AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1446180

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1446180 MtrunA17_Chr3g0136801 99.000 100 1 0 1 100 1 100 5.00e-70 204
Msa1446180 MtrunA17_Chr6g0460501 54.082 98 45 0 2 99 77 174 9.57e-37 122
Msa1446180 MtrunA17_Chr6g0470661 53.608 97 45 0 2 98 72 168 2.40e-33 115
Msa1446180 MtrunA17_Chr1g0203511 53.608 97 45 0 2 98 107 203 9.31e-33 114
Msa1446180 MtrunA17_Chr3g0120151 44.330 97 54 0 3 99 35 131 8.69e-24 90.9
Msa1446180 MtrunA17_Chr6g0460431 49.180 61 31 0 36 96 26 86 1.12e-15 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1446180 AT2G24940.1 81.000 100 19 0 1 100 1 100 4.17e-57 171
Msa1446180 AT5G52240.2 53.608 97 45 0 2 98 74 170 6.13e-35 118
Msa1446180 AT5G52240.1 53.608 97 45 0 2 98 74 170 2.37e-34 117
Msa1446180 AT3G48890.1 52.577 97 46 0 2 98 70 166 1.72e-32 113
Msa1446180 AT4G14965.1 42.268 97 56 0 3 99 42 138 1.21e-20 83.2
Msa1446180 AT4G14965.2 45.783 83 45 0 3 85 42 124 4.43e-20 80.5

