AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0004540


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0004540 MtrunA17_Chr1g0157151 91.250 160 5 3 1 152 1 159 3.12e-94 269
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0004540 AT1G76060.1 65.101 149 42 4 4 144 8 154 7.09e-58 177

Find 32 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACACCGTGGAAGAGCTTC+TGG 0.320024 1_1:+7051289 Msa0004540:CDS
ATTGTCACTCGGTTGCTTAT+CGG 0.353596 1_1:+7051542 Msa0004540:CDS
CCGCCACGCGCAACCGTTTG+CGG 0.355220 1_1:-7051249 None:intergenic
ACGATGCCAAAGGCGTTCTA+TGG 0.381120 1_1:+7051453 Msa0004540:CDS
CAGTGCTTCTCGGCGCGTGC+TGG 0.390621 1_1:-7051384 None:intergenic
GAGGAAAATGGCGAAGCCTT+TGG 0.391236 1_1:+7051204 Msa0004540:CDS
AAGGATCGTCGCGGTGGCAG+TGG 0.428548 1_1:+7051617 Msa0004540:CDS
AGAAGCTCTTCCACGGTGTC+AGG 0.435099 1_1:-7051287 None:intergenic
TGTAGAGACTCAGTGCTTCT+CGG 0.445236 1_1:-7051394 None:intergenic
AAGAAGAAGAGTTGCTGAAT+CGG 0.468368 1_1:+7051351 Msa0004540:CDS
ATCACGCCATAGAACGCCTT+TGG 0.477887 1_1:-7051459 None:intergenic
TGCGAGGTTTGAGACGGATC+CGG 0.482393 1_1:+7051517 Msa0004540:CDS
AGCAACCGAGTGACAATCTC+CGG 0.496816 1_1:-7051536 None:intergenic
GATCGTCGCGGTGGCAGTGG+CGG 0.542143 1_1:+7051620 Msa0004540:CDS
TTCACATGGCACGATGCCAA+AGG 0.565614 1_1:+7051443 Msa0004540:CDS
GTTTCAGATTCGAATTCCAA+AGG 0.567422 1_1:-7051220 None:intergenic
CCGTTCCAGAAGCTCTTCCA+CGG 0.587827 1_1:-7051294 None:intergenic
TGAGCTTGCGAGGTTTGAGA+CGG 0.591164 1_1:+7051511 Msa0004540:CDS
CCGCAAACGGTTGCGCGTGG+CGG 0.594281 1_1:+7051249 Msa0004540:CDS
GTCACTCGGTTGCTTATCGG+TGG 0.599413 1_1:+7051545 Msa0004540:CDS
GTAAAGAGTTTGAGCTTGCG+AGG 0.613271 1_1:+7051501 Msa0004540:CDS
CCGTGGAAGAGCTTCTGGAA+CGG 0.622869 1_1:+7051294 Msa0004540:CDS
AAACCGCAAACGGTTGCGCG+TGG 0.625582 1_1:+7051246 Msa0004540:CDS
GTTGCTTATCGGTGGACGTG+AGG 0.631369 1_1:+7051553 Msa0004540:CDS
CAACGCTATTGATAAGCTTG+CGG 0.647873 1_1:+7051583 Msa0004540:CDS
AAGAAGAGTTGCTGAATCGG+CGG 0.650336 1_1:+7051354 Msa0004540:CDS
ATTCAGAAGGATCGTCGCGG+TGG 0.657849 1_1:+7051611 Msa0004540:CDS
GCTTGCGGAACAGATTCAGA+AGG 0.661253 1_1:+7051598 Msa0004540:CDS
CGGATCCGGAGATTGTCACT+CGG 0.686306 1_1:+7051531 Msa0004540:CDS
ACACGACGGTCCTGACACCG+TGG 0.698737 1_1:+7051277 Msa0004540:CDS
GCGTGGCGGTTATTACACGA+CGG 0.720396 1_1:+7051263 Msa0004540:CDS
CAGATTCAGAAGGATCGTCG+CGG 0.756987 1_1:+7051608 Msa0004540:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GTTTCAGATTCGAATTCCAA+AGG - chr1_1:7051223-7051242 None:intergenic 35.0%
AAGAAGAAGAGTTGCTGAAT+CGG + chr1_1:7051351-7051370 Msa0004540:CDS 35.0%
CTGAAACCAAAAACCGCAAA+CGG + chr1_1:7051236-7051255 Msa0004540:CDS 40.0%
! GTGCTTCACGATTTTTCACA+TGG + chr1_1:7051429-7051448 Msa0004540:CDS 40.0%
ATTGTCACTCGGTTGCTTAT+CGG + chr1_1:7051542-7051561 Msa0004540:CDS 40.0%
CAACGCTATTGATAAGCTTG+CGG + chr1_1:7051583-7051602 Msa0004540:CDS 40.0%
AAGAAGAGTTGCTGAATCGG+CGG + chr1_1:7051354-7051373 Msa0004540:CDS 45.0%
TGTAGAGACTCAGTGCTTCT+CGG - chr1_1:7051397-7051416 None:intergenic 45.0%
GTAAAGAGTTTGAGCTTGCG+AGG + chr1_1:7051501-7051520 Msa0004540:CDS 45.0%
GAGGAAAATGGCGAAGCCTT+TGG + chr1_1:7051204-7051223 Msa0004540:CDS 50.0%
TTCACATGGCACGATGCCAA+AGG + chr1_1:7051443-7051462 Msa0004540:CDS 50.0%
!! ACGATGCCAAAGGCGTTCTA+TGG + chr1_1:7051453-7051472 Msa0004540:CDS 50.0%
ATCACGCCATAGAACGCCTT+TGG - chr1_1:7051462-7051481 None:intergenic 50.0%
TGAGCTTGCGAGGTTTGAGA+CGG + chr1_1:7051511-7051530 Msa0004540:CDS 50.0%
AGCAACCGAGTGACAATCTC+CGG - chr1_1:7051539-7051558 None:intergenic 50.0%
GCTTGCGGAACAGATTCAGA+AGG + chr1_1:7051598-7051617 Msa0004540:CDS 50.0%
CAGATTCAGAAGGATCGTCG+CGG + chr1_1:7051608-7051627 Msa0004540:CDS 50.0%
! GCGCAACCGTTTGCGGTTTT+TGG - chr1_1:7051245-7051264 None:intergenic 55.0%
GCGTGGCGGTTATTACACGA+CGG + chr1_1:7051263-7051282 Msa0004540:CDS 55.0%
AGAAGCTCTTCCACGGTGTC+AGG - chr1_1:7051290-7051309 None:intergenic 55.0%
TGACACCGTGGAAGAGCTTC+TGG + chr1_1:7051289-7051308 Msa0004540:CDS 55.0%
CCGTTCCAGAAGCTCTTCCA+CGG - chr1_1:7051297-7051316 None:intergenic 55.0%
! CCGTGGAAGAGCTTCTGGAA+CGG + chr1_1:7051294-7051313 Msa0004540:CDS 55.0%
! TGCGAGGTTTGAGACGGATC+CGG + chr1_1:7051517-7051536 Msa0004540:CDS 55.0%
CGGATCCGGAGATTGTCACT+CGG + chr1_1:7051531-7051550 Msa0004540:CDS 55.0%
GTCACTCGGTTGCTTATCGG+TGG + chr1_1:7051545-7051564 Msa0004540:CDS 55.0%
GTTGCTTATCGGTGGACGTG+AGG + chr1_1:7051553-7051572 Msa0004540:CDS 55.0%
ATTCAGAAGGATCGTCGCGG+TGG + chr1_1:7051611-7051630 Msa0004540:CDS 55.0%
AAACCGCAAACGGTTGCGCG+TGG + chr1_1:7051246-7051265 Msa0004540:CDS 60.0%
ACACGACGGTCCTGACACCG+TGG + chr1_1:7051277-7051296 Msa0004540:CDS 65.0%
AAGGATCGTCGCGGTGGCAG+TGG + chr1_1:7051617-7051636 Msa0004540:CDS 65.0%
CCGCCACGCGCAACCGTTTG+CGG - chr1_1:7051252-7051271 None:intergenic 70.0%
CCGCAAACGGTTGCGCGTGG+CGG + chr1_1:7051249-7051268 Msa0004540:CDS 70.0%
CAGTGCTTCTCGGCGCGTGC+TGG - chr1_1:7051387-7051406 None:intergenic 70.0%
GATCGTCGCGGTGGCAGTGG+CGG + chr1_1:7051620-7051639 Msa0004540:CDS 70.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 7051200 7051658 7051200 ID=Msa0004540;Name=Msa0004540
chr1_1 mRNA 7051200 7051658 7051200 ID=Msa0004540-mRNA-1;Parent=Msa0004540;Name=Msa0004540-mRNA-1;_AED=0.37;_eAED=0.37;_QI=0|-1|0|1|-1|1|1|0|152
chr1_1 exon 7051200 7051658 7051200 ID=Msa0004540-mRNA-1:exon:2426;Parent=Msa0004540-mRNA-1
chr1_1 CDS 7051200 7051658 7051200 ID=Msa0004540-mRNA-1:cds;Parent=Msa0004540-mRNA-1
Gene Sequence

