AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0099210


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0099210 MtrunA17_Chr1g0151181 97.115 104 3 0 1 104 16 119 2.47e-70 205
Msa0099210 MtrunA17_Chr4g0071001 58.407 113 29 7 2 101 14 121 4.11e-27 96.3
Msa0099210 MtrunA17_Chr3g0135901 70.297 101 23 4 1 101 15 108 4.88e-27 95.9
Msa0099210 MtrunA17_Chr2g0329951 47.115 104 46 4 2 104 13 108 1.76e-22 84.3
Msa0099210 MtrunA17_Chr8g0342841 48.315 89 36 4 16 104 26 104 1.92e-16 68.6
Msa0099210 MtrunA17_Chr8g0342831 48.315 89 36 4 16 104 26 104 1.92e-16 68.6
Msa0099210 MtrunA17_Chr7g0269811 34.694 98 55 3 4 101 1 89 1.25e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0099210 AT5G11970.1 55.340 103 34 5 2 104 15 105 6.07e-23 85.5
Msa0099210 AT3G13910.1 51.852 81 35 3 15 94 20 97 2.41e-16 68.6
Msa0099210 AT3G13910.2 51.852 81 35 3 15 94 20 97 4.31e-16 68.6
Msa0099210 AT2G19460.1 55.000 80 28 3 16 95 39 110 1.82e-14 64.3
Msa0099210 AT2G19460.2 55.000 80 28 3 16 95 91 162 3.44e-14 64.7
Msa0099210 AT1G72720.1 43.158 95 48 2 12 104 37 127 1.27e-13 62.4
Msa0099210 AT2G47480.1 45.161 62 32 1 42 101 47 108 1.14e-12 59.7
Msa0099210 AT3G05725.1 43.478 69 36 2 35 103 59 124 1.17e-11 57.4
Msa0099210 AT3G62640.1 51.163 43 21 0 60 102 68 110 1.28e-11 57.0

