AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0582710


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582710 MtrunA17_Chr4g0015681 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa0582710 MtrunA17_CPg0492901 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa0582710 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
Msa0582710 ATCG00070.1 76.667 60 14 0 1 60 1 60 3.76e-26 92.0
Msa0582710 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 4_2:-1170587 Msa0582710:CDS
ACTGGCATAAAATCTACAAT+TGG 0.453871 4_2:+1170484 None:intergenic
AATGATCCAGGACGTAATCC+TGG 0.474800 4_2:-1169937 Msa0582710:CDS
GGATTCCTATCTAATGATCC+AGG 0.536202 4_2:-1169949 Msa0582710:CDS
TCACGTCCAGGATTACGTCC+TGG 0.548081 4_2:+1169931 None:intergenic
TACGTCCTGGATCATTAGAT+AGG 0.581605 4_2:+1169944 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTCCAAATATTAAAATTTT+TGG - chr4_2:1170213-1170232 Msa0582710:intron 10.0%
!!! TATCCAAAAATTTTAATATT+TGG + chr4_2:1170219-1170238 None:intergenic 10.0%
!! ATTTCAAAAAAAAAAAACTT+AGG + chr4_2:1170370-1170389 None:intergenic 10.0%
!!! AATTTTAATATTTGGAATCA+AGG + chr4_2:1170211-1170230 None:intergenic 15.0%
!!! CGTTTTTTTTTTAATTATCT+TGG - chr4_2:1170465-1170484 Msa0582710:CDS 15.0%
!! GAAAAAACTACTTGAATAAA+GGG + chr4_2:1169970-1169989 None:intergenic 20.0%
!! AGAAAAAACTACTTGAATAA+AGG + chr4_2:1169971-1169990 None:intergenic 20.0%
!!! TTATTCAAGTAGTTTTTTCT+TGG - chr4_2:1169971-1169990 Msa0582710:CDS 20.0%
!! TGAAAATTCTATTATTCGAT+TGG - chr4_2:1170257-1170276 Msa0582710:intron 20.0%
!!! TGTGGATATGAAAAAAATTT+TGG - chr4_2:1170308-1170327 Msa0582710:intron 20.0%
!! TCTTATAAACTTAGTATCAA+AGG - chr4_2:1170399-1170418 Msa0582710:intron 20.0%
!!! TTTTTCTCTTAGCTTTTGTT+TGG - chr4_2:1170063-1170082 Msa0582710:intron 25.0%
!!! TTTGTTTCTCTTTTCATCTT+CGG - chr4_2:1170540-1170559 Msa0582710:CDS 25.0%
! AATTGGATTCAAAAAAGCGT+AGG + chr4_2:1170012-1170031 None:intergenic 30.0%
ACTGGCATAAAATCTACAAT+TGG + chr4_2:1170029-1170048 None:intergenic 30.0%
!! AAAAAGAGTAAGGGTATTAC+TGG + chr4_2:1170047-1170066 None:intergenic 30.0%
GCTAAGAGAAAAAAGAGTAA+GGG + chr4_2:1170056-1170075 None:intergenic 30.0%
AGCTAAGAGAAAAAAGAGTA+AGG + chr4_2:1170057-1170076 None:intergenic 30.0%
!! AATCAAGATCTAGGTATTGG+TGG + chr4_2:1170289-1170308 None:intergenic 35.0%
CACAATCAAGATCTAGGTAT+TGG + chr4_2:1170292-1170311 None:intergenic 35.0%
CAATACCTAGATCTTGATTG+TGG - chr4_2:1170290-1170309 Msa0582710:intron 35.0%
CATATCCACAATCAAGATCT+AGG + chr4_2:1170298-1170317 None:intergenic 35.0%
GAGAATCTATTCTCTTTCTC+TGG - chr4_2:1170442-1170461 Msa0582710:CDS 35.0%
! TTCAAAAAAGCGTAGGCTTC+AGG + chr4_2:1170005-1170024 None:intergenic 40.0%
GGATTCCTATCTAATGATCC+AGG - chr4_2:1170561-1170580 Msa0582710:CDS 40.0%
TACGTCCTGGATCATTAGAT+AGG + chr4_2:1170569-1170588 None:intergenic 40.0%
!! CAAGATCTAGGTATTGGTGG+TGG + chr4_2:1170286-1170305 None:intergenic 45.0%
AATGATCCAGGACGTAATCC+TGG - chr4_2:1170573-1170592 Msa0582710:CDS 45.0%
!!! AATAAATTCTTAATTTTTTT+CGG + chr4_2:1170134-1170153 None:intergenic 5.0%
TCACGTCCAGGATTACGTCC+TGG + chr4_2:1170582-1170601 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 1169924 1170608 1169924 ID=Msa0582710;Name=Msa0582710
chr4_2 mRNA 1169924 1170608 1169924 ID=Msa0582710-mRNA-1;Parent=Msa0582710;Name=Msa0582710-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|0|0|1|0|0|2|0|97
chr4_2 exon 1170434 1170608 1170434 ID=Msa0582710-mRNA-1:exon:264;Parent=Msa0582710-mRNA-1
chr4_2 exon 1169924 1170042 1169924 ID=Msa0582710-mRNA-1:exon:263;Parent=Msa0582710-mRNA-1
chr4_2 CDS 1170434 1170608 1170434 ID=Msa0582710-mRNA-1:cds;Parent=Msa0582710-mRNA-1
chr4_2 CDS 1169924 1170042 1169924 ID=Msa0582710-mRNA-1:cds;Parent=Msa0582710-mRNA-1
Gene Sequence

>Msa0582710

ATGCTTAATATCTTTAGCTTGGTCTGTATTTGTATTGACTCTGCCCTTTATTCAAGTAGTTTTTTCTTGGCAAAATTACCTGAAGCCTACGCTTTTTTGAATCCAATTGTAGATTTTATGCCAGTAATACCCTTACTCTTTTTTCTCTTAGCTTTTGTTTGGCAAGCTGCTGTAAATTTTGTAATGCTTACTCTAAAACTATTTGTTTACACGATAGTGATATTCTTTGTTTCTCTTTTCATCTTCGGATTCCTATCTAATGATCCAGGACGTAATCCTGGACGTGAAGAATAA

Protein sequence

>Msa0582710

MLNIFSLVCICIDSALYSSSFFLAKLPEAYAFLNPIVDFMPVIPLLFFLLAFVWQAAVNFVMLTLKLFVYTIVIFFVSLFIFGFLSNDPGRNPGREE*