AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1109890


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1109890 MtrunA17_Chr7g0244341 94.505 91 5 0 1 91 1 91 8.30e-58 177
Msa1109890 MtrunA17_Chr7g0244331 80.220 91 18 0 1 91 1 91 1.48e-47 151
Msa1109890 MtrunA17_Chr7g0244321 81.522 92 15 2 1 91 1 91 1.07e-45 146
Msa1109890 MtrunA17_Chr7g0244371 74.725 91 21 2 1 91 1 89 2.11e-41 135
Msa1109890 MtrunA17_Chr7g0244361 60.396 101 25 3 1 91 25 120 9.05e-31 109
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1109890 AT5G01750.1 45.361 97 49 2 1 93 1 97 1.67e-25 94.4
Msa1109890 AT5G01750.2 45.361 97 49 2 1 93 1 97 5.95e-25 94.0
Msa1109890 AT3G11740.1 50.633 79 39 0 23 101 3 81 7.98e-23 87.8
Msa1109890 AT1G33840.2 40.000 95 53 2 1 91 1 95 5.11e-19 77.8
Msa1109890 AT1G33840.1 40.000 95 53 2 1 91 1 95 1.06e-18 77.8
Msa1109890 AT2G14560.2 43.056 72 41 0 20 91 4 75 1.57e-17 73.9
Msa1109890 AT2G14560.1 43.056 72 41 0 20 91 4 75 2.42e-17 73.9
Msa1109890 AT2G14560.4 43.056 72 41 0 20 91 64 135 3.89e-17 73.9
Msa1109890 AT2G14560.3 43.056 72 41 0 20 91 64 135 5.17e-17 73.9

