AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG013401


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 92 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGAACGTGGCTAATTTC+TGG 0.218063 3:+51646343 MsaT013401.1:CDS
CAGCGGCATTAATTTGAAAT+TGG 0.244639 3:-51646103 None:intergenic
AGAGCATAGAGTTTGGTTTC+AGG 0.263168 3:+51645767 MsaT013401.1:CDS
GGCGGTGGTTGCTTCTATTC+AGG 0.264711 3:+51645834 MsaT013401.1:CDS
TGTTCTTCCACCACTGGTAC+TGG 0.276664 3:-51646288 None:intergenic
AATTAGCCACGTTCTGAATC+TGG 0.296437 3:-51646338 None:intergenic
GAGGAACCTGCTTTCGATAT+TGG 0.318864 3:+51646375 MsaT013401.1:CDS
AAATTTGCTCGGCGAGCATT+TGG 0.329497 3:+51646656 MsaT013401.1:CDS
TGATAATGAGGAGGCTGATA+TGG 0.331856 3:+51646398 MsaT013401.1:CDS
GTCAAATAGAGCATAGAGTT+TGG 0.371033 3:+51645760 MsaT013401.1:CDS
TTAAAACATGTGTCTCCAAC+TGG 0.380379 3:-51646467 None:intergenic
CGATGTTGAATACCCTCCTT+TGG 0.387542 3:-51643921 None:intergenic
GATCATTATGAGCAACCATT+AGG 0.389483 3:+51645873 MsaT013401.1:CDS
GCACGTGAGGCAGGTCGTTA+TGG 0.400336 3:+51646877 MsaT013401.1:CDS
AATACCGATGTAGCTTTATC+CGG 0.408209 3:-51646758 None:intergenic
TCAGAACGTGGCTAATTTCT+GGG 0.416922 3:+51646344 MsaT013401.1:CDS
GTGTTCATTGGTGGTGATAA+TGG 0.427824 3:+51646140 MsaT013401.1:CDS
GCTACTGCAGCGGCAGTTTG+TGG 0.430209 3:-51646315 None:intergenic
ATTAGAGCACCATACCGTTT+GGG 0.432642 3:-51643950 None:intergenic
AATTAATGCCGCTGCTATTG+TGG 0.433129 3:+51646112 MsaT013401.1:CDS
AATCGTAGGTTTAGACCTAA+TGG 0.433227 3:-51645888 None:intergenic
AAACATCCCGTTATCGTCAT+AGG 0.435778 3:-51645913 None:intergenic
ATTGTGGGTTACGTGTTCAT+TGG 0.435990 3:+51646128 MsaT013401.1:CDS
AATTTGCTCGGCGAGCATTT+GGG 0.441935 3:+51646657 MsaT013401.1:CDS
GCCTCACGTGCAGGACAGTT+GGG 0.444919 3:-51646865 None:intergenic
TCATTCCACTTAATATCGAT+TGG 0.456651 3:-51646731 None:intergenic
CGTTAGAGAGAACAGATTTG+TGG 0.458615 3:+51646805 MsaT013401.1:CDS
TCCACCACTGGTACTGGGTC+AGG 0.460719 3:-51646282 None:intergenic
GATACCAGAGGGTCTAGGTT+TGG 0.463429 3:+51645789 MsaT013401.1:CDS
GTTCTTCCACCACTGGTACT+GGG 0.464509 3:-51646287 None:intergenic
GATTGACCTATGACGATAAC+GGG 0.465542 3:+51645907 MsaT013401.1:CDS
TGCCTCACGTGCAGGACAGT+TGG 0.476556 3:-51646866 None:intergenic
TCGTCTTCGCCATCCGATGA+TGG 0.480487 3:+51646080 MsaT013401.1:CDS
ATTAATGCCGCTGCTATTGT+GGG 0.481499 3:+51646113 MsaT013401.1:CDS
AGTATCCAATCGATATTAAG+TGG 0.481943 3:+51646726 MsaT013401.1:CDS
TCATCCATGTCAAGAGTGAA+TGG 0.486104 3:-51645945 None:intergenic
CTCATCTCGGATCGTGATGA+AGG 0.492063 3:-51646693 None:intergenic
GGCTGATATGGATGTCGAAA+TGG 0.496866 3:+51646410 MsaT013401.1:CDS
TCTAGGTTTGGAGTATGTTA+CGG 0.497585 3:+51645801 MsaT013401.1:CDS
CGATTGACCTATGACGATAA+CGG 0.500068 3:+51645906 MsaT013401.1:CDS
AACTGTCCTGCACGTGAGGC+AGG 0.503776 3:+51646868 MsaT013401.1:CDS
TTCAGGATACCAGAGGGTCT+AGG 0.513988 3:+51645784 MsaT013401.1:CDS
TACTCCAAACCTAGACCCTC+TGG 0.515790 3:-51645793 None:intergenic
ATTAGCCACGTTCTGAATCT+GGG 0.515846 3:-51646337 None:intergenic
CAACATCGCGTCAACCCAAA+CGG 0.515982 3:+51643936 MsaT013401.1:CDS
TTTCGATATTGGTGATAATG+AGG 0.526872 3:+51646386 MsaT013401.1:CDS
TTTAACGCTTGCTGCGTACA+TGG 0.531915 3:+51646485 MsaT013401.1:CDS
AATTTGAAATTGGCCATCAT+CGG 0.533132 3:-51646093 None:intergenic
AGCTTACGGCTCGTGTCCCA+TGG 0.534486 3:+51645715 MsaT013401.1:intron
TAACGACCTGCCTCACGTGC+AGG 0.537930 3:-51646874 None:intergenic
TCTCGGATCGTGATGAAGGT+TGG 0.548455 3:-51646689 None:intergenic
