AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG003201


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003201 MtrunA17_Chr1g0182611 88.950 362 37 1 1 359 88 449 0.0 645
MsaG003201 MtrunA17_Chr1g0182621 64.577 319 98 4 44 359 246 552 1.99e-119 358
MsaG003201 MtrunA17_Chr1g0182621 51.568 287 125 3 1 284 92 367 8.25e-83 264
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 87 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTACCATCAGATGATATTTC+TGG 0.152483 1:+53340399 None:intergenic
CGGTAACAGGCTGTTTCTTC+TGG 0.258466 1:+53340094 None:intergenic
CTCAGTTTCTCCAGAGTCAT+TGG 0.268603 1:-53339749 MsaT003201.1:CDS
AAGGTTGTTATAAGAGAAAA+AGG 0.277388 1:-53339894 MsaT003201.1:CDS
TGTCAAGAAATCTTGTTTGA+TGG 0.311615 1:-53340838 MsaT003201.1:intron
CGGAAGCAGCAGCCTGCATC+TGG 0.314800 1:-53340525 MsaT003201.1:CDS
AGTGCATAGCTTTCCCAGTT+TGG 0.320250 1:+53340934 None:intergenic
GAGCAGCGCACGCTGGAAAA+TGG 0.336004 1:-53341143 MsaT003201.1:CDS
TGATTCGGCCAATGCTGTTC+CGG 0.339045 1:-53340878 MsaT003201.1:CDS
GGAATAGTAAACACATTGTC+TGG 0.341105 1:-53339973 MsaT003201.1:CDS
AGTGGGGTTGATGTTACTTA+TGG 0.365193 1:-53340600 MsaT003201.1:CDS
GTGGAGATCTGGTATTTATC+TGG 0.372945 1:+53340054 None:intergenic
TATTTATCTGGATGTGTTGC+CGG 0.380047 1:+53340066 None:intergenic
CAGAAGAAACAGCCTGTTAC+CGG 0.388877 1:-53340093 MsaT003201.1:CDS
AGAGTTTAACATTATGCAAC+CGG 0.398439 1:+53340118 None:intergenic
AACCCCACTCATCTCCTTTG+AGG 0.416310 1:+53340614 None:intergenic
GAGGATTCTCTTCCACTGTA+TGG 0.421691 1:-53338769 MsaT003201.1:CDS
GGTGTTGCCTGACGAGGCCC+TGG 0.428575 1:-53340676 MsaT003201.1:CDS
TCAGTTTCTCCAGAGTCATT+GGG 0.439624 1:-53339748 MsaT003201.1:CDS
CAATCTCCCGTGGTCTTATC+CGG 0.440181 1:+53340234 None:intergenic
TCCTACTTCTTTGGTATCAC+CGG 0.443039 1:-53340253 MsaT003201.1:CDS
GGTGAGGTCAATGTTGTTCA+TGG 0.450542 1:-53340165 MsaT003201.1:CDS
GACACCCATTCAGTCACAAA+AGG 0.454994 1:-53339995 MsaT003201.1:CDS
GTTGCCGGATCTCCGGTAAC+AGG 0.455494 1:+53340081 None:intergenic
ACATGTCCCGTTCATCTTCG+AGG 0.466823 1:+53340199 None:intergenic
GATCTCCACCTTACCAGCCT+TGG 0.478185 1:-53340040 MsaT003201.1:CDS
ACAGCCTGTTACCGGAGATC+CGG 0.478659 1:-53340085 MsaT003201.1:CDS
