AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1362880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1362880 MtrunA17_Chr6g0455241 97.701 87 2 0 19 105 56 142 2.32e-60 181
Msa1362880 MtrunA17_Chr6g0455271 95.833 96 4 0 1 96 2 97 2.48e-52 160
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 19 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATGCAGCAAGAATGCTTT+TGG 0.265450 tig0017975:+19208 Msa1362880:CDS
ACAACATCATTGAAGATAAA+AGG 0.287321 tig0017975:+19122 Msa1362880:CDS
TTGTCTGATCAACAATGATT+TGG 0.352096 tig0017975:+19160 Msa1362880:CDS
TAAGTACCACACCTATTGTT+AGG 0.386678 tig0017975:-19341 None:intergenic
GTACGATAGCCTTGACGTAT+TGG 0.444086 tig0017975:-19290 None:intergenic
CAAACACAAACTGGTAGAAC+TGG 0.449515 tig0017975:+19239 Msa1362880:CDS
GATTTGAGTCAAACACAAAC+TGG 0.464256 tig0017975:+19230 Msa1362880:CDS
ACTTGCTTGCCTTCTCAGAA+TGG 0.483184 tig0017975:+19311 Msa1362880:CDS
ATGGAGGTGGACCTAACAAT+AGG 0.493318 tig0017975:+19330 Msa1362880:CDS
TTGCCTTCTCAGAATGGAGG+TGG 0.512101 tig0017975:+19317 Msa1362880:CDS
GTAATTGGATCAATAAGATA+AGG 0.536107 tig0017975:-19088 None:intergenic
TGCTTGCCTTCTCAGAATGG+AGG 0.570153 tig0017975:+19314 Msa1362880:CDS
GGTCCACCTCCATTCTGAGA+AGG 0.625898 tig0017975:-19320 None:intergenic
ACCAAAGAAGAAAATGAACA+AGG 0.627471 tig0017975:+19049 None:intergenic
GGTAGAACTGGTAATAACAA+TGG 0.632835 tig0017975:+19251 Msa1362880:CDS
CCAAAGAAGAAAATGAACAA+GGG 0.643796 tig0017975:+19050 None:intergenic
GTTAAGTGTCCAATACGTCA+AGG 0.658926 tig0017975:+19281 Msa1362880:CDS
GATAAAAGGTTGTACCTCAG+AGG 0.662136 tig0017975:+19136 Msa1362880:CDS
GGTGGACCTAACAATAGGTG+TGG 0.694293 tig0017975:+19335 Msa1362880:CDS
GTTGATCAGACAATCCTCTG+AGG 0.737752 tig0017975:-19150 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GTAATTGGATCAATAAGATA+AGG - tig0017975:19091-19110 None:intergenic 25.0%
!!! TTGTTTTGCTTAGATGTAAT+TGG - tig0017975:19106-19125 None:intergenic 25.0%
! ACAACATCATTGAAGATAAA+AGG + tig0017975:19122-19141 Msa1362880:CDS 25.0%
TTGTCTGATCAACAATGATT+TGG + tig0017975:19160-19179 Msa1362880:CDS 30.0%
GATTTGAGTCAAACACAAAC+TGG + tig0017975:19230-19249 Msa1362880:CDS 35.0%
GGTAGAACTGGTAATAACAA+TGG + tig0017975:19251-19270 Msa1362880:CDS 35.0%
TAAGTACCACACCTATTGTT+AGG - tig0017975:19344-19363 None:intergenic 35.0%
GATAAAAGGTTGTACCTCAG+AGG + tig0017975:19136-19155 Msa1362880:CDS 40.0%
! TCATGCAGCAAGAATGCTTT+TGG + tig0017975:19208-19227 Msa1362880:CDS 40.0%
CAAACACAAACTGGTAGAAC+TGG + tig0017975:19239-19258 Msa1362880:CDS 40.0%
GTTAAGTGTCCAATACGTCA+AGG + tig0017975:19281-19300 Msa1362880:CDS 40.0%
GTTGATCAGACAATCCTCTG+AGG - tig0017975:19153-19172 None:intergenic 45.0%
! GTACGATAGCCTTGACGTAT+TGG - tig0017975:19293-19312 None:intergenic 45.0%
ACTTGCTTGCCTTCTCAGAA+TGG + tig0017975:19311-19330 Msa1362880:CDS 45.0%
ATGGAGGTGGACCTAACAAT+AGG + tig0017975:19330-19349 Msa1362880:CDS 45.0%
TGCTTGCCTTCTCAGAATGG+AGG + tig0017975:19314-19333 Msa1362880:CDS 50.0%
TTGCCTTCTCAGAATGGAGG+TGG + tig0017975:19317-19336 Msa1362880:CDS 50.0%
GGTGGACCTAACAATAGGTG+TGG + tig0017975:19335-19354 Msa1362880:CDS 50.0%
! GGTCCACCTCCATTCTGAGA+AGG - tig0017975:19323-19342 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0017975 gene 19062 19379 19062 ID=Msa1362880;Name=Msa1362880
tig0017975 mRNA 19062 19379 19062 ID=Msa1362880-mRNA-1;Parent=Msa1362880;Name=Msa1362880-mRNA-1;_AED=0.18;_eAED=0.19;_QI=0|-1|0|1|-1|1|1|0|105
tig0017975 exon 19062 19379 19062 ID=Msa1362880-mRNA-1:exon:13279;Parent=Msa1362880-mRNA-1
tig0017975 CDS 19062 19379 19062 ID=Msa1362880-mRNA-1:cds;Parent=Msa1362880-mRNA-1
Gene Sequence

>Msa1362880

ATGAACAAGGGTGTATCACTATTGTTCCTTATCTTATTGATCCAATTACATCTAAGCAAAACAACATCATTGAAGATAAAAGGTTGTACCTCAGAGGATTGTCTGATCAACAATGATTTGGAATCAGAAGAATTTTCTATGAGTTCTCATGCAGCAAGAATGCTTTTGGATTTGAGTCAAACACAAACTGGTAGAACTGGTAATAACAATGGTGCTGCTGTTAAGTGTCCAATACGTCAAGGCTATCGTACTTGCTTGCCTTCTCAGAATGGAGGTGGACCTAACAATAGGTGTGGTACTTATAATAGAGTTTGCTAA

Protein sequence

>Msa1362880

MNKGVSLLFLILLIQLHLSKTTSLKIKGCTSEDCLINNDLESEEFSMSSHAARMLLDLSQTQTGRTGNNNGAAVKCPIRQGYRTCLPSQNGGGPNNRCGTYNRVC*