AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1366760

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1366760 MtrunA17_Chr4g0057011 98.214 168 3 0 1 168 1 168 4.02e-120 335
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1366760 AT4G12340.1 46.341 164 81 4 1 161 1 160 1.02e-38 130

Find 49 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACCTTACGTTTAACCCTTC+TGG 0.110791 tig0018481:-114673 None:intergenic
CATGGAGGTCCTTTGCCTTT+TGG 0.128221 tig0018481:-114914 None:intergenic
GCCGTGCAACGCTCAGGCTT+TGG 0.255174 tig0018481:-114960 None:intergenic
TTCTTCAGCTACATTAGGTT+GGG 0.280071 tig0018481:-114715 None:intergenic
TTACGTAGGCTTGGTCCTTT+AGG 0.283433 tig0018481:+115071 Msa1366760:CDS
TCAGGAAAGTGAGAAGGTTT+TGG 0.292107 tig0018481:+114848 Msa1366760:CDS
ACCTTACGTTTAACCCTTCT+GGG 0.292509 tig0018481:-114672 None:intergenic
CCGTGCAACGCTCAGGCTTT+GGG 0.326501 tig0018481:-114959 None:intergenic
TCAGGTTCTTCAGCTACATT+AGG 0.334051 tig0018481:-114720 None:intergenic
AGGCATTCGAACTGTGCTTC+AGG 0.363412 tig0018481:+114830 Msa1366760:CDS
CTGGGTTTCTTCTTCACCAC+AGG 0.385753 tig0018481:-114654 None:intergenic
GCAAGAGAAGCAAATGTTGC+AGG 0.389405 tig0018481:+114884 Msa1366760:CDS
CTCTCAGCCGTGCAACGCTC+AGG 0.393105 tig0018481:-114966 None:intergenic
GGGTGTGCAGGCAATGTTGC+AGG 0.407000 tig0018481:-114789 None:intergenic
TGCACTGGCCACACTGGAGC+AGG 0.421988 tig0018481:-114750 None:intergenic
CCTTCCCAGTCCGAGTTAGA+AGG 0.426504 tig0018481:+114810 Msa1366760:CDS
GTTCTTCAGCTACATTAGGT+TGG 0.436982 tig0018481:-114716 None:intergenic
ATAACTTATTTGCCACCTAA+AGG 0.471447 tig0018481:-115086 None:intergenic
GCAGATTGCTTACGTAGGCT+TGG 0.472496 tig0018481:+115062 Msa1366760:CDS
AAGGACCCTTTGAAGTGTGC+TGG 0.474153 tig0018481:+115023 Msa1366760:CDS
GCAGGCTGCACTGGCCACAC+TGG 0.476427 tig0018481:-114756 None:intergenic
GAATGCCTTCTAACTCGGAC+TGG 0.491128 tig0018481:-114815 None:intergenic
ACTGGAGCAGGTGCAATCTC+AGG 0.492416 tig0018481:-114738 None:intergenic
TCTTCAGCTACATTAGGTTG+GGG 0.497120 tig0018481:-114714 None:intergenic
TGCTTCGTTAACATGTTACA+AGG 0.498659 tig0018481:+114992 Msa1366760:CDS
GAAGCTTATACTCTTTCTCA+TGG 0.498978 tig0018481:-114932 None:intergenic
TCGGACTGGGAAGGGTGTGC+AGG 0.505034 tig0018481:-114801 None:intergenic
CAAAACCAGCACACTTCAAA+GGG 0.511503 tig0018481:-115028 None:intergenic
ACAAAACCAGCACACTTCAA+AGG 0.512279 tig0018481:-115029 None:intergenic
ACATACAGAGCAGGCTGCAC+TGG 0.517633 tig0018481:-114765 None:intergenic
CGTAGGCTTGGTCCTTTAGG+TGG 0.525700 tig0018481:+115074 Msa1366760:CDS
CCCAAAGCCTGAGCGTTGCA+CGG 0.534896 tig0018481:+114959 Msa1366760:CDS
ACCCAGAAGGGTTAAACGTA+AGG 0.537921 tig0018481:+114671 Msa1366760:CDS
CTTCTAACTCGGACTGGGAA+GGG 0.542616 tig0018481:-114809 None:intergenic
AGTTCGAATGCCTTCTAACT+CGG 0.544009 tig0018481:-114820 None:intergenic
ATGTTACAAGGAACATATCA+AGG 0.555082 tig0018481:+115004 Msa1366760:CDS
AATGCCTTCTAACTCGGACT+GGG 0.556237 tig0018481:-114814 None:intergenic
CCTTCTAACTCGGACTGGGA+AGG 0.556756 tig0018481:-114810 None:intergenic
GTTGCAGGAAGTAACCCAAA+AGG 0.568701 tig0018481:+114899 Msa1366760:CDS
GTTGCAGGTACATACAGAGC+AGG 0.591774 tig0018481:-114774 None:intergenic
CATCAACAAGCTTATTAACA+AGG 0.592884 tig0018481:-114629 None:intergenic
GGAAGTAACCCAAAAGGCAA+AGG 0.617788 tig0018481:+114905 Msa1366760:CDS
TGTGCTTCAGGAAAGTGAGA+AGG 0.619368 tig0018481:+114842 Msa1366760:CDS
CAGAAGGGTTAAACGTAAGG+TGG 0.629015 tig0018481:+114674 Msa1366760:CDS
TGGTGAAGAAGAAACCCAGA+AGG 0.640121 tig0018481:+114658 Msa1366760:CDS
GCTTATACTCTTTCTCATGG+AGG 0.652605 tig0018481:-114929 None:intergenic
AGATTGCACCTGCTCCAGTG+TGG 0.655551 tig0018481:+114742 Msa1366760:CDS
TAAGCTTGTTGATGATCCTG+TGG 0.678601 tig0018481:+114638 Msa1366760:CDS
GGTGAAGAAGAAACCCAGAA+GGG 0.704616 tig0018481:+114659 Msa1366760:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CATCAACAAGCTTATTAACA+AGG - tig0018481:114632-114651 None:intergenic 30.0%
ATGTTACAAGGAACATATCA+AGG + tig0018481:115004-115023 Msa1366760:CDS 30.0%
TTCTTCAGCTACATTAGGTT+GGG - tig0018481:114718-114737 None:intergenic 35.0%
GAAGCTTATACTCTTTCTCA+TGG - tig0018481:114935-114954 None:intergenic 35.0%