TGGATGTGTTGCCGGATCTC+CGG 0.481700 1:+53340074 None:intergenic
AGGCTGGTAAGGTGGAGATC+TGG 0.482190 1:+53340043 None:intergenic
GGTATTCCTCGAAGATGAAC+GGG 0.483907 1:-53340205 MsaT003201.1:CDS
ATCTGAAGCTGATATTGATT+CGG 0.486466 1:-53340893 MsaT003201.1:CDS
GACCACGGGAGATTGCAATA+AGG 0.494999 1:-53340226 MsaT003201.1:CDS
GCACTAGAATGCACCGGAGA+AGG 0.506282 1:-53340916 MsaT003201.1:CDS
GTCAATGTTGTTCATGGTAG+TGG 0.510692 1:-53340159 MsaT003201.1:CDS
AGAAGTGGAAACTCGTGATT+CGG 0.511753 1:-53340457 MsaT003201.1:CDS
AAATTTCATTCCTGCTTCGT+TGG 0.514310 1:-53340697 MsaT003201.1:CDS
CTGTAAAATCTCCACAAGGA+AGG 0.520970 1:-53339813 MsaT003201.1:CDS
TGTATGGAGCTGAGCTCCCT+AGG 0.525355 1:-53338753 MsaT003201.1:intron
TACACTATCCGGAACAGCAT+TGG 0.528438 1:+53340870 None:intergenic
CTACGATGACCTCCAGATGC+AGG 0.528905 1:+53340513 None:intergenic
ACACCCATTCAGTCACAAAA+GGG 0.532185 1:-53339994 MsaT003201.1:CDS
GTTGATGTTACTTATGGTAG+TGG 0.532246 1:-53340594 MsaT003201.1:CDS
GGAAAATGCAAGAAACCATT+CGG 0.536222 1:-53340654 MsaT003201.1:CDS
TTCGTTGGTGTTGCCTGACG+AGG 0.536527 1:-53340682 MsaT003201.1:CDS
AAAAGAATGCAAAGCCTCAA+AGG 0.537351 1:-53340628 MsaT003201.1:CDS
TGTAAAATCTCCACAAGGAA+GGG 0.537405 1:-53339812 MsaT003201.1:CDS
CAAATTGCAGATACACTATC+CGG 0.539970 1:+53340859 None:intergenic
TCAGGCAACACCAACGAAGC+AGG 0.540212 1:+53340687 None:intergenic
AACATTAATAGCACGTAACC+TGG 0.544388 1:+53340554 None:intergenic
GAGCTCTACCTCAACAGAAG+TGG 0.545818 1:-53340472 MsaT003201.1:CDS
AGTAAACACATTGTCTGGGC+AGG 0.549663 1:-53339968 MsaT003201.1:CDS
ATGTTGTTCATGGTAGTGGC+AGG 0.553357 1:-53340155 MsaT003201.1:CDS
ATCAGCTTCAGATCCTTCTC+CGG 0.554639 1:+53340903 None:intergenic
GCGAAAATAGACATGGTACC+AGG 0.560344 1:-53340572 MsaT003201.1:CDS
AAGCCTCAAAGGAGATGAGT+GGG 0.564158 1:-53340617 MsaT003201.1:CDS
AGGTATTCCTCGAAGATGAA+CGG 0.564929 1:-53340206 MsaT003201.1:CDS
GCATAGCTTTCCCAGTTTGG+AGG 0.565501 1:+53340937 None:intergenic
AAGCAGCAGCCTGCATCTGG+AGG 0.566088 1:-53340522 MsaT003201.1:CDS
GCAGGAATAGACGTAGTGCC+CGG 0.566956 1:-53340137 MsaT003201.1:CDS
TCCGGTGATACCAAAGAAGT+AGG 0.573504 1:+53340252 None:intergenic
GGATACAAGTCACTCGAACA+AGG 0.576987 1:-53339791 MsaT003201.1:CDS
ACGAGTTTCCACTTCTGTTG+AGG 0.577453 1:+53340464 None:intergenic
