AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1385090


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1385090 MtrunA17_Chr1g0151181 97.479 119 3 0 1 119 1 119 1.87e-82 236
Msa1385090 MtrunA17_Chr3g0135901 66.379 116 31 5 1 116 1 108 2.05e-30 105
Msa1385090 MtrunA17_Chr4g0071001 54.264 129 38 9 1 116 1 121 4.77e-27 96.7
Msa1385090 MtrunA17_Chr2g0329951 47.115 104 46 4 17 119 13 108 3.25e-22 84.0
Msa1385090 MtrunA17_Chr8g0342841 48.315 89 36 4 31 119 26 104 3.16e-16 68.6
Msa1385090 MtrunA17_Chr8g0342831 48.315 89 36 4 31 119 26 104 3.16e-16 68.6
Msa1385090 MtrunA17_Chr7g0269811 34.694 98 55 3 19 116 1 89 2.02e-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
Msa1385090 AT5G11970.1 54.622 119 40 7 1 119 1 105 1.16e-26 95.5
Msa1385090 AT3G13910.1 44.554 101 44 4 10 109 8 97 3.77e-16 68.9
Msa1385090 AT3G13910.2 44.554 101 44 4 10 109 8 97 7.11e-16 68.6
Msa1385090 AT2G19460.1 43.333 120 48 5 1 110 1 110 1.26e-15 67.8
Msa1385090 AT2G19460.2 43.333 120 48 5 1 110 53 162 2.32e-15 68.6
Msa1385090 AT1G72720.1 43.158 95 48 2 27 119 37 127 2.88e-13 62.0
Msa1385090 AT2G47480.1 45.161 62 32 1 57 116 47 108 1.54e-12 59.7
Msa1385090 AT3G05725.1 43.478 69 36 2 50 118 59 124 1.59e-11 57.4
Msa1385090 AT3G62640.1 51.163 43 21 0 75 117 68 110 1.86e-11 57.0

