AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0603060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0603060 MtrunA17_Chr4g0031671 98.649 148 2 0 1 148 1 148 1.61e-101 287
Msa0603060 MtrunA17_Chr4g0031631 98.649 148 2 0 1 148 1 148 1.61e-101 287
Msa0603060 MtrunA17_Chr4g0030941 98.649 148 2 0 1 148 1 148 1.61e-101 287
Msa0603060 MtrunA17_Chr4g0035061 98.649 148 2 0 1 148 1 148 2.92e-101 286
Msa0603060 MtrunA17_Chr4g0035631 98.649 148 2 0 1 148 1 148 2.92e-101 286
Msa0603060 MtrunA17_Chr4g0031061 97.973 148 3 0 1 148 1 148 1.03e-100 285
Msa0603060 MtrunA17_Chr4g0032321 97.973 148 3 0 1 148 1 148 1.03e-100 285
Msa0603060 MtrunA17_Chr4g0035071 97.297 148 4 0 1 148 1 148 8.85e-100 283
Msa0603060 MtrunA17_Chr4g0030981 97.973 148 2 1 1 148 1 147 2.86e-99 281
Msa0603060 MtrunA17_Chr4g0030951 98.611 144 2 0 5 148 4 147 1.44e-98 280
Msa0603060 MtrunA17_Chr4g0046191 94.595 148 3 1 1 148 1 143 2.57e-95 271
Msa0603060 MtrunA17_Chr1g0197451 89.189 148 5 3 1 148 1 137 1.52e-78 228
Msa0603060 MtrunA17_Chr1g0198251 88.514 148 6 3 1 148 1 137 6.84e-78 227
Msa0603060 MtrunA17_Chr1g0182361 92.793 111 4 1 38 148 30 136 2.73e-64 192
Msa0603060 MtrunA17_Chr7g0263031 92.793 111 5 1 38 148 31 138 5.55e-64 192
Msa0603060 MtrunA17_Chr2g0320511 61.798 89 34 0 59 147 136 224 4.13e-37 126
Msa0603060 MtrunA17_Chr8g0368781 67.742 93 22 3 15 107 4 88 1.13e-33 114
Msa0603060 MtrunA17_Chr4g0031051 90.196 51 5 0 86 136 1 51 4.20e-27 95.9
Msa0603060 MtrunA17_Chr7g0228831 92.500 40 3 0 57 96 42 81 8.42e-23 86.3
Msa0603060 MtrunA17_Chr4g0014401 36.792 106 63 2 31 132 5 110 2.77e-13 62.8
Msa0603060 MtrunA17_Chr4g0075141 37.349 83 51 1 64 145 34 116 5.44e-12 59.3
Msa0603060 MtrunA17_Chr4g0062361 33.010 103 61 4 33 134 4 99 2.79e-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
Msa0603060 AT3G45980.1 88.742 151 13 2 1 148 1 150 2.11e-83 241
Msa0603060 AT2G28720.1 86.093 151 18 1 1 148 1 151 1.35e-80 234
Msa0603060 AT1G07790.1 86.275 153 11 3 1 148 1 148 1.25e-79 232
Msa0603060 AT5G59910.1 91.176 136 9 2 13 148 18 150 2.63e-77 226
Msa0603060 AT3G46030.1 94.444 126 6 1 23 148 21 145 1.07e-75 222
Msa0603060 AT2G37470.1 81.757 148 16 3 1 147 1 138 7.74e-71 209
Msa0603060 AT3G53650.1 81.879 149 15 3 1 148 1 138 1.02e-69 207
Msa0603060 AT5G22880.1 86.897 145 17 2 4 148 3 145 6.04e-67 200
Msa0603060 AT5G02570.1 79.730 148 14 1 1 148 1 132 1.14e-66 199
Msa0603060 AT3G09480.1 84.127 126 16 1 23 148 5 126 2.63e-62 187
