None:intergenic
ATCGCCTGTATTAAGCTCTA+CGG 0.548367 tig0020612:-55869 Msa1383770:CDS
TCTGTTGTGGAATTCTGAAA+CGG 0.550614 tig0020612:+55642 None:intergenic
ATGATATCAACCACCGTGGT+GGG 0.553215 tig0020612:-55806 Msa1383770:CDS
GGACCTGAGAAGCCGGTGAT+CGG 0.556230 tig0020612:+55663 None:intergenic
CTGAGAAGCCGGTGATCGGA+CGG 0.557696 tig0020612:+55667 None:intergenic
AAGGGAGGTATTTGTTGGCA+CGG 0.595376 tig0020612:-55695 Msa1383770:CDS
CATCCACCGTTGAATTGTAA+GGG 0.599993 tig0020612:-55713 Msa1383770:CDS
TCAACGGTGGATGATGGTAG+CGG 0.620485 tig0020612:+55723 None:intergenic
CCTAATGGCAACGCTGACGT+GGG 0.634171 tig0020612:-55777 Msa1383770:CDS
ATACCTCCCTTACAATTCAA+CGG 0.637027 tig0020612:+55707 None:intergenic
ATCTCACTATCATTAGAAAG+CGG 0.641809 tig0020612:+55601 None:intergenic
CATGATATCAACCACCGTGG+TGG 0.657627 tig0020612:-55807 Msa1383770:CDS
CCACCGTTGAATTGTAAGGG+AGG 0.677032 tig0020612:-55710 Msa1383770:CDS
GTAGCGGTTGATAGCATACG+TGG 0.718415 tig0020612:+55739 None:intergenic
CAACCTTACAACAATCTACG+TGG 0.719583 tig0020612:-55897 Msa1383770:CDS
CATTAGGATAAAGCCCACCA+CGG 0.727327 tig0020612:+55793 None:intergenic
CCTCCCTTACAATTCAACGG+TGG 0.751522 tig0020612:+55710 None:intergenic
TAGGATAAAGCCCACCACGG+TGG 0.764291 tig0020612:+55796 None:intergenic
TGTCATGATATCAACCACCG+TGG 0.843191 tig0020612:-55810 Msa1383770:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TATCATGACAACAAAAACGC+CGG + tig0020612:55716-55735 None:intergenic 35.0%
ATACCTCCCTTACAATTCAA+CGG + tig0020612:55832-55851 None:intergenic 35.0%
!! ATTGTAAGGGAGGTATTTGT+TGG - tig0020612:55836-55855 Msa1383770:CDS 35.0%
! TCTGTTGTGGAATTCTGAAA+CGG + tig0020612:55897-55916 None:intergenic 35.0%
GGAATAGGAAATATCTGTTG+TGG + tig0020612:55910-55929 None:intergenic 35.0%
CAACCTTACAACAATCTACG+TGG - tig0020612:55639-55658 Msa1383770:CDS 40.0%
ATCGCCTGTATTAAGCTCTA+CGG - tig0020612:55667-55686 Msa1383770:CDS 40.0%
AAAGCCGTAGAGCTTAATAC+AGG + tig0020612:55674-55693 None:intergenic 40.0%
TACAATTCAACGGTGGATGA+TGG + tig0020612:55822-55841 None:intergenic 40.0%
TCATCCACCGTTGAATTGTA+AGG - tig0020612:55822-55841 Msa1383770:CDS 40.0%
CATCCACCGTTGAATTGTAA+GGG - tig0020612:55823-55842 Msa1383770:CDS 40.0%
CAGCCACGTAGATTGTTGTA+AGG + tig0020612:55645-55664 None:intergenic 45.0%
TGTCATGATATCAACCACCG+TGG - tig0020612:55726-55745 Msa1383770:CDS 45.0%
ATGATATCAACCACCGTGGT+GGG - tig0020612:55730-55749 Msa1383770:CDS 45.0%
