AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1379550

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1379550 MtrunA17_Chr2g0290101 92.500 120 6 2 1 120 1 117 8.13e-72 209
Msa1379550 MtrunA17_Chr4g0076001 66.667 87 29 0 33 119 29 115 1.55e-39 128
Msa1379550 MtrunA17_Chr4g0007361 55.046 109 46 2 14 119 6 114 3.31e-33 112
Msa1379550 MtrunA17_Chr4g0053921 44.538 119 59 1 1 119 1 112 4.21e-29 101
Msa1379550 MtrunA17_Chr4g0019791 53.846 91 40 1 30 120 22 110 2.55e-28 99.8
Msa1379550 MtrunA17_Chr2g0333041 52.174 92 42 1 27 118 20 109 2.63e-28 99.8
Msa1379550 MtrunA17_Chr2g0315951 44.167 120 58 2 1 119 1 112 1.27e-27 98.2
Msa1379550 MtrunA17_Chr5g0443061 42.857 119 58 5 1 117 1 111 1.29e-24 90.5
Msa1379550 MtrunA17_Chr2g0315931 42.241 116 59 1 1 116 1 108 7.57e-23 85.9
Msa1379550 MtrunA17_Chr8g0374521 48.889 90 42 2 32 117 25 114 6.02e-22 83.6
Msa1379550 MtrunA17_Chr4g0028791 43.617 94 52 1 27 119 19 112 2.56e-20 79.3
Msa1379550 MtrunA17_Chr5g0448281 40.187 107 60 3 12 116 5 109 2.57e-20 79.3
Msa1379550 MtrunA17_Chr5g0443051 48.864 88 42 3 34 119 27 113 5.80e-20 78.6
Msa1379550 MtrunA17_Chr5g0443081 38.938 113 63 4 9 119 5 113 1.66e-16 69.7
Msa1379550 MtrunA17_Chr8g0354141 39.326 89 47 1 36 117 40 128 8.34e-16 70.5
Msa1379550 MtrunA17_Chr1g0174391 45.570 79 40 3 40 116 26 103 2.67e-15 66.6
Msa1379550 MtrunA17_Chr1g0174351 45.570 79 40 3 40 116 26 103 3.98e-15 65.9
Msa1379550 MtrunA17_Chr1g0174381 47.826 69 34 2 40 106 26 94 7.78e-15 65.1
Msa1379550 MtrunA17_Chr3g0093771 38.462 91 55 1 30 119 26 116 9.50e-15 65.5
Msa1379550 MtrunA17_Chr1g0174371 44.304 79 41 3 40 116 26 103 1.04e-14 65.1
Msa1379550 MtrunA17_Chr5g0441261 36.957 92 57 1 30 120 2 93 1.32e-14 64.7
Msa1379550 MtrunA17_Chr1g0174321 44.304 79 41 3 40 116 26 103 2.17e-14 64.3
Msa1379550 MtrunA17_Chr1g0174331 43.038 79 42 3 40 116 26 103 8.87e-14 62.8
Msa1379550 MtrunA17_Chr3g0097041 34.862 109 69 2 12 119 43 150 1.05e-13 63.9
Msa1379550 MtrunA17_Chr2g0291121 50.000 68 32 2 40 105 26 93 2.97e-13 61.2
Msa1379550 MtrunA17_Chr5g0443101 43.038 79 42 3 40 116 32 109 4.22e-13 60.8
Msa1379550 MtrunA17_Chr4g0019971 44.578 83 43 3 40 120 26 107 5.24e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1379550 AT5G47550.1 64.835 91 31 1 30 119 26 116 9.71e-37 121
Msa1379550 AT4G16500.2 62.195 82 30 1 37 117 34 115 2.33e-26 95.1
Msa1379550 AT4G16500.1 62.195 82 30 1 37 117 34 115 2.33e-26 95.1
Msa1379550 AT2G40880.1 40.860 93 54 1 27 118 30 122 2.53e-20 80.1
Msa1379550 AT3G12490.2 37.931 116 69 2 8 120 11 126 1.76e-17 75.5
Msa1379550 AT3G12490.1 42.391 92 52 1 30 120 2 93 3.55e-17 72.8
Msa1379550 AT5G12140.1 40.000 90 53 1 31 119 9 98 1.57e-15 67.0
Msa1379550 AT5G05110.1 37.778 90 54 1 32 119 45 134 5.58e-14 65.9