Msa0603060 AT1G08170.1 56.989 93 40 0 53 145 143 235 1.79e-37 128

Find 45 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTGTCAGGCTTGTTCTTCC+CGG 0.318826 4_2:-47217816 Msa0603060:CDS
GGAAGCTTCTTCCCTGCCTT+TGG 0.324723 4_2:+47218083 None:intergenic
TTGCTTGAGATACCAATGTC+TGG 0.335174 4_2:+47217957 None:intergenic
CTTCTCCGCCGGAGCTTTCT+CGG 0.336863 4_2:+47218109 None:intergenic
GCTTGTTCTTCCCGGTGAAT+TGG 0.368237 4_2:-47217808 Msa0603060:CDS
GCTGGCTTCTTCTCTCCCTT+TGG 0.368494 4_2:+47218170 None:intergenic
GCCTTTGGCTTCTTCTCCGC+CGG 0.402654 4_2:+47218098 None:intergenic
ATTTCCCTGGAAGTGATTGT+TGG 0.430207 4_2:+47217846 None:intergenic
CTCTGATTCAATGGCACCAA+AGG 0.436385 4_2:-47218186 None:intergenic
GCGGAGAAGAAGCCAAAGGC+AGG 0.445065 4_2:-47218095 Msa0603060:CDS
ATACAAGATCTACATCTTCA+AGG 0.451479 4_2:-47217997 Msa0603060:CDS
GTGGACTTCTTCTCCTCAGC+GGG 0.452143 4_2:+47218137 None:intergenic
TCAGCGGGTTTCTTCTCCGC+TGG 0.467762 4_2:+47218152 None:intergenic
GCAGCTGAACCACCTTCCTT+AGG 0.469489 4_2:+47218062 None:intergenic
GGGAAATTCAGACTGCTGTC+AGG 0.472146 4_2:-47217830 Msa0603060:CDS
TCTCTTCTTCTTCTTGTCTC+CGG 0.474508 4_2:+47218040 None:intergenic
ACCCTCAGAGACAGCATGCT+TGG 0.475334 4_2:+47217785 None:intergenic
AGAAGCCAACAATCACTTCC+AGG 0.480188 4_2:-47217851 Msa0603060:CDS
AGCATGCTTGGCCAATTCAC+CGG 0.481273 4_2:+47217797 None:intergenic
AAGGAAGGTGGTTCAGCTGC+CGG 0.489603 4_2:-47218059 Msa0603060:CDS
GACAGCAGTCTGAATTTCCC+TGG 0.496873 4_2:+47217833 None:intergenic
GATCTAAGAACTAGTAAACT+TGG 0.511385 4_2:+47217749 None:intergenic
CACAGTCGCCGAGAAAGCTC+CGG 0.525595 4_2:-47218117 Msa0603060:CDS
TGCTTGAGATACCAATGTCT+GGG 0.532971 4_2:+47217958 None:intergenic
TGGTATCTCAAGCAAAGCCA+TGG 0.533917 4_2:-47217949 Msa0603060:CDS
GCATGCTTGGCCAATTCACC+GGG 0.547334 4_2:+47217798 None:intergenic
TCTGATTCAATGGCACCAAA+GGG 0.547354 4_2:-47218185 None:intergenic
AGTAAACTTGGTCACAGCCT+TGG 0.548318 4_2:+47217761 None:intergenic
CGGAGAAGAAGCCAAAGGCA+GGG 0.564014 4_2:-47218094 Msa0603060:CDS
GCCAAGCATGCTGTCTCTGA+GGG 0.566391 4_2:-47217786 Msa0603060:CDS
TGCTGTCTCTGAGGGTACCA+AGG 0.572597 4_2:-47217778 Msa0603060:CDS
GGCAGGGAAGAAGCTTCCTA+AGG 0.584355 4_2:-47218078 Msa0603060:CDS
GGCCAAGCATGCTGTCTCTG+AGG 0.598295 4_2:-47217787 Msa0603060:CDS
GGGAAGAAGCTTCCTAAGGA+AGG 0.609466 4_2:-47218074 Msa0603060:CDS
AAACAAGTTCACCCAGACAT+TGG 0.612279 4_2:-47217969 Msa0603060:CDS
TCCGGCGGAGAAGAAGCCAA+AGG 0.620050 4_2:-47218099 Msa0603060:CDS
