AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280008113.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280008113.01.T01 MTR_2g035810 100.000 41 0 0 44 84 1 41 1.78e-23 90.5
MsG0280008113.01.T01 MTR_4g064813 90.000 40 4 0 44 83 1 40 5.74e-20 82.4
MsG0280008113.01.T01 MTR_3g081530 96.552 29 1 0 56 84 15 43 5.56e-14 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280008113.01.T01 AT2G32260 96.296 27 1 0 56 82 32 58 1.03e-12 62.0

Find 13 sgRNAs with CRISPR-Local

Find 117 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCAAAGTTAATGATGTTAT+TGG 0.194035 2:-25602137 MsG0280008113.01.T01:intron
TAGTTGAAATTACGATTTCT+TGG 0.309549 2:+25599715 None:intergenic
ACCAATAACATCATTAACTT+TGG 0.362275 2:+25602136 None:intergenic
TAACACAAATTTGTGTAGAT+TGG 0.363308 2:+25602204 None:intergenic
CTTGGCTTGTTCAAGAGAAC+GGG 0.379292 2:+25599733 None:intergenic
CCATCAGCATAAACACGAAC+AGG 0.422644 2:+25599785 None:intergenic
ATTTACGATCTCTTTCACTT+TGG 0.443426 2:-25599761 MsG0280008113.01.T01:CDS
CCTGTTCGTGTTTATGCTGA+TGG 0.469877 2:-25599785 MsG0280008113.01.T01:CDS
GAACAAGATGACTCTGAAGT+TGG 0.491101 2:-25599821 MsG0280008113.01.T01:CDS
TCTTGGCTTGTTCAAGAGAA+CGG 0.511606 2:+25599732 None:intergenic
CGCGCGCAGTTTAGCGTGGA+AGG 0.535080 2:-25602236 MsG0280008113.01.T01:CDS
CTTGTTCAAGAGAACGGGCA+TGG 0.557740 2:+25599738 None:intergenic
AATGCGCGCGCAGTTTAGCG+TGG 0.627716 2:-25602240 MsG0280008113.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATTATTTATCTATATAG+AGG - Chr2:25600141-25600160 MsG0280008113.01.T01:intron 10.0%
!!! CGTATTTTTTTTTTTTTTTT+TGG - Chr2:25601909-25601928 MsG0280008113.01.T01:intron 10.0%
!!! TATTAATTTATGATTTTCTT+GGG + Chr2:25600703-25600722 None:intergenic 10.0%
!!! TTATTAATTTATGATTTTCT+TGG + Chr2:25600704-25600723 None:intergenic 10.0%
!!! TTTTTTTTTTTTTTTTTGGA+AGG - Chr2:25601913-25601932 MsG0280008113.01.T01:intron 10.0%
!! AAAAAAAAAAAAAAATACGG+TGG + Chr2:25601908-25601927 None:intergenic 15.0%
!! AAAAAAAAAAAAAATACGGT+GGG + Chr2:25601907-25601926 None:intergenic 15.0%
!! TCTAAATTAATAAATTTCTC+CGG - Chr2:25601036-25601055 MsG0280008113.01.T01:intron 15.0%
!!! AGTTTTTCAATTTTTTACAT+TGG + Chr2:25600627-25600646 None:intergenic 15.0%
!!! ATTCATATCTAATTTGTTTA+CGG + Chr2:25601092-25601111 None:intergenic 15.0%
!!! TCTAAAATAATAAATTTGTC+CGG - Chr2:25600589-25600608 MsG0280008113.01.T01:intron 15.0%
!!! TGTGTTTTAAATATTGAAAA+TGG - Chr2:25599988-25600007 MsG0280008113.01.T01:intron 15.0%
!! AAAAAAAAAAAAATACGGTG+GGG + Chr2:25601906-25601925 None:intergenic 20.0%
!! AAAAAAACAAGAAACAAAAG+AGG - Chr2:25602041-25602060 MsG0280008113.01.T01:intron 20.0%
!! AATATTCCTATATGAGAATA+TGG + Chr2:25600127-25600146 None:intergenic 20.0%
!! CTCTATAAATTAATAATGTC+AGG + Chr2:25601063-25601082 None:intergenic 20.0%
!! GTTTAAATGAAAGAAAACAT+AGG + Chr2:25601987-25602006 None:intergenic 20.0%
!! TATTTGTATTCAACAGTAAT+TGG + Chr2:25600057-25600076 None:intergenic 20.0%
