AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180005291.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005291.01.T01 MTR_1g096460 92.800 125 9 0 1 125 1 125 3.41e-72 215
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005291.01.T01 AT1G35680 36.943 157 79 7 1 145 1 149 2.35e-18 78.2

Find 42 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTCTCTCTTTGTTCAAAA+TGG 0.252859 1:-89735022 MsG0180005291.01.T01:exon
AACAGCAGATTCAGTGGATT+TGG 0.261606 1:+89734831 None:intergenic
ACTTGAGAGTCGGGCTCAAC+AGG 0.374565 1:+89734805 None:intergenic
ACAGCAGATTCAGTGGATTT+GGG 0.380963 1:+89734832 None:intergenic
AAATTGTTCAGTCTCCTTCA+TGG 0.399185 1:-89734762 MsG0180005291.01.T01:CDS
GGCCAGGGTGAACAATATAT+TGG 0.416675 1:+89734132 None:intergenic
GATTCAGTGGATTTGGGAAC+GGG 0.427167 1:+89734838 None:intergenic
AGAGGATAGAGTTGAGAGAG+AGG 0.436596 1:-89735046 MsG0180005291.01.T01:five_prime_UTR
GTAAATAAATGGATAGGAAG+AGG 0.447418 1:-89735079 None:intergenic
GACTCCGACACTTGAGAGTC+GGG 0.447669 1:+89734796 None:intergenic
TGAACAACAAGCCAGCGGCC+AGG 0.470564 1:+89734116 None:intergenic
CTTGTTGTTCAGAGGCTCAA+AGG 0.473982 1:-89734104 MsG0180005291.01.T01:CDS
GGAAGAGGAAGAACATAAAG+AGG 0.475604 1:-89735064 MsG0180005291.01.T01:five_prime_UTR
AATTGTTCAGTCTCCTTCAT+GGG 0.484994 1:-89734761 MsG0180005291.01.T01:CDS
GAACAACAAGCCAGCGGCCA+GGG 0.488250 1:+89734117 None:intergenic
AAGAAGTGCAACATGTCAAA+TGG 0.488885 1:+89734033 None:intergenic
TTGAGGCTTTGTTGAACAAT+GGG 0.491609 1:+89734951 None:intergenic
CAGTCTCCTTCATGGGAGAA+AGG 0.493689 1:-89734754 MsG0180005291.01.T01:CDS
GCCGCTGGCTTGTTGTTCAG+AGG 0.515615 1:-89734112 MsG0180005291.01.T01:CDS
TGATGAGAAATAGAGAATTG+AGG 0.517104 1:+89734934 None:intergenic
ATATTGTTCACCCTGGCCGC+TGG 0.519617 1:-89734127 MsG0180005291.01.T01:CDS
TGGAAAGAGAGGTTGTGAGA+AGG 0.523157 1:+89734892 None:intergenic
AGGCAAGCGTTGTGAGAAAG+TGG 0.533199 1:+89734867 None:intergenic
TGTGAAAGAAGAACAGAGAG+TGG 0.542220 1:+89734975 None:intergenic
ATTGAGGCTTTGTTGAACAA+TGG 0.545857 1:+89734950 None:intergenic
TTGTGAGAAGGAACACGAGA+AGG 0.551095 1:+89734904 None:intergenic
AAAAGACCTTTCTCCCATGA+AGG 0.553345 1:+89734748 None:intergenic
GTAAGAGTAAATAAATGGAT+AGG 0.553474 1:-89735085 None:intergenic
AGATTCAGTGGATTTGGGAA+CGG 0.556307 1:+89734837 None:intergenic
AGACTCCGACACTTGAGAGT+CGG 0.579540 1:+89734795 None:intergenic