Find 32 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATATTGTCTTCAAAGTTAA+AGG 0.162900 7_3:-54349321 Msa1109890:CDS
GTGCTTCCGACCACCATATT+TGG 0.296063 7_3:-54349441 Msa1109890:CDS
TGCTCCATATCCATTGGATT+TGG 0.348058 7_3:-54349406 Msa1109890:CDS
ACAATATTGAGGGCCAAATA+TGG 0.348290 7_3:+54349428 None:intergenic
ACAGCCAAATCCAATGGATA+TGG 0.371690 7_3:+54349402 None:intergenic
GGATTTGGCTGTGGTCAAAA+AGG 0.380756 7_3:-54349391 Msa1109890:CDS
TTGCGACGTAGGGTGGTGAT+AGG 0.450531 7_3:+54349246 None:intergenic
ATATCCATTGGATTTGGCTG+TGG 0.476662 7_3:-54349400 Msa1109890:CDS
AGAAGAGAGTATAACGTTGA+AGG 0.493942 7_3:+54349219 None:intergenic
ATATTGTGCTCCATATCCAT+TGG 0.499976 7_3:-54349412 Msa1109890:CDS
TGCCTCTGCACCACCGATGT+CGG 0.506015 7_3:-54349463 Msa1109890:CDS
GCAGATGGTTGTGGTTGATA+AGG 0.518139 7_3:+54349483 None:intergenic
GGATATGGAGCACAATATTG+AGG 0.540481 7_3:+54349417 None:intergenic
CACCGACATCGGTGGTGCAG+AGG 0.548461 7_3:+54349461 None:intergenic
GGTGCAGAGGCAGATGGTTG+TGG 0.549880 7_3:+54349474 None:intergenic
TTGAAGGTACCTTGCGACGT+AGG 0.551744 7_3:+54349235 None:intergenic
TGAAGGTACCTTGCGACGTA+GGG 0.554387 7_3:+54349236 None:intergenic
GATATGGAGCACAATATTGA+GGG 0.554691 7_3:+54349418 None:intergenic
TTGACCACAGCCAAATCCAA+TGG 0.558143 7_3:+54349396 None:intergenic
CAAGACACGGCGGTCACGAA+AGG 0.581276 7_3:+54349287 None:intergenic
TGCGACGTAGGGTGGTGATA+GGG 0.606682 7_3:+54349247 None:intergenic
ATCGGTGGTGCAGAGGCAGA+TGG 0.609454 7_3:+54349468 None:intergenic
GTCGGAAGCACCGACATCGG+TGG 0.614411 7_3:+54349453 None:intergenic
TGAGGGCCAAATATGGTGGT+CGG 0.625346 7_3:+54349435 None:intergenic
AGGTACCTTGCGACGTAGGG+TGG 0.633675 7_3:+54349239 None:intergenic
TATCACCACCCTACGTCGCA+AGG 0.636481 7_3:-54349244 Msa1109890:CDS
AAGGTGATAGCAATTTCAGA+CGG 0.662704 7_3:-54349372 Msa1109890:CDS
ATATTGAGGGCCAAATATGG+TGG 0.664652 7_3:+54349431 None:intergenic
GTGGTCGGAAGCACCGACAT+CGG 0.667721 7_3:+54349450 None:intergenic
CTGCGGCATCAACCAAGACA+CGG 0.671998 7_3:+54349274 None:intergenic
GGTGGTGATAGGGTTATCTG+CGG 0.701861 7_3:+54349257 None:intergenic
CGGCATCAACCAAGACACGG+CGG 0.795295 7_3:+54349277 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATTGTCTTCAAAGTTAA+AGG - chr7_3:54349359-54349378 Msa1109890:CDS 20.0%
ACAATATTGAGGGCCAAATA+TGG + chr7_3:54349255-54349274 None:intergenic 35.0%
GATATGGAGCACAATATTGA+GGG + chr7_3:54349265-54349284 None:intergenic 35.0%
ATATTGTGCTCCATATCCAT+TGG - chr7_3:54349268-54349287 Msa1109890:CDS 35.0%
AAGGTGATAGCAATTTCAGA+CGG - chr7_3:54349308-54349327 Msa1109890:CDS 35.0%
! AGAAGAGAGTATAACGTTGA+AGG + chr7_3:54349464-54349483 None:intergenic 35.0%
ATATTGAGGGCCAAATATGG+TGG + chr7_3:54349252-54349271 None:intergenic 40.0%
GGATATGGAGCACAATATTG+AGG + chr7_3:54349266-54349285 None:intergenic 40.0%
TGCTCCATATCCATTGGATT+TGG - chr7_3:54349274-54349293 Msa1109890:CDS 40.0%
ACAGCCAAATCCAATGGATA+TGG + chr7_3:54349281-54349300 None:intergenic 40.0%
ATATCCATTGGATTTGGCTG+TGG - chr7_3:54349280-54349299 Msa1109890:CDS 40.0%
! GCAGATGGTTGTGGTTGATA+AGG + chr7_3:54349200-54349219 None:intergenic 45.0%
TTGACCACAGCCAAATCCAA+TGG + chr7_3:54349287-54349306 None:intergenic 45.0%
GGATTTGGCTGTGGTCAAAA+AGG - chr7_3:54349289-54349308 Msa1109890:CDS 45.0%
GTGCTTCCGACCACCATATT+TGG - chr7_3:54349239-54349258 Msa1109890:CDS 50.0%
TGAGGGCCAAATATGGTGGT+CGG + chr7_3:54349248-54349267 None:intergenic 50.0%
GGTGGTGATAGGGTTATCTG+CGG + chr7_3:54349426-54349445 None:intergenic 50.0%
!! TGAAGGTACCTTGCGACGTA+GGG + chr7_3:54349447-54349466 None:intergenic 50.0%
!! TTGAAGGTACCTTGCGACGT+AGG + chr7_3:54349448-54349467 None:intergenic 50.0%
CTGCGGCATCAACCAAGACA+CGG + chr7_3:54349409-54349428 None:intergenic 55.0%
TGCGACGTAGGGTGGTGATA+GGG + chr7_3:54349436-54349455 None:intergenic 55.0%
TTGCGACGTAGGGTGGTGAT+AGG + chr7_3:54349437-54349456 None:intergenic 55.0%
TATCACCACCCTACGTCGCA+AGG - chr7_3:54349436-54349455 Msa1109890:CDS 55.0%
GGTGCAGAGGCAGATGGTTG+TGG + chr7_3:54349209-54349228 None:intergenic 60.0%
ATCGGTGGTGCAGAGGCAGA+TGG + chr7_3:54349215-54349234 None:intergenic 60.0%
TGCCTCTGCACCACCGATGT+CGG - chr7_3:54349217-54349236 Msa1109890:CDS 60.0%
!! GTGGTCGGAAGCACCGACAT+CGG + chr7_3:54349233-54349252 None:intergenic 60.0%
CAAGACACGGCGGTCACGAA+AGG + chr7_3:54349396-54349415 None:intergenic 60.0%
CTTTCGTGACCGCCGTGTCT+TGG - chr7_3:54349394-54349413 Msa1109890:CDS 60.0%
CGGCATCAACCAAGACACGG+CGG + chr7_3:54349406-54349425 None:intergenic 60.0%
AGGTACCTTGCGACGTAGGG+TGG + chr7_3:54349444-54349463 None:intergenic 60.0%
CACCGACATCGGTGGTGCAG+AGG + chr7_3:54349222-54349241 None:intergenic 65.0%
!! GTCGGAAGCACCGACATCGG+TGG + chr7_3:54349230-54349249 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 54349188 54349514 54349188 ID=Msa1109890;Name=Msa1109890
chr7_3 mRNA 54349188 54349514 54349188 ID=Msa1109890-mRNA-1;Parent=Msa1109890;Name=Msa1109890-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|108
chr7_3 exon 54349188 54349514 54349188 ID=Msa1109890-mRNA-1:exon:11432;Parent=Msa1109890-mRNA-1
chr7_3 CDS 54349188 54349514 54349188 ID=Msa1109890-mRNA-1:cds;Parent=Msa1109890-mRNA-1
Gene Sequence

>Msa1109890

ATGGCTCATCCTTATCAACCACAACCATCTGCCTCTGCACCACCGATGTCGGTGCTTCCGACCACCATATTTGGCCCTCAATATTGTGCTCCATATCCATTGGATTTGGCTGTGGTCAAAAAGGTGATAGCAATTTCAGACGGAAACTTCGTCGTCACTGATGTCAACAGCAATATTGTCTTCAAAGTTAAAGGTTCTCTTTTAACCTTTCGTGACCGCCGTGTCTTGGTTGATGCCGCAGATAACCCTATCACCACCCTACGTCGCAAGGTACCTTCAACGTTATACTCTCTTCTTTCTTATTTTCTTTCATTTATGTACAAATAG

Protein sequence

>Msa1109890

MAHPYQPQPSASAPPMSVLPTTIFGPQYCAPYPLDLAVVKKVIAISDGNFVVTDVNSNIVFKVKGSLLTFRDRRVLVDAADNPITTLRRKVPSTLYSLLSYFLSFMYK*