AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0317540

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0317540 MtrunA17_Chr2g0290931 98.630 146 2 0 1 146 1 146 6.28e-103 290
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGCTTGAAGCAGAAGATT+TGG 0.301631 2_4:+15442646 Msa0317540:CDS
GAGAAAGGTTGTTTAGCATT+TGG 0.326273 2_4:+15442404 Msa0317540:CDS
GCCATTTGAGGTTAATAGAT+TGG 0.344754 2_4:+15442625 Msa0317540:CDS
CCAAGACAACACTTGTTTCA+AGG 0.366636 2_4:+15442523 Msa0317540:CDS
AAATCCTCCATTGATCCCTT+TGG 0.386929 2_4:-15442596 None:intergenic
TTCTGGTATTGATTTCTTTG+AGG 0.395501 2_4:+15442550 Msa0317540:CDS
ACTTGTTTCAAGGTTTCTTC+TGG 0.404656 2_4:+15442533 Msa0317540:CDS
TCCAATCTATTAACCTCAAA+TGG 0.414962 2_4:-15442626 None:intergenic
CCTTGAAACAAGTGTTGTCT+TGG 0.422034 2_4:-15442523 None:intergenic
TTGGAGTGTTTGATTTCCCT+TGG 0.432978 2_4:+15442423 Msa0317540:CDS
ATGATGTTGAAGCAAAGATT+TGG 0.461294 2_4:+15442297 Msa0317540:CDS
AGGGATCAATGGAGGATTTG+TGG 0.464367 2_4:+15442600 Msa0317540:CDS
GGATTTGTGGCTGCCATTTG+AGG 0.474098 2_4:+15442613 Msa0317540:CDS
GATTTCCCTTGGTTGAAAGA+TGG 0.486271 2_4:+15442434 Msa0317540:CDS
TGAGGCTCCAAAGGGATCAA+TGG 0.510645 2_4:+15442589 Msa0317540:CDS
AAGAATGAAGTGGAAGAGAA+AGG 0.519180 2_4:+15442389 Msa0317540:CDS
TAGATTGTGTGAGGCTCCAA+AGG 0.564320 2_4:+15442580 Msa0317540:CDS
AGATTGTGTGAGGCTCCAAA+GGG 0.596314 2_4:+15442581 Msa0317540:CDS
CACCAAGGAAAAGAATGAAG+TGG 0.603149 2_4:+15442379 Msa0317540:CDS
TGACACCATCTTTCAACCAA+GGG 0.626669 2_4:-15442439 None:intergenic
ATGACACCATCTTTCAACCA+AGG 0.654692 2_4:-15442440 None:intergenic
GGCTCCAAAGGGATCAATGG+AGG 0.655913 2_4:+15442592 Msa0317540:CDS
GGAAAATGATAGATTGTGTG+AGG 0.713281 2_4:+15442571 Msa0317540:CDS
ATGTGGCACAAGTTTCACCA+AGG 0.735233 2_4:+15442364 Msa0317540:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATGATGTTGAAGCAAAGATT+TGG + chr2_4:15442297-15442316 Msa0317540:CDS 30.0%
GCTAAAAAAAGAGATGTATG+TGG + chr2_4:15442347-15442366 Msa0317540:CDS 30.0%
!! TTCTGGTATTGATTTCTTTG+AGG + chr2_4:15442550-15442569 Msa0317540:CDS 30.0%
TCCAATCTATTAACCTCAAA+TGG - chr2_4:15442629-15442648 None:intergenic 30.0%
! TTCCACTTCATTCTTTTCCT+TGG - chr2_4:15442384-15442403 None:intergenic 35.0%
AAGAATGAAGTGGAAGAGAA+AGG + chr2_4:15442389-15442408 Msa0317540:CDS 35.0%
GAGAAAGGTTGTTTAGCATT+TGG + chr2_4:15442404-15442423 Msa0317540:CDS 35.0%
ACTTGTTTCAAGGTTTCTTC+TGG + chr2_4:15442533-15442552 Msa0317540:CDS 35.0%
GGAAAATGATAGATTGTGTG+AGG + chr2_4:15442571-15442590 Msa0317540:CDS 35.0%
! GCCATTTGAGGTTAATAGAT+TGG + chr2_4:15442625-15442644 Msa0317540:CDS 35.0%
CACCAAGGAAAAGAATGAAG+TGG + chr2_4:15442379-15442398 Msa0317540:CDS 40.0%
! TTGGAGTGTTTGATTTCCCT+TGG + chr2_4:15442423-15442442 Msa0317540:CDS 40.0%
GATTTCCCTTGGTTGAAAGA+TGG + chr2_4:15442434-15442453 Msa0317540:CDS 40.0%
TGACACCATCTTTCAACCAA+GGG - chr2_4:15442442-15442461 None:intergenic 40.0%
ATGACACCATCTTTCAACCA+AGG - chr2_4:15442443-15442462 None:intergenic 40.0%
! CCTTGAAACAAGTGTTGTCT+TGG - chr2_4:15442526-15442545 None:intergenic 40.0%
CCAAGACAACACTTGTTTCA+AGG + chr2_4:15442523-15442542 Msa0317540:CDS 40.0%
AAATCCTCCATTGATCCCTT+TGG - chr2_4:15442599-15442618 None:intergenic 40.0%
ATGTGGCACAAGTTTCACCA+AGG + chr2_4:15442364-15442383 Msa0317540:CDS 45.0%
TAGATTGTGTGAGGCTCCAA+AGG + chr2_4:15442580-15442599 Msa0317540:CDS 45.0%
AGATTGTGTGAGGCTCCAAA+GGG + chr2_4:15442581-15442600 Msa0317540:CDS 45.0%
AGGGATCAATGGAGGATTTG+TGG + chr2_4:15442600-15442619 Msa0317540:CDS 45.0%
GGAGCTTGAAGCAGAAGATT+TGG + chr2_4:15442646-15442665 Msa0317540:CDS 45.0%
TGAGGCTCCAAAGGGATCAA+TGG + chr2_4:15442589-15442608 Msa0317540:CDS 50.0%
! GGATTTGTGGCTGCCATTTG+AGG + chr2_4:15442613-15442632 Msa0317540:CDS 50.0%
GGCTCCAAAGGGATCAATGG+AGG + chr2_4:15442592-15442611 Msa0317540:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 15442260 15442700 15442260 ID=Msa0317540;Name=Msa0317540
chr2_4 mRNA 15442260 15442700 15442260 ID=Msa0317540-mRNA-1;Parent=Msa0317540;Name=Msa0317540-mRNA-1;_AED=0.17;_eAED=0.17;_QI=0|-1|0|1|-1|1|1|0|146
chr2_4 exon 15442260 15442700 15442260 ID=Msa0317540-mRNA-1:exon:5740;Parent=Msa0317540-mRNA-1
chr2_4 CDS 15442260 15442700 15442260 ID=Msa0317540-mRNA-1:cds;Parent=Msa0317540-mRNA-1
Gene Sequence

