AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene91297

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene91297.t1 MTR_5g005130 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene91297.t1 MTR_3g115330 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene91297.t1 MTR_1g106755 100.000 56 0 0 1 56 1 56 9.62e-38 119
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene91297.t1 AT4G33865 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene91297.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene91297.t1 AT3G43980 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene91297.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109

Find 25 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAGCAATGCCAAGGAAAT+TGG 0.216340 1.3:-73106863 MS.gene91297:CDS
CAAGGAAATTGGCTTCATTA+AGG 0.276234 1.3:-73106852 MS.gene91297:intron
CATGGATTGATAAGGAAGTA+TGG 0.378864 1.3:-73106911 MS.gene91297:CDS
CCATGGGACACTCAAATGTT+TGG 0.382308 1.3:-73107570 MS.gene91297:CDS
GAACCAGGACCATAGGTCTT+GGG 0.410602 1.3:+73107538 None:intergenic
CTTAATGAAGCCAATTTCCT+TGG 0.421882 1.3:+73106853 None:intergenic
AGCATTGCCTGCAGCACATA+AGG 0.453112 1.3:+73106888 None:intergenic
GGAACCAGGACCATAGGTCT+TGG 0.464100 1.3:+73107537 None:intergenic
ATGGTCCTGGTTCCCGCACT+TGG 0.475887 1.3:-73107528 MS.gene91297:intron
CACCCCAAGACCTATGGTCC+TGG 0.491604 1.3:-73107541 MS.gene91297:CDS
AACTCTCACCCCAAGACCTA+TGG 0.505813 1.3:-73107547 MS.gene91297:CDS
GGAATTCACATGGATTGATA+AGG 0.515737 1.3:-73106919 MS.gene91297:CDS
ATATACCAAGTGCGGGAACC+AGG 0.531737 1.3:+73107523 None:intergenic
AGTATGGCCTTATGTGCTGC+AGG 0.540472 1.3:-73106895 MS.gene91297:CDS
CCAAACATTTGAGTGTCCCA+TGG 0.543494 1.3:+73107570 None:intergenic
TAACTTGTAGCCGTGTGTGC+GGG 0.573381 1.3:-73106940 MS.gene91297:intron
CATGTGAATTCCCGCACACA+CGG 0.574250 1.3:+73106930 None:intergenic
AAGAATGAATATACCAAGTG+CGG 0.579658 1.3:+73107515 None:intergenic
AGTGCGGGAACCAGGACCAT+AGG 0.585453 1.3:+73107531 None:intergenic
CAATTTCCTTGGCATTGCTG+TGG 0.593734 1.3:+73106864 None:intergenic
AACCAGGACCATAGGTCTTG+GGG 0.597207 1.3:+73107539 None:intergenic
CGTGTGTGCGGGAATTCACA+TGG 0.601988 1.3:-73106929 MS.gene91297:CDS
AGAATGAATATACCAAGTGC+GGG 0.603783 1.3:+73107516 None:intergenic
ATGCTTCCACAGCAATGCCA+AGG 0.620494 1.3:-73106870 MS.gene91297:CDS
ATAACTTGTAGCCGTGTGTG+CGG 0.665136 1.3:-73106941 MS.gene91297:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTATTGATAATATGTTTT+GGG - chr1.3:73107028-73107047 MS.gene91297:intron 15.0%
!!! TTATGTTATTGCTATTATAT+CGG - chr1.3:73107215-73107234 MS.gene91297:intron 15.0%
!! AAACCTAAATGAATTGAAAA+AGG + chr1.3:73106857-73106876 None:intergenic 20.0%
!! GATATAATAGCAATAACATA+AGG + chr1.3:73107216-73107235 None:intergenic 20.0%
!! GATTCAAAATTCATAAAAGA+GGG + chr1.3:73106927-73106946 None:intergenic 20.0%
!! GCAAGAAAAATAAAAACAAA+AGG + chr1.3:73107560-73107579 None:intergenic 20.0%
!!! ATTTAGGTTTCTAGTATTTT+GGG - chr1.3:73106867-73106886 MS.gene91297:CDS 20.0%
!!! GTGTTATTGATAATATGTTT+TGG - chr1.3:73107027-73107046 MS.gene91297:intron 20.0%
!!! GTTATTGATAATATGTTTTG+GGG - chr1.3:73107029-73107048 MS.gene91297:intron 20.0%
!!! TAACCTTTTTCAATTCATTT+AGG - chr1.3:73106851-73106870 MS.gene91297:intron 20.0%
!!! TTGGGGATTTTTATTTTATT+GGG - chr1.3:73107046-73107065 MS.gene91297:intron 20.0%
!!! TTTGGGGATTTTTATTTTAT+TGG - chr1.3:73107045-73107064 MS.gene91297:intron 20.0%
