AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG004034

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG004034 MtrunA17_Chr1g0192841 75.127 197 35 1 56 238 47 243 5.93e-90 265
MsaG004034 MtrunA17_Chr5g0435401 50.794 189 68 7 55 238 244 412 1.05e-39 141
MsaG004034 MtrunA17_Chr5g0435401 67.568 74 24 0 76 149 193 266 1.55e-26 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 54 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTCGTTGGATATGTTAAA+TGG 0.182684 1:+64985058 MsaT004034.1:CDS
CACAATTCCATTGGTGAGTT+TGG 0.209381 1:-64983082 None:intergenic
TCCCTTCTTCCCAGTTGATT+TGG 0.271998 1:+64985027 MsaT004034.1:CDS
TTCTTGCTTTCCTCCACATA+TGG 0.365771 1:-64984776 None:intergenic
CAGTAAGTATCCAAATCAAC+TGG 0.378693 1:-64985037 None:intergenic
GAAGAGCACTCAAGATCTTA+AGG 0.392322 1:+64984877 MsaT004034.1:CDS
CAACCGCTAGTATAGTCATT+TGG 0.413628 1:-64985086 None:intergenic
GGAGGAAAGCAAGAAGATAA+AGG 0.418994 1:+64984784 MsaT004034.1:CDS
TGGTGACTTCCAAGTAAAAC+AGG 0.431064 1:-64983446 None:intergenic
AATGGAAGGCAACAAGACTA+TGG 0.438680 1:+64983038 None:intergenic
CTGGTGAAAACCTCCTCTTC+TGG 0.440306 1:-64983466 None:intergenic
CCCATTGGACACAATTCCAT+TGG 0.444629 1:-64983091 None:intergenic
ATCCAAATCAACTGGGAAGA+AGG 0.454997 1:-64985029 None:intergenic
GCTCAAGATCCGGACATTGA+TGG 0.455328 1:+64984576 MsaT004034.1:CDS
GTTCGTTGGATATGTTAAAT+GGG 0.459203 1:+64985059 MsaT004034.1:CDS
TATTTGATATCCACTTTGTC+CGG 0.459963 1:-64984523 None:intergenic
AAGACAAAGAAAAGAAGAAA+CGG 0.466286 1:+64984487 MsaT004034.1:CDS
ATGACTATCTCTAAGTCATC+AGG 0.469356 1:-64983129 None:intergenic
TTTGGATACTTACTGTTCGT+TGG 0.489477 1:+64985045 MsaT004034.1:CDS
ACAGAAGAATAGTTTGGTAG+TGG 0.492096 1:-64984950 None:intergenic
CCAATGGAATTGTGTCCAAT+GGG 0.492590 1:+64983091 MsaT004034.1:CDS
TACGCATGGCTATTGATGCT+TGG 0.512694 1:+64984610 MsaT004034.1:CDS
ACCAATGGAATTGTGTCCAA+TGG 0.516036 1:+64983090 MsaT004034.1:CDS
ATCGAGCACATTCATGCTTG+AGG 0.516753 1:-64984548 None:intergenic
CAACAATGCAGCTGTGGAGT+TGG 0.523389 1:+64984973 MsaT004034.1:CDS
TTGTTGACAGAAGAATAGTT+TGG 0.526138 1:-64984956 None:intergenic
TCCAAATCAACTGGGAAGAA+GGG 0.526508 1:-64985028 None:intergenic
TTCTGTCAACAATGCAGCTG+TGG 0.527890 1:+64984967 MsaT004034.1:CDS
TTGGCATCTGAAGGTGATGA+TGG 0.536024 1:-64983063 None:intergenic
TACTTGGAAGTCACCAGAAG+AGG 0.540823 1:+64983453 MsaT004034.1:CDS
GATCATTGACAATAAACAGA+TGG 0.543332 1:+64984826 MsaT004034.1:CDS
TCGATTAAAAGCTCAAGATC+CGG 0.550386 1:+64984566 MsaT004034.1:CDS
TGATATCCACTTTGTCCGGT+AGG 0.555314 1:-64984519 None:intergenic
AGAAGAGTACTGTTTCCCAT+TGG 0.564784 1:-64983106 None:intergenic
AAGATCTTAAGGAGGAAAAG+AGG 0.571062 1:+64984888 MsaT004034.1:CDS
ACTGAAGATCTTAAGAAGGA+TGG 0.571447 1:+64984851 MsaT004034.1:CDS
AAACGGCGAGGTCCTCCTAC+CGG 0.572639 1:+64984504 MsaT004034.1:CDS
TTCCTAGCTCAAACAATGGA+AGG 0.574513 1:+64983024 None:intergenic
TAGTCGTAACCGCACACACT+AGG 0.575038 1:-64984911 None:intergenic
GGGCACTGAAGATCTTAAGA+AGG 0.581617 1:+64984847 MsaT004034.1:CDS
ATCATTGACAATAAACAGAT+GGG 0.586725 1:+64984827 MsaT004034.1:CDS
TTGGAAGTCACCAGAAGAGG+AGG 0.590853 1:+64983456 MsaT004034.1:CDS
TATCCACTTTGTCCGGTAGG+AGG 0.594215 1:-64984516 None:intergenic
TTGGTGAGTTTGGCATCTGA+AGG 0.614422 1:-64983072 None:intergenic
TCAGATGCCAAACTCACCAA+TGG 0.618895 1:+64983075 MsaT004034.1:CDS
TTTCATGTAGCCATATGTGG+AGG 0.619171 1:+64984766 MsaT004034.1:intron
GGTCCTCCTACCGGACAAAG+TGG 0.623840 1:+64984513 MsaT004034.1:CDS
AAGCATCAATAGCCATGCGT+AGG 0.630888 1:-64984608 None:intergenic
ACAAGTCTAAGATTGTCTCT+CGG 0.631739 1:-64983422 None:intergenic
GAAAAGAGGCCTAGTGTGTG+CGG 0.639000 1:+64984902 MsaT004034.1:CDS
GATGACTTAGAGATAGTCAT+CGG 0.643924 1:+64983132 MsaT004034.1:CDS
AGTAAGTATCCAAATCAACT+GGG 0.663991 1:-64985036 None:intergenic
GAGCACTCAAGATCTTAAGG+AGG 0.665195 1:+64984880 MsaT004034.1:CDS
AAAGAAAAGAAGAAACGGCG+AGG 0.681943 1:+64984492 MsaT004034.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 64983039 64985093 64983039 ID=MsaG004034
Chr1 mRNA 64983039 64985093 64983039 ID=MsaT004034.1;Parent=MsaG004034
Chr1 exon 64983039 64983158 64983039 ID=MsaT004034.1.exon1;Parent=MsaT004034.1
Chr1 CDS 64983039 64983158 64983039 ID=cds.MsaT004034.1;Parent=MsaT004034.1
Chr1 exon 64983413 64983488 64983413 ID=MsaT004034.1.exon2;Parent=MsaT004034.1
Chr1 CDS 64983413 64983488 64983413 ID=cds.MsaT004034.1;Parent=MsaT004034.1
Chr1 exon 64984457 64984659 64984457 ID=MsaT004034.1.exon3;Parent=MsaT004034.1
Chr1 CDS 64984457 64984659 64984457 ID=cds.MsaT004034.1;Parent=MsaT004034.1
Chr1 exon 64984776 64985093 64984776 ID=MsaT004034.1.exon4;Parent=MsaT004034.1
Chr1 CDS 64984776 64985093 64984776 ID=cds.MsaT004034.1;Parent=MsaT004034.1
Gene Sequence