Find 26 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCCTTCACCGCCACGTAGA+TGG 0.304041 tig0031290:+4217 None:intergenic
TGCTCTGCTAGCGTCTTTGC+CGG 0.356636 tig0031290:+4130 None:intergenic
AGATCGGAGTTCTCAATGAT+TGG 0.393020 tig0031290:-4043 Msa1446180:CDS
CTAACGATGGTGGCAACAAC+AGG 0.396192 tig0031290:+3996 None:intergenic
GAGAACTCCGATCTCTTTCT+CGG 0.397488 tig0031290:+4052 None:intergenic
GCCCATCTACGTGGCGGTGA+AGG 0.412629 tig0031290:-4219 Msa1446180:CDS
AGCGTCTTTGCCGGCGAACA+TGG 0.474656 tig0031290:+4139 None:intergenic
GATCGGAGTTCTCAATGATT+GGG 0.479187 tig0031290:-4042 Msa1446180:CDS
AGGGTACTTAGCTACGAACT+TGG 0.494927 tig0031290:+4016 None:intergenic
GCCACGTAGATGGGCTTCGA+TGG 0.508678 tig0031290:+4227 None:intergenic
GGTAAATCGTTCTACGGTCC+AGG 0.513945 tig0031290:-4173 Msa1446180:CDS
GGAGCCTACGCCATGTTCGC+CGG 0.517126 tig0031290:-4149 Msa1446180:CDS
GATATCACCTCGTCGCTCGA+TGG 0.532549 tig0031290:-4080 Msa1446180:CDS
TGGACCGTAGAACGATTTAC+CGG 0.538773 tig0031290:+4175 None:intergenic
CCCATCTACGTGGCGGTGAA+GGG 0.540433 tig0031290:-4218 Msa1446180:CDS
CCACGTAGATGGGCTTCGAT+GGG 0.568442 tig0031290:+4228 None:intergenic
GGACTCACCGAGAAAGAGAT+CGG 0.584108 tig0031290:-4059 Msa1446180:CDS
ACCACCGGTAAATCGTTCTA+CGG 0.585309 tig0031290:-4179 Msa1446180:CDS
TTGAATTAATTAGCTAACGA+TGG 0.596468 tig0031290:+3983 None:intergenic
AATTAATTAGCTAACGATGG+TGG 0.596842 tig0031290:+3986 None:intergenic
TTTGCCGGCGAACATGGCGT+AGG 0.602453 tig0031290:+4145 None:intergenic
AAATCGTTCTACGGTCCAGG+TGG 0.624678 tig0031290:-4170 Msa1446180:CDS
TAACGATGGTGGCAACAACA+GGG 0.689123 tig0031290:+3997 None:intergenic
ATCGAAGCCCATCTACGTGG+CGG 0.707583 tig0031290:-4225 Msa1446180:CDS
ACCGTAGAACGATTTACCGG+TGG 0.721812 tig0031290:+4178 None:intergenic
CAACAACTGAGCGAATACAA+CGG 0.745415 tig0031290:-4257 Msa1446180:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAACAACTGAGCGAATACAA+CGG - tig0031290:4007-4026 Msa1446180:CDS 40.0%
AGATCGGAGTTCTCAATGAT+TGG - tig0031290:4221-4240 Msa1446180:CDS 40.0%
GATCGGAGTTCTCAATGATT+GGG - tig0031290:4222-4241 Msa1446180:CDS 40.0%
ACCACCGGTAAATCGTTCTA+CGG - tig0031290:4085-4104 Msa1446180:CDS 45.0%
TGGACCGTAGAACGATTTAC+CGG + tig0031290:4092-4111 None:intergenic 45.0%
GAGAACTCCGATCTCTTTCT+CGG + tig0031290:4215-4234 None:intergenic 45.0%
! AGGGTACTTAGCTACGAACT+TGG + tig0031290:4251-4270 None:intergenic 45.0%
! TAACGATGGTGGCAACAACA+GGG + tig0031290:4270-4289 None:intergenic 45.0%
ACCGTAGAACGATTTACCGG+TGG + tig0031290:4089-4108 None:intergenic 50.0%
GGTAAATCGTTCTACGGTCC+AGG - tig0031290:4091-4110 Msa1446180:CDS 50.0%
AAATCGTTCTACGGTCCAGG+TGG - tig0031290:4094-4113 Msa1446180:CDS 50.0%
GGACTCACCGAGAAAGAGAT+CGG - tig0031290:4205-4224 Msa1446180:CDS 50.0%
! CTAACGATGGTGGCAACAAC+AGG + tig0031290:4271-4290 None:intergenic 50.0%
! CCACGTAGATGGGCTTCGAT+GGG + tig0031290:4039-4058 None:intergenic 55.0%
ATCGAAGCCCATCTACGTGG+CGG - tig0031290:4039-4058 Msa1446180:CDS 55.0%
TGCTCTGCTAGCGTCTTTGC+CGG + tig0031290:4137-4156 None:intergenic 55.0%
GATATCACCTCGTCGCTCGA+TGG - tig0031290:4184-4203 Msa1446180:CDS 55.0%
CCCATCGAAGCCCATCTACG+TGG - tig0031290:4036-4055 Msa1446180:CDS 60.0%
! GCCACGTAGATGGGCTTCGA+TGG + tig0031290:4040-4059 None:intergenic 60.0%
CCCTTCACCGCCACGTAGAT+GGG + tig0031290:4049-4068 None:intergenic 60.0%
CCCATCTACGTGGCGGTGAA+GGG - tig0031290:4046-4065 Msa1446180:CDS 60.0%
ACCCTTCACCGCCACGTAGA+TGG + tig0031290:4050-4069 None:intergenic 60.0%
! CGCGTTTTCGACGTCACCAC+CGG - tig0031290:4070-4089 Msa1446180:CDS 60.0%
AACATGGCGTAGGCTCCACC+TGG + tig0031290:4112-4131 None:intergenic 60.0%
TTTGCCGGCGAACATGGCGT+AGG + tig0031290:4122-4141 None:intergenic 60.0%
AGCGTCTTTGCCGGCGAACA+TGG + tig0031290:4128-4147 None:intergenic 60.0%
GCCCATCTACGTGGCGGTGA+AGG - tig0031290:4045-4064 Msa1446180:CDS 65.0%
GGAGCCTACGCCATGTTCGC+CGG - tig0031290:4115-4134 Msa1446180:CDS 65.0%
GGTGAGTCCATCGAGCGACG+AGG + tig0031290:4194-4213 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0031290 gene 3992 4294 3992 ID=Msa1446180;Name=Msa1446180
tig0031290 mRNA 3992 4294 3992 ID=Msa1446180-mRNA-1;Parent=Msa1446180;Name=Msa1446180-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|100
tig0031290 exon 3992 4294 3992 ID=Msa1446180-mRNA-1:exon:15350;Parent=Msa1446180-mRNA-1
tig0031290 CDS 3992 4294 3992 ID=Msa1446180-mRNA-1:cds;Parent=Msa1446180-mRNA-1
Gene Sequence

>Msa1446180

ATGGAGATGACAGCACAACAACTGAGCGAATACAACGGTACAGACCCATCGAAGCCCATCTACGTGGCGGTGAAGGGTCGCGTTTTCGACGTCACCACCGGTAAATCGTTCTACGGTCCAGGTGGAGCCTACGCCATGTTCGCCGGCAAAGACGCTAGCAGAGCACTTGCAAAGATGAGCAAGAACGAAGAAGATATCACCTCGTCGCTCGATGGACTCACCGAGAAAGAGATCGGAGTTCTCAATGATTGGGAAACCAAGTTCGTAGCTAAGTACCCTGTTGTTGCCACCATCGTTAGCTAA
Protein sequence

>Msa1446180

MEMTAQQLSEYNGTDPSKPIYVAVKGRVFDVTTGKSFYGPGGAYAMFAGKDASRALAKMSKNEEDITSSLDGLTEKEIGVLNDWETKFVAKYPVVATIVS*