AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG016291


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG016291 MtrunA17_Chr1g0182631 64.444 270 57 5 1 269 1 232 6.22e-116 334
MsaG016291 MtrunA17_Chr3g0127001 64.444 270 55 5 1 269 30 259 1.20e-113 330
MsaG016291 MtrunA17_Chr3g0092141 47.368 114 54 1 164 271 59 172 2.07e-29 111
MsaG016291 MtrunA17_Chr4g0060761 45.370 108 50 1 169 267 160 267 3.55e-27 107
MsaG016291 MtrunA17_Chr5g0406901 37.037 135 67 2 158 274 190 324 3.89e-21 92.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG016291 AT5G53040.1 52.381 105 50 0 164 268 148 252 4.63e-32 120
MsaG016291 AT5G66990.1 49.550 111 45 1 169 268 164 274 6.18e-31 118
MsaG016291 AT1G18790.1 44.094 127 54 2 149 265 120 239 1.77e-27 108
MsaG016291 AT1G74480.1 46.364 110 49 1 162 261 133 242 1.15e-26 107
MsaG016291 AT4G35590.2 33.824 136 70 2 150 265 171 306 2.53e-17 81.6
MsaG016291 AT4G35590.1 33.824 136 70 2 150 265 221 356 3.03e-17 82.0
MsaG016291 AT5G16100.2 38.462 91 48 1 158 240 348 438 3.76e-12 67.4

Find 54 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGGTAAAGCAACATTTA+AGG 0.169846 3:+96399714 None:intergenic
CATTGCAATTTGATGATATA+AGG 0.198698 3:-96399393 MsaT016291.1:CDS
TCGGTGTAATGCCCCATTTC+AGG 0.239025 3:+96399697 None:intergenic
AAATGTTGCTTTACCTGAAA+TGG 0.239415 3:-96399710 MsaT016291.1:CDS
TCTTCATTCAATTCCATTTC+AGG 0.242189 3:+96398907 None:intergenic
TAGTTGGATATAACCGTAAA+AGG 0.331612 3:-96398792 MsaT016291.1:CDS
AACTACTTTGATCAAGGTAT+TGG 0.343714 3:+96399755 None:intergenic
TCAGGTAAAGCAACATTTAA+GGG 0.355156 3:+96399715 None:intergenic
AATGTTGCTTTACCTGAAAT+GGG 0.356567 3:-96399709 MsaT016291.1:CDS
TTGTGAACAAACAAGAGAAA+TGG 0.359147 3:-96399603 MsaT016291.1:CDS
ATGATTTCATTGAGTTTGAT+TGG 0.364629 3:-96399861 MsaT016291.1:CDS
AGCAATACTCTTCCCTTTGT+CGG 0.387658 3:+96399678 None:intergenic
GTTGAGGCTTCCAAGAAAAC+AGG 0.393183 3:-96399643 MsaT016291.1:CDS
CCCTGCATCTATTCTTCAAA+AGG 0.394587 3:+96399314 None:intergenic
GTTAGAGAAACTTCCTGAAA+TGG 0.395826 3:-96398920 MsaT016291.1:CDS
CAATTTGATCCCAATCATAA+GGG 0.401066 3:+96398677 None:intergenic
TCAATTTGATCCCAATCATA+AGG 0.419469 3:+96398676 None:intergenic
GAGTGGATTTGTTGAAGCTT+CGG 0.430431 3:-96399539 MsaT016291.1:CDS
TGTTGTGTGATGCAGGAAAT+GGG 0.433682 3:-96398985 MsaT016291.1:intron
GGCAAACGAGGTTGCTATGA+TGG 0.435987 3:-96398959 MsaT016291.1:CDS
TGTGAACAAACAAGAGAAAT+GGG 0.437906 3:-96399602 MsaT016291.1:CDS
TGTACTCATCGACAACCTTA+AGG 0.442882 3:-96399245 MsaT016291.1:intron
GTACTAGAACTAGTATCATA+AGG 0.476033 3:-96399429 MsaT016291.1:CDS
AACTCAATGAAATCATCAAA+TGG 0.477184 3:+96399868 None:intergenic
CTGCTACTTGGCAATGGTAG+TGG 0.480934 3:+96399451 None:intergenic
TGATTTCATTGAGTTTGATT+GGG 0.486276 3:-96399860 MsaT016291.1:CDS
CTAGTTCTAGTACTGCTACT+TGG 0.488715 3:+96399439 None:intergenic
GGGAGCTCAACATCACTAGA+TGG 0.489772 3:-96399294 MsaT016291.1:CDS
GAGGTTGAAGCTCAAGGTTG+AGG 0.499590 3:+96398824 None:intergenic
TGTGATGCAGGAAATGGGTT+TGG 0.499818 3:-96398980 MsaT016291.1:intron
TTGTGAAGAAAGAGGTTGAA+GGG 0.507686 3:-96399489 MsaT016291.1:CDS
TATCCAACTACAAGCAAAAG+AGG 0.508092 3:+96398805 None:intergenic
TCTCAAAACTACTTTGATCA+AGG 0.511922 3:+96399749 None:intergenic
CTATGATGGAGAAGAAGAAA+AGG 0.520048 3:-96398945 MsaT016291.1:CDS
AAGATCATTGAACCACCCAT+TGG 0.537266 3:+96399801 None:intergenic
AGGTTGAAGCTCAAGGTTGA+GGG 0.539779 3:+96398825 None:intergenic
TTTGTGAAGAAAGAGGTTGA+AGG 0.545050 3:-96399490 MsaT016291.1:CDS
TGTGAAGAAAGAGGTTGAAG+GGG 0.555743 3:-96399488 MsaT016291.1:CDS
ATGGGGCATTACACCGACAA+AGG 0.558093 3:-96399691 MsaT016291.1:CDS
TGGGGCATTACACCGACAAA+GGG 0.567564 3:-96399690 MsaT016291.1:CDS
GAACTAGTATCATAAGGAAG+AGG 0.575464 3:-96399423 MsaT016291.1:CDS
CTAGTACTGCTACTTGGCAA+TGG 0.587993 3:+96399445 None:intergenic
CCTGCATCTATTCTTCAAAA+GGG 0.589493 3:+96399315 None:intergenic
GCAAAAGAGGTTGAAGCTCA+AGG 0.593736 3:+96398818 None:intergenic
ACATTGAGTGCTGCTGAGAG+TGG 0.594289 3:-96399556 MsaT016291.1:CDS
GGGAAGAGTATTGCTGAGAG+TGG 0.605279 3:-96399670 MsaT016291.1:CDS
GGAAATGGGTTTGGCAAACG+AGG 0.606744 3:-96398971 MsaT016291.1:CDS
ATGTTGCTTTACCTGAAATG+GGG 0.616338 3:-96399708 MsaT016291.1:CDS
GATGGCCTCACAGAAAATTG+AGG 0.623093 3:-96399276 MsaT016291.1:CDS
ATGAAGAAATCAAGAAGCTG+AGG 0.626377 3:-96398891 MsaT016291.1:CDS
GCTGCTAAGAAAATGAATGT+TGG 0.631864 3:-96399343 MsaT016291.1:CDS
AATTTGATCCCAATCATAAG+GGG 0.655111 3:+96398678 None:intergenic
TCACACAAAGAGTATAGTGA+AGG 0.665552 3:-96398754 MsaT016291.1:CDS
GCACTCAATGTCAATGACAG+TGG 0.693921 3:+96399568 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 96398672 96399902 96398672 ID=MsaG016291
Chr3 mRNA 96398672 96399902 96398672 ID=MsaT016291.1;Parent=MsaG016291
Chr3 exon 96398672 96398992 96398672 ID=MsaT016291.1.exon2;Parent=MsaT016291.1
Chr3 CDS 96398672 96398992 96398672 ID=cds.MsaT016291.1;Parent=MsaT016291.1
Chr3 exon 96399246 96399902 96399246 ID=MsaT016291.1.exon1;Parent=MsaT016291.1
Chr3 CDS 96399246 96399902 96399246 ID=cds.MsaT016291.1;Parent=MsaT016291.1
Gene Sequence