Find 34 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTTCAAGTCCTTATTATT+AGG 0.268756 tig0020711:+29065 None:intergenic
GAAAAGTGAAAGGTTCATTT+AGG 0.301962 tig0020711:-28923 Msa1385090:CDS
TCAAAGGGGTCCTAATAATA+AGG 0.325607 tig0020711:-29075 Msa1385090:CDS
TAAGACCTAATATCATAATT+AGG 0.344095 tig0020711:+29122 None:intergenic
ATTTCCAAGTCTTGGAGCTT+TGG 0.345743 tig0020711:-29008 Msa1385090:CDS
CTAAGCCTAATTATGATATT+AGG 0.367646 tig0020711:-29127 Msa1385090:CDS
CTGAATTTCAAAGAAAGAAA+AGG 0.382930 tig0020711:-28977 Msa1385090:CDS
GGTCTTCAATTTCCAAGTCT+TGG 0.385601 tig0020711:-29016 Msa1385090:CDS
AGGATTACAACAAACAAATT+AGG 0.424144 tig0020711:-29199 Msa1385090:CDS
TTCCTATGCACAAACTCAAA+GGG 0.443805 tig0020711:-29090 Msa1385090:CDS
AACAAACAAATTAGGCCCTA+TGG 0.456268 tig0020711:-29191 Msa1385090:CDS
AGTGGCTAAAGAATAGGTAT+TGG 0.458659 tig0020711:-28890 Msa1385090:CDS
TGAATTTCAAAGAAAGAAAA+GGG 0.462597 tig0020711:-28976 Msa1385090:CDS
GCTTTAAGTGGCTAAAGAAT+AGG 0.471892 tig0020711:-28896 Msa1385090:CDS
CATCATTTGACTATTTCCAT+AGG 0.472718 tig0020711:+29175 None:intergenic
ATCACCAAAGCTCCAAGACT+TGG 0.492773 tig0020711:+29004 None:intergenic
AGGACTTGAAGTTGAAGAAA+GGG 0.493735 tig0020711:-29055 Msa1385090:CDS
CATTTAGGAAAAGCTTTAAG+TGG 0.499586 tig0020711:-28908 Msa1385090:CDS
AAGGACTTGAAGTTGAAGAA+AGG 0.504271 tig0020711:-29056 Msa1385090:CDS
TACAAAATGTATTCTGTGGA+AGG 0.507359 tig0020711:-28945 Msa1385090:CDS
ATCATTTGACTATTTCCATA+GGG 0.507995 tig0020711:+29176 None:intergenic
TTGTTTGTTGTAATCCTCCA+TGG 0.515361 tig0020711:+29205 None:intergenic
TTTCCTATGCACAAACTCAA+AGG 0.521927 tig0020711:-29091 Msa1385090:CDS
ATGCAGATGGAGGGCTACAA+TGG 0.544528 tig0020711:-29155 Msa1385090:CDS
GGCATGTGGTTTATAACTTG+TGG 0.581423 tig0020711:-28869 Msa1385090:CDS
AAATAGTCAAATGATGCAGA+TGG 0.594245 tig0020711:-29168 Msa1385090:CDS
AAGGGAAAAGCATTTCATCA+AGG 0.598189 tig0020711:-29037 Msa1385090:CDS
TAGTCAAATGATGCAGATGG+AGG 0.613440 tig0020711:-29165 Msa1385090:CDS
AGTCAAATGATGCAGATGGA+GGG 0.615864 tig0020711:-29164 Msa1385090:CDS
TCTGTGGAAGGAAAAGTGAA+AGG 0.617851 tig0020711:-28933 Msa1385090:CDS
AAAGAATAGGTATTGGCATG+TGG 0.618847 tig0020711:-28883 Msa1385090:CDS
TAGCTACAAAATGTATTCTG+TGG 0.631804 tig0020711:-28949 Msa1385090:CDS
ACCCCTTTGAGTTTGTGCAT+AGG 0.638318 tig0020711:+29088 None:intergenic
TCCTATGCACAAACTCAAAG+GGG 0.640633 tig0020711:-29089 Msa1385090:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAGACCTAATATCATAATT+AGG + tig0020711:28950-28969 None:intergenic 20.0%
!! TGAATTTCAAAGAAAGAAAA+GGG - tig0020711:29093-29112 Msa1385090:CDS 20.0%
! AGGATTACAACAAACAAATT+AGG - tig0020711:28870-28889 Msa1385090:CDS 25.0%
! ATCATTTGACTATTTCCATA+GGG + tig0020711:28896-28915 None:intergenic 25.0%
! CTAAGCCTAATTATGATATT+AGG - tig0020711:28942-28961 Msa1385090:CDS 25.0%
! AACTTCAAGTCCTTATTATT+AGG + tig0020711:29007-29026 None:intergenic 25.0%
!!! CTTTTCTTTCTTTGAAATTC+AGG + tig0020711:29094-29113 None:intergenic 25.0%
