AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0285790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0285790 MtrunA17_Chr2g0302091 78.610 187 27 2 1 187 16 189 9.15e-96 276
Msa0285790 MtrunA17_Chr3g0093131 60.526 190 63 6 1 188 1 180 1.78e-63 194
Msa0285790 MtrunA17_Chr8g0345001 49.438 178 83 5 15 188 3 177 4.70e-45 147
Msa0285790 MtrunA17_Chr4g0018951 33.824 136 76 3 47 181 31 153 1.13e-17 76.3
Msa0285790 MtrunA17_Chr2g0333981 36.810 163 89 7 27 181 5 161 1.30e-17 76.3
Msa0285790 MtrunA17_Chr8g0379021 35.220 159 92 7 27 181 10 161 1.09e-14 68.6
Msa0285790 MtrunA17_Chr8g0355091 33.918 171 87 8 15 175 2 156 1.01e-13 67.0
Msa0285790 MtrunA17_Chr1g0206991 34.568 162 86 8 28 178 7 159 4.39e-13 64.3
Msa0285790 MtrunA17_Chr5g0422421 33.121 157 95 7 28 178 7 159 5.85e-13 65.1
Msa0285790 MtrunA17_Chr2g0292791 33.908 174 89 8 15 178 2 159 1.16e-12 64.3
Msa0285790 MtrunA17_Chr3g0099421 33.333 162 88 6 28 178 32 184 1.69e-12 63.9
Msa0285790 MtrunA17_Chr2g0317481 31.176 170 89 8 28 182 7 163 5.41e-12 62.4
Msa0285790 MtrunA17_Chr2g0317451 31.176 170 89 8 28 182 7 163 6.23e-12 62.4
Msa0285790 MtrunA17_Chr1g0206701 33.333 156 90 7 28 175 7 156 6.82e-12 62.0
Msa0285790 MtrunA17_Chr3g0119901 30.061 163 93 7 29 181 11 162 9.44e-12 61.2
Msa0285790 MtrunA17_Chr5g0422941 29.167 168 94 7 20 175 2 156 1.37e-11 61.2
Msa0285790 MtrunA17_Chr1g0149391 31.677 161 92 8 28 178 7 159 2.97e-11 60.5
Msa0285790 MtrunA17_Chr3g0085241 28.834 163 95 7 29 181 43 194 5.35e-11 59.7
Msa0285790 MtrunA17_Chr5g0419601 29.487 156 91 7 29 175 11 156 7.80e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0285790 AT2G24840.1 28.289 152 105 4 29 178 65 214 2.13e-13 67.0
Msa0285790 AT5G60440.1 31.875 160 91 7 29 178 9 160 6.12e-13 66.2