>MsaT004034.1

ATGGAAGGCAACAAGACTATGGTTCCATCATCACCTTCAGATGCCAAACTCACCAATGGAATTGTGTCCAATGGGAAACAGTACTCTTCTCCTGATGACTTAGAGATAGTCATCGGCAAATTTCAATGTCCGAGAGACAATCTTAGACTTGTACCTGTTTTACTTGGAAGTCACCAGAAGAGGAGGTTTTCACCAGCACCCTCAAATGACAAAGAAAACAAGAAACAAGACAAAGAAAAGAAGAAACGGCGAGGTCCTCCTACCGGACAAAGTGGATATCAAATATTCCTCAAGCATGAATGTGCTCGATTAAAAGCTCAAGATCCGGACATTGATGGCAAAAAAGTCCTACGCATGGCTATTGATGCTTGGCAGAAGATGTCTGCCACTGAAAAACAGCCATATGTGGAGGAAAGCAAGAAGATAAAGGAAAAAAAGAAGGAAGCAGTGATCATTGACAATAAACAGATGGGCACTGAAGATCTTAAGAAGGATGGAAAGAAGAGCACTCAAGATCTTAAGGAGGAAAAGAGGCCTAGTGTGTGCGGTTACGACTACTGTGCAACTTCGCAACCACTACCAAACTATTCTTCTGTCAACAATGCAGCTGTGGAGTTGGCTTTGAAAATGACTGAAAAAGCACTCAAGGATCCCTTCTTCCCAGTTGATTTGGATACTTACTGTTCGTTGGATATGTTAAATGGGAAATCCAAATGA
Protein sequence

>MsaT004034.1

MEGNKTMVPSSPSDAKLTNGIVSNGKQYSSPDDLEIVIGKFQCPRDNLRLVPVLLGSHQKRRFSPAPSNDKENKKQDKEKKKRRGPPTGQSGYQIFLKHECARLKAQDPDIDGKKVLRMAIDAWQKMSATEKQPYVEESKKIKEKKKEAVIIDNKQMGTEDLKKDGKKSTQDLKEEKRPSVCGYDYCATSQPLPNYSSVNNAAVELALKMTEKALKDPFFPVDLDTYCSLDMLNGKSK*