AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086160


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086160 MtrunA17_Chr4g0015681 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa1086160 MtrunA17_CPg0492901 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa1086160 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
Msa1086160 ATCG00070.1 76.667 60 14 0 1 60 1 60 3.76e-26 92.0
Msa1086160 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 7_2:-87212282 Msa1086160:CDS
ACTGGCATAAAATCTACAAT+TGG 0.453871 7_2:+87212179 None:intergenic
AATGATCCAGGACGTAATCC+TGG 0.474800 7_2:-87211633 Msa1086160:CDS
GGATTCCTATCTAATGATCC+AGG 0.536202 7_2:-87211645 Msa1086160:CDS
TCACGTCCAGGATTACGTCC+TGG 0.548081 7_2:+87211627 None:intergenic
TACGTCCTGGATCATTAGAT+AGG 0.581605 7_2:+87211640 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAATAAATTCTTAATTTTTT+CGG + chr7_2:87211830-87211849 None:intergenic 10.0%
!!! ATTCCAAATATTAAAATTTT+TGG - chr7_2:87211908-87211927 Msa1086160:intron 10.0%
!!! TATCCAAAAATTTTAATATT+TGG + chr7_2:87211914-87211933 None:intergenic 10.0%
!! ATTTCAAAAAAAAAAAACTT+AGG + chr7_2:87212065-87212084 None:intergenic 10.0%
!!! AATTTTAATATTTGGAATCA+AGG + chr7_2:87211906-87211925 None:intergenic 15.0%
!!! CGTTTTTTTTTTAATTATCT+TGG - chr7_2:87212160-87212179 Msa1086160:CDS 15.0%
!! GAAAAAACTACTTGAATAAA+GGG + chr7_2:87211666-87211685 None:intergenic 20.0%
!! AGAAAAAACTACTTGAATAA+AGG + chr7_2:87211667-87211686 None:intergenic 20.0%
!!! TTATTCAAGTAGTTTTTTCT+TGG - chr7_2:87211667-87211686 Msa1086160:CDS 20.0%
!! TGAAAATTCTATTATTCGAT+TGG - chr7_2:87211952-87211971 Msa1086160:intron 20.0%
!!! TGTGGATATGAAAAAAATTT+TGG - chr7_2:87212003-87212022 Msa1086160:intron 20.0%
!! TCTTATAAACTTAGTATCAA+AGG - chr7_2:87212094-87212113 Msa1086160:intron 20.0%
!!! TTTTTCTCTTAGCTTTTGTT+TGG - chr7_2:87211759-87211778 Msa1086160:intron 25.0%
!!! TTTGTTTCTCTTTTCATCTT+CGG - chr7_2:87212235-87212254 Msa1086160:CDS 25.0%
! AATTGGATTCAAAAAAGCGT+AGG + chr7_2:87211708-87211727 None:intergenic 30.0%
ACTGGCATAAAATCTACAAT+TGG + chr7_2:87211725-87211744 None:intergenic 30.0%
!! AAAAAGAGTAAGGGTATTAC+TGG + chr7_2:87211743-87211762 None:intergenic 30.0%
GCTAAGAGAAAAAAGAGTAA+GGG + chr7_2:87211752-87211771 None:intergenic 30.0%
AGCTAAGAGAAAAAAGAGTA+AGG + chr7_2:87211753-87211772 None:intergenic 30.0%
!! AATCAAGATCTAGGTATTGG+TGG + chr7_2:87211984-87212003 None:intergenic 35.0%
CACAATCAAGATCTAGGTAT+TGG + chr7_2:87211987-87212006 None:intergenic 35.0%
CAATACCTAGATCTTGATTG+TGG - chr7_2:87211985-87212004 Msa1086160:intron 35.0%
CATATCCACAATCAAGATCT+AGG + chr7_2:87211993-87212012 None:intergenic 35.0%
GAGAATCTATTCTCTTTCTC+TGG - chr7_2:87212137-87212156 Msa1086160:CDS 35.0%
! TTCAAAAAAGCGTAGGCTTC+AGG + chr7_2:87211701-87211720 None:intergenic 40.0%
GGATTCCTATCTAATGATCC+AGG - chr7_2:87212256-87212275 Msa1086160:CDS 40.0%
TACGTCCTGGATCATTAGAT+AGG + chr7_2:87212264-87212283 None:intergenic 40.0%
!! CAAGATCTAGGTATTGGTGG+TGG + chr7_2:87211981-87212000 None:intergenic 45.0%
AATGATCCAGGACGTAATCC+TGG - chr7_2:87212268-87212287 Msa1086160:CDS 45.0%
TCACGTCCAGGATTACGTCC+TGG + chr7_2:87212277-87212296 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87211620 87212303 87211620 ID=Msa1086160;Name=Msa1086160
chr7_2 mRNA 87211620 87212303 87211620 ID=Msa1086160-mRNA-1;Parent=Msa1086160;Name=Msa1086160-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|0|0|1|0|0|2|0|97
chr7_2 exon 87212129 87212303 87212129 ID=Msa1086160-mRNA-1:exon:23737;Parent=Msa1086160-mRNA-1
chr7_2 exon 87211620 87211738 87211620 ID=Msa1086160-mRNA-1:exon:23736;Parent=Msa1086160-mRNA-1
chr7_2 CDS 87212129 87212303 87212129 ID=Msa1086160-mRNA-1:cds;Parent=Msa1086160-mRNA-1
chr7_2 CDS 87211620 87211738 87211620 ID=Msa1086160-mRNA-1:cds;Parent=Msa1086160-mRNA-1
Gene Sequence

>Msa1086160

ATGCTTAATATCTTTAGCTTGGTCTGTATTTGTATTGACTCTGCCCTTTATTCAAGTAGTTTTTTCTTGGCAAAATTACCTGAAGCCTACGCTTTTTTGAATCCAATTGTAGATTTTATGCCAGTAATACCCTTACTCTTTTTTCTCTTAGCTTTTGTTTGGCAAGCTGCTGTAAATTTTGTAATGCTTACTCTAAAACTATTTGTTTACACGATAGTGATATTCTTTGTTTCTCTTTTCATCTTCGGATTCCTATCTAATGATCCAGGACGTAATCCTGGACGTGAAGAATAA

Protein sequence

>Msa1086160

MLNIFSLVCICIDSALYSSSFFLAKLPEAYAFLNPIVDFMPVIPLLFFLLAFVWQAAVNFVMLTLKLFVYTIVIFFVSLFIFGFLSNDPGRNPGREE*