!! TCCAATTAACATAAAACTTA+TGG + Chr2:25599939-25599958 None:intergenic 20.0%
!! TTCAAAATTAAAACGAAGAA+CGG - Chr2:25600427-25600446 MsG0280008113.01.T01:intron 20.0%
!! TTTAGTATACTATTGAGTTA+TGG - Chr2:25600318-25600337 MsG0280008113.01.T01:intron 20.0%
!! TTTGTCAAAAAGTTATTCAA+CGG + Chr2:25600208-25600227 None:intergenic 20.0%
!!! TCCATAAGTTTTATGTTAAT+TGG - Chr2:25599935-25599954 MsG0280008113.01.T01:intron 20.0%
!!! TCGTTTTAATTTTGAAACAT+GGG + Chr2:25600423-25600442 None:intergenic 20.0%
!!! TTCGTTTTAATTTTGAAACA+TGG + Chr2:25600424-25600443 None:intergenic 20.0%
! AATCACAACTGTATTACAAA+TGG + Chr2:25599962-25599981 None:intergenic 25.0%
! ACAATGTTAACTAATTAGAG+GGG + Chr2:25601590-25601609 None:intergenic 25.0%
! ACCAATAACATCATTAACTT+TGG + Chr2:25599830-25599849 None:intergenic 25.0%
! AGAGGAGAATTAGATTATAA+GGG - Chr2:25600159-25600178 MsG0280008113.01.T01:intron 25.0%
! ATGAGAGTTGTATCATATTT+AGG - Chr2:25601352-25601371 MsG0280008113.01.T01:intron 25.0%
! CAATGATTCATGATTCAATA+TGG - Chr2:25601429-25601448 MsG0280008113.01.T01:intron 25.0%
! CTTTAAACAAAGTTGTACAA+GGG - Chr2:25601165-25601184 MsG0280008113.01.T01:intron 25.0%
! GACAATGTTAACTAATTAGA+GGG + Chr2:25601591-25601610 None:intergenic 25.0%
! GGGTATTATACAATTTGATA+CGG + Chr2:25601659-25601678 None:intergenic 25.0%
! TAAAGAGTTTCTACTGTATA+TGG + Chr2:25600541-25600560 None:intergenic 25.0%
! TAAATTAATAATGTCAGGAC+CGG + Chr2:25601058-25601077 None:intergenic 25.0%
! TAACACAAATTTGTGTAGAT+TGG + Chr2:25599762-25599781 None:intergenic 25.0%
! TAGAGGAGAATTAGATTATA+AGG - Chr2:25600158-25600177 MsG0280008113.01.T01:intron 25.0%
! TATCTACAAAGACTCTAATA+AGG + Chr2:25601561-25601580 None:intergenic 25.0%
! TCCAAAGTTAATGATGTTAT+TGG - Chr2:25599826-25599845 MsG0280008113.01.T01:CDS 25.0%
! TCTTTAAACAAAGTTGTACA+AGG - Chr2:25601164-25601183 MsG0280008113.01.T01:intron 25.0%
! TGAGTTATGGCTAAAATTAA+TGG - Chr2:25600331-25600350 MsG0280008113.01.T01:intron 25.0%
! TTACTACATACCAAACAAAA+AGG + Chr2:25600909-25600928 None:intergenic 25.0%
! TTGTTACCATATTCTCATAT+AGG - Chr2:25600118-25600137 MsG0280008113.01.T01:intron 25.0%
!! AGAGATCCCTTTATAATTTT+CGG - Chr2:25600676-25600695 MsG0280008113.01.T01:intron 25.0%
!! GACTAATTTTCCTTTTTGTT+TGG - Chr2:25600896-25600915 MsG0280008113.01.T01:intron 25.0%
!! TTTCAGATTGAATAAGTTGA+AGG - Chr2:25600093-25600112 MsG0280008113.01.T01:intron 25.0%
!! TTTTTGACAAAATGCTTTAC+TGG - Chr2:25600217-25600236 MsG0280008113.01.T01:intron 25.0%
!! TTTTTGTATATTTGCGAGTT+TGG - Chr2:25601251-25601270 MsG0280008113.01.T01:intron 25.0%
!!! CGTTTTAATTTTGAAACATG+GGG + Chr2:25600422-25600441 None:intergenic 25.0%
!!! TTTAAGCAATTCTAAAGTGA+TGG + Chr2:25601518-25601537 None:intergenic 25.0%
AATGAGAGAGTAAAAAAGAG+AGG - Chr2:25602017-25602036 MsG0280008113.01.T01:intron 30.0%
ACTGTACATACCAAACAAAA+AGG + Chr2:25600956-25600975 None:intergenic 30.0%
ATTTACGATCTCTTTCACTT+TGG - Chr2:25602202-25602221 MsG0280008113.01.T01:CDS 30.0%
CAATGTTAACTAATTAGAGG+GGG + Chr2:25601589-25601608 None:intergenic 30.0%