GTGGGTTACGTGTTCATTGG+TGG 0.549075 3:+51646131 MsaT013401.1:CDS
TAAAACATGTGTCTCCAACT+GGG 0.552768 3:-51646466 None:intergenic
TTGTACCAGCAAAATTTGCT+CGG 0.557897 3:+51646645 MsaT013401.1:CDS
TGAAATTGGCCATCATCGGA+TGG 0.563008 3:-51646089 None:intergenic
GGCAGGTCGTTATGGTGTAA+AGG 0.566786 3:+51646885 MsaT013401.1:CDS
ATTCACTCTTGACATGGATG+AGG 0.568212 3:+51645947 MsaT013401.1:CDS
GCTTCCATTCACTCTTGACA+TGG 0.570881 3:+51645941 MsaT013401.1:CDS
GTATGTTACGGAGAGATCAA+TGG 0.580224 3:+51645813 MsaT013401.1:CDS
ACAGATTTGTGGAAGGCACA+AGG 0.581028 3:+51646816 MsaT013401.1:CDS
TGACATGCAACCTTGAGCTA+TGG 0.582304 3:-51645998 None:intergenic
GTTGCTCATAATGATCAAGC+AGG 0.585077 3:-51645866 None:intergenic
TTATCACCAATATCGAAAGC+AGG 0.592587 3:-51646381 None:intergenic
GAGCGAAGACGAAGATGAGT+CGG 0.593776 3:-51646054 None:intergenic
ACCCAACTGTCCTGCACGTG+AGG 0.595873 3:+51646864 MsaT013401.1:CDS
TGCACATGGCAATCCCCAGT+TGG 0.598828 3:+51646452 MsaT013401.1:CDS
AAAACATGTGTCTCCAACTG+GGG 0.599659 3:-51646465 None:intergenic
AGGTAACTAATCGTCAATTG+AGG 0.606077 3:+51645967 MsaT013401.1:CDS
CGATATTGGTGATAATGAGG+AGG 0.613156 3:+51646389 MsaT013401.1:CDS
TGTTCCTGACCCAGTACCAG+TGG 0.613436 3:+51646278 MsaT013401.1:CDS
TACGGAGAGATCAATGGCGG+TGG 0.619550 3:+51645819 MsaT013401.1:CDS
CAGATTTGTGGAAGGCACAA+GGG 0.620094 3:+51646817 MsaT013401.1:CDS
CTGAATCTGGGCTACTGCAG+CGG 0.621166 3:-51646325 None:intergenic
TATCGTCATAGGTCAATCGT+AGG 0.623984 3:-51645902 None:intergenic
ACTCACGGTGGAACTCATCT+CGG 0.624872 3:-51646706 None:intergenic
TCCTGACCCAGTACCAGTGG+TGG 0.629390 3:+51646281 MsaT013401.1:CDS
TAATATCGATTGGATACTCA+CGG 0.630661 3:-51646721 None:intergenic
CAAAGTATCTAAATGTACGC+AGG 0.631169 3:-51646028 None:intergenic
AGAGAGAACAGATTTGTGGA+AGG 0.635968 3:+51646809 MsaT013401.1:CDS
GTTTGGTTTCAGGATACCAG+AGG 0.643279 3:+51645777 MsaT013401.1:CDS
TTTGGTTTCAGGATACCAGA+GGG 0.645318 3:+51645778 MsaT013401.1:CDS
TAATTTCTGGGATGATGATG+AGG 0.648095 3:+51646356 MsaT013401.1:CDS
GGAACTATGACCATAGCTCA+AGG 0.651950 3:+51645988 MsaT013401.1:CDS
CACGTAACCCACAATAGCAG+CGG 0.655702 3:-51646120 None:intergenic
TATGGATGTCGAAATGGATG+TGG 0.657183 3:+51646416 MsaT013401.1:CDS
AAAACCGGATAAAGCTACAT+CGG 0.665649 3:+51646754 MsaT013401.1:CDS
CATGGTGAAATGCAGCAACA+TGG 0.687154 3:+51646503 MsaT013401.1:CDS
AATGGATGTGGTAGATGCTG+AGG 0.688566 3:+51646428 MsaT013401.1:CDS
AGTAGCCCAGATTCAGAACG+TGG 0.698194 3:+51646332 MsaT013401.1:CDS
TGTTACGGAGAGATCAATGG+CGG 0.735510 3:+51645816 MsaT013401.1:CDS
GTAGATGCTGAGGATGCACA+TGG 0.739903 3:+51646438 MsaT013401.1:CDS
TATCGATTGGATACTCACGG+TGG 0.816467 3:-51646718 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 51643913 51646904 51643913 ID=MsaG013401
Chr3 mRNA 51643913 51646904 51643913 ID=MsaT013401.1;Parent=MsaG013401
Chr3 exon 51643913 51643957 51643913 ID=MsaT013401.1.exon1;Parent=MsaT013401.1
Chr3 CDS 51643913 51643957 51643913 ID=cds.MsaT013401.1;Parent=MsaT013401.1
Chr3 exon 51645717 51646161 51645717 ID=MsaT013401.1.exon2;Parent=MsaT013401.1
Chr3 CDS 51645717 51646161 51645717 ID=cds.MsaT013401.1;Parent=MsaT013401.1
Chr3 exon 51646277 51646524 51646277 ID=MsaT013401.1.exon3;Parent=MsaT013401.1
Chr3 CDS 51646277 51646524 51646277 ID=cds.MsaT013401.1;Parent=MsaT013401.1
Chr3 exon 51646644 51646904 51646644 ID=MsaT013401.1.exon4;Parent=MsaT013401.1
Chr3 CDS 51646644 51646904 51646644 ID=cds.MsaT013401.1;Parent=MsaT013401.1
Gene Sequence

