AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1400110

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1400110 MtrunA17_Chr8g0388791 94.186 86 2 1 1 83 1 86 3.43e-51 155
Msa1400110 MtrunA17_Chr8g0346591 61.905 42 16 0 3 44 8 49 4.67e-13 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1400110 AT4G10810.1 62.500 48 18 0 4 51 16 63 3.06e-13 59.3

Find 32 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAACTTCTCTTTAGATATC+AGG 0.264418 tig0022414:+95164 None:intergenic
TTCCGCTTTCTTCTCTTCCT+TGG 0.296008 tig0022414:-95107 Msa1400110:CDS
TCATCGTCTTCGTCGTTATC+AGG 0.344564 tig0022414:+95046 None:intergenic
GGAGGTTGGTGATATCGTTT+GGG 0.357316 tig0022414:+94960 None:intergenic
GGGAGGTTGGTGATATCGTT+TGG 0.364836 tig0022414:+94959 None:intergenic
GATCAGATGGCAACCTGGGT+GGG 0.426814 tig0022414:-95142 Msa1400110:CDS
GGGGTCTTAACGGAGGGATC+AGG 0.428723 tig0022414:+94980 None:intergenic
GGTGGTGGTGGTGACGGAGT+CGG 0.448510 tig0022414:+95018 None:intergenic
ATCAGATGGCAACCTGGGTG+GGG 0.454986 tig0022414:-95141 Msa1400110:CDS
CCTGATATCTAAAGAGAAGT+TGG 0.455522 tig0022414:-95164 Msa1400110:CDS
GTTGACGGTGGTGGTGGTGG+TGG 0.455838 tig0022414:+95006 None:intergenic
ATTGTTGACGGTGGTGGTGG+TGG 0.457641 tig0022414:+95003 None:intergenic
ATCAGGATTGTTGACGGTGG+TGG 0.467123 tig0022414:+94997 None:intergenic
GATATCGTTTGGGGTCTTAA+CGG 0.478557 tig0022414:+94970 None:intergenic
AGGATTGTTGACGGTGGTGG+TGG 0.495328 tig0022414:+95000 None:intergenic
TAAAGAGAAGTTGGATCAGA+TGG 0.515604 tig0022414:-95155 Msa1400110:CDS
AGAGAAGAAAGCGGAAGAGA+CGG 0.533991 tig0022414:+95114 None:intergenic
AGTTGGATCAGATGGCAACC+TGG 0.543370 tig0022414:-95147 Msa1400110:CDS
GACGCAAGAAAAGCGTTCCA+AGG 0.548791 tig0022414:+95090 None:intergenic
GGATCAGATGGCAACCTGGG+TGG 0.570514 tig0022414:-95143 Msa1400110:CDS
GAAGAAAGCGGAAGAGACGG+TGG 0.578991 tig0022414:+95117 None:intergenic
GTTGGATCAGATGGCAACCT+GGG 0.581479 tig0022414:-95146 Msa1400110:CDS
GGAGGGATCAGGATTGTTGA+CGG 0.583608 tig0022414:+94991 None:intergenic
TCGTTTGGGGTCTTAACGGA+GGG 0.589276 tig0022414:+94974 None:intergenic
ATCGTTTGGGGTCTTAACGG+AGG 0.613773 tig0022414:+94973 None:intergenic
AGAGACGGTGGACCCCACCC+AGG 0.649497 tig0022414:+95129 None:intergenic
TCGTCTTCGTCGTTATCAGG+AGG 0.685685 tig0022414:+95049 None:intergenic
TTCCAAGGAAGAGAAGAAAG+CGG 0.690072 tig0022414:+95105 None:intergenic
GTTATCAGGAGGATCAGAAG+TGG 0.695959 tig0022414:+95060 None:intergenic
GAGGTTGGTGATATCGTTTG+GGG 0.715129 tig0022414:+94961 None:intergenic
GGGATCAGGATTGTTGACGG+TGG 0.721497 tig0022414:+94994 None:intergenic
TCGACCACGATGGAGAACAA+CGG 0.739992 tig0022414:-95190 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CCAACTTCTCTTTAGATATC+AGG + tig0022414:94972-94991 None:intergenic 35.0%
CCTGATATCTAAAGAGAAGT+TGG - tig0022414:94969-94988 Msa1400110:CDS 35.0%
TAAAGAGAAGTTGGATCAGA+TGG - tig0022414:94978-94997 Msa1400110:CDS 35.0%
TTCCAAGGAAGAGAAGAAAG+CGG + tig0022414:95031-95050 None:intergenic 40.0%