GAAACTGTTCATGATTCCCA+TGG 0.633384 4_2:+47217932 None:intergenic
GAAGCCAACAATCACTTCCA+GGG 0.639164 4_2:-47217850 Msa0603060:CDS
CGGAGCTTTCTCGGCGACTG+TGG 0.639450 4_2:+47218118 None:intergenic
AAAGGGAGAGAAGAAGCCAG+CGG 0.642633 4_2:-47218168 Msa0603060:CDS
GGTATCTCAAGCAAAGCCAT+GGG 0.654333 4_2:-47217948 Msa0603060:CDS
TGTGGACTTCTTCTCCTCAG+CGG 0.655377 4_2:+47218136 None:intergenic
AAGAAGCTTCCTAAGGAAGG+TGG 0.656480 4_2:-47218071 Msa0603060:CDS
AGTCGCCGAGAAAGCTCCGG+CGG 0.659369 4_2:-47218114 Msa0603060:CDS
AGCGGAGAAGAAACCCGCTG+AGG 0.708553 4_2:-47218150 Msa0603060:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATACAAGATCTACATCTTCA+AGG - chr4_2:47217931-47217950 Msa0603060:CDS 30.0%
TCTCTTCTTCTTCTTGTCTC+CGG + chr4_2:47217891-47217910 None:intergenic 40.0%
AAACAAGTTCACCCAGACAT+TGG - chr4_2:47217959-47217978 Msa0603060:CDS 40.0%
TGCTTGAGATACCAATGTCT+GGG + chr4_2:47217973-47217992 None:intergenic 40.0%
TTGCTTGAGATACCAATGTC+TGG + chr4_2:47217974-47217993 None:intergenic 40.0%
GAAACTGTTCATGATTCCCA+TGG + chr4_2:47217999-47218018 None:intergenic 40.0%
ATTTCCCTGGAAGTGATTGT+TGG + chr4_2:47218085-47218104 None:intergenic 40.0%
AAGAAGCTTCCTAAGGAAGG+TGG - chr4_2:47217857-47217876 Msa0603060:CDS 45.0%
TGGTATCTCAAGCAAAGCCA+TGG - chr4_2:47217979-47217998 Msa0603060:CDS 45.0%
GGTATCTCAAGCAAAGCCAT+GGG - chr4_2:47217980-47217999 Msa0603060:CDS 45.0%
AGAAGCCAACAATCACTTCC+AGG - chr4_2:47218077-47218096 Msa0603060:CDS 45.0%
GAAGCCAACAATCACTTCCA+GGG - chr4_2:47218078-47218097 Msa0603060:CDS 45.0%
AGTAAACTTGGTCACAGCCT+TGG + chr4_2:47218170-47218189 None:intergenic 45.0%
AAAGGGAGAGAAGAAGCCAG+CGG - chr4_2:47217760-47217779 Msa0603060:CDS 50.0%
TGTGGACTTCTTCTCCTCAG+CGG + chr4_2:47217795-47217814 None:intergenic 50.0%
GGGAAGAAGCTTCCTAAGGA+AGG - chr4_2:47217854-47217873 Msa0603060:CDS 50.0%
GACAGCAGTCTGAATTTCCC+TGG + chr4_2:47218098-47218117 None:intergenic 50.0%
GGGAAATTCAGACTGCTGTC+AGG - chr4_2:47218098-47218117 Msa0603060:CDS 50.0%
GCTTGTTCTTCCCGGTGAAT+TGG - chr4_2:47218120-47218139 Msa0603060:CDS 50.0%
AGCATGCTTGGCCAATTCAC+CGG + chr4_2:47218134-47218153 None:intergenic 50.0%
! GCTGGCTTCTTCTCTCCCTT+TGG + chr4_2:47217761-47217780 None:intergenic 55.0%
GTGGACTTCTTCTCCTCAGC+GGG + chr4_2:47217794-47217813 None:intergenic 55.0%
CGGAGAAGAAGCCAAAGGCA+GGG - chr4_2:47217834-47217853 Msa0603060:CDS 55.0%
GGAAGCTTCTTCCCTGCCTT+TGG + chr4_2:47217848-47217867 None:intergenic 55.0%
