AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0825340


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0825340 MtrunA17_Chr5g0446481 56.250 112 30 3 3 95 269 380 1.33e-15 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCCATGACTTCTAATT+CGG 0.254904 5_3:-65107132 None:intergenic
CTGTTCTCACATTTGACTTC+AGG 0.259207 5_3:-65107346 None:intergenic
CTGCCCTCATCGTTATCTTC+AGG 0.326793 5_3:-65107164 None:intergenic
TACCATCCAACTCCTCTTCT+CGG 0.356543 5_3:-65107384 None:intergenic
TCTTCCATGACTTCTAATTC+GGG 0.395461 5_3:-65107131 None:intergenic
GGAGTTGGATGGTAAGGATA+AGG 0.416898 5_3:+65107393 Msa0825340:CDS
TGTTCTCACATTTGACTTCA+GGG 0.423382 5_3:-65107345 None:intergenic
AAGGAGAAAAGTCAAGAAGA+GGG 0.437816 5_3:+65107191 Msa0825340:CDS
GAAGATATTGAAGTTGAGAA+AGG 0.451322 5_3:+65107448 Msa0825340:CDS
TGCCCTCATCGTTATCTTCA+GGG 0.458026 5_3:-65107163 None:intergenic
TGTCAAAGTGGAGGAAGGAT+TGG 0.460101 5_3:+65107238 Msa0825340:CDS
GAAACCCGAATTAGAAGTCA+TGG 0.483277 5_3:+65107127 Msa0825340:CDS
GAAAAGCCGAGAAGAGGAGT+TGG 0.483883 5_3:+65107378 Msa0825340:CDS
CAAATGTGAGAACAGTGAAA+AGG 0.511793 5_3:+65107354 Msa0825340:CDS
GAGAGGAGGAAACAACCATT+AGG 0.513456 5_3:+65107486 Msa0825340:CDS
AGAAGAGGAGTTGGATGGTA+AGG 0.515883 5_3:+65107387 Msa0825340:CDS
TAACGATGAGGGCAGTGAAA+AGG 0.525846 5_3:+65107172 Msa0825340:CDS
GACGATAAGTCAAATGAAGA+TGG 0.529347 5_3:+65107418 Msa0825340:CDS
GGAGAAAAGTCAAGAAGAGG+GGG 0.533848 5_3:+65107193 Msa0825340:CDS
AGGAGAAAAGTCAAGAAGAG+GGG 0.535131 5_3:+65107192 Msa0825340:CDS
GAAGATGTCAAAGTGGAGGA+AGG 0.545672 5_3:+65107233 Msa0825340:CDS
AAAGGAGAAAAGTCAAGAAG+AGG 0.574837 5_3:+65107190 Msa0825340:CDS
TGCAGGAAAGGAAAGGTCGA+AGG 0.593802 5_3:+65107266 Msa0825340:CDS
GTCAAATGAAGATGTCAAAG+TGG 0.615078 5_3:+65107226 Msa0825340:CDS
AAAGGAGAAAAGCCGAGAAG+AGG 0.615277 5_3:+65107372 Msa0825340:CDS
AAATGAAGATGTCAAAGTGG+AGG 0.626631 5_3:+65107229 Msa0825340:CDS
ATCCCTGAAGATAACGATGA+GGG 0.631291 5_3:+65107161 Msa0825340:CDS
AGCCGAGAAGAGGAGTTGGA+TGG 0.655744 5_3:+65107382 Msa0825340:CDS
GCAGGAAAGGAAAGGTCGAA+GGG 0.655802 5_3:+65107267 Msa0825340:CDS
TATCCCTGAAGATAACGATG+AGG 0.683408 5_3:+65107160 Msa0825340:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAAGGAATAAAAAAGTGT+GGG + chr5_3:65107464-65107483 Msa0825340:CDS 25.0%
TTCTTCCATGACTTCTAATT+CGG - chr5_3:65107135-65107154 None:intergenic 30.0%
AAGGTGAAAAAGGAAAACAA+AGG + chr5_3:65107293-65107312 Msa0825340:intron 30.0%
AAAGGAACAAAAAGAGATAG+AGG + chr5_3:65107311-65107330 Msa0825340:intron 30.0%
GAAGATATTGAAGTTGAGAA+AGG + chr5_3:65107448-65107467 Msa0825340:CDS 30.0%
GAGAAAGGAATAAAAAAGTG+TGG + chr5_3:65107463-65107482 Msa0825340:CDS 30.0%
TCTTCCATGACTTCTAATTC+GGG - chr5_3:65107134-65107153 None:intergenic 35.0%
AAAGGAGAAAAGTCAAGAAG+AGG + chr5_3:65107190-65107209 Msa0825340:CDS 35.0%
AAGGAGAAAAGTCAAGAAGA+GGG + chr5_3:65107191-65107210 Msa0825340:CDS 35.0%
GTCAAATGAAGATGTCAAAG+TGG + chr5_3:65107226-65107245 Msa0825340:CDS 35.0%
AAATGAAGATGTCAAAGTGG+AGG + chr5_3:65107229-65107248 Msa0825340:CDS 35.0%
CAAAAAGAGATAGAGGATAG+AGG + chr5_3:65107318-65107337 Msa0825340:intron 35.0%
! TGTTCTCACATTTGACTTCA+GGG - chr5_3:65107348-65107367 None:intergenic 35.0%
CAAATGTGAGAACAGTGAAA+AGG + chr5_3:65107354-65107373 Msa0825340:CDS 35.0%
