AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268850


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268850 MtrunA17_Chr4g0015681 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa0268850 MtrunA17_CPg0492901 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa0268850 MtrunA17_Chr4g0016771 96.667 60 2 0 1 60 1 60 7.64e-35 113
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268850 ATCG00070.1 76.667 60 14 0 1 60 1 60 3.76e-26 92.0
Msa0268850 ATCG00080.1 97.222 36 1 0 62 97 1 36 2.92e-19 73.9

Find 6 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATGCTTAATATCTTTAGCT+TGG 0.440922 2_2:-70418569 Msa0268850:CDS
ACTGGCATAAAATCTACAAT+TGG 0.453871 2_2:+70418466 None:intergenic
AATGATCCAGGACGTAATCC+TGG 0.474800 2_2:-70417920 Msa0268850:CDS
GGATTCCTATCTAATGATCC+AGG 0.536202 2_2:-70417932 Msa0268850:CDS
TCACGTCCAGGATTACGTCC+TGG 0.548081 2_2:+70417914 None:intergenic
TACGTCCTGGATCATTAGAT+AGG 0.581605 2_2:+70417927 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTCCAAATATTAAAATTTT+TGG - chr2_2:70418196-70418215 Msa0268850:intron 10.0%
!!! TATCCAAAAATTTTAATATT+TGG + chr2_2:70418202-70418221 None:intergenic 10.0%
!! ATTTCAAAAAAAAAAAACTT+AGG + chr2_2:70418353-70418372 None:intergenic 10.0%
!!! AATTTTAATATTTGGAATCA+AGG + chr2_2:70418194-70418213 None:intergenic 15.0%
!! GAAAAAACTACTTGAATAAA+GGG + chr2_2:70417953-70417972 None:intergenic 20.0%
!! AGAAAAAACTACTTGAATAA+AGG + chr2_2:70417954-70417973 None:intergenic 20.0%
!!! TTATTCAAGTAGTTTTTTCT+TGG - chr2_2:70417954-70417973 Msa0268850:CDS 20.0%
!! TGAAAATTCTATTATTCGAT+TGG - chr2_2:70418240-70418259 Msa0268850:intron 20.0%
!!! TGTGGATATGAAAAAAATTT+TGG - chr2_2:70418291-70418310 Msa0268850:intron 20.0%
!! TCTTATAAACTTAGTATCAA+AGG - chr2_2:70418382-70418401 Msa0268850:intron 20.0%
!!! GCGTTTTTTTTTAATTATCT+TGG - chr2_2:70418447-70418466 Msa0268850:CDS 20.0%
!!! TTTTTCTCTTAGCTTTTGTT+TGG - chr2_2:70418046-70418065 Msa0268850:intron 25.0%
!!! TTTGTTTCTCTTTTCATCTT+CGG - chr2_2:70418522-70418541 Msa0268850:CDS 25.0%
! AATTGGATTCAAAAAAGCGT+AGG + chr2_2:70417995-70418014 None:intergenic 30.0%
ACTGGCATAAAATCTACAAT+TGG + chr2_2:70418012-70418031 None:intergenic 30.0%
!! AAAAAGAGTAAGGGTATTAC+TGG + chr2_2:70418030-70418049 None:intergenic 30.0%
GCTAAGAGAAAAAAGAGTAA+GGG + chr2_2:70418039-70418058 None:intergenic 30.0%
AGCTAAGAGAAAAAAGAGTA+AGG + chr2_2:70418040-70418059 None:intergenic 30.0%
!! AATCAAGATCTAGGTATTGG+TGG + chr2_2:70418272-70418291 None:intergenic 35.0%
CACAATCAAGATCTAGGTAT+TGG + chr2_2:70418275-70418294 None:intergenic 35.0%
CAATACCTAGATCTTGATTG+TGG - chr2_2:70418273-70418292 Msa0268850:intron 35.0%
CATATCCACAATCAAGATCT+AGG + chr2_2:70418281-70418300 None:intergenic 35.0%
GAGAATCTATTCTCTTTCTC+TGG - chr2_2:70418425-70418444 Msa0268850:CDS 35.0%
! TTCAAAAAAGCGTAGGCTTC+AGG + chr2_2:70417988-70418007 None:intergenic 40.0%
GGATTCCTATCTAATGATCC+AGG - chr2_2:70418543-70418562 Msa0268850:CDS 40.0%
TACGTCCTGGATCATTAGAT+AGG + chr2_2:70418551-70418570 None:intergenic 40.0%
!! CAAGATCTAGGTATTGGTGG+TGG + chr2_2:70418269-70418288 None:intergenic 45.0%
AATGATCCAGGACGTAATCC+TGG - chr2_2:70418555-70418574 Msa0268850:CDS 45.0%
!!! AATAAATTCTTAATTTTTTT+CGG + chr2_2:70418117-70418136 None:intergenic 5.0%
TCACGTCCAGGATTACGTCC+TGG + chr2_2:70418564-70418583 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70417907 70418590 70417907 ID=Msa0268850;Name=Msa0268850
chr2_2 mRNA 70417907 70418590 70417907 ID=Msa0268850-mRNA-1;Parent=Msa0268850;Name=Msa0268850-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|0|0|1|0|0|2|0|97
chr2_2 exon 70418416 70418590 70418416 ID=Msa0268850-mRNA-1:exon:22695;Parent=Msa0268850-mRNA-1
chr2_2 exon 70417907 70418025 70417907 ID=Msa0268850-mRNA-1:exon:22694;Parent=Msa0268850-mRNA-1
chr2_2 CDS 70418416 70418590 70418416 ID=Msa0268850-mRNA-1:cds;Parent=Msa0268850-mRNA-1
chr2_2 CDS 70417907 70418025 70417907 ID=Msa0268850-mRNA-1:cds;Parent=Msa0268850-mRNA-1
Gene Sequence

>Msa0268850

ATGCTTAATATCTTTAGCTTGGTCTGTATTTGTATTGACTCTGCCCTTTATTCAAGTAGTTTTTTCTTGGCAAAATTACCTGAAGCCTACGCTTTTTTGAATCCAATTGTAGATTTTATGCCAGTAATACCCTTACTCTTTTTTCTCTTAGCTTTTGTTTGGCAAGCTGCTGTAAATTTTGTAATGCTTACTCTAAAACTATTTGTTTACACGATAGTGATATTCTTTGTTTCTCTTTTCATCTTCGGATTCCTATCTAATGATCCAGGACGTAATCCTGGACGTGAAGAATAA

Protein sequence

>Msa0268850

MLNIFSLVCICIDSALYSSSFFLAKLPEAYAFLNPIVDFMPVIPLLFFLLAFVWQAAVNFVMLTLKLFVYTIVIFFVSLFIFGFLSNDPGRNPGREE*