GGCAGGGAAGAAGCTTCCTA+AGG - chr4_2:47217850-47217869 Msa0603060:CDS 55.0%
GCAGCTGAACCACCTTCCTT+AGG + chr4_2:47217869-47217888 None:intergenic 55.0%
AAGGAAGGTGGTTCAGCTGC+CGG - chr4_2:47217869-47217888 Msa0603060:CDS 55.0%
! GCTGTCAGGCTTGTTCTTCC+CGG - chr4_2:47218112-47218131 Msa0603060:CDS 55.0%
GCATGCTTGGCCAATTCACC+GGG + chr4_2:47218133-47218152 None:intergenic 55.0%
GCCAAGCATGCTGTCTCTGA+GGG - chr4_2:47218142-47218161 Msa0603060:CDS 55.0%
ACCCTCAGAGACAGCATGCT+TGG + chr4_2:47218146-47218165 None:intergenic 55.0%
!! TGCTGTCTCTGAGGGTACCA+AGG - chr4_2:47218150-47218169 Msa0603060:CDS 55.0%
! TCAGCGGGTTTCTTCTCCGC+TGG + chr4_2:47217779-47217798 None:intergenic 60.0%
AGCGGAGAAGAAACCCGCTG+AGG - chr4_2:47217778-47217797 Msa0603060:CDS 60.0%
CACAGTCGCCGAGAAAGCTC+CGG - chr4_2:47217811-47217830 Msa0603060:CDS 60.0%
CTTCTCCGCCGGAGCTTTCT+CGG + chr4_2:47217822-47217841 None:intergenic 60.0%
TCCGGCGGAGAAGAAGCCAA+AGG - chr4_2:47217829-47217848 Msa0603060:CDS 60.0%
! GCCTTTGGCTTCTTCTCCGC+CGG + chr4_2:47217833-47217852 None:intergenic 60.0%
GCGGAGAAGAAGCCAAAGGC+AGG - chr4_2:47217833-47217852 Msa0603060:CDS 60.0%
GGCCAAGCATGCTGTCTCTG+AGG - chr4_2:47218141-47218160 Msa0603060:CDS 60.0%
CGGAGCTTTCTCGGCGACTG+TGG + chr4_2:47217813-47217832 None:intergenic 65.0%
AGTCGCCGAGAAAGCTCCGG+CGG - chr4_2:47217814-47217833 Msa0603060:CDS 65.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 47217752 47218198 47217752 ID=Msa0603060;Name=Msa0603060
chr4_2 mRNA 47217752 47218198 47217752 ID=Msa0603060-mRNA-1;Parent=Msa0603060;Name=Msa0603060-mRNA-1;_AED=0.18;_eAED=0.18;_QI=0|-1|0|1|-1|1|1|0|148
chr4_2 exon 47217752 47218198 47217752 ID=Msa0603060-mRNA-1:exon:10817;Parent=Msa0603060-mRNA-1
chr4_2 CDS 47217752 47218198 47217752 ID=Msa0603060-mRNA-1:cds;Parent=Msa0603060-mRNA-1
Gene Sequence

>Msa0603060

ATGGCACCAAAGGGAGAGAAGAAGCCAGCGGAGAAGAAACCCGCTGAGGAGAAGAAGTCCACAGTCGCCGAGAAAGCTCCGGCGGAGAAGAAGCCAAAGGCAGGGAAGAAGCTTCCTAAGGAAGGTGGTTCAGCTGCCGGAGACAAGAAGAAGAAGAGAAACAAGAAGAGTGTAGAAACATACAAGATCTACATCTTCAAGGTTCTGAAACAAGTTCACCCAGACATTGGTATCTCAAGCAAAGCCATGGGAATCATGAACAGTTTCATCAATGACATCTTCGAGAAACTCGCTCAAGAATCTTCAAGACTTGCTCGATACAACAAGAAGCCAACAATCACTTCCAGGGAAATTCAGACTGCTGTCAGGCTTGTTCTTCCCGGTGAATTGGCCAAGCATGCTGTCTCTGAGGGTACCAAGGCTGTGACCAAGTTTACTAGTTCTTAG
Protein sequence

>Msa0603060

MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGDKKKKRNKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS*