AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1385530

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1385530 MtrunA17_Chr4g0037781 84.733 131 20 0 1 131 58 188 2.98e-80 234
Msa1385530 MtrunA17_Chr7g0236851 80.153 131 26 0 1 131 296 426 1.85e-70 223
Msa1385530 MtrunA17_Chr4g0037771 81.034 116 22 0 1 116 1 116 2.00e-68 201
Msa1385530 MtrunA17_Chr6g0468561 53.488 129 56 2 1 128 297 422 3.47e-36 130
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1385530 AT5G52510.1 46.565 131 64 2 1 131 270 394 3.62e-26 102

Find 19 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGCTGCCACCGCAATTTC+TGG 0.192643 tig0020757:+56792 Msa1385530:CDS
TTGCTTCAAGCTCTCTTTCA+TGG 0.245115 tig0020757:+57019 Msa1385530:CDS
GAAATTTGATCGTTGGTTAT+TGG 0.249208 tig0020757:+56878 Msa1385530:CDS
AGCTTCGAGGATTGCAATAT+TGG 0.276395 tig0020757:-57045 None:intergenic
AACGATCAAATTTCAGTCTT+GGG 0.364738 tig0020757:-56869 None:intergenic
CAACGATCAAATTTCAGTCT+TGG 0.369194 tig0020757:-56870 None:intergenic
TGAAATTCCACCTGCAATAG+TGG 0.402615 tig0020757:+56941 Msa1385530:CDS
TGTGTTGTGGAGTTTGATAA+TGG 0.448667 tig0020757:+57104 Msa1385530:CDS
TGAAGCAAATAGAGTGATCA+AGG 0.451795 tig0020757:-57004 None:intergenic
TATCTTCAAATGTAGCTTCG+AGG 0.464718 tig0020757:-57058 None:intergenic
GTGGAGTTTGATAATGGTAA+TGG 0.467419 tig0020757:+57110 Msa1385530:CDS
CAAGACTGAAATTTGATCGT+TGG 0.476052 tig0020757:+56871 Msa1385530:CDS
AAACTCCATGCACGTTTCAA+CGG 0.532071 tig0020757:+57158 Msa1385530:CDS
TCGTTGGTTATTGGATTGCA+TGG 0.560143 tig0020757:+56887 Msa1385530:CDS
CGTGAAGAATCTTTGTGTTG+TGG 0.574036 tig0020757:+57091 Msa1385530:CDS
AAATAGAGTGATCAAGGAGA+AGG 0.585337 tig0020757:-56998 None:intergenic
GTTAACCGTTGAAACGTGCA+TGG 0.614346 tig0020757:-57163 None:intergenic
GTGTTTGAGAGAAACGAGAG+AGG 0.625259 tig0020757:-56842 None:intergenic
GCTGCCACCGCAATTTCTGG+AGG 0.664192 tig0020757:+56795 Msa1385530:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AACGATCAAATTTCAGTCTT+GGG - tig0020757:56872-56891 None:intergenic 30.0%
! GAAATTTGATCGTTGGTTAT+TGG + tig0020757:56878-56897 Msa1385530:CDS 30.0%
! CATTTTTCCTCCAGAAATTG+CGG - tig0020757:56805-56824 None:intergenic 35.0%
TGGAGGAAAAATGGAATATG+CGG + tig0020757:56812-56831 Msa1385530:CDS 35.0%
CAACGATCAAATTTCAGTCT+TGG - tig0020757:56873-56892 None:intergenic 35.0%
CAAGACTGAAATTTGATCGT+TGG + tig0020757:56871-56890 Msa1385530:CDS 35.0%
AAAAATTCCACTATTGCAGG+TGG - tig0020757:56951-56970 None:intergenic 35.0%
