AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG009040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG009040 MtrunA17_Chr5g0394621 90.184 163 15 1 1 162 1 163 2.85e-103 294
MsaG009040 MtrunA17_Chr5g0394631 73.171 164 43 1 1 163 1 164 4.17e-77 235
MsaG009040 MtrunA17_Chr5g0394631 65.169 178 51 6 1 173 214 385 6.96e-62 196
MsaG009040 MtrunA17_Chr1g0204951 57.386 176 70 3 1 173 1 174 6.06e-62 189
MsaG009040 MtrunA17_Chr1g0204971 55.114 176 74 3 1 173 1 174 8.63e-59 181
MsaG009040 MtrunA17_Chr7g0273661 35.000 140 88 1 16 155 3 139 3.24e-27 100
MsaG009040 MtrunA17_Chr7g0223361 31.818 154 100 3 17 169 4 153 1.30e-20 84.0
MsaG009040 MtrunA17_Chr7g0223351 34.559 136 84 3 20 155 7 137 5.01e-20 82.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG009040 AT2G32030.1 46.104 154 68 4 3 155 14 153 7.14e-40 134
MsaG009040 AT2G32020.1 47.794 136 64 2 21 155 19 148 2.48e-36 124
MsaG009040 AT3G22560.1 33.553 152 95 3 21 169 7 155 6.79e-21 84.7

Find 42 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCAAGGTCAGAAAGATTA+AGG 0.227074 2:-52247174 None:intergenic
CTCTTCTTTGTCACGTGGTT+TGG 0.270188 2:-52247119 None:intergenic
ATGTTCTAGGCTCTAAATAT+TGG 0.292142 2:+52247413 MsaT009040.1:CDS
GCAGAACTTGGCTATGTTCT+AGG 0.302641 2:+52247400 MsaT009040.1:CDS
TAAGGGGTCGGAGTGTGATT+TGG 0.307480 2:-52247156 None:intergenic
TGTTCTAGGCTCTAAATATT+GGG 0.316974 2:+52247414 MsaT009040.1:CDS
AAGGGGTCGGAGTGTGATTT+GGG 0.320072 2:-52247155 None:intergenic
ATATAGCTTCAAAGTTTCTA+TGG 0.332117 2:+52247290 MsaT009040.1:CDS
TCCATCAATGATCGTGCAAT+TGG 0.335248 2:+52247325 MsaT009040.1:CDS
CCCAATTGCACGATCATTGA+TGG 0.338330 2:-52247326 None:intergenic
AATGTTGGGTCTCAGAGTTT+TGG 0.354229 2:+52247535 MsaT009040.1:CDS
GCTCTAAATATTGGGGTAAA+GGG 0.356917 2:+52247422 MsaT009040.1:CDS
GGCTCTAAATATTGGGGTAA+AGG 0.422886 2:+52247421 MsaT009040.1:CDS
AGTTGCCAAGTTCTGCTCTT+GGG 0.428431 2:+52247225 MsaT009040.1:CDS
GTTGATGCCATCATCCTTGC+TGG 0.429573 2:-52247257 None:intergenic
CACTTGTTTCACAACACACT+TGG 0.439429 2:-52247449 None:intergenic
ATTCTGTGAGTTGTCTTACT+TGG 0.446468 2:+52247483 MsaT009040.1:CDS
AAGTTGCCAAGTTCTGCTCT+TGG 0.477212 2:+52247224 MsaT009040.1:CDS
AGGAACAAATGTGCAGAACT+TGG 0.481600 2:+52247388 MsaT009040.1:CDS
CCATCAATGATCGTGCAATT+GGG 0.483539 2:+52247326 MsaT009040.1:CDS
GTGAGTTGTCTTACTTGGAA+AGG 0.487957 2:+52247488 MsaT009040.1:CDS
GCTTGAAGCTTTAGTTGATG+TGG 0.488968 2:+52247510 MsaT009040.1:CDS
TTCTGACCTTGATGATCTCA+TGG 0.490514 2:+52247183 MsaT009040.1:CDS
ATCAAGGTCAGAAAGATTAA+GGG 0.492658 2:-52247173 None:intergenic
TAGTTGATGTGGAAAATGTT+GGG 0.494202 2:+52247521 MsaT009040.1:CDS
TTGTTCCTTGATTTATCACC+AGG 0.502130 2:-52247373 None:intergenic
GTTCACCTGGTGATAAATCA+AGG 0.507986 2:+52247368 MsaT009040.1:CDS
TTAGTTGATGTGGAAAATGT+TGG 0.523001 2:+52247520 MsaT009040.1:CDS
ACCTTGATGATCTCATGGTA+TGG 0.538119 2:+52247188 MsaT009040.1:CDS
TGTTGTGAAACAAGTGGTTA+AGG 0.541729 2:+52247456 MsaT009040.1:CDS
TCTCTATCCTCAAGTTCACC+TGG 0.545696 2:+52247355 MsaT009040.1:CDS
CTCTACACCAGCAAGGATGA+TGG 0.559987 2:+52247250 MsaT009040.1:CDS
CTCTAAATATTGGGGTAAAG+GGG 0.564900 2:+52247423 MsaT009040.1:CDS
GAGTTCCCAAGAGCAGAACT+TGG 0.571214 2:-52247230 None:intergenic
TTTATCACCAGGTGAACTTG+AGG 0.579933 2:-52247362 None:intergenic
ATTCTCTCTTCTTTGTCACG+TGG 0.580393 2:-52247124 None:intergenic
GGTCAGAAAGATTAAGGGGT+CGG 0.585362 2:-52247168 None:intergenic
GTTCTAGGCTCTAAATATTG+GGG 0.619040 2:+52247415 MsaT009040.1:CDS
TCCATACCATGAGATCATCA+AGG 0.632686 2:-52247189 None:intergenic
TCAAGGTCAGAAAGATTAAG+GGG 0.633672 2:-52247172 None:intergenic
TTGGGAACTCTACACCAGCA+AGG 0.679749 2:+52247243 MsaT009040.1:CDS
CAAGTGTGTTGTGAAACAAG+TGG 0.740021 2:+52247450 MsaT009040.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 52247097 52247621 52247097 ID=MsaG009040
Chr2 mRNA 52247097 52247621 52247097 ID=MsaT009040.1;Parent=MsaG009040
Chr2 exon 52247097 52247621 52247097 ID=MsaT009040.1.exon1;Parent=MsaT009040.1
Chr2 CDS 52247097 52247621 52247097 ID=cds.MsaT009040.1;Parent=MsaT009040.1
Gene Sequence