TGCTTCGTTAACATGTTACA+AGG + tig0018481:114992-115011 Msa1366760:CDS 35.0%
! ATTTTGCAGATTGCTTACGT+AGG + tig0018481:115057-115076 Msa1366760:CDS 35.0%
!! TAAGCTTGTTGATGATCCTG+TGG + tig0018481:114638-114657 Msa1366760:CDS 40.0%
ACCTTACGTTTAACCCTTCT+GGG - tig0018481:114675-114694 None:intergenic 40.0%
! TCTTCAGCTACATTAGGTTG+GGG - tig0018481:114717-114736 None:intergenic 40.0%
GTTCTTCAGCTACATTAGGT+TGG - tig0018481:114719-114738 None:intergenic 40.0%
TCAGGTTCTTCAGCTACATT+AGG - tig0018481:114723-114742 None:intergenic 40.0%
AGTTCGAATGCCTTCTAACT+CGG - tig0018481:114823-114842 None:intergenic 40.0%
! TCAGGAAAGTGAGAAGGTTT+TGG + tig0018481:114848-114867 Msa1366760:CDS 40.0%
GCTTATACTCTTTCTCATGG+AGG - tig0018481:114932-114951 None:intergenic 40.0%
CAAAACCAGCACACTTCAAA+GGG - tig0018481:115031-115050 None:intergenic 40.0%
ACAAAACCAGCACACTTCAA+AGG - tig0018481:115032-115051 None:intergenic 40.0%
TGGTGAAGAAGAAACCCAGA+AGG + tig0018481:114658-114677 Msa1366760:CDS 45.0%
GGTGAAGAAGAAACCCAGAA+GGG + tig0018481:114659-114678 Msa1366760:CDS 45.0%
ACCCAGAAGGGTTAAACGTA+AGG + tig0018481:114671-114690 Msa1366760:CDS 45.0%
CACCTTACGTTTAACCCTTC+TGG - tig0018481:114676-114695 None:intergenic 45.0%
CAGAAGGGTTAAACGTAAGG+TGG + tig0018481:114674-114693 Msa1366760:CDS 45.0%
AATGCCTTCTAACTCGGACT+GGG - tig0018481:114817-114836 None:intergenic 45.0%
TGTGCTTCAGGAAAGTGAGA+AGG + tig0018481:114842-114861 Msa1366760:CDS 45.0%
GCAAGAGAAGCAAATGTTGC+AGG + tig0018481:114884-114903 Msa1366760:CDS 45.0%
GTTGCAGGAAGTAACCCAAA+AGG + tig0018481:114899-114918 Msa1366760:CDS 45.0%
GGAAGTAACCCAAAAGGCAA+AGG + tig0018481:114905-114924 Msa1366760:CDS 45.0%
! ATGGAGGTCCTTTGCCTTTT+GGG - tig0018481:114916-114935 None:intergenic 45.0%
! TTACGTAGGCTTGGTCCTTT+AGG + tig0018481:115071-115090 Msa1366760:CDS 45.0%
CTGGGTTTCTTCTTCACCAC+AGG - tig0018481:114657-114676 None:intergenic 50.0%
GTTGCAGGTACATACAGAGC+AGG - tig0018481:114777-114796 None:intergenic 50.0%
! CTTCTAACTCGGACTGGGAA+GGG - tig0018481:114812-114831 None:intergenic 50.0%
GAATGCCTTCTAACTCGGAC+TGG - tig0018481:114818-114837 None:intergenic 50.0%
AGGCATTCGAACTGTGCTTC+AGG + tig0018481:114830-114849 Msa1366760:CDS 50.0%
! CATGGAGGTCCTTTGCCTTT+TGG - tig0018481:114917-114936 None:intergenic 50.0%
!! AAGGACCCTTTGAAGTGTGC+TGG + tig0018481:115023-115042 Msa1366760:CDS 50.0%
GCAGATTGCTTACGTAGGCT+TGG + tig0018481:115062-115081 Msa1366760:CDS 50.0%
ACTGGAGCAGGTGCAATCTC+AGG - tig0018481:114741-114760 None:intergenic 55.0%
AGATTGCACCTGCTCCAGTG+TGG + tig0018481:114742-114761 Msa1366760:CDS 55.0%
ACATACAGAGCAGGCTGCAC+TGG - tig0018481:114768-114787 None:intergenic 55.0%
! CCTTCTAACTCGGACTGGGA+AGG - tig0018481:114813-114832 None:intergenic 55.0%
CCTTCCCAGTCCGAGTTAGA+AGG + tig0018481:114810-114829 Msa1366760:CDS 55.0%
! CGTAGGCTTGGTCCTTTAGG+TGG + tig0018481:115074-115093 Msa1366760:CDS 55.0%
GGGTGTGCAGGCAATGTTGC+AGG - tig0018481:114792-114811 None:intergenic 60.0%
!! CAACGCTCAGGCTTTGGGTC+TGG - tig0018481:114957-114976 None:intergenic 60.0%
CCGTGCAACGCTCAGGCTTT+GGG - tig0018481:114962-114981 None:intergenic 60.0%
! CCCAAAGCCTGAGCGTTGCA+CGG + tig0018481:114959-114978 Msa1366760:CDS 60.0%
! TGCACTGGCCACACTGGAGC+AGG - tig0018481:114753-114772 None:intergenic 65.0%
! TCGGACTGGGAAGGGTGTGC+AGG - tig0018481:114804-114823 None:intergenic 65.0%
GCCGTGCAACGCTCAGGCTT+TGG - tig0018481:114963-114982 None:intergenic 65.0%
CTCTCAGCCGTGCAACGCTC+AGG - tig0018481:114969-114988 None:intergenic 65.0%
! CTGAGCGTTGCACGGCTGAG+AGG + tig0018481:114967-114986 Msa1366760:CDS 65.0%
! GCAGGCTGCACTGGCCACAC+TGG - tig0018481:114759-114778 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
tig0018481 gene 114597 115103 114597 ID=Msa1366760;Name=Msa1366760
tig0018481 mRNA 114597 115103 114597 ID=Msa1366760-mRNA-1;Parent=Msa1366760;Name=Msa1366760-mRNA-1;_AED=0.26;_eAED=0.27;_QI=0|-1|0|1|-1|1|1|0|168
tig0018481 exon 114597 115103 114597 ID=Msa1366760-mRNA-1:exon:15221;Parent=Msa1366760-mRNA-1
tig0018481 CDS 114597 115103 114597 ID=Msa1366760-mRNA-1:cds;Parent=Msa1366760-mRNA-1
Gene Sequence

