AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0050820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0050820 MtrunA17_Chr1g0155551 98.125 160 3 0 1 160 1 160 1.90e-115 323
Msa0050820 MtrunA17_Chr4g0035414 60.544 147 52 4 15 160 15 156 8.05e-55 170
Msa0050820 MtrunA17_Chr3g0144941 62.676 142 46 4 18 159 18 152 3.57e-48 153
Msa0050820 MtrunA17_Chr8g0378901 50.000 166 71 6 1 160 1 160 1.01e-42 139
Msa0050820 MtrunA17_Chr3g0141881 62.500 88 30 1 18 105 54 138 3.16e-32 112
Msa0050820 MtrunA17_Chr1g0194681 38.411 151 85 4 9 159 7 149 5.80e-24 91.3
Msa0050820 MtrunA17_Chr7g0225661 41.237 97 56 1 5 100 58 154 5.84e-17 74.3
Msa0050820 MtrunA17_Chr6g0456061 42.045 88 50 1 18 105 79 165 3.41e-16 72.4
Msa0050820 MtrunA17_Chr8g0341311 40.426 94 55 1 8 100 51 144 1.77e-15 70.1
Msa0050820 MtrunA17_Chr3g0139301 33.898 118 78 0 2 119 98 215 2.23e-15 71.6
Msa0050820 MtrunA17_Chr4g0054291 37.931 116 58 1 8 109 39 154 3.41e-15 68.9
Msa0050820 MtrunA17_Chr7g0220571 46.988 83 43 1 18 100 76 157 6.00e-15 68.9
Msa0050820 MtrunA17_Chr5g0400901 38.095 105 61 1 1 105 36 136 7.15e-13 62.8
Msa0050820 MtrunA17_Chr8g0369161 40.789 76 45 0 23 98 302 377 5.93e-12 62.4
Msa0050820 MtrunA17_Chr1g0152241 41.860 86 47 1 29 114 59 141 3.67e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0050820 AT1G75390.1 52.727 165 68 6 2 158 9 171 7.66e-48 153
Msa0050820 AT4G34590.1 56.618 136 57 1 27 160 24 159 5.45e-46 148
Msa0050820 AT2G18160.1 47.917 144 62 3 22 153 23 165 1.27e-35 122
Msa0050820 AT1G75390.2 62.887 97 32 3 2 94 9 105 2.48e-32 112
Msa0050820 AT3G62420.1 42.857 133 63 3 28 158 23 144 3.19e-25 94.7
Msa0050820 AT5G49450.1 38.519 135 71 5 27 154 13 142 6.27e-16 70.9
Msa0050820 AT5G38800.1 44.444 90 50 0 11 100 53 142 4.66e-15 68.9
Msa0050820 AT3G30530.1 45.946 74 40 0 27 100 78 151 1.15e-14 68.2
Msa0050820 AT2G04038.1 51.515 66 26 1 27 92 71 130 1.72e-14 67.4
Msa0050820 AT5G15830.1 34.545 110 72 0 27 136 71 180 2.40e-14 67.4
Msa0050820 AT1G13600.1 44.048 84 45 1 19 100 73 156 2.23e-13 65.1
Msa0050820 AT4G37730.1 43.750 80 37 2 17 88 176 255 1.44e-11 61.6
Msa0050820 AT1G68880.1 46.269 67 36 0 28 94 45 111 1.83e-11 58.9
Msa0050820 AT2G22850.1 47.561 82 32 2 28 109 127 197 4.88e-11 59.3
Msa0050820 AT2G22850.2 47.561 82 32 2 28 109 127 197 4.88e-11 59.3
Msa0050820 AT1G32150.1 44.304 79 40 2 18 92 281 359 6.43e-11 59.7