Find 29 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTTCAAGTCCTTATTATT+AGG 0.268756 1_3:+5285067 None:intergenic
GAAAAGTGAAAGGTTCATTT+AGG 0.301962 1_3:-5284925 Msa0099210:CDS
TCAAAGGGGTCCTAATAATA+AGG 0.325607 1_3:-5285077 Msa0099210:CDS
TAAGACCTAATATCATAATT+AGG 0.344095 1_3:+5285124 None:intergenic
ATTTCCAAGTCTTGGAGCTT+TGG 0.345743 1_3:-5285010 Msa0099210:CDS
CTAAGCCTAATTATGATATT+AGG 0.367646 1_3:-5285129 Msa0099210:CDS
CTGAATTTCAAAGAAAGAAA+AGG 0.382930 1_3:-5284979 Msa0099210:CDS
GGTCTTCAATTTCCAAGTCT+TGG 0.385601 1_3:-5285018 Msa0099210:CDS
TTCCTATGCACAAACTCAAA+GGG 0.443805 1_3:-5285092 Msa0099210:CDS
AGTGGCTAAAGAATAGGTAT+TGG 0.458659 1_3:-5284892 Msa0099210:CDS
TGAATTTCAAAGAAAGAAAA+GGG 0.462597 1_3:-5284978 Msa0099210:CDS
GCTTTAAGTGGCTAAAGAAT+AGG 0.471892 1_3:-5284898 Msa0099210:CDS
ATCACCAAAGCTCCAAGACT+TGG 0.492773 1_3:+5285006 None:intergenic
AGGACTTGAAGTTGAAGAAA+GGG 0.493735 1_3:-5285057 Msa0099210:CDS
CATTTAGGAAAAGCTTTAAG+TGG 0.499586 1_3:-5284910 Msa0099210:CDS
AAGGACTTGAAGTTGAAGAA+AGG 0.504271 1_3:-5285058 Msa0099210:CDS
TACAAAATGTATTCTGTGGA+AGG 0.507359 1_3:-5284947 Msa0099210:CDS
TTTCCTATGCACAAACTCAA+AGG 0.521927 1_3:-5285093 Msa0099210:CDS
ATGCAGATGGAGGGCTACAA+TGG 0.544528 1_3:-5285157 Msa0099210:CDS
CCCTAATCAAATGATGCAGA+TGG 0.581218 1_3:-5285170 None:intergenic
GGCATGTGGTTTATAACTTG+TGG 0.581423 1_3:-5284871 Msa0099210:CDS
AAGGGAAAAGCATTTCATCA+AGG 0.598189 1_3:-5285039 Msa0099210:CDS
TAATCAAATGATGCAGATGG+AGG 0.606249 1_3:-5285167 None:intergenic
TCTGTGGAAGGAAAAGTGAA+AGG 0.617851 1_3:-5284935 Msa0099210:CDS
AAAGAATAGGTATTGGCATG+TGG 0.618847 1_3:-5284885 Msa0099210:CDS
AATCAAATGATGCAGATGGA+GGG 0.622764 1_3:-5285166 None:intergenic
TAGCTACAAAATGTATTCTG+TGG 0.631804 1_3:-5284951 Msa0099210:CDS
ACCCCTTTGAGTTTGTGCAT+AGG 0.638318 1_3:+5285090 None:intergenic
TCCTATGCACAAACTCAAAG+GGG 0.640633 1_3:-5285091 Msa0099210:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAGACCTAATATCATAATT+AGG + chr1_3:5284907-5284926 None:intergenic 20.0%
!! TGAATTTCAAAGAAAGAAAA+GGG - chr1_3:5285050-5285069 Msa0099210:CDS 20.0%
! CTAAGCCTAATTATGATATT+AGG - chr1_3:5284899-5284918 Msa0099210:CDS 25.0%
! AACTTCAAGTCCTTATTATT+AGG + chr1_3:5284964-5284983 None:intergenic 25.0%
!!! CTTTTCTTTCTTTGAAATTC+AGG + chr1_3:5285051-5285070 None:intergenic 25.0%
! CTGAATTTCAAAGAAAGAAA+AGG - chr1_3:5285049-5285068 Msa0099210:CDS 25.0%
TAGCTACAAAATGTATTCTG+TGG - chr1_3:5285077-5285096 Msa0099210:CDS 30.0%
TACAAAATGTATTCTGTGGA+AGG - chr1_3:5285081-5285100 Msa0099210:CDS 30.0%
GAAAAGTGAAAGGTTCATTT+AGG - chr1_3:5285103-5285122 Msa0099210:CDS 30.0%
!! CATTTAGGAAAAGCTTTAAG+TGG - chr1_3:5285118-5285137 Msa0099210:CDS 30.0%
TTTCCTATGCACAAACTCAA+AGG - chr1_3:5284935-5284954 Msa0099210:CDS 35.0%
TTCCTATGCACAAACTCAAA+GGG - chr1_3:5284936-5284955 Msa0099210:CDS 35.0%
TCAAAGGGGTCCTAATAATA+AGG - chr1_3:5284951-5284970 Msa0099210:CDS 35.0%
AAGGACTTGAAGTTGAAGAA+AGG - chr1_3:5284970-5284989 Msa0099210:CDS 35.0%
AGGACTTGAAGTTGAAGAAA+GGG - chr1_3:5284971-5284990 Msa0099210:CDS 35.0%
!! AAGGGAAAAGCATTTCATCA+AGG - chr1_3:5284989-5285008 Msa0099210:CDS 35.0%
! GCTTTAAGTGGCTAAAGAAT+AGG - chr1_3:5285130-5285149 Msa0099210:CDS 35.0%
AGTGGCTAAAGAATAGGTAT+TGG - chr1_3:5285136-5285155 Msa0099210:CDS 35.0%
!! AAAGAATAGGTATTGGCATG+TGG - chr1_3:5285143-5285162 Msa0099210:CDS 35.0%
TCCTATGCACAAACTCAAAG+GGG - chr1_3:5284937-5284956 Msa0099210:CDS 40.0%
GGTCTTCAATTTCCAAGTCT+TGG - chr1_3:5285010-5285029 Msa0099210:CDS 40.0%
ATTTCCAAGTCTTGGAGCTT+TGG - chr1_3:5285018-5285037 Msa0099210:CDS 40.0%
TCTGTGGAAGGAAAAGTGAA+AGG - chr1_3:5285093-5285112 Msa0099210:CDS 40.0%
GGCATGTGGTTTATAACTTG+TGG - chr1_3:5285157-5285176 Msa0099210:CDS 40.0%
! ACCCCTTTGAGTTTGTGCAT+AGG + chr1_3:5284941-5284960 None:intergenic 45.0%
ATCACCAAAGCTCCAAGACT+TGG + chr1_3:5285025-5285044 None:intergenic 45.0%
ATGCAGATGGAGGGCTACAA+TGG - chr1_3:5284871-5284890 Msa0099210:CDS 50.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 5284868 5285182 5284868 ID=Msa0099210;Name=Msa0099210
chr1_3 mRNA 5284868 5285182 5284868 ID=Msa0099210-mRNA-1;Parent=Msa0099210;Name=Msa0099210-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|104
chr1_3 exon 5284868 5285182 5284868 ID=Msa0099210-mRNA-1:exon:1909;Parent=Msa0099210-mRNA-1
chr1_3 CDS 5284868 5285182 5284868 ID=Msa0099210-mRNA-1:cds;Parent=Msa0099210-mRNA-1
Gene Sequence

>Msa0099210

ATGATGCAGATGGAGGGCTACAATGGAGCAACTAAGCCTAATTATGATATTAGGTCTTATAGTGATTTTTCCTATGCACAAACTCAAAGGGGTCCTAATAATAAGGACTTGAAGTTGAAGAAAGGGAAAAGCATTTCATCAAGGTCTTCAATTTCCAAGTCTTGGAGCTTTGGTGATGATCCTGAATTTCAAAGAAAGAAAAGGGTTGCTAGCTACAAAATGTATTCTGTGGAAGGAAAAGTGAAAGGTTCATTTAGGAAAAGCTTTAAGTGGCTAAAGAATAGGTATTGGCATGTGGTTTATAACTTGTGGTGA

Protein sequence

>Msa0099210

MMQMEGYNGATKPNYDIRSYSDFSYAQTQRGPNNKDLKLKKGKSISSRSSISKSWSFGDDPEFQRKKRVASYKMYSVEGKVKGSFRKSFKWLKNRYWHVVYNLW*