CTGAAAAATTCCACTATTGC+AGG - tig0020757:56954-56973 None:intergenic 35.0%
AAATAGAGTGATCAAGGAGA+AGG - tig0020757:57001-57020 None:intergenic 35.0%
TGAAGCAAATAGAGTGATCA+AGG - tig0020757:57007-57026 None:intergenic 35.0%
TATCTTCAAATGTAGCTTCG+AGG - tig0020757:57061-57080 None:intergenic 35.0%
TGTGTTGTGGAGTTTGATAA+TGG + tig0020757:57104-57123 Msa1385530:CDS 35.0%
!! GTGGAGTTTGATAATGGTAA+TGG + tig0020757:57110-57129 Msa1385530:CDS 35.0%
! CGCAATTTCTGGAGGAAAAA+TGG + tig0020757:56803-56822 Msa1385530:CDS 40.0%
AGGAAAAATGGAATATGCGG+AGG + tig0020757:56815-56834 Msa1385530:CDS 40.0%
! TCGTTGGTTATTGGATTGCA+TGG + tig0020757:56887-56906 Msa1385530:CDS 40.0%
TGAAATTCCACCTGCAATAG+TGG + tig0020757:56941-56960 Msa1385530:CDS 40.0%
TTGCTTCAAGCTCTCTTTCA+TGG + tig0020757:57019-57038 Msa1385530:CDS 40.0%
AGCTTCGAGGATTGCAATAT+TGG - tig0020757:57048-57067 None:intergenic 40.0%
CGTGAAGAATCTTTGTGTTG+TGG + tig0020757:57091-57110 Msa1385530:CDS 40.0%
! TGAAACGTGCATGGAGTTTT+TGG - tig0020757:57157-57176 None:intergenic 40.0%
AAACTCCATGCACGTTTCAA+CGG + tig0020757:57158-57177 Msa1385530:CDS 40.0%
! TTTTCCTCCAGAAATTGCGG+TGG - tig0020757:56802-56821 None:intergenic 45.0%
GTGTTTGAGAGAAACGAGAG+AGG - tig0020757:56845-56864 None:intergenic 45.0%
!! GTGCATGGAGTTTTTGGAGA+AGG - tig0020757:57151-57170 None:intergenic 45.0%
GAAGCTGCCACCGCAATTTC+TGG + tig0020757:56792-56811 Msa1385530:CDS 55.0%
! GCTGCCACCGCAATTTCTGG+AGG + tig0020757:56795-56814 Msa1385530:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0020757 gene 56789 57184 56789 ID=Msa1385530;Name=Msa1385530
tig0020757 mRNA 56789 57184 56789 ID=Msa1385530-mRNA-1;Parent=Msa1385530;Name=Msa1385530-mRNA-1;_AED=0.30;_eAED=0.31;_QI=0|-1|0|1|-1|1|1|0|131
tig0020757 exon 56789 57184 56789 ID=Msa1385530-mRNA-1:exon:9638;Parent=Msa1385530-mRNA-1
tig0020757 CDS 56789 57184 56789 ID=Msa1385530-mRNA-1:cds;Parent=Msa1385530-mRNA-1
Gene Sequence

>Msa1385530

ATGGAAGCTGCCACCGCAATTTCTGGAGGAAAAATGGAATATGCGGAGGAGATCCTCTCTCGTTTCTCTCAAACACAAAACCCAAGACTGAAATTTGATCGTTGGTTATTGGATTGCATGGCTTTAGCGCTGAAATCGCGTGTGAATAACATTGAAATTCCACCTGCAATAGTGGAATTTTTCAGCAAAGAACATGCTAAGTCGACTCACCTTCTCCTTGATCACTCTATTTGCTTCAAGCTCTCTTTCATGGCTGCCAATATTGCAATCCTCGAAGCTACATTTGAAGATACAACAAAGAGCGTGAAGAATCTTTGTGTTGTGGAGTTTGATAATGGTAATGGAAAACAATACATAAACCTTCTCCAAAAACTCCATGCACGTTTCAACGGTTAA
Protein sequence

>Msa1385530

MEAATAISGGKMEYAEEILSRFSQTQNPRLKFDRWLLDCMALALKSRVNNIEIPPAIVEFFSKEHAKSTHLLLDHSICFKLSFMAANIAILEATFEDTTKSVKNLCVVEFDNGNGKQYINLLQKLHARFNG*