>Msa1366760

ATGGGTGAGTTTACAATTCAAATTAGCAATGACCTTGTTAATAAGCTTGTTGATGATCCTGTGGTGAAGAAGAAACCCAGAAGGGTTAAACGTAAGGTGGCAAGAGAGATTGAAAAGCCCCAACCTAATGTAGCTGAAGAACCTGAGATTGCACCTGCTCCAGTGTGGCCAGTGCAGCCTGCTCTGTATGTACCTGCAACATTGCCTGCACACCCTTCCCAGTCCGAGTTAGAAGGCATTCGAACTGTGCTTCAGGAAAGTGAGAAGGTTTTGGAAAGATTGCAGAAGCAAGAGAAGCAAATGTTGCAGGAAGTAACCCAAAAGGCAAAGGACCTCCATGAGAAAGAGTATAAGCTTCCAGACCCAAAGCCTGAGCGTTGCACGGCTGAGAGGCTTGCTTCGTTAACATGTTACAAGGAACATATCAAGGACCCTTTGAAGTGTGCTGGTTTTGTTAACAATTTTGCAGATTGCTTACGTAGGCTTGGTCCTTTAGGTGGCAAATAA
Protein sequence

>Msa1366760

MGEFTIQISNDLVNKLVDDPVVKKKPRRVKRKVAREIEKPQPNVAEEPEIAPAPVWPVQPALYVPATLPAHPSQSELEGIRTVLQESEKVLERLQKQEKQMLQEVTQKAKDLHEKEYKLPDPKPERCTAERLASLTCYKEHIKDPLKCAGFVNNFADCLRRLGPLGGK*