Find 23 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTAATCAACAACCAATTA+TGG 0.294562 1_2:+4860082 Msa0050820:CDS
AGGCAGAGAATTGTGTTCTA+AGG 0.304006 1_2:+4859901 Msa0050820:CDS
AACACCACAACAACTACTAA+TGG 0.383416 1_2:+4859984 Msa0050820:CDS
ATGTCTGCAGAGGCCATAAT+TGG 0.394626 1_2:-4860095 None:intergenic
GGAAGATTTGCAGCTTCAAA+TGG 0.446632 1_2:+4859707 Msa0050820:CDS
AAAGCAATCGAATCGCGAAT+CGG 0.496834 1_2:+4859749 Msa0050820:CDS
TATCCTATGGCCACATCTAG+TGG 0.505899 1_2:+4859642 None:intergenic
AACTCCATTAGTAGTTGTTG+TGG 0.516849 1_2:-4859988 None:intergenic
TCAACAAAATCTCAAAGCTA+TGG 0.521179 1_2:+4859678 Msa0050820:CDS
GGCAGAGAATTGTGTTCTAA+GGG 0.540590 1_2:+4859902 Msa0050820:CDS
TTCAAATGGATCAAAGAAAG+AGG 0.542675 1_2:+4859721 Msa0050820:CDS
TAGTTGTTGTGGTGTTGATG+AGG 0.546016 1_2:-4859977 None:intergenic
GCGAATCGGCAAGAAGATCA+AGG 0.559935 1_2:+4859763 Msa0050820:CDS
ACAACACTATCTTAAAATTG+AGG 0.562515 1_2:+4859881 Msa0050820:CDS
CGGCAAGAAGATCAAGGATG+AGG 0.573196 1_2:+4859769 Msa0050820:CDS
AAATGTGTGAACTTAATCAA+AGG 0.582994 1_2:+4859928 Msa0050820:CDS
ATCTCAAAGCTATGGCTCTG+AGG 0.614327 1_2:+4859686 Msa0050820:CDS
TTTCCACTAGATGTGGCCAT+AGG 0.620229 1_2:-4859645 None:intergenic
GATGAGGAAGCAGAAGCACA+TGG 0.623986 1_2:+4859785 Msa0050820:CDS
CCTCTGCAGACATGTTTATG+TGG 0.636770 1_2:+4860105 Msa0050820:CDS
ACTAGAGTTTCCACTAGATG+TGG 0.653981 1_2:-4859652 None:intergenic
CCACATAAACATGTCTGCAG+AGG 0.669420 1_2:-4860105 None:intergenic
AAAACAGTGAAATACTCACA+AGG 0.723410 1_2:+4859844 Msa0050820:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACAACACTATCTTAAAATTG+AGG + chr1_2:4859881-4859900 Msa0050820:CDS 25.0%
! AAATGTGTGAACTTAATCAA+AGG + chr1_2:4859928-4859947 Msa0050820:CDS 25.0%
! TCTTAATCAACAACCAATTA+TGG + chr1_2:4860082-4860101 Msa0050820:CDS 25.0%
TCAACAAAATCTCAAAGCTA+TGG + chr1_2:4859678-4859697 Msa0050820:CDS 30.0%
TTCAAATGGATCAAAGAAAG+AGG + chr1_2:4859721-4859740 Msa0050820:CDS 30.0%
AAAACAGTGAAATACTCACA+AGG + chr1_2:4859844-4859863 Msa0050820:CDS 30.0%
AACACCACAACAACTACTAA+TGG + chr1_2:4859984-4860003 Msa0050820:CDS 35.0%
AACTCCATTAGTAGTTGTTG+TGG - chr1_2:4859991-4860010 None:intergenic 35.0%
ACTAGAGTTTCCACTAGATG+TGG - chr1_2:4859655-4859674 None:intergenic 40.0%
GGAAGATTTGCAGCTTCAAA+TGG + chr1_2:4859707-4859726 Msa0050820:CDS 40.0%
AAAGCAATCGAATCGCGAAT+CGG + chr1_2:4859749-4859768 Msa0050820:CDS 40.0%
AGGCAGAGAATTGTGTTCTA+AGG + chr1_2:4859901-4859920 Msa0050820:CDS 40.0%
GGCAGAGAATTGTGTTCTAA+GGG + chr1_2:4859902-4859921 Msa0050820:CDS 40.0%
!! TAGTTGTTGTGGTGTTGATG+AGG - chr1_2:4859980-4859999 None:intergenic 40.0%
! ATCTCAAAGCTATGGCTCTG+AGG + chr1_2:4859686-4859705 Msa0050820:CDS 45.0%
ATGTCTGCAGAGGCCATAAT+TGG - chr1_2:4860098-4860117 None:intergenic 45.0%
CCACATAAACATGTCTGCAG+AGG - chr1_2:4860108-4860127 None:intergenic 45.0%
CCTCTGCAGACATGTTTATG+TGG + chr1_2:4860105-4860124 Msa0050820:CDS 45.0%
GCGAATCGGCAAGAAGATCA+AGG + chr1_2:4859763-4859782 Msa0050820:CDS 50.0%
CGGCAAGAAGATCAAGGATG+AGG + chr1_2:4859769-4859788 Msa0050820:CDS 50.0%
! GATGAGGAAGCAGAAGCACA+TGG + chr1_2:4859785-4859804 Msa0050820:CDS 50.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 4859648 4860130 4859648 ID=Msa0050820;Name=Msa0050820
chr1_2 mRNA 4859648 4860130 4859648 ID=Msa0050820-mRNA-1;Parent=Msa0050820;Name=Msa0050820-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|160
chr1_2 exon 4859648 4860130 4859648 ID=Msa0050820-mRNA-1:exon:1313;Parent=Msa0050820-mRNA-1
chr1_2 CDS 4859648 4860130 4859648 ID=Msa0050820-mRNA-1:cds;Parent=Msa0050820-mRNA-1
Gene Sequence

>Msa0050820

ATGGCCACATCTAGTGGAAACTCTAGTGTGTCAACAAAATCTCAAAGCTATGGCTCTGAGGAAGATTTGCAGCTTCAAATGGATCAAAGAAAGAGGAAGAGAAAGCAATCGAATCGCGAATCGGCAAGAAGATCAAGGATGAGGAAGCAGAAGCACATGGATGATTTAGTTGCTGAAGTTGAAAGACTAAGAAATGAAAACAGTGAAATACTCACAAGGATGAACATGACAACACAACACTATCTTAAAATTGAGGCAGAGAATTGTGTTCTAAGGGCTCAAATGTGTGAACTTAATCAAAGGCTACAATCATTGAATGATATCATCAACCTCATCAACACCACAACAACTACTAATGGAGTTAATTATCAAAATAATGATTGTTTTTTAACAATTTCAGATAATTGCTTCATGAATCAAATGAATATGTCATATCTTAATCAACAACCAATTATGGCCTCTGCAGACATGTTTATGTGGTGA

Protein sequence

>Msa0050820

MATSSGNSSVSTKSQSYGSEEDLQLQMDQRKRKRKQSNRESARRSRMRKQKHMDDLVAEVERLRNENSEILTRMNMTTQHYLKIEAENCVLRAQMCELNQRLQSLNDIINLINTTTTTNGVNYQNNDCFLTISDNCFMNQMNMSYLNQQPIMASADMFMW*