AGCGTTGTGAGAAAGTGGAT+TGG 0.591056 1:+89734872 None:intergenic
AGGTGCAACAGCAGATTCAG+TGG 0.593123 1:+89734825 None:intergenic
CGCCAATATATTGTTCACCC+TGG 0.594986 1:-89734134 MsG0180005291.01.T01:CDS
TGTGAGAAGGAACACGAGAA+GGG 0.611777 1:+89734905 None:intergenic
AGAAAGTGGATTGGAAAGAG+AGG 0.617691 1:+89734881 None:intergenic
TGAGCCCGACTCTCAAGTGT+CGG 0.618629 1:-89734800 MsG0180005291.01.T01:CDS
GTATACCTTGTCGTTAACGT+TGG 0.621234 1:+89734079 None:intergenic
GAAGGAACACGAGAAGGGAA+AGG 0.624230 1:+89734910 None:intergenic
AGGAGACTGAACAATTTGAG+AGG 0.639275 1:+89734768 None:intergenic
AGGTGCCAACGTTAACGACA+AGG 0.654570 1:-89734084 MsG0180005291.01.T01:CDS
GCCTCTGAACAACAAGCCAG+CGG 0.664752 1:+89734111 None:intergenic
GATTTGGGAACGGGTAACAG+AGG 0.673707 1:+89734847 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAACCTATATTTTTTAACTT+GGG - Chr1:89734719-89734738 MsG0180005291.01.T01:intron 15.0%
!! CAATCAATTAGTTAGTAAAA+GGG - Chr1:89734790-89734809 MsG0180005291.01.T01:CDS 20.0%
!! TCAATCAATTAGTTAGTAAA+AGG - Chr1:89734789-89734808 MsG0180005291.01.T01:CDS 20.0%
!! TGTTAATATAGATTGTTCTA+TGG - Chr1:89734463-89734482 MsG0180005291.01.T01:intron 20.0%
!! TTTGAACAATTCAAACAAAA+GGG + Chr1:89734421-89734440 None:intergenic 20.0%
!!! AGGTATTTGTTTATTGTTTT+GGG - Chr1:89734850-89734869 MsG0180005291.01.T01:CDS 20.0%
!!! CTAACCTATATTTTTTAACT+TGG - Chr1:89734718-89734737 MsG0180005291.01.T01:intron 20.0%
!!! TAGGTATTTGTTTATTGTTT+TGG - Chr1:89734849-89734868 MsG0180005291.01.T01:CDS 20.0%
!!! TTTTGAACAATTCAAACAAA+AGG + Chr1:89734422-89734441 None:intergenic 20.0%
! AAAGATATGCAAACTCAATT+GGG + Chr1:89734499-89734518 None:intergenic 25.0%
! AGTATTGCACATTAAAGATT+AGG - Chr1:89734586-89734605 MsG0180005291.01.T01:intron 25.0%
! ATATAGGTTAGAACAATCAT+TGG + Chr1:89734709-89734728 None:intergenic 25.0%
! GAACCCAAGTTAAAAAATAT+AGG + Chr1:89734725-89734744 None:intergenic 25.0%
! GTGGTTAATAAACTCAATTA+TGG + Chr1:89734763-89734782 None:intergenic 25.0%
! TAGGAATGGTTAAGTAAAAT+GGG - Chr1:89734605-89734624 MsG0180005291.01.T01:intron 25.0%
! TTAGGAATGGTTAAGTAAAA+TGG - Chr1:89734604-89734623 MsG0180005291.01.T01:intron 25.0%
!!! GGTATTTGTTTATTGTTTTG+GGG - Chr1:89734851-89734870 MsG0180005291.01.T01:CDS 25.0%
!!! TTGTGTTGTTTTGTTTAGAT+TGG - Chr1:89734923-89734942 MsG0180005291.01.T01:CDS 25.0%
ACTAATTGATTGAGCTTAAG+TGG + Chr1:89734782-89734801 None:intergenic 30.0%