>MsaT009040.1

ATGGAGATAACTTCTATTTCTTCCAAACCACGTGACAAAGAAGAGAGAATTGATCTAACCCAAATCACACTCCGACCCCTTAATCTTTCTGACCTTGATGATCTCATGGTATGGACAACTGATGAAAAAGTTGCCAAGTTCTGCTCTTGGGAACTCTACACCAGCAAGGATGATGGCATCAACTTCATTGAAAATATAGCTTCAAAGTTTCTATGGTGCAAAGCAATATCCATCAATGATCGTGCAATTGGGTGTGTTTCTCTATCCTCAAGTTCACCTGGTGATAAATCAAGGAACAAATGTGCAGAACTTGGCTATGTTCTAGGCTCTAAATATTGGGGTAAAGGGGTTGCCAAGTGTGTTGTGAAACAAGTGGTTAAGGCTGCATTCTGTGAGTTGTCTTACTTGGAAAGGCTTGAAGCTTTAGTTGATGTGGAAAATGTTGGGTCTCAGAGTTTTGGAGAAAGCTGGTTTCCAAAAAGAGGGAGTTCTGAGGAAATATTTTTTCATGAAAGGAAAAAGTAG
Protein sequence

>MsaT009040.1

MEITSISSKPRDKEERIDLTQITLRPLNLSDLDDLMVWTTDEKVAKFCSWELYTSKDDGINFIENIASKFLWCKAISINDRAIGCVSLSSSSPGDKSRNKCAELGYVLGSKYWGKGVAKCVVKQVVKAAFCELSYLERLEALVDVENVGSQSFGESWFPKRGSSEEIFFHERKK*