AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0796820

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0796820 MtrunA17_Chr5g0399701 73.643 129 25 3 1 127 1 122 9.30e-32 108
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 47 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCTCATGATTGGGCTTCC+TGG 0.247172 5_3:+8840904 None:intergenic
CTTCCTGGTGGCAGTGATAC+AGG 0.253219 5_3:+8840919 None:intergenic
GTGATACAGGGGAGGGTGCT+TGG 0.269078 5_3:+8840932 None:intergenic
CTCGGGCCCATGCTCATGCT+TGG 0.274606 5_3:+8840835 None:intergenic
CTCATGCTTGGGCTCATGCT+CGG 0.309614 5_3:+8840877 None:intergenic
CTCGGGCTCATGCTCATGAT+TGG 0.309691 5_3:+8840895 None:intergenic
ATGCTACCATTATTCTTTGC+TGG 0.315901 5_3:-8840658 Msa0796820:CDS
CTCATGCTTGGGCTCATACT+TGG 0.360267 5_3:+8840847 None:intergenic
CTGTGAACAACCGCGTTGCT+TGG 0.369585 5_3:+8840694 None:intergenic
TCATGCTTGGGCTCATGCTC+GGG 0.375831 5_3:+8840878 None:intergenic
TTGCTTGGACTTGAAGCAAC+TGG 0.388265 5_3:+8840709 None:intergenic
GAAGGTGATGGTGAGGAAGC+TGG 0.389101 5_3:+8840757 None:intergenic
CTTGGACTCATGCTCATGCT+TGG 0.391770 5_3:+8840865 None:intergenic
TGATACAGGGGAGGGTGCTT+GGG 0.395750 5_3:+8840933 None:intergenic
TCGGGCCCATGCTCATGCTT+GGG 0.410770 5_3:+8840836 None:intergenic
GGGAAAGGTGGGCTCATACT+TGG 0.429231 5_3:+8840799 None:intergenic
CTTGGACTCCTGCTCATGCT+CGG 0.443131 5_3:+8840817 None:intergenic
TTGGACTCATGCTCATGCTT+GGG 0.445374 5_3:+8840866 None:intergenic
GCTAGCCATGTCTCTTGCTC+TGG 0.451838 5_3:-8840971 Msa0796820:CDS
GCAGTACCAGCAAAGAATAA+TGG 0.458474 5_3:+8840652 None:intergenic
TTCCTGGTGGCAGTGATACA+GGG 0.459768 5_3:+8840920 None:intergenic
AGGGGAGGGTGCTTGGGCTA+TGG 0.461739 5_3:+8840939 None:intergenic
TCGGGCTCATGCTCATGATT+GGG 0.467264 5_3:+8840896 None:intergenic
TTGGACTCCTGCTCATGCTC+GGG 0.483287 5_3:+8840818 None:intergenic
GCATGGGCCCGAGCATGAGC+AGG 0.497816 5_3:-8840825 Msa0796820:CDS
GGAGATGGTGAAGCAGCAGT+AGG 0.535138 5_3:+8840778 None:intergenic
GGTGGCAGTGATACAGGGGA+GGG 0.541381 5_3:+8840925 None:intergenic
ATTATCAGACATCGATTCTC+CGG 0.547569 5_3:+8840732 None:intergenic
GATTCTCCGGTGGAAGGTGA+TGG 0.549766 5_3:+8840745 None:intergenic
TATGAGCCCAAGCATGAGCA+TGG 0.552073 5_3:-8840842 Msa0796820:CDS
TCCTGGTGGCAGTGATACAG+GGG 0.558755 5_3:+8840921 None:intergenic
TGGTGGCAGTGATACAGGGG+AGG 0.573893 5_3:+8840924 None:intergenic
TCCCCTGTATCACTGCCACC+AGG 0.577522 5_3:-8840922 Msa0796820:CDS
GAAGCAGCAGTAGGGAAAGG+TGG 0.580658 5_3:+8840787 None:intergenic
AAGCAGCAGTAGGGAAAGGT+GGG 0.588458 5_3:+8840788 None:intergenic
TCCTCACCATCACCTTCCAC+CGG 0.596602 5_3:-8840751 Msa0796820:CDS