Find 25 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAAGACTTTAAGAATTCTT+TGG 0.239126 2_3:+25761364 Msa0285790:CDS
GTGCTTCATATTGAAGCCTT+AGG 0.338858 2_3:-25761214 None:intergenic
TAGAATTATTCCACCAATCA+TGG 0.397833 2_3:-25761316 None:intergenic
TGCTTCATATTGAAGCCTTA+GGG 0.444644 2_3:-25761213 None:intergenic
GCATAGAACTTGTTCTTGTC+CGG 0.453036 2_3:-25761089 None:intergenic
GTGATGTCAATTTCCATGAT+TGG 0.461626 2_3:+25761303 Msa0285790:CDS
ACGATGAATGACAGCATCAC+AGG 0.499770 2_3:-25761123 None:intergenic
ATCCTCGACCATCATATGTC+CGG 0.509285 2_3:-25761153 None:intergenic
ATGAAATTGCTGAAACCCTA+AGG 0.533334 2_3:+25761198 Msa0285790:CDS
GGACATATGATGGTCGAGGA+TGG 0.552906 2_3:+25761155 Msa0285790:CDS
GAGTTCTCAAGACGCAAACT+CGG 0.557665 2_3:+25760999 Msa0285790:CDS
TGTCTGAAAAGAACACTGCT+AGG 0.558447 2_3:+25760883 Msa0285790:CDS
GACATATGATGGTCGAGGAT+GGG 0.560153 2_3:+25761156 Msa0285790:CDS
TCTTGTCCGGCGATTTGACG+AGG 0.561634 2_3:-25761076 None:intergenic
TGCACTCCTCGTCAAATCGC+CGG 0.565424 2_3:+25761070 Msa0285790:CDS
GAACAACACTTAACAACACT+CGG 0.575251 2_3:+25760928 Msa0285790:CDS
GCTTCTGAGAGAAAGAATGC+TGG 0.579951 2_3:+25760906 Msa0285790:CDS
AATTTACGTGCAGCAAGCGA+AGG 0.589056 2_3:+25761401 Msa0285790:CDS
CGATGAATGACAGCATCACA+GGG 0.591570 2_3:-25761122 None:intergenic
CACCGGACATATGATGGTCG+AGG 0.592373 2_3:+25761151 Msa0285790:CDS
GTCTGAAAAGAACACTGCTA+GGG 0.626438 2_3:+25760884 Msa0285790:CDS
ATGTCAATTTCCATGATTGG+TGG 0.630551 2_3:+25761306 Msa0285790:CDS
AAGAACAAGTTCTATGCATG+TGG 0.639320 2_3:+25761095 Msa0285790:CDS
GAAAGCTGTCAAAGTCACCA+AGG 0.688984 2_3:+25761271 Msa0285790:CDS
GATGAATGACAGCATCACAG+GGG 0.800398 2_3:-25761121 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGAAAGAAGAAAAACTGAA+CGG + chr2_3:25760972-25760991 Msa0285790:CDS 25.0%
!! TGAAGACTTTAAGAATTCTT+TGG + chr2_3:25761364-25761383 Msa0285790:CDS 25.0%
!!! AATTCTTTGGAGAGTTTTAA+GGG + chr2_3:25761377-25761396 Msa0285790:CDS 25.0%
TCAAGAAAAACTTGAAGAAG+AGG + chr2_3:25761238-25761257 Msa0285790:CDS 30.0%
TAGAATTATTCCACCAATCA+TGG - chr2_3:25761319-25761338 None:intergenic 30.0%
!! GAATTCTTTGGAGAGTTTTA+AGG + chr2_3:25761376-25761395 Msa0285790:CDS 30.0%
GAACAACACTTAACAACACT+CGG + chr2_3:25760928-25760947 Msa0285790:CDS 35.0%
AAGAACAAGTTCTATGCATG+TGG + chr2_3:25761095-25761114 Msa0285790:CDS 35.0%
ATGAAATTGCTGAAACCCTA+AGG + chr2_3:25761198-25761217 Msa0285790:CDS 35.0%
TGCTTCATATTGAAGCCTTA+GGG - chr2_3:25761216-25761235 None:intergenic 35.0%
AGAAAAACTTGAAGAAGAGG+AGG + chr2_3:25761241-25761260 Msa0285790:CDS 35.0%
GTGATGTCAATTTCCATGAT+TGG + chr2_3:25761303-25761322 Msa0285790:CDS 35.0%
ATGTCAATTTCCATGATTGG+TGG + chr2_3:25761306-25761325 Msa0285790:CDS 35.0%
TGTCTGAAAAGAACACTGCT+AGG + chr2_3:25760883-25760902 Msa0285790:CDS 40.0%
GTCTGAAAAGAACACTGCTA+GGG + chr2_3:25760884-25760903 Msa0285790:CDS 40.0%
! GCATAGAACTTGTTCTTGTC+CGG - chr2_3:25761092-25761111 None:intergenic 40.0%
! GTCATTCATCGTTTTCTCAC+CGG + chr2_3:25761134-25761153 Msa0285790:CDS 40.0%
! TTTTCTCACCGGACATATGA+TGG + chr2_3:25761145-25761164 Msa0285790:CDS 40.0%
GTGCTTCATATTGAAGCCTT+AGG - chr2_3:25761217-25761236 None:intergenic 40.0%
! GCTTCTGAGAGAAAGAATGC+TGG + chr2_3:25760906-25760925 Msa0285790:CDS 45.0%
GAGTTCTCAAGACGCAAACT+CGG + chr2_3:25760999-25761018 Msa0285790:CDS 45.0%
!! CGAGGAGTGCAGTTTTTGAT+TGG - chr2_3:25761061-25761080 None:intergenic 45.0%
GATGAATGACAGCATCACAG+GGG - chr2_3:25761124-25761143 None:intergenic 45.0%
CGATGAATGACAGCATCACA+GGG - chr2_3:25761125-25761144 None:intergenic 45.0%
ACGATGAATGACAGCATCAC+AGG - chr2_3:25761126-25761145 None:intergenic 45.0%
ATCCTCGACCATCATATGTC+CGG - chr2_3:25761156-25761175 None:intergenic 45.0%
GACATATGATGGTCGAGGAT+GGG + chr2_3:25761156-25761175 Msa0285790:CDS 45.0%
GAAAGCTGTCAAAGTCACCA+AGG + chr2_3:25761271-25761290 Msa0285790:CDS 45.0%
! GACATCACTCTTTTGTGCCT+TGG - chr2_3:25761291-25761310 None:intergenic 45.0%
AATTTACGTGCAGCAAGCGA+AGG + chr2_3:25761401-25761420 Msa0285790:CDS 45.0%
GGACATATGATGGTCGAGGA+TGG + chr2_3:25761155-25761174 Msa0285790:CDS 50.0%
TGCACTCCTCGTCAAATCGC+CGG + chr2_3:25761070-25761089 Msa0285790:CDS 55.0%
TCTTGTCCGGCGATTTGACG+AGG - chr2_3:25761079-25761098 None:intergenic 55.0%
CACCGGACATATGATGGTCG+AGG + chr2_3:25761151-25761170 Msa0285790:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 25760864 25761430 25760864 ID=Msa0285790;Name=Msa0285790
chr2_3 mRNA 25760864 25761430 25760864 ID=Msa0285790-mRNA-1;Parent=Msa0285790;Name=Msa0285790-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|188
chr2_3 exon 25760864 25761430 25760864 ID=Msa0285790-mRNA-1:exon:9513;Parent=Msa0285790-mRNA-1
chr2_3 CDS 25760864 25761430 25760864 ID=Msa0285790-mRNA-1:cds;Parent=Msa0285790-mRNA-1
Gene Sequence