>Msa0317540

ATGGAGCAAGAGAAGAATAAGAGAGCAAGAGAATATGATGATGTTGAAGCAAAGATTTGGTTTTCTTTTGAGAATAATAACAAGAAAGCTAAAAAAAGAGATGTATGTGGCACAAGTTTCACCAAGGAAAAGAATGAAGTGGAAGAGAAAGGTTGTTTAGCATTTGGAGTGTTTGATTTCCCTTGGTTGAAAGATGGTGTCATATACAAATTAGAAGATTGTTTAATTGATTTTGAAGACAATTTCTTGTCATCATTACAAGACCAAGACAACACTTGTTTCAAGGTTTCTTCTGGTATTGATTTCTTTGAGGAAAATGATAGATTGTGTGAGGCTCCAAAGGGATCAATGGAGGATTTGTGGCTGCCATTTGAGGTTAATAGATTGGAGCTTGAAGCAGAAGATTTGGATTGTATTTGTAGCTCTTTGCTAAACAATTAA
Protein sequence

>Msa0317540

MEQEKNKRAREYDDVEAKIWFSFENNNKKAKKRDVCGTSFTKEKNEVEEKGCLAFGVFDFPWLKDGVIYKLEDCLIDFEDNFLSSLQDQDNTCFKVSSGIDFFEENDRLCEAPKGSMEDLWLPFEVNRLELEAEDLDCICSSLLNN*