GGTGAAGCAGCAGTAGGGAA+AGG 0.605004 5_3:+8840784 None:intergenic
GATGGTGAGGAAGCTGGAGA+TGG 0.605949 5_3:+8840763 None:intergenic
GAGATGGTGAAGCAGCAGTA+GGG 0.615443 5_3:+8840779 None:intergenic
CTCATGATTGGGCTTCCTGG+TGG 0.617444 5_3:+8840907 None:intergenic
GACATCGATTCTCCGGTGGA+AGG 0.621189 5_3:+8840739 None:intergenic
TCCGGTGGAAGGTGATGGTG+AGG 0.623620 5_3:+8840750 None:intergenic
ATGAGCCCAAGCATGAGCAT+GGG 0.631721 5_3:-8840841 Msa0796820:CDS
TGTCACCAGAGCAAGAGACA+TGG 0.667198 5_3:+8840966 None:intergenic
AGACATGGCTAGCATGAGTG+TGG 0.667612 5_3:+8840981 None:intergenic
ATCAGACATCGATTCTCCGG+TGG 0.683845 5_3:+8840735 None:intergenic
TGCTTCAAGTCCAAGCAACG+CGG 0.698866 5_3:-8840704 Msa0796820:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATCAGACATCGATTCTC+CGG + chr5_3:8840904-8840923 None:intergenic 35.0%
ATGCTACCATTATTCTTTGC+TGG - chr5_3:8840975-8840994 Msa0796820:CDS 35.0%
GCAGTACCAGCAAAGAATAA+TGG + chr5_3:8840984-8841003 None:intergenic 40.0%
TTGGACTCATGCTCATGCTT+GGG + chr5_3:8840770-8840789 None:intergenic 45.0%
TTGCTTGGACTTGAAGCAAC+TGG + chr5_3:8840927-8840946 None:intergenic 45.0%
AGACATGGCTAGCATGAGTG+TGG + chr5_3:8840655-8840674 None:intergenic 50.0%
TGTCACCAGAGCAAGAGACA+TGG + chr5_3:8840670-8840689 None:intergenic 50.0%
TTCCTGGTGGCAGTGATACA+GGG + chr5_3:8840716-8840735 None:intergenic 50.0%
ATGCTCATGATTGGGCTTCC+TGG + chr5_3:8840732-8840751 None:intergenic 50.0%
TCGGGCTCATGCTCATGATT+GGG + chr5_3:8840740-8840759 None:intergenic 50.0%
CTTGGACTCATGCTCATGCT+TGG + chr5_3:8840771-8840790 None:intergenic 50.0%
CTCATGCTTGGGCTCATACT+TGG + chr5_3:8840789-8840808 None:intergenic 50.0%
TATGAGCCCAAGCATGAGCA+TGG - chr5_3:8840791-8840810 Msa0796820:CDS 50.0%
ATGAGCCCAAGCATGAGCAT+GGG - chr5_3:8840762-8840781 Msa0796820:CDS 50.0%
AAGCAGCAGTAGGGAAAGGT+GGG + chr5_3:8840848-8840867 None:intergenic 50.0%
GAGATGGTGAAGCAGCAGTA+GGG + chr5_3:8840857-8840876 None:intergenic 50.0%
!! ATCAGACATCGATTCTCCGG+TGG + chr5_3:8840901-8840920 None:intergenic 50.0%
TGCTTCAAGTCCAAGCAACG+CGG - chr5_3:8840929-8840948 Msa0796820:CDS 50.0%
GCTAGCCATGTCTCTTGCTC+TGG - chr5_3:8840662-8840681 Msa0796820:CDS 55.0%
!! TGATACAGGGGAGGGTGCTT+GGG + chr5_3:8840703-8840722 None:intergenic 55.0%
TCCTGGTGGCAGTGATACAG+GGG + chr5_3:8840715-8840734 None:intergenic 55.0%
CTTCCTGGTGGCAGTGATAC+AGG + chr5_3:8840717-8840736 None:intergenic 55.0%
CTCATGATTGGGCTTCCTGG+TGG + chr5_3:8840729-8840748 None:intergenic 55.0%
CTCGGGCTCATGCTCATGAT+TGG + chr5_3:8840741-8840760 None:intergenic 55.0%
TCATGCTTGGGCTCATGCTC+GGG + chr5_3:8840758-8840777 None:intergenic 55.0%
