AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1305340


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 12 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACAATTTATGGGATTAAA+TGG 0.170061 8_3:-68770190 Msa1305340:CDS
AGAGTTTATAGAACAATTTA+TGG 0.254847 8_3:-68770200 Msa1305340:CDS
AAAGATCAACTTAGCATTGT+TGG 0.297378 8_3:+68770223 None:intergenic
AGTTCATCGGATTCTGCATT+TGG 0.303861 8_3:-68770283 Msa1305340:CDS
ATCAAGAGAATGCTTCAAAC+TGG 0.364802 8_3:-68770250 Msa1305340:CDS
GAGTTTATAGAACAATTTAT+GGG 0.389704 8_3:-68770199 Msa1305340:CDS
GTTCATCGGATTCTGCATTT+GGG 0.414475 8_3:-68770282 Msa1305340:CDS
TCTTGTTCTTATGTTGAAGC+TGG 0.444656 8_3:-68770165 Msa1305340:CDS
AAATGCAGAATCCGATGAAC+TGG 0.458650 8_3:+68770285 None:intergenic
GGTCTTAATTGTAGTATGAT+AGG 0.475415 8_3:-68770788 None:intergenic
ATCGGATTCTGCATTTGGGA+TGG 0.499346 8_3:-68770278 Msa1305340:CDS
TCAAGAGAATGCTTCAAACT+GGG 0.611932 8_3:-68770249 Msa1305340:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCAAAACATAACTTATTATT+TGG - chr8_3:68770446-68770465 Msa1305340:intron 15.0%
!!! TACATATGTTCTCAAAATTT+TGG + chr8_3:68770539-68770558 None:intergenic 20.0%
!!! AATTTTGAGAACATATGTAT+TGG - chr8_3:68770540-68770559 Msa1305340:intron 20.0%
!!! ATTTTGAGAACATATGTATT+GGG - chr8_3:68770541-68770560 Msa1305340:intron 20.0%
!! AGAGTTTATAGAACAATTTA+TGG - chr8_3:68770724-68770743 Msa1305340:intron 20.0%
!! GAGTTTATAGAACAATTTAT+GGG - chr8_3:68770725-68770744 Msa1305340:intron 20.0%
! TAAATTAGTGACATCAGAAT+AGG + chr8_3:68770204-68770223 None:intergenic 25.0%
!! TTTACAGAATTCTTTTCCAA+TGG + chr8_3:68770250-68770269 None:intergenic 25.0%
!! AATCAACAAGTTGAATGTTT+AGG - chr8_3:68770268-68770287 Msa1305340:CDS 25.0%
!! ATCAACAAGTTGAATGTTTA+GGG - chr8_3:68770269-68770288 Msa1305340:CDS 25.0%
! GAACAATTTATGGGATTAAA+TGG - chr8_3:68770734-68770753 Msa1305340:intron 25.0%
!! ACAGTTATTTTGTGAAAACC+CGG + chr8_3:68770296-68770315 None:intergenic 30.0%
GCAACGATGAAAATTTGAAA+AGG + chr8_3:68770478-68770497 None:intergenic 30.0%
! TCAAATTTTCATCGTTGCAT+TGG - chr8_3:68770480-68770499 Msa1305340:intron 30.0%
!!! GATGTTTTTTACCAGTTCAT+CGG - chr8_3:68770628-68770647 Msa1305340:intron 30.0%
AAAGATCAACTTAGCATTGT+TGG + chr8_3:68770704-68770723 None:intergenic 30.0%
TAACTGTATGATATCTGTCC+TGG - chr8_3:68770309-68770328 Msa1305340:intron 35.0%
TTAATGACACTTCAGCAGTT+CGG + chr8_3:68770351-68770370 None:intergenic 35.0%