! CAAAATGTAAACTTTAACAG+CGG + chr1.3:73106902-73106921 None:intergenic 25.0%
! CGATTCAAAATTCATAAAAG+AGG + chr1.3:73106928-73106947 None:intergenic 25.0%
! TTTGAACATATGTAGTTTAG+TGG - chr1.3:73107186-73107205 MS.gene91297:intron 25.0%
!! ATTTTACATGATTGTATCTG+AGG + chr1.3:73107521-73107540 None:intergenic 25.0%
!! TAATGGTTTTCTATTGCTTT+GGG - chr1.3:73106973-73106992 MS.gene91297:intron 25.0%
!! TAATTAAGCTTTGATTCAGA+TGG - chr1.3:73107110-73107129 MS.gene91297:intron 25.0%
!!! CATTTAGGTTTCTAGTATTT+TGG - chr1.3:73106866-73106885 MS.gene91297:CDS 25.0%
AAGAATGAATATACCAAGTG+CGG + chr1.3:73106815-73106834 None:intergenic 30.0%
! CTAATGGTTTTCTATTGCTT+TGG - chr1.3:73106972-73106991 MS.gene91297:intron 30.0%
!! GTGTTGTTTCTATGTTCTAA+TGG - chr1.3:73106956-73106975 MS.gene91297:intron 30.0%
AGAATGAATATACCAAGTGC+GGG + chr1.3:73106814-73106833 None:intergenic 35.0%
CTTAATGAAGCCAATTTCCT+TGG + chr1.3:73107477-73107496 None:intergenic 35.0%
TGCTATTATATCGGTACTAG+AGG - chr1.3:73107224-73107243 MS.gene91297:intron 35.0%
! CAAGGAAATTGGCTTCATTA+AGG - chr1.3:73107475-73107494 MS.gene91297:intron 35.0%
! CATGGATTGATAAGGAAGTA+TGG - chr1.3:73107416-73107435 MS.gene91297:intron 35.0%
! GGAATTCACATGGATTGATA+AGG - chr1.3:73107408-73107427 MS.gene91297:intron 35.0%
!! TGCTTTGGGTTGTACTGTTA+TGG - chr1.3:73106987-73107006 MS.gene91297:intron 40.0%
CAATTTCCTTGGCATTGCTG+TGG + chr1.3:73107466-73107485 None:intergenic 45.0%
CACAGCAATGCCAAGGAAAT+TGG - chr1.3:73107464-73107483 MS.gene91297:intron 45.0%
! ATAACTTGTAGCCGTGTGTG+CGG - chr1.3:73107386-73107405 MS.gene91297:intron 45.0%
AACCAGGACCATAGGTCTTG+GGG + chr1.3:73106791-73106810 None:intergenic 50.0%
AACTCTCACCCCAAGACCTA+TGG - chr1.3:73106780-73106799 MS.gene91297:intron 50.0%
AGCATTGCCTGCAGCACATA+AGG + chr1.3:73107442-73107461 None:intergenic 50.0%
ATATACCAAGTGCGGGAACC+AGG + chr1.3:73106807-73106826 None:intergenic 50.0%
ATGCTTCCACAGCAATGCCA+AGG - chr1.3:73107457-73107476 MS.gene91297:intron 50.0%
CATGTGAATTCCCGCACACA+CGG + chr1.3:73107400-73107419 None:intergenic 50.0%
GAACCAGGACCATAGGTCTT+GGG + chr1.3:73106792-73106811 None:intergenic 50.0%
! TAACTTGTAGCCGTGTGTGC+GGG - chr1.3:73107387-73107406 MS.gene91297:intron 50.0%
!! AGTATGGCCTTATGTGCTGC+AGG - chr1.3:73107432-73107451 MS.gene91297:intron 50.0%
CGTGTGTGCGGGAATTCACA+TGG - chr1.3:73107398-73107417 MS.gene91297:intron 55.0%
GGAACCAGGACCATAGGTCT+TGG + chr1.3:73106793-73106812 None:intergenic 55.0%
AGTGCGGGAACCAGGACCAT+AGG + chr1.3:73106799-73106818 None:intergenic 60.0%
ATGGTCCTGGTTCCCGCACT+TGG - chr1.3:73106799-73106818 MS.gene91297:intron 60.0%
CACCCCAAGACCTATGGTCC+TGG - chr1.3:73106786-73106805 MS.gene91297:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 73106759 73107590 73106759 ID=MS.gene91297
chr1.3 mRNA 73106759 73107590 73106759 ID=MS.gene91297.t1;Parent=MS.gene91297
chr1.3 exon 73107529 73107590 73107529 ID=MS.gene91297.t1.exon1;Parent=MS.gene91297.t1
chr1.3 CDS 73107529 73107590 73107529 ID=cds.MS.gene91297.t1;Parent=MS.gene91297.t1
chr1.3 exon 73106853 73106952 73106853 ID=MS.gene91297.t1.exon2;Parent=MS.gene91297.t1
chr1.3 CDS 73106853 73106952 73106853 ID=cds.MS.gene91297.t1;Parent=MS.gene91297.t1
chr1.3 exon 73106759 73106767 73106759 ID=MS.gene91297.t1.exon3;Parent=MS.gene91297.t1
chr1.3 CDS 73106759 73106767 73106759 ID=cds.MS.gene91297.t1;Parent=MS.gene91297.t1
Gene Sequence

