AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380016057.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016057.01.T01 MTR_3g082690 98.571 70 1 0 5 74 428 497 1.17e-41 141
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016057.01.T01 AT3G07670 75.000 68 17 0 7 74 299 366 1.17e-21 86.3
MsG0380016057.01.T01 AT3G07670 75.000 68 17 0 7 74 437 504 1.73e-21 86.3

Find 27 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTCATCACTTCATGTTAT+TGG 0.159601 3:+78496220 MsG0380016057.01.T01:three_prime_UTR
AAAGGCTTGAAAATCTTTAA+TGG 0.210155 3:+78496099 MsG0380016057.01.T01:CDS
TGAAAATCTTTAATGGGTTC+TGG 0.228182 3:+78496106 MsG0380016057.01.T01:CDS
GTCTTCTGTTGAGTTGTTTC+GGG 0.232871 3:-78495880 None:intergenic
AGTCTTCTGTTGAGTTGTTT+CGG 0.314214 3:-78495881 None:intergenic
ATGAGGACTGGTGAATTAAA+AGG 0.337001 3:+78496081 MsG0380016057.01.T01:CDS
AAGGCTTGAAAATCTTTAAT+GGG 0.349585 3:+78496100 MsG0380016057.01.T01:CDS
GGTAAGTGGATCGCTAGATT+TGG 0.375776 3:+78495847 MsG0380016057.01.T01:CDS
AAAATAATGAATGGCCTCAT+TGG 0.414490 3:-78496137 None:intergenic
AATGAAAACAAGAAAAGAAA+AGG 0.460861 3:+78496312 MsG0380016057.01.T01:three_prime_UTR
TTTCCATTTGATCGATCCAC+AGG 0.496273 3:+78495826 MsG0380016058.01.T01:intron
GAAGAAGACTGAGGGATATG+AGG 0.527158 3:+78496064 MsG0380016057.01.T01:CDS
TTGATCGATCCACAGGTAAG+TGG 0.549849 3:+78495833 MsG0380016057.01.T01:CDS
AACAAGAAAAGAAAAGGCCG+TGG 0.551947 3:+78496318 MsG0380016057.01.T01:three_prime_UTR
GTTTAGATGCAATAATTCCA+CGG 0.556900 3:-78496335 None:intergenic
TTCTGGAATCGTTTCCAATG+AGG 0.561253 3:+78496123 MsG0380016057.01.T01:CDS
CAACGGTGGAAAATAATGAA+TGG 0.562616 3:-78496146 None:intergenic
AGACTGAGGGATATGAGGAC+TGG 0.586138 3:+78496069 MsG0380016057.01.T01:CDS
CTTTCTAAAGCAGCTAGCCG+TGG 0.603623 3:+78495904 MsG0380016057.01.T01:CDS
GATATTGCGAAGAAGACTGA+GGG 0.640825 3:+78496056 MsG0380016057.01.T01:intron
AGATGTTTCCAAGCAAGCAA+CGG 0.640892 3:-78496163 None:intergenic
TGTTTCCAAGCAAGCAACGG+TGG 0.643563 3:-78496160 None:intergenic
ACTTGTGTAATAGCGAGCGC+AGG 0.651320 3:+78495927 MsG0380016057.01.T01:CDS
TCTAGCGATCCACTTACCTG+TGG 0.663437 3:-78495842 None:intergenic
TCTTCTGTTGAGTTGTTTCG+GGG 0.672386 3:-78495879 None:intergenic
AGATATTGCGAAGAAGACTG+AGG 0.673237 3:+78496055 MsG0380016057.01.T01:intron
CTCGCTATTACACAAGTCCA+CGG 0.710247 3:-78495921 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTAATTTCTACTTACAA+AGG + Chr3:78495991-78496010 MsG0380016057.01.T01:intron 15.0%
!! AATGAAAACAAGAAAAGAAA+AGG + Chr3:78496312-78496331 MsG0380016057.01.T01:three_prime_UTR 20.0%
!!! TTATTGGTTTTTGTTTTTGA+TGG + Chr3:78496236-78496255 MsG0380016057.01.T01:three_prime_UTR 20.0%
!!! TTTTTGTTTTTGATGGAAAT+AGG + Chr3:78496243-78496262 MsG0380016057.01.T01:three_prime_UTR 20.0%
! AAAGGCTTGAAAATCTTTAA+TGG + Chr3:78496099-78496118 MsG0380016057.01.T01:CDS 25.0%
! AAGGCTTGAAAATCTTTAAT+GGG + Chr3:78496100-78496119 MsG0380016057.01.T01:CDS 25.0%
!!! AATTTAGCACTATTTTGAAG+AGG + Chr3:78496415-78496434 MsG0380016057.01.T01:three_prime_UTR 25.0%
AAAATAATGAATGGCCTCAT+TGG - Chr3:78496140-78496159 None:intergenic 30.0%