GACGATAAGTCAAATGAAGA+TGG + chr5_3:65107418-65107437 Msa0825340:CDS 35.0%
GAAACCCGAATTAGAAGTCA+TGG + chr5_3:65107127-65107146 Msa0825340:CDS 40.0%
TATCCCTGAAGATAACGATG+AGG + chr5_3:65107160-65107179 Msa0825340:CDS 40.0%
ATCCCTGAAGATAACGATGA+GGG + chr5_3:65107161-65107180 Msa0825340:CDS 40.0%
AGGAGAAAAGTCAAGAAGAG+GGG + chr5_3:65107192-65107211 Msa0825340:CDS 40.0%
AGGAAGGATTGGAAAAATGC+AGG + chr5_3:65107249-65107268 Msa0825340:CDS 40.0%
GGATTGGAAAAATGCAGGAA+AGG + chr5_3:65107254-65107273 Msa0825340:CDS 40.0%
GGAAAAATGCAGGAAAGGAA+AGG + chr5_3:65107259-65107278 Msa0825340:CDS 40.0%
! CTGTTCTCACATTTGACTTC+AGG - chr5_3:65107349-65107368 None:intergenic 40.0%
! GGAATAAAAAAGTGTGGGAG+AGG + chr5_3:65107469-65107488 Msa0825340:CDS 40.0%
! ATAAAAAAGTGTGGGAGAGG+AGG + chr5_3:65107472-65107491 Msa0825340:CDS 40.0%
TGCCCTCATCGTTATCTTCA+GGG - chr5_3:65107166-65107185 None:intergenic 45.0%
TAACGATGAGGGCAGTGAAA+AGG + chr5_3:65107172-65107191 Msa0825340:CDS 45.0%
GGAGAAAAGTCAAGAAGAGG+GGG + chr5_3:65107193-65107212 Msa0825340:CDS 45.0%
GAAGATGTCAAAGTGGAGGA+AGG + chr5_3:65107233-65107252 Msa0825340:CDS 45.0%
TGTCAAAGTGGAGGAAGGAT+TGG + chr5_3:65107238-65107257 Msa0825340:CDS 45.0%
CGAAGGGTAGAAGGTGAAAA+AGG + chr5_3:65107283-65107302 Msa0825340:intron 45.0%
AAAGGAGAAAAGCCGAGAAG+AGG + chr5_3:65107372-65107391 Msa0825340:CDS 45.0%
TACCATCCAACTCCTCTTCT+CGG - chr5_3:65107387-65107406 None:intergenic 45.0%
AGAAGAGGAGTTGGATGGTA+AGG + chr5_3:65107387-65107406 Msa0825340:CDS 45.0%
GGAGTTGGATGGTAAGGATA+AGG + chr5_3:65107393-65107412 Msa0825340:CDS 45.0%
CTGCCCTCATCGTTATCTTC+AGG - chr5_3:65107167-65107186 None:intergenic 50.0%
GAAAAGTCAAGAAGAGGGGG+AGG + chr5_3:65107196-65107215 Msa0825340:CDS 50.0%
TGCAGGAAAGGAAAGGTCGA+AGG + chr5_3:65107266-65107285 Msa0825340:CDS 50.0%
GCAGGAAAGGAAAGGTCGAA+GGG + chr5_3:65107267-65107286 Msa0825340:CDS 50.0%
AGGAAAGGTCGAAGGGTAGA+AGG + chr5_3:65107274-65107293 Msa0825340:intron 50.0%
GAAAAGCCGAGAAGAGGAGT+TGG + chr5_3:65107378-65107397 Msa0825340:CDS 50.0%
AGCCGAGAAGAGGAGTTGGA+TGG + chr5_3:65107382-65107401 Msa0825340:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 65107089 65107507 65107089 ID=Msa0825340;Name=Msa0825340
chr5_3 mRNA 65107089 65107507 65107089 ID=Msa0825340-mRNA-1;Parent=Msa0825340;Name=Msa0825340-mRNA-1;_AED=0.40;_eAED=0.57;_QI=0|0|0|1|0|0.5|2|0|124
chr5_3 exon 65107089 65107288 65107089 ID=Msa0825340-mRNA-1:exon:20390;Parent=Msa0825340-mRNA-1
chr5_3 exon 65107333 65107507 65107333 ID=Msa0825340-mRNA-1:exon:20391;Parent=Msa0825340-mRNA-1
chr5_3 CDS 65107089 65107288 65107089 ID=Msa0825340-mRNA-1:cds;Parent=Msa0825340-mRNA-1
chr5_3 CDS 65107333 65107507 65107333 ID=Msa0825340-mRNA-1:cds;Parent=Msa0825340-mRNA-1
Gene Sequence

>Msa0825340

ATGGATAGTAAAAAAGCGAGAGAAAGCGTTGAAGCTAAGAAACCCGAATTAGAAGTCATGGAAGAAGAGATTATCCCTGAAGATAACGATGAGGGCAGTGAAAAGGAGAAAAGTCAAGAAGAGGGGGAGGATGATAAGTCAAATGAAGATGTCAAAGTGGAGGAAGGATTGGAAAAATGCAGGAAAGGAAAGGTCGAAGGGATAGAGGATATCCCTGAAGTCAAATGTGAGAACAGTGAAAAGGAGAAAAGCCGAGAAGAGGAGTTGGATGGTAAGGATAAGGTTGACGATAAGTCAAATGAAGATGGTTCTTCTGAAGATATTGAAGTTGAGAAAGGAATAAAAAAGTGTGGGAGAGGAGGAAACAACCATTAG

Protein sequence

>Msa0825340

MDSKKARESVEAKKPELEVMEEEIIPEDNDEGSEKEKSQEEGEDDKSNEDVKVEEGLEKCRKGKVEGIEDIPEVKCENSEKEKSREEELDGKDKVDDKSNEDGSSEDIEVEKGIKKCGRGGNNH*