CATGAACGAGCAGCGCACGC+TGG 0.579334 1:-53341150 MsaT003201.1:CDS
CATCCAGAAATATCATCTGA+TGG 0.590199 1:-53340402 MsaT003201.1:intron
ACGGGACATGTCAATTAAGA+CGG 0.591957 1:-53340187 MsaT003201.1:CDS
CGGGACATGTCAATTAAGAC+GGG 0.595490 1:-53340186 MsaT003201.1:CDS
TGACTTGTATCCCTTCCTTG+TGG 0.599408 1:+53339802 None:intergenic
GAATAGTAAACACATTGTCT+GGG 0.607705 1:-53339972 MsaT003201.1:CDS
CCAGCCTTGGAAAAGAGTGA+TGG 0.608271 1:-53340027 MsaT003201.1:CDS
GATACAAGTCACTCGAACAA+GGG 0.609110 1:-53339790 MsaT003201.1:CDS
GGGAGCTCAGCTCCATACAG+TGG 0.610473 1:+53338757 None:intergenic
AGCTATGCACTAGAATGCAC+CGG 0.615493 1:-53340922 MsaT003201.1:CDS
CTGCATCTGGAGGTCATCGT+AGG 0.620919 1:-53340512 MsaT003201.1:CDS
TACCTTATTGCAATCTCCCG+TGG 0.621061 1:+53340224 None:intergenic
GCCTTGGAAAAGAGTGATGG+AGG 0.621071 1:-53340024 MsaT003201.1:CDS
GTATCACCGGATAAGACCAC+GGG 0.626364 1:-53340240 MsaT003201.1:CDS
GTGTTGCCTGACGAGGCCCT+GGG 0.635492 1:-53340675 MsaT003201.1:CDS
CATGTCAATTAAGACGGGTG+AGG 0.637260 1:-53340181 MsaT003201.1:CDS
GAGTTTAACATTATGCAACC+GGG 0.641017 1:+53340119 None:intergenic
CAATGACTCTGGAGAAACTG+AGG 0.645689 1:+53339750 None:intergenic
AAAGCCTCAAAGGAGATGAG+TGG 0.652543 1:-53340618 MsaT003201.1:CDS
GTGCTATTAATGTTTGTCAG+CGG 0.670687 1:-53340545 MsaT003201.1:CDS
ACAGTTGAAACAGAAGCAGT+CGG 0.677484 1:-53339868 MsaT003201.1:CDS
GGTATCACCGGATAAGACCA+CGG 0.680385 1:-53340241 MsaT003201.1:CDS
TCTTCTGTAAAATCTCCACA+AGG 0.702540 1:-53339817 MsaT003201.1:CDS
GGTAGTGGCGAAAATAGACA+TGG 0.702887 1:-53340579 MsaT003201.1:CDS
AGCCTCAAAGGAGATGAGTG+GGG 0.721063 1:-53340616 MsaT003201.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 53338616 53341171 53338616 ID=MsaG003201
Chr1 mRNA 53338616 53341171 53338616 ID=MsaT003201.1;Parent=MsaG003201
Chr1 exon 53338616 53338664 53338616 ID=MsaT003201.1.exon6;Parent=MsaT003201.1
Chr1 CDS 53338616 53338664 53338616 ID=cds.MsaT003201.1;Parent=MsaT003201.1
Chr1 exon 53338754 53338790 53338754 ID=MsaT003201.1.exon5;Parent=MsaT003201.1
Chr1 CDS 53338754 53338790 53338754 ID=cds.MsaT003201.1;Parent=MsaT003201.1
Chr1 exon 53339728 53340291 53339728 ID=MsaT003201.1.exon4;Parent=MsaT003201.1