AGTTCTCTCTTTGTTCAAAA+TGG - Chr1:89734062-89734081 MsG0180005291.01.T01:CDS 30.0%
CAAAGATATGCAAACTCAAT+TGG + Chr1:89734500-89734519 None:intergenic 30.0%
CAATTGAGTTTGCATATCTT+TGG - Chr1:89734498-89734517 MsG0180005291.01.T01:intron 30.0%
TCAATTATGGACGAATCATT+CGG + Chr1:89734750-89734769 None:intergenic 30.0%
TGATGAGAAATAGAGAATTG+AGG + Chr1:89734153-89734172 None:intergenic 30.0%
TGCACATTAAAGATTAGGAA+TGG - Chr1:89734591-89734610 MsG0180005291.01.T01:intron 30.0%
!! AGTTAGTAAAAGGGTTAGTT+TGG - Chr1:89734799-89734818 MsG0180005291.01.T01:CDS 30.0%
!!! GAGAGGCTTTTTTTAATGTT+GGG - Chr1:89734381-89734400 MsG0180005291.01.T01:intron 30.0%
!!! TGAGAGGCTTTTTTTAATGT+TGG - Chr1:89734380-89734399 MsG0180005291.01.T01:intron 30.0%
!!! TGTTGTTTTGTTTAGATTGG+TGG - Chr1:89734926-89734945 MsG0180005291.01.T01:CDS 30.0%
!!! TTGGATGGTTTTGTATTGTT+GGG - Chr1:89734818-89734837 MsG0180005291.01.T01:CDS 30.0%
!!! TTTGGATGGTTTTGTATTGT+TGG - Chr1:89734817-89734836 MsG0180005291.01.T01:CDS 30.0%
AAATTGTTCAGTCTCCTTCA+TGG - Chr1:89734322-89734341 MsG0180005291.01.T01:intron 35.0%
AATTGTTCAGTCTCCTTCAT+GGG - Chr1:89734323-89734342 MsG0180005291.01.T01:intron 35.0%
GACAGACTTTACTTACGTTT+CGG + Chr1:89734687-89734706 None:intergenic 35.0%
TTTAATGTTGGGTGTGGATT+GGG - Chr1:89734392-89734411 MsG0180005291.01.T01:intron 35.0%
! AAGAAGTGCAACATGTCAAA+TGG + Chr1:89735054-89735073 None:intergenic 35.0%
! CAAAAGTTACATGCTTTGAG+TGG - Chr1:89734437-89734456 MsG0180005291.01.T01:intron 35.0%
! TTTTAATGTTGGGTGTGGAT+TGG - Chr1:89734391-89734410 MsG0180005291.01.T01:intron 35.0%
!! AGTAAAAGGGTTAGTTTGGA+TGG - Chr1:89734803-89734822 MsG0180005291.01.T01:CDS 35.0%
!! ATTGAGGCTTTGTTGAACAA+TGG + Chr1:89734137-89734156 None:intergenic 35.0%
!! GTATTGTTGGGTTGGTAAAT+AGG - Chr1:89734830-89734849 MsG0180005291.01.T01:CDS 35.0%
!! TTGAGGCTTTGTTGAACAAT+GGG + Chr1:89734136-89734155 None:intergenic 35.0%
!!! AGGTCTTTTTGCTGTTGTAA+TGG - Chr1:89734350-89734369 MsG0180005291.01.T01:intron 35.0%
!!! ATGGTTTTGTATTGTTGGGT+TGG - Chr1:89734822-89734841 MsG0180005291.01.T01:CDS 35.0%
!!! GCTTTTTTTAATGTTGGGTG+TGG - Chr1:89734386-89734405 MsG0180005291.01.T01:intron 35.0%
!!! TTGTAATGGTGAGTTTTGAG+AGG - Chr1:89734364-89734383 MsG0180005291.01.T01:intron 35.0%
AAAAGACCTTTCTCCCATGA+AGG + Chr1:89734339-89734358 None:intergenic 40.0%
AGGAGACTGAACAATTTGAG+AGG + Chr1:89734319-89734338 None:intergenic 40.0%
