AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268930


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268930 MtrunA17_Chr4g0015681 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa0268930 MtrunA17_CPg0492901 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa0268930 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
Msa0268930 ATCG00070.1 76.667 60 14 0 1 60 1 60 3.76e-26 92.0
Msa0268930 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:+70454860 None:intergenic
ACTGGCATAAAATCTACAAT+TGG 0.453871 2_2:-70454963 None:intergenic
AATGATCCAGGACGTAATCC+TGG 0.474800 2_2:+70455509 Msa0268930:CDS
GGATTCCTATCTAATGATCC+AGG 0.536202 2_2:+70455497 Msa0268930:CDS
TCACGTCCAGGATTACGTCC+TGG 0.548081 2_2:-70455515 None:intergenic
TACGTCCTGGATCATTAGAT+AGG 0.581605 2_2:-70455502 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTCCAAATATTAAAATTTT+TGG + chr2_2:70455150-70455169 Msa0268930:intron 10.0%
!!! TATCCAAAAATTTTAATATT+TGG - chr2_2:70455156-70455175 None:intergenic 10.0%
!! ATTTCAAAAAAAAAAAACTT+AGG - chr2_2:70455306-70455325 None:intergenic 10.0%
!!! AATTTTAATATTTGGAATCA+AGG - chr2_2:70455148-70455167 None:intergenic 15.0%
!!! CGTTTTTTTTTTAATTATCT+TGG + chr2_2:70455401-70455420 Msa0268930:intron 15.0%
!! GAAAAAACTACTTGAATAAA+GGG - chr2_2:70454907-70454926 None:intergenic 20.0%
!! AGAAAAAACTACTTGAATAA+AGG - chr2_2:70454908-70454927 None:intergenic 20.0%
!!! TTATTCAAGTAGTTTTTTCT+TGG + chr2_2:70454908-70454927 Msa0268930:CDS 20.0%
!! TGAAAATTCTATTATTCGAT+TGG + chr2_2:70455194-70455213 Msa0268930:intron 20.0%
!! TTGTGGATATGAAAAAAATT+TGG + chr2_2:70455244-70455263 Msa0268930:intron 20.0%
!! TCTTATAAACTTAGTATCAA+AGG + chr2_2:70455335-70455354 Msa0268930:intron 20.0%
!!! TTTTTCTCTTAGCTTTTGTT+TGG + chr2_2:70455000-70455019 Msa0268930:CDS 25.0%
!!! TTTGTTTCTCTTTTCATCTT+CGG + chr2_2:70455476-70455495 Msa0268930:CDS 25.0%
! AATTGGATTCAAAAAAGCGT+AGG - chr2_2:70454949-70454968 None:intergenic 30.0%
ACTGGCATAAAATCTACAAT+TGG - chr2_2:70454966-70454985 None:intergenic 30.0%
!! AAAAAGAGTAAGGGTATTAC+TGG - chr2_2:70454984-70455003 None:intergenic 30.0%
GCTAAGAGAAAAAAGAGTAA+GGG - chr2_2:70454993-70455012 None:intergenic 30.0%
AGCTAAGAGAAAAAAGAGTA+AGG - chr2_2:70454994-70455013 None:intergenic 30.0%
!! AATCAAGATCTAGGTATTGG+TGG - chr2_2:70455226-70455245 None:intergenic 35.0%
CACAATCAAGATCTAGGTAT+TGG - chr2_2:70455229-70455248 None:intergenic 35.0%
CAATACCTAGATCTTGATTG+TGG + chr2_2:70455227-70455246 Msa0268930:intron 35.0%
CATATCCACAATCAAGATCT+AGG - chr2_2:70455235-70455254 None:intergenic 35.0%
GAGAATCTATTCTCTTTCTC+TGG + chr2_2:70455378-70455397 Msa0268930:intron 35.0%
! TTCAAAAAAGCGTAGGCTTC+AGG - chr2_2:70454942-70454961 None:intergenic 40.0%
GGATTCCTATCTAATGATCC+AGG + chr2_2:70455497-70455516 Msa0268930:CDS 40.0%
TACGTCCTGGATCATTAGAT+AGG - chr2_2:70455505-70455524 None:intergenic 40.0%
!! CAAGATCTAGGTATTGGTGG+TGG - chr2_2:70455223-70455242 None:intergenic 45.0%
AATGATCCAGGACGTAATCC+TGG + chr2_2:70455509-70455528 Msa0268930:CDS 45.0%
!!! AATAAATTCTTAATTTTTTT+CGG - chr2_2:70455071-70455090 None:intergenic 5.0%
TCACGTCCAGGATTACGTCC+TGG - chr2_2:70455518-70455537 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70454861 70455544 70454861 ID=Msa0268930;Name=Msa0268930
chr2_2 mRNA 70454861 70455544 70454861 ID=Msa0268930-mRNA-1;Parent=Msa0268930;Name=Msa0268930-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|0|0|1|0|0|2|0|97
chr2_2 exon 70454861 70455035 70454861 ID=Msa0268930-mRNA-1:exon:22692;Parent=Msa0268930-mRNA-1
chr2_2 exon 70455426 70455544 70455426 ID=Msa0268930-mRNA-1:exon:22693;Parent=Msa0268930-mRNA-1
chr2_2 CDS 70454861 70455035 70454861 ID=Msa0268930-mRNA-1:cds;Parent=Msa0268930-mRNA-1
chr2_2 CDS 70455426 70455544 70455426 ID=Msa0268930-mRNA-1:cds;Parent=Msa0268930-mRNA-1
Gene Sequence

>Msa0268930

ATGCTTAATATCTTTAGCTTGGTCTGTATTTGTATTGACTCTGCCCTTTATTCAAGTAGTTTTTTCTTGGCAAAATTACCTGAAGCCTACGCTTTTTTGAATCCAATTGTAGATTTTATGCCAGTAATACCCTTACTCTTTTTTCTCTTAGCTTTTGTTTGGCAAGCTGCTGTAAATTTTGTAATGCTTACTCTAAAACTATTTGTTTACACGATAGTGATATTCTTTGTTTCTCTTTTCATCTTCGGATTCCTATCTAATGATCCAGGACGTAATCCTGGACGTGAAGAATAA

Protein sequence

>Msa0268930

MLNIFSLVCICIDSALYSSSFFLAKLPEAYAFLNPIVDFMPVIPLLFFLLAFVWQAAVNFVMLTLKLFVYTIVIFFVSLFIFGFLSNDPGRNPGREE*