AGTTCATCACTTCATGTTAT+TGG + Chr3:78496220-78496239 MsG0380016057.01.T01:three_prime_UTR 30.0%
GTTTAGATGCAATAATTCCA+CGG - Chr3:78496338-78496357 None:intergenic 30.0%
!! TGAAAATCTTTAATGGGTTC+TGG + Chr3:78496106-78496125 MsG0380016057.01.T01:CDS 30.0%
CAACGGTGGAAAATAATGAA+TGG - Chr3:78496149-78496168 None:intergenic 35.0%
! AGTCTTCTGTTGAGTTGTTT+CGG - Chr3:78495884-78495903 None:intergenic 35.0%
! ATGAGGACTGGTGAATTAAA+AGG + Chr3:78496081-78496100 MsG0380016057.01.T01:CDS 35.0%
AACAAGAAAAGAAAAGGCCG+TGG + Chr3:78496318-78496337 MsG0380016057.01.T01:three_prime_UTR 40.0%
AGATATTGCGAAGAAGACTG+AGG + Chr3:78496055-78496074 MsG0380016057.01.T01:intron 40.0%
AGATGTTTCCAAGCAAGCAA+CGG - Chr3:78496166-78496185 None:intergenic 40.0%
GATATTGCGAAGAAGACTGA+GGG + Chr3:78496056-78496075 MsG0380016057.01.T01:intron 40.0%
! GTCTTCTGTTGAGTTGTTTC+GGG - Chr3:78495883-78495902 None:intergenic 40.0%
! TCTTCTGTTGAGTTGTTTCG+GGG - Chr3:78495882-78495901 None:intergenic 40.0%
!! TTCTGGAATCGTTTCCAATG+AGG + Chr3:78496123-78496142 MsG0380016057.01.T01:CDS 40.0%
CTCGCTATTACACAAGTCCA+CGG - Chr3:78495924-78495943 None:intergenic 45.0%
GAAGAAGACTGAGGGATATG+AGG + Chr3:78496064-78496083 MsG0380016057.01.T01:CDS 45.0%
GGTAAGTGGATCGCTAGATT+TGG + Chr3:78495847-78495866 MsG0380016057.01.T01:CDS 45.0%
TTGATCGATCCACAGGTAAG+TGG + Chr3:78495833-78495852 MsG0380016057.01.T01:CDS 45.0%
! ATTTTCCACCGTTGCTTGCT+TGG + Chr3:78496155-78496174 MsG0380016057.01.T01:three_prime_UTR 45.0%
ACTTGTGTAATAGCGAGCGC+AGG + Chr3:78495927-78495946 MsG0380016057.01.T01:CDS 50.0%
AGACTGAGGGATATGAGGAC+TGG + Chr3:78496069-78496088 MsG0380016057.01.T01:CDS 50.0%
TCTAGCGATCCACTTACCTG+TGG - Chr3:78495845-78495864 None:intergenic 50.0%
TGTTTCCAAGCAAGCAACGG+TGG - Chr3:78496163-78496182 None:intergenic 50.0%
!! CTTTCTAAAGCAGCTAGCCG+TGG + Chr3:78495904-78495923 MsG0380016057.01.T01:CDS 50.0%
Chromosome Type Strat End Strand Name
Chr3 gene 78495833 78496499 78495833 ID=MsG0380016057.01;Name=MsG0380016057.01
Chr3 mRNA 78495833 78496499 78495833 ID=MsG0380016057.01.T01;Parent=MsG0380016057.01;Name=MsG0380016057.01.T01;_AED=0.49;_eAED=0.50;_QI=0|1|0.5|1|1|1|2|356|74
Chr3 exon 78495833 78495970 78495833 ID=MsG0380016057.01.T01:exon:17399;Parent=MsG0380016057.01.T01
Chr3 exon 78496057 78496499 78496057 ID=MsG0380016057.01.T01:exon:17400;Parent=MsG0380016057.01.T01
Chr3 CDS 78495833 78495970 78495833 ID=MsG0380016057.01.T01:cds;Parent=MsG0380016057.01.T01
Chr3 CDS 78496057 78496143 78496057 ID=MsG0380016057.01.T01:cds;Parent=MsG0380016057.01.T01
Chr3 three_prime_UTR 78496144 78496499 78496144 ID=MsG0380016057.01.T01:three_prime_utr;Parent=MsG0380016057.01.T01
Gene Sequence

>MsG0380016057.01.T01

TTGATCGATCCACAGGTAAGTGGATCGCTAGATTTGGATGTGACTTCCCCGAAACAACTCAACAGAAGACTCTTTCTAAAGCAGCTAGCCGTGGACTTGTGTAATAGCGAGCGCAGGATATTGTTTCGTGCTCAATATATATTGCGAAGAAGACTGAGGGATATGAGGACTGGTGAATTAAAAGGCTTGAAAATCTTTAATGGGTTCTGGAATCGTTTCCAATGA

Protein sequence

>MsG0380016057.01.T01

LIDPQVSGSLDLDVTSPKQLNRRLFLKQLAVDLCNSERRILFRAQYILRRRLRDMRTGELKGLKIFNGFWNRFQ*