GGAAGAGGAAGAACATAAAG+AGG - Chr1:89734020-89734039 MsG0180005291.01.T01:CDS 40.0%
GTATACCTTGTCGTTAACGT+TGG + Chr1:89735008-89735027 None:intergenic 40.0%
TGTCTTATCCCTCCAATTCT+TGG - Chr1:89734640-89734659 MsG0180005291.01.T01:intron 40.0%
TGTGAAAGAAGAACAGAGAG+TGG + Chr1:89734112-89734131 None:intergenic 40.0%
! AACAGCAGATTCAGTGGATT+TGG + Chr1:89734256-89734275 None:intergenic 40.0%
! ACAGCAGATTCAGTGGATTT+GGG + Chr1:89734255-89734274 None:intergenic 40.0%
! AGATTCAGTGGATTTGGGAA+CGG + Chr1:89734250-89734269 None:intergenic 40.0%
!! AGAAAGTGGATTGGAAAGAG+AGG + Chr1:89734206-89734225 None:intergenic 40.0%
!! TATCTTTGGCTCTATGAGCA+TGG - Chr1:89734512-89734531 MsG0180005291.01.T01:intron 40.0%
AGAGGATAGAGTTGAGAGAG+AGG - Chr1:89734038-89734057 MsG0180005291.01.T01:CDS 45.0%
AGCGTTGTGAGAAAGTGGAT+TGG + Chr1:89734215-89734234 None:intergenic 45.0%
ATCCCTCCAATTCTTGGAGA+AGG - Chr1:89734646-89734665 MsG0180005291.01.T01:intron 45.0%
CGCCAATATATTGTTCACCC+TGG - Chr1:89734950-89734969 MsG0180005291.01.T01:CDS 45.0%
GGCCAGGGTGAACAATATAT+TGG + Chr1:89734955-89734974 None:intergenic 45.0%
TCCCTCCAATTCTTGGAGAA+GGG - Chr1:89734647-89734666 MsG0180005291.01.T01:intron 45.0%
TCCCTTCTCCAAGAATTGGA+GGG + Chr1:89734651-89734670 None:intergenic 45.0%
TGGAAAGAGAGGTTGTGAGA+AGG + Chr1:89734195-89734214 None:intergenic 45.0%
TGTGAGAAGGAACACGAGAA+GGG + Chr1:89734182-89734201 None:intergenic 45.0%
TTGTGAGAAGGAACACGAGA+AGG + Chr1:89734183-89734202 None:intergenic 45.0%
! GATTCAGTGGATTTGGGAAC+GGG + Chr1:89734249-89734268 None:intergenic 45.0%
!! CTTGTTGTTCAGAGGCTCAA+AGG - Chr1:89734980-89734999 MsG0180005291.01.T01:CDS 45.0%
AATTCTTGGAGAAGGGACCC+TGG - Chr1:89734654-89734673 MsG0180005291.01.T01:intron 50.0%
AGACTCCGACACTTGAGAGT+CGG + Chr1:89734292-89734311 None:intergenic 50.0%
AGGGTCCCTTCTCCAAGAAT+TGG + Chr1:89734655-89734674 None:intergenic 50.0%
AGGTGCAACAGCAGATTCAG+TGG + Chr1:89734262-89734281 None:intergenic 50.0%
AGGTGCCAACGTTAACGACA+AGG - Chr1:89735000-89735019 MsG0180005291.01.T01:CDS 50.0%
CAGTCTCCTTCATGGGAGAA+AGG - Chr1:89734330-89734349 MsG0180005291.01.T01:intron 50.0%
GAAGGAACACGAGAAGGGAA+AGG + Chr1:89734177-89734196 None:intergenic 50.0%
GATTTGGGAACGGGTAACAG+AGG + Chr1:89734240-89734259 None:intergenic 50.0%
GTCCCTTCTCCAAGAATTGG+AGG + Chr1:89734652-89734671 None:intergenic 50.0%