GAGTTGCAAAACAAATTAGA+GGG - Chr2:25600482-25600501 MsG0280008113.01.T01:intron 30.0%
GGACAATGTTAACTAATTAG+AGG + Chr2:25601592-25601611 None:intergenic 30.0%
GTAAAACTTCGGTAAAAGTA+CGG - Chr2:25601187-25601206 MsG0280008113.01.T01:intron 30.0%
GTACAGTAAATGTAAACAAG+AGG + Chr2:25600778-25600797 None:intergenic 30.0%
TTATACAATTTGATACGGAG+TGG + Chr2:25601654-25601673 None:intergenic 30.0%
TTCAATGTTCAGAGTCAAAA+CGG + Chr2:25602094-25602113 None:intergenic 30.0%
TTGGGACCGAAAATTATAAA+GGG + Chr2:25600685-25600704 None:intergenic 30.0%
TTTGTACAAGGGTAAAACTT+CGG - Chr2:25601213-25601232 MsG0280008113.01.T01:intron 30.0%
! AATGTGGATTTTTGTGCTTT+TGG + Chr2:25601327-25601346 None:intergenic 30.0%
! TAAAACTTCGGTAAAAGTAC+GGG - Chr2:25601188-25601207 MsG0280008113.01.T01:intron 30.0%
! TGTTGCAGTTAGTTTATCAA+AGG + Chr2:25601765-25601784 None:intergenic 30.0%
!! GACTAATTTGCCTTTTTGTT+TGG - Chr2:25600943-25600962 MsG0280008113.01.T01:intron 30.0%
!!! TTTTTTACATTGGCCCAAAT+CGG + Chr2:25600617-25600636 None:intergenic 30.0%
AAATGATGATTGGAGTTGCT+CGG + Chr2:25601625-25601644 None:intergenic 35.0%
ACAACTCTCATAGTTGAATG+TGG + Chr2:25601343-25601362 None:intergenic 35.0%
ACGGCTAAAAATGCAGAAAA+AGG - Chr2:25600446-25600465 MsG0280008113.01.T01:intron 35.0%
ACTACTGTGTTCATATGCAT+TGG + Chr2:25600822-25600841 None:intergenic 35.0%
CATAGAGATGACAATGAGTA+GGG + Chr2:25601679-25601698 None:intergenic 35.0%
CGGCTAAAAATGCAGAAAAA+GGG - Chr2:25600447-25600466 MsG0280008113.01.T01:intron 35.0%
CTTGGGACCGAAAATTATAA+AGG + Chr2:25600686-25600705 None:intergenic 35.0%
GGAGTTGCAAAACAAATTAG+AGG - Chr2:25600481-25600500 MsG0280008113.01.T01:intron 35.0%
GTGGACATGAAAATGATGAT+TGG + Chr2:25601635-25601654 None:intergenic 35.0%
GTTGTACAAGGGTAAAACTT+CGG - Chr2:25601176-25601195 MsG0280008113.01.T01:intron 35.0%
TGGAGAACACTTGAATGAAA+TGG + Chr2:25600521-25600540 None:intergenic 35.0%
! AAAGTACGGGATTTTGTACA+AGG - Chr2:25601201-25601220 MsG0280008113.01.T01:intron 35.0%
! AACTGACTTTGGATCTGAAT+CGG + Chr2:25601474-25601493 None:intergenic 35.0%
! AAGTACGGGATTTTGTACAA+GGG - Chr2:25601202-25601221 MsG0280008113.01.T01:intron 35.0%
! AGATGTCATGTAACTGACTT+TGG + Chr2:25601485-25601504 None:intergenic 35.0%
! TTTTTACATTGGCCCAAATC+GGG + Chr2:25600616-25600635 None:intergenic 35.0%
AATGCAGAAAAAGGGTCAGT+CGG - Chr2:25600455-25600474 MsG0280008113.01.T01:intron 40.0%
ACATGGGGTCCAATAAATTG+TGG + Chr2:25600407-25600426 None:intergenic 40.0%
ATCTTGGACGAATTGAGCTT+TGG + Chr2:25601298-25601317 None:intergenic 40.0%
CTAATTTACGTTGAGTCCCA+AGG - Chr2:25600844-25600863 MsG0280008113.01.T01:intron 40.0%
GCATAGAGATGACAATGAGT+AGG + Chr2:25601680-25601699 None:intergenic 40.0%
GCTCTAGTAGCTTGAGATTT+GGG + Chr2:25600035-25600054 None:intergenic 40.0%
TGTTAACTAATTAGAGGGGG+TGG + Chr2:25601586-25601605 None:intergenic 40.0%
!! GAACAAGATGACTCTGAAGT+TGG - Chr2:25602142-25602161 MsG0280008113.01.T01:CDS 40.0%
!! TCTTGGCTTGTTCAAGAGAA+CGG + Chr2:25602234-25602253 None:intergenic 40.0%