! GATATCGTTTGGGGTCTTAA+CGG + tig0022414:95166-95185 None:intergenic 40.0%
AGAGAAGAAAGCGGAAGAGA+CGG + tig0022414:95022-95041 None:intergenic 45.0%
TTCCGCTTTCTTCTCTTCCT+TGG - tig0022414:95026-95045 Msa1400110:CDS 45.0%
GTTATCAGGAGGATCAGAAG+TGG + tig0022414:95076-95095 None:intergenic 45.0%
TCATCGTCTTCGTCGTTATC+AGG + tig0022414:95090-95109 None:intergenic 45.0%
!! GAGGTTGGTGATATCGTTTG+GGG + tig0022414:95175-95194 None:intergenic 45.0%
!! GGAGGTTGGTGATATCGTTT+GGG + tig0022414:95176-95195 None:intergenic 45.0%
AGTTGGATCAGATGGCAACC+TGG - tig0022414:94986-95005 Msa1400110:CDS 50.0%
GTTGGATCAGATGGCAACCT+GGG - tig0022414:94987-95006 Msa1400110:CDS 50.0%
!! GACGCAAGAAAAGCGTTCCA+AGG + tig0022414:95046-95065 None:intergenic 50.0%
TCGTCTTCGTCGTTATCAGG+AGG + tig0022414:95087-95106 None:intergenic 50.0%
ATCAGGATTGTTGACGGTGG+TGG + tig0022414:95139-95158 None:intergenic 50.0%
GGAGGGATCAGGATTGTTGA+CGG + tig0022414:95145-95164 None:intergenic 50.0%
! TCGTTTGGGGTCTTAACGGA+GGG + tig0022414:95162-95181 None:intergenic 50.0%
! ATCGTTTGGGGTCTTAACGG+AGG + tig0022414:95163-95182 None:intergenic 50.0%
!! GGGAGGTTGGTGATATCGTT+TGG + tig0022414:95177-95196 None:intergenic 50.0%
GATCAGATGGCAACCTGGGT+GGG - tig0022414:94991-95010 Msa1400110:CDS 55.0%
ATCAGATGGCAACCTGGGTG+GGG - tig0022414:94992-95011 Msa1400110:CDS 55.0%
GAAGAAAGCGGAAGAGACGG+TGG + tig0022414:95019-95038 None:intergenic 55.0%
!! ATTGTTGACGGTGGTGGTGG+TGG + tig0022414:95133-95152 None:intergenic 55.0%
! AGGATTGTTGACGGTGGTGG+TGG + tig0022414:95136-95155 None:intergenic 55.0%
GGGATCAGGATTGTTGACGG+TGG + tig0022414:95142-95161 None:intergenic 55.0%
GGATCAGATGGCAACCTGGG+TGG - tig0022414:94990-95009 Msa1400110:CDS 60.0%
GGGGTCTTAACGGAGGGATC+AGG + tig0022414:95156-95175 None:intergenic 60.0%
!! GGTGGTGGTGGTGACGGAGT+CGG + tig0022414:95118-95137 None:intergenic 65.0%
!! GGTGGTGGTGGTGGTGGTGA+CGG + tig0022414:95124-95143 None:intergenic 65.0%
!! GTTGACGGTGGTGGTGGTGG+TGG + tig0022414:95130-95149 None:intergenic 65.0%
AGAGACGGTGGACCCCACCC+AGG + tig0022414:95007-95026 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
tig0022414 gene 94952 95203 94952 ID=Msa1400110;Name=Msa1400110
tig0022414 mRNA 94952 95203 94952 ID=Msa1400110-mRNA-1;Parent=Msa1400110;Name=Msa1400110-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|-1|0|1|-1|1|1|0|83
tig0022414 exon 94952 95203 94952 ID=Msa1400110-mRNA-1:exon:17554;Parent=Msa1400110-mRNA-1
tig0022414 CDS 94952 95203 94952 ID=Msa1400110-mRNA-1:cds;Parent=Msa1400110-mRNA-1
Gene Sequence

>Msa1400110

ATGGAGAACAACGGCAGCCTGATATCTAAAGAGAAGTTGGATCAGATGGCAACCTGGGTGGGGTCCACCGTCTCTTCCGCTTTCTTCTCTTCCTTGGAACGCTTTTCTTGCGTCAACGTCACCACTTCTGATCCTCCTGATAACGACGAAGACGATGATTACTCCGACTCCGTCACCACCACCACCACCACCGTCAACAATCCTGATCCCTCCGTTAAGACCCCAAACGATATCACCAACCTCCCCGTTTGA
Protein sequence

>Msa1400110

MENNGSLISKEKLDQMATWVGSTVSSAFFSSLERFSCVNVTTSDPPDNDEDDDYSDSVTTTTTTVNNPDPSVKTPNDITNLPV*