! CTGAATTTCAAAGAAAGAAA+AGG - tig0020711:29092-29111 Msa1385090:CDS 25.0%
CATCATTTGACTATTTCCAT+AGG + tig0020711:28897-28916 None:intergenic 30.0%
AAATAGTCAAATGATGCAGA+TGG - tig0020711:28901-28920 Msa1385090:CDS 30.0%
TAGCTACAAAATGTATTCTG+TGG - tig0020711:29120-29139 Msa1385090:CDS 30.0%
TACAAAATGTATTCTGTGGA+AGG - tig0020711:29124-29143 Msa1385090:CDS 30.0%
GAAAAGTGAAAGGTTCATTT+AGG - tig0020711:29146-29165 Msa1385090:CDS 30.0%
!! CATTTAGGAAAAGCTTTAAG+TGG - tig0020711:29161-29180 Msa1385090:CDS 30.0%
AACAAACAAATTAGGCCCTA+TGG - tig0020711:28878-28897 Msa1385090:CDS 35.0%
TTTCCTATGCACAAACTCAA+AGG - tig0020711:28978-28997 Msa1385090:CDS 35.0%
TTCCTATGCACAAACTCAAA+GGG - tig0020711:28979-28998 Msa1385090:CDS 35.0%
TCAAAGGGGTCCTAATAATA+AGG - tig0020711:28994-29013 Msa1385090:CDS 35.0%
AAGGACTTGAAGTTGAAGAA+AGG - tig0020711:29013-29032 Msa1385090:CDS 35.0%
AGGACTTGAAGTTGAAGAAA+GGG - tig0020711:29014-29033 Msa1385090:CDS 35.0%
!! AAGGGAAAAGCATTTCATCA+AGG - tig0020711:29032-29051 Msa1385090:CDS 35.0%
! GCTTTAAGTGGCTAAAGAAT+AGG - tig0020711:29173-29192 Msa1385090:CDS 35.0%
AGTGGCTAAAGAATAGGTAT+TGG - tig0020711:29179-29198 Msa1385090:CDS 35.0%
!! AAAGAATAGGTATTGGCATG+TGG - tig0020711:29186-29205 Msa1385090:CDS 35.0%
TAGTCAAATGATGCAGATGG+AGG - tig0020711:28904-28923 Msa1385090:CDS 40.0%
AGTCAAATGATGCAGATGGA+GGG - tig0020711:28905-28924 Msa1385090:CDS 40.0%
TCCTATGCACAAACTCAAAG+GGG - tig0020711:28980-28999 Msa1385090:CDS 40.0%
GGTCTTCAATTTCCAAGTCT+TGG - tig0020711:29053-29072 Msa1385090:CDS 40.0%
ATTTCCAAGTCTTGGAGCTT+TGG - tig0020711:29061-29080 Msa1385090:CDS 40.0%
TCTGTGGAAGGAAAAGTGAA+AGG - tig0020711:29136-29155 Msa1385090:CDS 40.0%
GGCATGTGGTTTATAACTTG+TGG - tig0020711:29200-29219 Msa1385090:CDS 40.0%
! ACCCCTTTGAGTTTGTGCAT+AGG + tig0020711:28984-29003 None:intergenic 45.0%
ATCACCAAAGCTCCAAGACT+TGG + tig0020711:29068-29087 None:intergenic 45.0%
ATGCAGATGGAGGGCTACAA+TGG - tig0020711:28914-28933 Msa1385090:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0020711 gene 28866 29225 28866 ID=Msa1385090;Name=Msa1385090
tig0020711 mRNA 28866 29225 28866 ID=Msa1385090-mRNA-1;Parent=Msa1385090;Name=Msa1385090-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|119
tig0020711 exon 28866 29225 28866 ID=Msa1385090-mRNA-1:exon:9439;Parent=Msa1385090-mRNA-1
tig0020711 CDS 28866 29225 28866 ID=Msa1385090-mRNA-1:cds;Parent=Msa1385090-mRNA-1
Gene Sequence

>Msa1385090

ATGGAGGATTACAACAAACAAATTAGGCCCTATGGAAATAGTCAAATGATGCAGATGGAGGGCTACAATGGAGCAACTAAGCCTAATTATGATATTAGGTCTTATAGTGATTTTTCCTATGCACAAACTCAAAGGGGTCCTAATAATAAGGACTTGAAGTTGAAGAAAGGGAAAAGCATTTCATCAAGGTCTTCAATTTCCAAGTCTTGGAGCTTTGGTGATGATCCTGAATTTCAAAGAAAGAAAAGGGTTGCTAGCTACAAAATGTATTCTGTGGAAGGAAAAGTGAAAGGTTCATTTAGGAAAAGCTTTAAGTGGCTAAAGAATAGGTATTGGCATGTGGTTTATAACTTGTGGTGA

Protein sequence

>Msa1385090

MEDYNKQIRPYGNSQMMQMEGYNGATKPNYDIRSYSDFSYAQTQRGPNNKDLKLKKGKSISSRSSISKSWSFGDDPEFQRKKRVASYKMYSVEGKVKGSFRKSFKWLKNRYWHVVYNLW*