CATTAGGATAAAGCCCACCA+CGG + tig0020612:55746-55765 None:intergenic 45.0%
!! AAGGGAGGTATTTGTTGGCA+CGG - tig0020612:55841-55860 Msa1383770:CDS 45.0%
GACAACAAAAACGCCGGTGA+AGG + tig0020612:55710-55729 None:intergenic 50.0%
CATGATATCAACCACCGTGG+TGG - tig0020612:55729-55748 Msa1383770:CDS 50.0%
!! CGTGGTGGGCTTTATCCTAA+TGG - tig0020612:55744-55763 Msa1383770:CDS 50.0%
!! GTAGCGGTTGATAGCATACG+TGG + tig0020612:55800-55819 None:intergenic 50.0%
! TCAACGGTGGATGATGGTAG+CGG + tig0020612:55816-55835 None:intergenic 50.0%
CCTCCCTTACAATTCAACGG+TGG + tig0020612:55829-55848 None:intergenic 50.0%
CCACCGTTGAATTGTAAGGG+AGG - tig0020612:55826-55845 Msa1383770:CDS 50.0%
! TAGAAAGCGGCGTTGGGAAT+AGG + tig0020612:55925-55944 None:intergenic 50.0%
CTCTGTGCTCGTACCTTCAC+CGG - tig0020612:55694-55713 Msa1383770:CDS 55.0%
TAGGATAAAGCCCACCACGG+TGG + tig0020612:55743-55762 None:intergenic 55.0%
TCCTAATGGCAACGCTGACG+TGG - tig0020612:55758-55777 Msa1383770:CDS 55.0%
CCTAATGGCAACGCTGACGT+GGG - tig0020612:55759-55778 Msa1383770:CDS 55.0%
CTGAAACGGACCTGAGAAGC+CGG + tig0020612:55883-55902 None:intergenic 55.0%
CCCACGTCAGCGTTGCCATT+AGG + tig0020612:55762-55781 None:intergenic 60.0%
CTGAGAAGCCGGTGATCGGA+CGG + tig0020612:55872-55891 None:intergenic 60.0%
GGACCTGAGAAGCCGGTGAT+CGG + tig0020612:55876-55895 None:intergenic 60.0%
!! CGTCCGATCACCGGCTTCTC+AGG - tig0020612:55870-55889 Msa1383770:CDS 65.0%
!! CGGTGTCGCCGTCCGATCAC+CGG - tig0020612:55861-55880 Msa1383770:CDS 70.0%
Chromosome Type Strat End Strand Name
tig0020612 gene 55613 55945 55613 ID=Msa1383770;Name=Msa1383770
tig0020612 mRNA 55613 55945 55613 ID=Msa1383770-mRNA-1;Parent=Msa1383770;Name=Msa1383770-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|110
tig0020612 exon 55613 55945 55613 ID=Msa1383770-mRNA-1:exon:8769;Parent=Msa1383770-mRNA-1
tig0020612 CDS 55613 55945 55613 ID=Msa1383770-mRNA-1:cds;Parent=Msa1383770-mRNA-1
Gene Sequence

>Msa1383770

ATGGCTCTATCTGATGCAGTTGTTAGCAACCTTACAACAATCTACGTGGCTGTGATCGCCTGTATTAAGCTCTACGGCTTTCTCTGTGCTCGTACCTTCACCGGCGTTTTTGTTGTCATGATATCAACCACCGTGGTGGGCTTTATCCTAATGGCAACGCTGACGTGGGATGTCTCTCGTAAAGCCACGTATGCTATCAACCGCTACCATCATCCACCGTTGAATTGTAAGGGAGGTATTTGTTGGCACGGTGTCGCCGTCCGATCACCGGCTTCTCAGGTCCGTTTCAGAATTCCACAACAGATATTTCCTATTCCCAACGCCGCTTTCTAA
Protein sequence

>Msa1383770

MALSDAVVSNLTTIYVAVIACIKLYGFLCARTFTGVFVVMISTTVVGFILMATLTWDVSRKATYAINRYHHPPLNCKGGICWHGVAVRSPASQVRFRIPQQIFPIPNAAF*