>MsaT013401.1

ATGGTTTTCCAAAGGAGGGTATTCAACATCGCGTCAACCCAAACGCTTACGGCTCGTGTCCCATGGTATTTTTACGAACGTTTCAAAGGTCAAATAGAGCATAGAGTTTGGTTTCAGGATACCAGAGGGTCTAGGTTTGGAGTATGTTACGGAGAGATCAATGGCGGTGGTTGCTTCTATTCAGGTCTTCAGAACCTGCTTGATCATTATGAGCAACCATTAGGTCTAAACCTACGATTGACCTATGACGATAACGGGATGTTTCATATGCTTCCATTCACTCTTGACATGGATGAGGTAACTAATCGTCAATTGAGGAACTATGACCATAGCTCAAGGTTGCATGTCAATGAGTTCCTGCGTACATTTAGATACTTTGATTCCGACTCATCTTCGTCTTCGCTCGCTTCGTCTTCGCCATCCGATGATGGCCAATTTCAAATTAATGCCGCTGCTATTGTGGGTTACGTGTTCATTGGTGGTGATAATGTTGTTCCTGACCCAGTACCAGTGGTGGAAGAACAAAATCCACAAACTGCCGCTGCAGTAGCCCAGATTCAGAACGTGGCTAATTTCTGGGATGATGATGAGGAACCTGCTTTCGATATTGGTGATAATGAGGAGGCTGATATGGATGTCGAAATGGATGTGGTAGATGCTGAGGATGCACATGGCAATCCCCAGTTGGAGACACATGTTTTAACGCTTGCTGCGTACATGGTGAAATGCAGCAACATGCTTGTACCAGCAAAATTTGCTCGGCGAGCATTTGGGAATACAAGACCAACCTTCATCACGATCCGAGATGAGTTCCACCGTGAGTATCCAATCGATATTAAGTGGAATGAAAAACCGGATAAAGCTACATCGGTATTTTTCAGGGGCGGTTGGGGTGAATTCGTTAGAGAGAACAGATTTGTGGAAGGCACAAGGGTGTTGCTCACTTTAAACAAGACTAACCCAACTGTCCTGCACGTGAGGCAGGTCGTTATGGTGTAA

Protein sequence

>MsaT013401.1

MVFQRRVFNIASTQTLTARVPWYFYERFKGQIEHRVWFQDTRGSRFGVCYGEINGGGCFYSGLQNLLDHYEQPLGLNLRLTYDDNGMFHMLPFTLDMDEVTNRQLRNYDHSSRLHVNEFLRTFRYFDSDSSSSSLASSSPSDDGQFQINAAAIVGYVFIGGDNVVPDPVPVVEEQNPQTAAAVAQIQNVANFWDDDEEPAFDIGDNEEADMDVEMDVVDAEDAHGNPQLETHVLTLAAYMVKCSNMLVPAKFARRAFGNTRPTFITIRDEFHREYPIDIKWNEKPDKATSVFFRGGWGEFVRENRFVEGTRVLLTLNKTNPTVLHVRQVVMV*