CTCATGCTTGGGCTCATGCT+CGG + chr5_3:8840759-8840778 None:intergenic 55.0%
TTGGACTCCTGCTCATGCTC+GGG + chr5_3:8840818-8840837 None:intergenic 55.0%
CTTGGACTCCTGCTCATGCT+CGG + chr5_3:8840819-8840838 None:intergenic 55.0%
! GGGAAAGGTGGGCTCATACT+TGG + chr5_3:8840837-8840856 None:intergenic 55.0%
GAAGCAGCAGTAGGGAAAGG+TGG + chr5_3:8840849-8840868 None:intergenic 55.0%
GGTGAAGCAGCAGTAGGGAA+AGG + chr5_3:8840852-8840871 None:intergenic 55.0%
GGAGATGGTGAAGCAGCAGT+AGG + chr5_3:8840858-8840877 None:intergenic 55.0%
GATGGTGAGGAAGCTGGAGA+TGG + chr5_3:8840873-8840892 None:intergenic 55.0%
! GAAGGTGATGGTGAGGAAGC+TGG + chr5_3:8840879-8840898 None:intergenic 55.0%
TCCTCACCATCACCTTCCAC+CGG - chr5_3:8840882-8840901 Msa0796820:CDS 55.0%
GATTCTCCGGTGGAAGGTGA+TGG + chr5_3:8840891-8840910 None:intergenic 55.0%
!! GACATCGATTCTCCGGTGGA+AGG + chr5_3:8840897-8840916 None:intergenic 55.0%
CTGTGAACAACCGCGTTGCT+TGG + chr5_3:8840942-8840961 None:intergenic 55.0%
!! GTGATACAGGGGAGGGTGCT+TGG + chr5_3:8840704-8840723 None:intergenic 60.0%
GGTGGCAGTGATACAGGGGA+GGG + chr5_3:8840711-8840730 None:intergenic 60.0%
TGGTGGCAGTGATACAGGGG+AGG + chr5_3:8840712-8840731 None:intergenic 60.0%
TCCCCTGTATCACTGCCACC+AGG - chr5_3:8840711-8840730 Msa0796820:CDS 60.0%
TCGGGCCCATGCTCATGCTT+GGG + chr5_3:8840800-8840819 None:intergenic 60.0%
! TCCGGTGGAAGGTGATGGTG+AGG + chr5_3:8840886-8840905 None:intergenic 60.0%
!! AGGGGAGGGTGCTTGGGCTA+TGG + chr5_3:8840697-8840716 None:intergenic 65.0%
CTCGGGCCCATGCTCATGCT+TGG + chr5_3:8840801-8840820 None:intergenic 65.0%
GCATGGGCCCGAGCATGAGC+AGG - chr5_3:8840808-8840827 Msa0796820:CDS 70.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 8840636 8841019 8840636 ID=Msa0796820;Name=Msa0796820
chr5_3 mRNA 8840636 8841019 8840636 ID=Msa0796820-mRNA-1;Parent=Msa0796820;Name=Msa0796820-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|127
chr5_3 exon 8840636 8841019 8840636 ID=Msa0796820-mRNA-1:exon:3775;Parent=Msa0796820-mRNA-1
chr5_3 CDS 8840636 8841019 8840636 ID=Msa0796820-mRNA-1:cds;Parent=Msa0796820-mRNA-1
Gene Sequence

>Msa0796820

ATGGCACTCACACGTGCCACACTCATGCTAGCCATGTCTCTTGCTCTGGTGACATTGTCCATAGCCCAAGCACCCTCCCCTGTATCACTGCCACCAGGAAGCCCAATCATGAGCATGAGCCCGAGCATGAGCCCAAGCATGAGCATGAGTCCAAGTATGAGCCCAAGCATGAGCATGGGCCCGAGCATGAGCAGGAGTCCAAGTATGAGCCCACCTTTCCCTACTGCTGCTTCACCATCTCCAGCTTCCTCACCATCACCTTCCACCGGAGAATCGATGTCTGATAATCCAGTTGCTTCAAGTCCAAGCAACGCGGTTGTTCACAGAAGCAGTGTTTTCATGCTACCATTATTCTTTGCTGGTACTGCACTGCTTCTTGCTTAA
Protein sequence

>Msa0796820

MALTRATLMLAMSLALVTLSIAQAPSPVSLPPGSPIMSMSPSMSPSMSMSPSMSPSMSMGPSMSRSPSMSPPFPTAASPSPASSPSPSTGESMSDNPVASSPSNAVVHRSSVFMLPLFFAGTALLLA*