>MS.gene91297

ATGGGACACTCAAATGTTTGGAACTCTCACCCCAAGACCTATGGTCCTGGTTCCCGCACTTGGTATATTCATTCTTCAATCTTCGATTCACATAACCTTTTTCAATTCATTTAGGTTTCTAGTATTTTGGGTTTTATTTTCCGCTGTTAAAGTTTACATTTTGATCCCTCTTTTATGAATTTTGAATCGTTTGACTAGTGTTGTTTCTATGTTCTAATGGTTTTCTATTGCTTTGGGTTGTACTGTTATGGTTTGAGATTGATGAATAGTGTTATTGATAATATGTTTTGGGGATTTTTATTTTATTGGGTCAGCTTTGATATCAGCTGATGTTATAGCTAAGCAGTGAACTAATTAAGCTTTGATTCAGATGGCTTAAGTTGATTATTAATTTCGTTCAATGTTGTTTTGTTCTCGTTGTTGATGATTTGAACATATGTAGTTTAGTGGAAAACCTTATGTTATTGCTATTATATCGGTACTAGAGGAACACTGAACAGTAATTTTTGAATAATAGTGTATACTATACACATTCTCACTATTCTGTAGAATAATAATTGATGTTGTATTGCAGATCAGTTGTTTTTTAATTTAGAATTGTCTTGCTGATTGTGATTCATTTTGTGTATAACTTGTAGCCGTGTGTGCGGGAATTCACATGGATTGATAAGGAAGTATGGCCTTATGTGCTGCAGGCAATGCTTCCACAGCAATGCCAAGGAAATTGGCTTCATTAAGGTAAACTTTTGATTATGTTGTCCTCAGATACAATCATGTAAAATGTATGCATTTTTAATGCCTTTTGTTTTTATTTTTCTTGCAGTACCGTTGA
Protein sequence

>MS.gene91297.t1

MGHSNVWNSHPKTYGPGSRTCRVCGNSHGLIRKYGLMCCRQCFHSNAKEIGFIKYR