AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0579340


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 15 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGCTGGACCTAACGATCTTT+TGG 0.317659 4_1:-84003183 Msa0579340:CDS
TTTGCCAATAGGATCTGGTT+TGG 0.364938 4_1:+84003016 None:intergenic
TTGCCAATAGGATCTGGTTT+GGG 0.376061 4_1:+84003017 None:intergenic
AGCATCATCAACCGCACCTT+TGG 0.404914 4_1:+84002992 None:intergenic
GTACTTGCCAAAAGATCGTT+AGG 0.439536 4_1:+84003176 None:intergenic
AAACCCAAACCAGATCCTAT+TGG 0.473112 4_1:-84003020 Msa0579340:CDS
GATGATGCTACAAAGTCTGC+TGG 0.547087 4_1:-84002978 Msa0579340:CDS
ACTGTAGGAAATCTTGCAGC+TGG 0.550456 4_1:-84003125 Msa0579340:CDS
GCTGGTGTTCATAAGACTGT+AGG 0.573068 4_1:-84003074 Msa0579340:CDS
GCATCAGCACAGAAAACTGT+AGG 0.588939 4_1:-84003140 Msa0579340:CDS
GTAGGAAATCTTGCAGCTGG+TGG 0.593110 4_1:-84003122 Msa0579340:CDS
GATCCTATTGGCAAAACCAA+AGG 0.604323 4_1:-84003008 Msa0579340:CDS
AATGTGGGAAATGCTGCAGC+TGG 0.619200 4_1:-84003092 Msa0579340:CDS
TATTGGCAAAACCAAAGGTG+CGG 0.679241 4_1:-84003003 Msa0579340:CDS
GATGCTACAAAGTCTGCTGG+AGG 0.702868 4_1:-84002975 Msa0579340:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTTTACAAAATCAGCAGCGT+TGG + chr4_1:84003110-84003129 None:intergenic 35.0%
GTACTTGCCAAAAGATCGTT+AGG + chr4_1:84002974-84002993 None:intergenic 40.0%
! CGATCTTTTGGCAAGTACAA+AGG - chr4_1:84002976-84002995 Msa0579340:CDS 40.0%
! CAGCATTTCCCACATTTTTC+TGG + chr4_1:84003051-84003070 None:intergenic 40.0%
AAACCCAAACCAGATCCTAT+TGG - chr4_1:84003127-84003146 Msa0579340:CDS 40.0%
! TTGCCAATAGGATCTGGTTT+GGG + chr4_1:84003133-84003152 None:intergenic 40.0%
TTTGCCAATAGGATCTGGTT+TGG + chr4_1:84003134-84003153 None:intergenic 40.0%
!!! TTGGTTTTGCCAATAGGATC+TGG + chr4_1:84003139-84003158 None:intergenic 40.0%
GATCCTATTGGCAAAACCAA+AGG - chr4_1:84003139-84003158 Msa0579340:CDS 40.0%
TATTGGCAAAACCAAAGGTG+CGG - chr4_1:84003144-84003163 Msa0579340:CDS 40.0%
GCATCAGCACAGAAAACTGT+AGG - chr4_1:84003007-84003026 Msa0579340:CDS 45.0%
ACTGTAGGAAATCTTGCAGC+TGG - chr4_1:84003022-84003041 Msa0579340:CDS 45.0%
GCTGGTGTTCATAAGACTGT+AGG - chr4_1:84003073-84003092 Msa0579340:CDS 45.0%
!!! GCACCTTTGGTTTTGCCAAT+AGG + chr4_1:84003145-84003164 None:intergenic 45.0%
GATGATGCTACAAAGTCTGC+TGG - chr4_1:84003169-84003188 Msa0579340:CDS 45.0%
! GGCTGGACCTAACGATCTTT+TGG - chr4_1:84002964-84002983 Msa0579340:CDS 50.0%
GTAGGAAATCTTGCAGCTGG+TGG - chr4_1:84003025-84003044 Msa0579340:CDS 50.0%
AGCTGGTGGCCAGAAAAATG+TGG - chr4_1:84003039-84003058 Msa0579340:CDS 50.0%
GCTGGTGGCCAGAAAAATGT+GGG - chr4_1:84003040-84003059 Msa0579340:CDS 50.0%
AATGTGGGAAATGCTGCAGC+TGG - chr4_1:84003055-84003074 Msa0579340:CDS 50.0%
AGCATCATCAACCGCACCTT+TGG + chr4_1:84003158-84003177 None:intergenic 50.0%
GATGCTACAAAGTCTGCTGG+AGG - chr4_1:84003172-84003191 Msa0579340:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 84002962 84003207 84002962 ID=Msa0579340;Name=Msa0579340
chr4_1 mRNA 84002962 84003207 84002962 ID=Msa0579340-mRNA-1;Parent=Msa0579340;Name=Msa0579340-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|81
chr4_1 exon 84002962 84003207 84002962 ID=Msa0579340-mRNA-1:exon:30785;Parent=Msa0579340-mRNA-1
chr4_1 CDS 84002962 84003207 84002962 ID=Msa0579340-mRNA-1:cds;Parent=Msa0579340-mRNA-1
Gene Sequence

>Msa0579340

ATGGCTGGACCTAACGATCTTTTGGCAAGTACAAAGGATGCAGCAGCATCAGCACAGAAAACTGTAGGAAATCTTGCAGCTGGTGGCCAGAAAAATGTGGGAAATGCTGCAGCTGGTGTTCATAAGACTGTAGGAGATTTTGCTACCAACGCTGCTGATTTTGTAAAACCCAAACCAGATCCTATTGGCAAAACCAAAGGTGCGGTTGATGATGCTACAAAGTCTGCTGGAGGCTTATTTAAATGA

Protein sequence

>Msa0579340

MAGPNDLLASTKDAAASAQKTVGNLAAGGQKNVGNAAAGVHKTVGDFATNAADFVKPKPDPIGKTKGAVDDATKSAGGLFK*