Find 30 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTGAGACACAAGTGGTTTC+TGG 0.279706 tig0020280:+1902 Msa1379550:CDS
GGGTCTTTCACGTTCTTGAT+TGG 0.308449 tig0020280:-1794 None:intergenic
GGTCTTTCACGTTCTTGATT+GGG 0.329181 tig0020280:-1793 None:intergenic
AGAATTATGAAGCACGTGTT+TGG 0.333246 tig0020280:+1972 Msa1379550:CDS
GAATTATGAAGCACGTGTTT+GGG 0.379153 tig0020280:+1973 Msa1379550:CDS
AGCATCCTTCTTCAAACCAT+TGG 0.422878 tig0020280:-1753 None:intergenic
GCACCGTTGTGAAGTTTCAT+TGG 0.424065 tig0020280:-1683 None:intergenic
CGTTTCCAATGGTTTGAAGA+AGG 0.442519 tig0020280:+1748 Msa1379550:CDS
CACGTGTTTGGGAGAAACCT+TGG 0.458351 tig0020280:+1984 Msa1379550:CDS
ACATCACATAATCAAGCAAC+AGG 0.465380 tig0020280:-2037 None:intergenic
ACAGAGTACGGGAAACAATC+TGG 0.483880 tig0020280:+1848 Msa1379550:CDS
CTTCTTCAAACCATTGGAAA+CGG 0.493775 tig0020280:-1747 None:intergenic
AAATTCGCAGTGACAGAGTA+CGG 0.494043 tig0020280:+1836 Msa1379550:CDS
TCGGTCTTTACCGTTTCCAA+TGG 0.496229 tig0020280:+1737 Msa1379550:CDS
TCTCTTTCTATCTGTTGTGT+CGG 0.500012 tig0020280:+1718 Msa1379550:CDS
GTCTTTCACGTTCTTGATTG+GGG 0.523162 tig0020280:-1792 None:intergenic
TTGAAGAAGGATGCTCTTGT+CGG 0.542380 tig0020280:+1761 Msa1379550:CDS
TTCGCGATCTCAACCACCTG+TGG 0.547556 tig0020280:-1815 None:intergenic
AAGAAGGATGCTCTTGTCGG+TGG 0.552279 tig0020280:+1764 Msa1379550:CDS
AGATTCTTCAAATGAAGCCA+AGG 0.557868 tig0020280:-2001 None:intergenic
AATTCGCAGTGACAGAGTAC+GGG 0.560575 tig0020280:+1837 Msa1379550:CDS
TACGAATTACCGTCTTGTGT+TGG 0.594867 tig0020280:+1925 Msa1379550:CDS
AGGATGCTCTTGTCGGTGGG+TGG 0.595498 tig0020280:+1768 Msa1379550:CDS
CTTTCGCAGCCAACACAAGA+CGG 0.634024 tig0020280:-1934 None:intergenic
CAAGAACGTGAAAGACCCAC+AGG 0.645956 tig0020280:+1799 Msa1379550:CDS
AGTTTCGTGAAAGTGATCAA+AGG 0.652758 tig0020280:+1881 Msa1379550:CDS
AGAAGGATGCTCTTGTCGGT+GGG 0.667040 tig0020280:+1765 Msa1379550:CDS
GATCAAAGGTGAGACACAAG+TGG 0.672303 tig0020280:+1895 Msa1379550:CDS
GAACGTGAAAGACCCACAGG+TGG 0.721214 tig0020280:+1802 Msa1379550:CDS
TTACCAATGAAACTTCACAA+CGG 0.778595 tig0020280:+1680 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCTCTTTCTATCTGTTGTGT+CGG + tig0020280:1718-1737 Msa1379550:CDS 35.0%
CTTCTTCAAACCATTGGAAA+CGG - tig0020280:1750-1769 None:intergenic 35.0%
AGTTTCGTGAAAGTGATCAA+AGG + tig0020280:1881-1900 Msa1379550:CDS 35.0%
AGAATTATGAAGCACGTGTT+TGG + tig0020280:1972-1991 Msa1379550:CDS 35.0%
GAATTATGAAGCACGTGTTT+GGG + tig0020280:1973-1992 Msa1379550:CDS 35.0%
AGATTCTTCAAATGAAGCCA+AGG - tig0020280:2004-2023 None:intergenic 35.0%
