AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268420


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268420 MtrunA17_Chr4g0015681 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa0268420 MtrunA17_CPg0492901 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa0268420 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
Msa0268420 ATCG00070.1 76.667 60 14 0 1 60 1 60 3.76e-26 92.0
Msa0268420 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:-70221295 Msa0268420:CDS
ACTGGCATAAAATCTACAAT+TGG 0.453871 2_2:+70221192 None:intergenic
AATGATCCAGGACGTAATCC+TGG 0.474800 2_2:-70220645 Msa0268420:CDS
GGATTCCTATCTAATGATCC+AGG 0.536202 2_2:-70220657 Msa0268420:CDS
TCACGTCCAGGATTACGTCC+TGG 0.548081 2_2:+70220639 None:intergenic
TACGTCCTGGATCATTAGAT+AGG 0.581605 2_2:+70220652 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTCCAAATATTAAAATTTT+TGG - chr2_2:70220921-70220940 Msa0268420:intron 10.0%
!!! TATCCAAAAATTTTAATATT+TGG + chr2_2:70220927-70220946 None:intergenic 10.0%
!! ATTTCAAAAAAAAAAAACTT+AGG + chr2_2:70221078-70221097 None:intergenic 10.0%
!!! AATTTTAATATTTGGAATCA+AGG + chr2_2:70220919-70220938 None:intergenic 15.0%
!!! CGTTTTTTTTTTAATTATCT+TGG - chr2_2:70221173-70221192 Msa0268420:CDS 15.0%
!! GAAAAAACTACTTGAATAAA+GGG + chr2_2:70220678-70220697 None:intergenic 20.0%
!! AGAAAAAACTACTTGAATAA+AGG + chr2_2:70220679-70220698 None:intergenic 20.0%
!!! TTATTCAAGTAGTTTTTTCT+TGG - chr2_2:70220679-70220698 Msa0268420:CDS 20.0%
!! TGAAAATTCTATTATTCGAT+TGG - chr2_2:70220965-70220984 Msa0268420:intron 20.0%
!!! TGTGGATATGAAAAAAATTT+TGG - chr2_2:70221016-70221035 Msa0268420:intron 20.0%
!! TCTTATAAACTTAGTATCAA+AGG - chr2_2:70221107-70221126 Msa0268420:intron 20.0%
!!! TTTTTCTCTTAGCTTTTGTT+TGG - chr2_2:70220771-70220790 Msa0268420:intron 25.0%
!!! TTTGTTTCTCTTTTCATCTT+CGG - chr2_2:70221248-70221267 Msa0268420:CDS 25.0%
! AATTGGATTCAAAAAAGCGT+AGG + chr2_2:70220720-70220739 None:intergenic 30.0%
ACTGGCATAAAATCTACAAT+TGG + chr2_2:70220737-70220756 None:intergenic 30.0%
!! AAAAAGAGTAAGGGTATTAC+TGG + chr2_2:70220755-70220774 None:intergenic 30.0%
GCTAAGAGAAAAAAGAGTAA+GGG + chr2_2:70220764-70220783 None:intergenic 30.0%
AGCTAAGAGAAAAAAGAGTA+AGG + chr2_2:70220765-70220784 None:intergenic 30.0%
!! AATCAAGATCTAGGTATTGG+TGG + chr2_2:70220997-70221016 None:intergenic 35.0%
CACAATCAAGATCTAGGTAT+TGG + chr2_2:70221000-70221019 None:intergenic 35.0%
CAATACCTAGATCTTGATTG+TGG - chr2_2:70220998-70221017 Msa0268420:intron 35.0%
CATATCCACAATCAAGATCT+AGG + chr2_2:70221006-70221025 None:intergenic 35.0%
GAGAATCTATTCTCTTTCTC+TGG - chr2_2:70221150-70221169 Msa0268420:CDS 35.0%
! TTCAAAAAAGCGTAGGCTTC+AGG + chr2_2:70220713-70220732 None:intergenic 40.0%
GGATTCCTATCTAATGATCC+AGG - chr2_2:70221269-70221288 Msa0268420:CDS 40.0%
TACGTCCTGGATCATTAGAT+AGG + chr2_2:70221277-70221296 None:intergenic 40.0%
!! CAAGATCTAGGTATTGGTGG+TGG + chr2_2:70220994-70221013 None:intergenic 45.0%
AATGATCCAGGACGTAATCC+TGG - chr2_2:70221281-70221300 Msa0268420:CDS 45.0%
!!! AATAAATTCTTAATTTTTTT+CGG + chr2_2:70220842-70220861 None:intergenic 5.0%
TCACGTCCAGGATTACGTCC+TGG + chr2_2:70221290-70221309 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70220632 70221316 70220632 ID=Msa0268420;Name=Msa0268420
chr2_2 mRNA 70220632 70221316 70220632 ID=Msa0268420-mRNA-1;Parent=Msa0268420;Name=Msa0268420-mRNA-1;_AED=0.48;_eAED=0.48;_QI=0|0|0|1|0|0|2|0|97
chr2_2 exon 70221142 70221316 70221142 ID=Msa0268420-mRNA-1:exon:22551;Parent=Msa0268420-mRNA-1
chr2_2 exon 70220632 70220750 70220632 ID=Msa0268420-mRNA-1:exon:22550;Parent=Msa0268420-mRNA-1
chr2_2 CDS 70221142 70221316 70221142 ID=Msa0268420-mRNA-1:cds;Parent=Msa0268420-mRNA-1
chr2_2 CDS 70220632 70220750 70220632 ID=Msa0268420-mRNA-1:cds;Parent=Msa0268420-mRNA-1
Gene Sequence

>Msa0268420

ATGCTTAATATCTTTAGCTTGGTCTGTATTTGTATTGACTCTGCCCTTTATTCAAGTAGTTTTTTCTTGGCAAAATTACCTGAAGCCTACGCTTTTTTGAATCCAATTGTAGATTTTATGCCAGTAATACCCTTACTCTTTTTTCTCTTAGCTTTTGTTTGGCAAGCTGCTGTAAATTTTGTAATGCTTACTCTAAAACTATTTGTTTACACGATAGTGATATTCTTTGTTTCTCTTTTCATCTTCGGATTCCTATCTAATGATCCAGGACGTAATCCTGGACGTGAAGAATAA

Protein sequence

>Msa0268420

MLNIFSLVCICIDSALYSSSFFLAKLPEAYAFLNPIVDFMPVIPLLFFLLAFVWQAAVNFVMLTLKLFVYTIVIFFVSLFIFGFLSNDPGRNPGREE*