Chr1 CDS 53339728 53340291 53339728 ID=cds.MsaT003201.1;Parent=MsaT003201.1
Chr1 exon 53340403 53340726 53340403 ID=MsaT003201.1.exon3;Parent=MsaT003201.1
Chr1 CDS 53340403 53340726 53340403 ID=cds.MsaT003201.1;Parent=MsaT003201.1
Chr1 exon 53340839 53340986 53340839 ID=MsaT003201.1.exon2;Parent=MsaT003201.1
Chr1 CDS 53340839 53340986 53340839 ID=cds.MsaT003201.1;Parent=MsaT003201.1
Chr1 exon 53341130 53341171 53341130 ID=MsaT003201.1.exon1;Parent=MsaT003201.1
Chr1 CDS 53341130 53341171 53341130 ID=cds.MsaT003201.1;Parent=MsaT003201.1
Gene Sequence

>MsaT003201.1

ATGAACGAGCAGCGCACGCTGGAAAATGGTTTTACTCCTCAGATTTCAAAGAATTTTTTATATGGTTTTCCTCCAAACTGGGAAAGCTATGCACTAGAATGCACCGGAGAAGGATCTGAAGCTGATATTGATTCGGCCAATGCTGTTCCGGATAGTGTATCTGCAATTTGTCAAGAAATCTTGTTTGATGGTGAGGAAAATTTCATTCCTGCTTCGTTGGTGTTGCCTGACGAGGCCCTGGGAAAATGCAAGAAACCATTCGGTACAAAAGAATGCAAAGCCTCAAAGGAGATGAGTGGGGTTGATGTTACTTATGGTAGTGGCGAAAATAGACATGGTACCAGGTTACGTGCTATTAATGTTTGTCAGCGGAAGCAGCAGCCTGCATCTGGAGGTCATCGTAGGCATCCAAATAAAAAACAGAGCTCTACCTCAACAGAAGTGGAAACTCGTGATTCGGATACTGCTATTTCTGAAAATGTATCAGTAAATCATCCAGAAATATCATCTGATGCTGTAGAGAAGTCTTTTCCTACTTCTTTGGTATCACCGGATAAGACCACGGGAGATTGCAATAAGGTATTCCTCGAAGATGAACGGGACATGTCAATTAAGACGGGTGAGGTCAATGTTGTTCATGGTAGTGGCAGGAATAGACGTAGTGCCCGGTTGCATAATGTTAAACTCTGCCAGAAGAAACAGCCTGTTACCGGAGATCCGGCAACACATCCAGATAAATACCAGATCTCCACCTTACCAGCCTTGGAAAAGAGTGATGGAGGACTTATGACACCCATTCAGTCACAAAAGGGAATAGTAAACACATTGTCTGGGCAGGTTACTAATAAATTCAGATCCAGAATTCCCCAAACTTTTTCAGCGAAGACTGAAGGTTGTTATAAGAGAAAAAGGGTGACAGTTGAAACAGAAGCAGTCGGACCTAAGAGAAAAAATATTAAACCCGCATCTTCTGTAAAATCTCCACAAGGAAGGGATACAAGTCACTCGAACAAGGGAAGCACACAGAGATTGTCCTCAGTTTCTCCAGAGTCATTGGGTCTCAAAAAATCAAGATCTGAGGATTCTCTTCCACTGTATGGAGCTGAGCTCCCTAGGAAGTGGAGCTTAATCCCAGAAAAAGTTAATAATGCAGTAGAGAACTAA

Protein sequence

>MsaT003201.1

MNEQRTLENGFTPQISKNFLYGFPPNWESYALECTGEGSEADIDSANAVPDSVSAICQEILFDGEENFIPASLVLPDEALGKCKKPFGTKECKASKEMSGVDVTYGSGENRHGTRLRAINVCQRKQQPASGGHRRHPNKKQSSTSTEVETRDSDTAISENVSVNHPEISSDAVEKSFPTSLVSPDKTTGDCNKVFLEDERDMSIKTGEVNVVHGSGRNRRSARLHNVKLCQKKQPVTGDPATHPDKYQISTLPALEKSDGGLMTPIQSQKGIVNTLSGQVTNKFRSRIPQTFSAKTEGCYKRKRVTVETEAVGPKRKNIKPASSVKSPQGRDTSHSNKGSTQRLSSVSPESLGLKKSRSEDSLPLYGAELPRKWSLIPEKVNNAVEN*