>Msa0285790

ATGAATAAGAATTGTGAACTGTCTGAAAAGAACACTGCTAGGGCTTCTGAGAGAAAGAATGCTGGAACAACACTTAACAACACTCGGAAGAGAAAGATGCATGAAATCAAGAAAGAAGAAAAACTGAACGGTTCTGAGTTCTCAAGACGCAAACTCGGAATATTCAACAAAGCAATAGAACTGTCTATTCTATGCCAATCAAAAACTGCACTCCTCGTCAAATCGCCGGACAAGAACAAGTTCTATGCATGTGGCTACCCCTGTGATGCTGTCATTCATCGTTTTCTCACCGGACATATGATGGTCGAGGATGGGAAAAAGAAGAAACAAGATGATGAAATTGCTGAAACCCTAAGGCTTCAATATGAAGCACTTCAAGAAAAACTTGAAGAAGAGGAGGATAATTTGAAAGCTGTCAAAGTCACCAAGGCACAAAAGAGTGATGTCAATTTCCATGATTGGTGGAATAATTCTATTGATGATATGAATTTAGCATCTCTTGAAGACTTTAAGAATTCTTTGGAGAGTTTTAAGGGTAATTTACGTGCAGCAAGCGAAGGAAAGTAG
Protein sequence

>Msa0285790

MNKNCELSEKNTARASERKNAGTTLNNTRKRKMHEIKKEEKLNGSEFSRRKLGIFNKAIELSILCQSKTALLVKSPDKNKFYACGYPCDAVIHRFLTGHMMVEDGKKKKQDDEIAETLRLQYEALQEKLEEEEDNLKAVKVTKAQKSDVNFHDWWNNSIDDMNLASLEDFKNSLESFKGNLRAASEGK*