AAATTTGTCCGGTCCCGATT+TGG - Chr2:25600600-25600619 MsG0280008113.01.T01:intron 45.0%
AATTACGTTGCAGCGAACCT+TGG + Chr2:25600864-25600883 None:intergenic 45.0%
AATTTGTCCGGTCCCGATTT+GGG - Chr2:25600601-25600620 MsG0280008113.01.T01:intron 45.0%
ATTACGTTGCAGCGAACCTT+GGG + Chr2:25600863-25600882 None:intergenic 45.0%
CCATCAGCATAAACACGAAC+AGG + Chr2:25602181-25602200 None:intergenic 45.0%
CCTGTTCGTGTTTATGCTGA+TGG - Chr2:25602178-25602197 MsG0280008113.01.T01:CDS 45.0%
CTCAATTCGTCCAAGATGCA+CGG - Chr2:25601301-25601320 MsG0280008113.01.T01:intron 45.0%
TCAGCCACGCCACAATTTAT+TGG - Chr2:25600395-25600414 MsG0280008113.01.T01:intron 45.0%
TTGGATCTGAATCGGTTACG+CGG + Chr2:25601466-25601485 None:intergenic 45.0%
! GGCTCTAGTAGCTTGAGATT+TGG + Chr2:25600036-25600055 None:intergenic 45.0%
!! CTTGGCTTGTTCAAGAGAAC+GGG + Chr2:25602233-25602252 None:intergenic 45.0%
!! CAAAAAAAAAAAAAAAAATA+CGG + Chr2:25601911-25601930 None:intergenic 5.0%
!!! TAAATATGTTATTTATTTAT+TGG + Chr2:25601139-25601158 None:intergenic 5.0%
AGAAAAAGGGTCAGTCGGCA+GGG - Chr2:25600460-25600479 MsG0280008113.01.T01:intron 50.0%
CTGCAGCAGTATGTAGTGGT+CGG + Chr2:25601880-25601899 None:intergenic 50.0%
CTTGTTCAAGAGAACGGGCA+TGG + Chr2:25602228-25602247 None:intergenic 50.0%
GGGTCCAATAAATTGTGGCG+TGG + Chr2:25600402-25600421 None:intergenic 50.0%
ACATTGGCCCAAATCGGGAC+CGG + Chr2:25600611-25600630 None:intergenic 55.0%
CAGAAAAAGGGTCAGTCGGC+AGG - Chr2:25600459-25600478 MsG0280008113.01.T01:intron 55.0%
GACGCTGCAGCAGTATGTAG+TGG + Chr2:25601884-25601903 None:intergenic 55.0%
! GTGCTTTTGGCCGTGCATCT+TGG + Chr2:25601314-25601333 None:intergenic 55.0%
TTGGAGTTGCTCGGACGCAG+TGG + Chr2:25601616-25601635 None:intergenic 60.0%
CGCGCGCAGTTTAGCGTGGA+AGG - Chr2:25599727-25599746 MsG0280008113.01.T01:CDS 65.0%
GAGTTGCTCGGACGCAGTGG+AGG + Chr2:25601613-25601632 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr2 gene 25599724 25602261 25599724 ID=MsG0280008113.01;Name=MsG0280008113.01
Chr2 mRNA 25599724 25602261 25599724 ID=MsG0280008113.01.T01;Parent=MsG0280008113.01;Name=MsG0280008113.01.T01;_AED=0.49;_eAED=0.75;_QI=0|0|0|1|0|0|2|0|84
Chr2 exon 25602138 25602261 25602138 ID=MsG0280008113.01.T01:exon:14112;Parent=MsG0280008113.01.T01
Chr2 exon 25599724 25599854 25599724 ID=MsG0280008113.01.T01:exon:14111;Parent=MsG0280008113.01.T01
Chr2 CDS 25602138 25602261 25602138 ID=MsG0280008113.01.T01:cds;Parent=MsG0280008113.01.T01
Chr2 CDS 25599724 25599854 25599724 ID=MsG0280008113.01.T01:cds;Parent=MsG0280008113.01.T01
Gene Sequence

>MsG0280008113.01.T01

ATGCGCGCGCAGTTTAGCGTGGAAGGCATGCATTTCCAATCTACACAAATTTGTGTTAGCTACTCTTTTACTCTAGTTGATACTAGAATTTGTAATGTCAAATCCAAAGTTAATGATGTTATTGTGATCATGAATGAACAAGATGACTCTGAAGTTGGCAAAAACGATAAACCTGTTCGTGTTTATGCTGATGGAATTTACGATCTCTTTCACTTTGGCCATGCCCGTTCTCTTGAACAAGCCAAGAAATCGTAA

Protein sequence

>MsG0280008113.01.T01

MRAQFSVEGMHFQSTQICVSYSFTLVDTRICNVKSKVNDVIVIMNEQDDSEVGKNDKPVRVYADGIYDLFHFGHARSLEQAKKS*