TACGTTTCGGCCAAACTCCA+GGG + Chr1:89734674-89734693 None:intergenic 50.0%
TTACGTTTCGGCCAAACTCC+AGG + Chr1:89734675-89734694 None:intergenic 50.0%
! AGGCAAGCGTTGTGAGAAAG+TGG + Chr1:89734220-89734239 None:intergenic 50.0%
ACTTGAGAGTCGGGCTCAAC+AGG + Chr1:89734282-89734301 None:intergenic 55.0%
ATATTGTTCACCCTGGCCGC+TGG - Chr1:89734957-89734976 MsG0180005291.01.T01:CDS 55.0%
GACTCCGACACTTGAGAGTC+GGG + Chr1:89734291-89734310 None:intergenic 55.0%
GCCTCTGAACAACAAGCCAG+CGG + Chr1:89734976-89734995 None:intergenic 55.0%
TGAGCCCGACTCTCAAGTGT+CGG - Chr1:89734284-89734303 MsG0180005291.01.T01:intron 55.0%
GAACAACAAGCCAGCGGCCA+GGG + Chr1:89734970-89734989 None:intergenic 60.0%
GGAGAAGGGACCCTGGAGTT+TGG - Chr1:89734661-89734680 MsG0180005291.01.T01:intron 60.0%
TGAACAACAAGCCAGCGGCC+AGG + Chr1:89734971-89734990 None:intergenic 60.0%
!! GCCGCTGGCTTGTTGTTCAG+AGG - Chr1:89734972-89734991 MsG0180005291.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr1 gene 89734013 89735093 89734013 ID=MsG0180005291.01;Name=MsG0180005291.01
Chr1 mRNA 89734013 89735093 89734013 ID=MsG0180005291.01.T01;Parent=MsG0180005291.01;Name=MsG0180005291.01.T01;_AED=0.50;_eAED=0.52;_QI=68|1|0.5|1|1|1|2|0|147
Chr1 exon 89734013 89734165 89734013 ID=MsG0180005291.01.T01:exon:17312;Parent=MsG0180005291.01.T01
Chr1 exon 89734735 89735093 89734735 ID=MsG0180005291.01.T01:exon:17311;Parent=MsG0180005291.01.T01
Chr1 five_prime_UTR 89735026 89735093 89735026 ID=MsG0180005291.01.T01:five_prime_utr;Parent=MsG0180005291.01.T01
Chr1 CDS 89734735 89735025 89734735 ID=MsG0180005291.01.T01:cds;Parent=MsG0180005291.01.T01
Chr1 CDS 89734013 89734165 89734013 ID=MsG0180005291.01.T01:cds;Parent=MsG0180005291.01.T01
Gene Sequence

>MsG0180005291.01.T01

ATGGCTTCTGCAACTGCTTCTACTCTTTCCACTCTCTGTTCTTCTTTCACAACCCATTGTTCAACAAAGCCTCAATTCTCTATTTCTCATCAACCTTTCCCTTCTCGTGTTCCTTCTCACAACCTCTCTTTCCAATCCACTTTCTCACAACGCTTGCCTCTGTTACCCGTTCCCAAATCCACTGAATCTGCTGTTGCACCTGTTGAGCCCGACTCTCAAGTGTCGGAGTCTGAATCCTCTCAAATTGTTCAGTCTCCTTCATGGGAGAAAGGTCTTTTTGCTGTTGTAATGATTGGTGGACGCCAATATATTGTTCACCCTGGCCGCTGGCTTGTTGTTCAGAGGCTCAAAGGTGCCAACGTTAACGACAAGGTATACAACTTGTTTGTTCTTAATTTCTGCCATTTGACATGTTGCACTTCTTATTCATTTTTAGTCTTTTAG

Protein sequence

>MsG0180005291.01.T01

MASATASTLSTLCSSFTTHCSTKPQFSISHQPFPSRVPSHNLSFQSTFSQRLPLLPVPKSTESAVAPVEPDSQVSESESSQIVQSPSWEKGLFAVVMIGGRQYIVHPGRWLVVQRLKGANVNDKVYNLFVLNFCHLTCCTSYSFLVF*