CGTTTCCAATGGTTTGAAGA+AGG + tig0020280:1748-1767 Msa1379550:CDS 40.0%
AGCATCCTTCTTCAAACCAT+TGG - tig0020280:1756-1775 None:intergenic 40.0%
TTGAAGAAGGATGCTCTTGT+CGG + tig0020280:1761-1780 Msa1379550:CDS 40.0%
GTCTTTCACGTTCTTGATTG+GGG - tig0020280:1795-1814 None:intergenic 40.0%
GGTCTTTCACGTTCTTGATT+GGG - tig0020280:1796-1815 None:intergenic 40.0%
AAATTCGCAGTGACAGAGTA+CGG + tig0020280:1836-1855 Msa1379550:CDS 40.0%
TACGAATTACCGTCTTGTGT+TGG + tig0020280:1925-1944 Msa1379550:CDS 40.0%
TCGGTCTTTACCGTTTCCAA+TGG + tig0020280:1737-1756 Msa1379550:CDS 45.0%
GGGTCTTTCACGTTCTTGAT+TGG - tig0020280:1797-1816 None:intergenic 45.0%
AATTCGCAGTGACAGAGTAC+GGG + tig0020280:1837-1856 Msa1379550:CDS 45.0%
ACAGAGTACGGGAAACAATC+TGG + tig0020280:1848-1867 Msa1379550:CDS 45.0%
GATCAAAGGTGAGACACAAG+TGG + tig0020280:1895-1914 Msa1379550:CDS 45.0%
AAGAAGGATGCTCTTGTCGG+TGG + tig0020280:1764-1783 Msa1379550:CDS 50.0%
AGAAGGATGCTCTTGTCGGT+GGG + tig0020280:1765-1784 Msa1379550:CDS 50.0%
CAAGAACGTGAAAGACCCAC+AGG + tig0020280:1799-1818 Msa1379550:CDS 50.0%
GGTGAGACACAAGTGGTTTC+TGG + tig0020280:1902-1921 Msa1379550:CDS 50.0%
CTTTCGCAGCCAACACAAGA+CGG - tig0020280:1937-1956 None:intergenic 50.0%
CACGTGTTTGGGAGAAACCT+TGG + tig0020280:1984-2003 Msa1379550:CDS 50.0%
GAACGTGAAAGACCCACAGG+TGG + tig0020280:1802-1821 Msa1379550:CDS 55.0%
TCGCGATCTCAACCACCTGT+GGG - tig0020280:1817-1836 None:intergenic 55.0%
TTCGCGATCTCAACCACCTG+TGG - tig0020280:1818-1837 None:intergenic 55.0%
AGGATGCTCTTGTCGGTGGG+TGG + tig0020280:1768-1787 Msa1379550:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0020280 gene 1686 2048 1686 ID=Msa1379550;Name=Msa1379550
tig0020280 mRNA 1686 2048 1686 ID=Msa1379550-mRNA-1;Parent=Msa1379550;Name=Msa1379550-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|120
tig0020280 exon 1686 2048 1686 ID=Msa1379550-mRNA-1:exon:6626;Parent=Msa1379550-mRNA-1
tig0020280 CDS 1686 2048 1686 ID=Msa1379550-mRNA-1:cds;Parent=Msa1379550-mRNA-1
Gene Sequence

>Msa1379550

ATGAAACTTCACAACGGTGCAATCTTTGTTCTTCTCTTTCTATCTGTTGTGTCGGTCTTTACCGTTTCCAATGGTTTGAAGAAGGATGCTCTTGTCGGTGGGTGGACCCCAATCAAGAACGTGAAAGACCCACAGGTGGTTGAGATCGCGAAATTCGCAGTGACAGAGTACGGGAAACAATCTGGTTCGAAACTGAGTTTCGTGAAAGTGATCAAAGGTGAGACACAAGTGGTTTCTGGTACGAATTACCGTCTTGTGTTGGCTGCGAAAGATGTTTCTGTGACGAAGAATTATGAAGCACGTGTTTGGGAGAAACCTTGGCTTCATTTGAAGAATCTTACTTCGTTTAAACCTGTTGCTTGA
Protein sequence

>Msa1379550

MKLHNGAIFVLLFLSVVSVFTVSNGLKKDALVGGWTPIKNVKDPQVVEIAKFAVTEYGKQSGSKLSFVKVIKGETQVVSGTNYRLVLAAKDVSVTKNYEARVWEKPWLHLKNLTSFKPVA*