>Msa0004540

ATGAGAGGAAAATGGCGAAGCCTTTGGAATTCGAATCTGAAACCAAAAACCGCAAACGGTTGCGCGTGGCGGTTATTACACGACGGTCCTGACACCGTGGAAGAGCTTCTGGAACGGCATCTAGTGAAGAAAGTTATCAACGATGATGAAGAAGAAGAAGAGTTGCTGAATCGGCGGCGACTCACCAGCACGCGCCGAGAAGCACTGAGTCTCTACAGAGACATTCTTCGTGCTTCACGATTTTTCACATGGCACGATGCCAAAGGCGTTCTATGGCGTGATCTTCTTAGAGATAGCGCTCGTAAAGAGTTTGAGCTTGCGAGGTTTGAGACGGATCCGGAGATTGTCACTCGGTTGCTTATCGGTGGACGTGAGGCTGTCAACAACGCTATTGATAAGCTTGCGGAACAGATTCAGAAGGATCGTCGCGGTGGCAGTGGCGGTTTTGATCAAACGTGA

Protein sequence

>Msa0004540

MRGKWRSLWNSNLKPKTANGCAWRLLHDGPDTVEELLERHLVKKVINDDEEEEELLNRRRLTSTRREALSLYRDILRASRFFTWHDAKGVLWRDLLRDSARKEFELARFETDPEIVTRLLIGGREAVNNAIDKLAEQIQKDRRGGSGGFDQT*