AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1367880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1367880 MtrunA17_Chr3g0145311 95.652 92 3 1 1 92 1 91 1.32e-58 174
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1367880 AT2G21290.1 62.651 83 29 1 10 92 18 98 1.25e-20 79.0

Find 26 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGATCATTTGTTCTCTCTT+CGG 0.404252 tig0018560:+9007 None:intergenic
AAAAGATTCAAGGGCTCGTA+TGG 0.464506 tig0018560:-9040 Msa1367880:CDS
AAAGAAAGGGAAAAGATTCA+AGG 0.481880 tig0018560:-9050 Msa1367880:CDS
TGAAATCAAATGAGCTTGAA+AGG 0.487197 tig0018560:+8935 None:intergenic
AAGTTCCCAGGTCTACTCCT+TGG 0.493148 tig0018560:-8964 Msa1367880:CDS
ACGCCTTGTGCTTCTTCTGC+CGG 0.494602 tig0018560:-9118 Msa1367880:CDS
GCTGCACGGTGGTTGATAAG+AGG 0.503001 tig0018560:-9154 Msa1367880:CDS
GATCGAACGAATCAAAGATA+AGG 0.533385 tig0018560:-8990 Msa1367880:CDS
CAAATGAGCTTGAAAGGAAG+AGG 0.534374 tig0018560:+8941 None:intergenic
GCTCCGATAGTGTGCGGACG+CGG 0.535798 tig0018560:-9085 Msa1367880:CDS
AGCTTGAAAGGAAGAGGCCA+AGG 0.539805 tig0018560:+8947 None:intergenic
TATCAACCACCGTGCAGCTA+CGG 0.541002 tig0018560:+9159 None:intergenic
AAGATAAGGTTGAAGTTCCC+AGG 0.546325 tig0018560:-8976 Msa1367880:CDS
AAGAGGCCAAGGAGTAGACC+TGG 0.562320 tig0018560:+8958 None:intergenic
TATCGGAGCAGCTGTTACGC+CGG 0.576176 tig0018560:+9099 None:intergenic
AAGAAAGGGAAAAGATTCAA+GGG 0.576778 tig0018560:-9049 Msa1367880:CDS
AGCGGTGCACCGTAGCTGCA+CGG 0.586905 tig0018560:-9168 Msa1367880:CDS
GTTGATAAGAGGAGCGTCGT+CGG 0.589779 tig0018560:-9143 Msa1367880:CDS
AGAGGCCAAGGAGTAGACCT+GGG 0.623067 tig0018560:+8959 None:intergenic
AAAGATTCAAGGGCTCGTAT+GGG 0.635720 tig0018560:-9039 Msa1367880:CDS
GTGGCGCTAGTGTGATGCAG+CGG 0.656151 tig0018560:-9186 Msa1367880:CDS
AAATTGTGTATGGCGAGTGG+TGG 0.695087 tig0018560:-9205 None:intergenic
ACAGCTGCTCCGATAGTGTG+CGG 0.696198 tig0018560:-9091 Msa1367880:CDS
AGAAAATTGTGTATGGCGAG+TGG 0.703620 tig0018560:-9208 None:intergenic
ACGCCGGCAGAAGAAGCACA+AGG 0.711011 tig0018560:+9115 None:intergenic
GGTGCACCGTAGCTGCACGG+TGG 0.772757 tig0018560:-9165 Msa1367880:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GTGATAAAAAGACAAAGAAA+GGG - tig0018560:9073-9092 Msa1367880:CDS 25.0%
GGTGATAAAAAGACAAAGAA+AGG - tig0018560:9072-9091 Msa1367880:CDS 30.0%
AAAGAAAGGGAAAAGATTCA+AGG - tig0018560:9086-9105 Msa1367880:CDS 30.0%
AAGAAAGGGAAAAGATTCAA+GGG - tig0018560:9087-9106 Msa1367880:CDS 30.0%