ATCAAGAGAATGCTTCAAAC+TGG - chr8_3:68770674-68770693 Msa1305340:intron 35.0%
TCAAGAGAATGCTTCAAACT+GGG - chr8_3:68770675-68770694 Msa1305340:intron 35.0%
TCTTGTTCTTATGTTGAAGC+TGG - chr8_3:68770759-68770778 Msa1305340:intron 35.0%
AAGGTCTGGAAGACTATGAT+TGG + chr8_3:68770173-68770192 None:intergenic 40.0%
ATCAGAATAGGCGATAGTGA+AGG + chr8_3:68770192-68770211 None:intergenic 40.0%
TTACTGACATGTTGAGCCAT+TGG - chr8_3:68770231-68770250 Msa1305340:CDS 40.0%
! CAAGTTGAATGTTTAGGGTC+CGG - chr8_3:68770274-68770293 Msa1305340:CDS 40.0%
! AAGTTGAATGTTTAGGGTCC+GGG - chr8_3:68770275-68770294 Msa1305340:CDS 40.0%
!! ATTTTCATCGTTGCATTGGC+TGG - chr8_3:68770484-68770503 Msa1305340:intron 40.0%
TGGGTGAAGATTTCTACTGT+AGG - chr8_3:68770560-68770579 Msa1305340:intron 40.0%
GGGTGAAGATTTCTACTGTA+GGG - chr8_3:68770561-68770580 Msa1305340:intron 40.0%
AAATGCAGAATCCGATGAAC+TGG + chr8_3:68770642-68770661 None:intergenic 40.0%
AGTTCATCGGATTCTGCATT+TGG - chr8_3:68770641-68770660 Msa1305340:intron 40.0%
GTTCATCGGATTCTGCATTT+GGG - chr8_3:68770642-68770661 Msa1305340:intron 40.0%
AATAGGCGATAGTGAAGGTC+TGG + chr8_3:68770187-68770206 None:intergenic 45.0%
! ATGATATCTGTCCTGGTTCG+TGG - chr8_3:68770316-68770335 Msa1305340:intron 45.0%
ATCGGATTCTGCATTTGGGA+TGG - chr8_3:68770646-68770665 Msa1305340:intron 45.0%
!! GTCCTGGTTCGTGGAACTTT+TGG - chr8_3:68770325-68770344 Msa1305340:intron 50.0%
GGCCAAAAGTTCCACGAACC+AGG + chr8_3:68770330-68770349 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 68770151 68770795 68770151 ID=Msa1305340;Name=Msa1305340
chr8_3 mRNA 68770151 68770795 68770151 ID=Msa1305340-mRNA-1;Parent=Msa1305340;Name=Msa1305340-mRNA-1;_AED=0.54;_eAED=1.00;_QI=0|0|0|0.5|1|1|2|0|60
chr8_3 exon 68770789 68770795 68770789 ID=Msa1305340-mRNA-1:exon:21306;Parent=Msa1305340-mRNA-1
chr8_3 exon 68770151 68770326 68770151 ID=Msa1305340-mRNA-1:exon:21305;Parent=Msa1305340-mRNA-1
chr8_3 CDS 68770789 68770795 68770789 ID=Msa1305340-mRNA-1:cds;Parent=Msa1305340-mRNA-1
chr8_3 CDS 68770151 68770326 68770151 ID=Msa1305340-mRNA-1:cds;Parent=Msa1305340-mRNA-1
Gene Sequence

>Msa1305340

ATGATAGTTAACACTGATGTTTTTTACCAGTTCATCGGATTCTGCATTTGGGATGGACATGATCAAGAGAATGCTTCAAACTGGGCATCCAACAATGCTAAGTTGATCTTTAGAGTTTATAGAACAATTTATGGGATTAAATGGATTCTTGTTCTTATGTTGAAGCTGGAAATCTGTTGCTAA

Protein sequence

>Msa1305340

MIVNTDVFYQFIGFCIWDGHDQENASNWASNNAKLIFRVYRTIYGIKWILVLMLKLEICC*