>MsaT016291.1

ATGGATATTTCACCATTTGATGATTTCATTGAGTTTGATTGGGCAACTCAGTTTTCATACCAAAGTAATCATTTTTACACCAATGGGTGGTTCAATGATCTTGAAAACTTCAACTTTGATTTCAACCAATACCTTGATCAAAGTAGTTTTGAGATCGATCAAAAGCCCTTAAATGTTGCTTTACCTGAAATGGGGCATTACACCGACAAAGGGAAGAGTATTGCTGAGAGTGGTTTTGTTGAGGCTTCCAAGAAAACAGGAAATCAGTTTGTGAGTTTTGTGAACAAACAAGAGAAATGGGAGAATCAAGAGCCACTGTCATTGACATTGAGTGCTGCTGAGAGTGGATTTGTTGAAGCTTCGGCAAAAACTGAAAGTGGGTTTGTGGATTTTGTGAAGAAAGAGGTTGAAGGGGAAAATCAAAAATTGCCACTACCATTGCCAAGTAGCAGTACTAGAACTAGTATCATAAGGAAGAGGTCAATTTCATTGCAATTTGATGATATAAGGAAACATTTTGATGTTCCTTTAAAAATGGCTGCTAAGAAAATGAATGTTGGTGTGACCCTTTTGAAGAATAGATGCAGGGAGCTCAACATCACTAGATGGCCTCACAGAAAATTGAGGAGCTTGACTGTACTCATCGACAACCTTAAGGAAATGGGTTTGGCAAACGAGGTTGCTATGATGGAGAAGAAGAAAAGGATGTTAGAGAAACTTCCTGAAATGGAATTGAATGAAGAAATCAAGAAGCTGAGGCAAGCATGCTTTAAAGCTAAATACAAGAAGAGAAGATTAATTGCCCTCAACCTTGAGCTTCAACCTCTTTTGCTTGTAGTTGGATATAACCGTAAAAGGAAATGTGAAGAAGTCTCACACAAAGAGTATAGTGAAGGACTCATTGACATACTAGTACTTGATTTTAATGTTCTATTTTTTTGGTTTTTTTCCCCTTATGATTGGGATCAAATTGAGTAG

Protein sequence

>MsaT016291.1

MDISPFDDFIEFDWATQFSYQSNHFYTNGWFNDLENFNFDFNQYLDQSSFEIDQKPLNVALPEMGHYTDKGKSIAESGFVEASKKTGNQFVSFVNKQEKWENQEPLSLTLSAAESGFVEASAKTESGFVDFVKKEVEGENQKLPLPLPSSSTRTSIIRKRSISLQFDDIRKHFDVPLKMAAKKMNVGVTLLKNRCRELNITRWPHRKLRSLTVLIDNLKEMGLANEVAMMEKKKRMLEKLPEMELNEEIKKLRQACFKAKYKKRRLIALNLELQPLLLVVGYNRKRKCEEVSHKEYSEGLIDILVLDFNVLFFWFFSPYDWDQIE*