TCGATCATTTGTTCTCTCTT+CGG + tig0018560:9132-9151 None:intergenic 35.0%
GATCGAACGAATCAAAGATA+AGG - tig0018560:9146-9165 Msa1367880:CDS 35.0%
AAAAGATTCAAGGGCTCGTA+TGG - tig0018560:9096-9115 Msa1367880:CDS 40.0%
AAAGATTCAAGGGCTCGTAT+GGG - tig0018560:9097-9116 Msa1367880:CDS 40.0%
AAGATAAGGTTGAAGTTCCC+AGG - tig0018560:9160-9179 Msa1367880:CDS 40.0%
CAAATGAGCTTGAAAGGAAG+AGG + tig0018560:9198-9217 None:intergenic 40.0%
TATCAACCACCGTGCAGCTA+CGG + tig0018560:8980-8999 None:intergenic 50.0%
!! GTTGATAAGAGGAGCGTCGT+CGG - tig0018560:8993-9012 Msa1367880:CDS 50.0%
AAGTTCCCAGGTCTACTCCT+TGG - tig0018560:9172-9191 Msa1367880:CDS 50.0%
AGCTTGAAAGGAAGAGGCCA+AGG + tig0018560:9192-9211 None:intergenic 50.0%
!! GCTGCACGGTGGTTGATAAG+AGG - tig0018560:8982-9001 Msa1367880:CDS 55.0%
ACGCCTTGTGCTTCTTCTGC+CGG - tig0018560:9018-9037 Msa1367880:CDS 55.0%
TATCGGAGCAGCTGTTACGC+CGG + tig0018560:9040-9059 None:intergenic 55.0%
ACAGCTGCTCCGATAGTGTG+CGG - tig0018560:9045-9064 Msa1367880:CDS 55.0%
AGAGGCCAAGGAGTAGACCT+GGG + tig0018560:9180-9199 None:intergenic 55.0%
AAGAGGCCAAGGAGTAGACC+TGG + tig0018560:9181-9200 None:intergenic 55.0%
GTGGCGCTAGTGTGATGCAG+CGG - tig0018560:8950-8969 Msa1367880:CDS 60.0%
! ACGCCGGCAGAAGAAGCACA+AGG + tig0018560:9024-9043 None:intergenic 60.0%
TCACCGCGTCCGCACACTAT+CGG + tig0018560:9057-9076 None:intergenic 60.0%
AGCGGTGCACCGTAGCTGCA+CGG - tig0018560:8968-8987 Msa1367880:CDS 65.0%
GCTCCGATAGTGTGCGGACG+CGG - tig0018560:9051-9070 Msa1367880:CDS 65.0%
GGTGCACCGTAGCTGCACGG+TGG - tig0018560:8971-8990 Msa1367880:CDS 70.0%
Chromosome Type Strat End Strand Name
tig0018560 gene 8940 9218 8940 ID=Msa1367880;Name=Msa1367880
tig0018560 mRNA 8940 9218 8940 ID=Msa1367880-mRNA-1;Parent=Msa1367880;Name=Msa1367880-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|92
tig0018560 exon 8940 9218 8940 ID=Msa1367880-mRNA-1:exon:194;Parent=Msa1367880-mRNA-1
tig0018560 CDS 8940 9218 8940 ID=Msa1367880-mRNA-1:cds;Parent=Msa1367880-mRNA-1
Gene Sequence

>Msa1367880

ATGGCGAGTGGTGGCGCTAGTGTGATGCAGCGGTGCACCGTAGCTGCACGGTGGTTGATAAGAGGAGCGTCGTCGGAGACGCCTTGTGCTTCTTCTGCCGGCGTAACAGCTGCTCCGATAGTGTGCGGACGCGGTGATAAAAAGACAAAGAAAGGGAAAAGATTCAAGGGCTCGTATGGGAAATCTCGTCCGAAGAGAGAACAAATGATCGAACGAATCAAAGATAAGGTTGAAGTTCCCAGGTCTACTCCTTGGCCTCTTCCTTTCAAGCTCATTTGA

Protein sequence

>Msa1367880

MASGGASVMQRCTVAARWLIRGASSETPCASSAGVTAAPIVCGRGDKKTKKGKRFKGSYGKSRPKREQMIERIKDKVEVPRSTPWPLPFKLI*