AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01564

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01564.t1 MTR_2g016150 97.312 186 3 1 1 184 1 186 9.07e-130 362
MS.gene01564.t1 MTR_3g031140 44.944 178 89 4 1 178 1 169 2.30e-44 145
MS.gene01564.t1 MTR_5g074290 38.798 183 81 5 1 178 1 157 7.14e-33 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01564.t1 AT1G29195 56.915 188 71 3 1 178 1 188 5.55e-68 206
MS.gene01564.t1 AT2G30230 40.642 187 89 6 1 178 1 174 4.37e-36 124
MS.gene01564.t1 AT1G06980 40.761 184 85 4 1 178 1 166 2.76e-35 122

Find 32 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCCGGTGGCGGCGGCGTT+GGG 0.349909 2.2:-67432201 None:intergenic
GGTTTCTTGAGAACATGTTT+TGG 0.350154 2.2:-67432076 None:intergenic
CACCTTCAGCGCAAGATGGC+GGG 0.354822 2.2:+67432104 MS.gene01564:CDS
TGCTGTGTGGAGACCTCATT+TGG 0.366621 2.2:+67432435 MS.gene01564:CDS
GGAGGGACAACAACAATCTT+AGG 0.387106 2.2:-67432133 None:intergenic
TTATCCGGTGGCGGCGGCGT+TGG 0.387250 2.2:-67432202 None:intergenic
AACCGTTATAGAAGATTTGT+TGG 0.403215 2.2:-67432475 None:intergenic
GACCGTTGCAGTGTACTATA+CGG 0.423911 2.2:-67432000 None:intergenic
GGTGGCGGCGGCGTTGGGAG+AGG 0.432082 2.2:-67432196 None:intergenic
TCTCCCAACGCCGCCGCCAC+CGG 0.479340 2.2:+67432198 MS.gene01564:CDS
ACCCCGCCATCTTGCGCTGA+AGG 0.489813 2.2:-67432106 None:intergenic
TCTTGCGCTGAAGGTGAAGA+AGG 0.505753 2.2:-67432097 None:intergenic
GACTGAGATTCTGTCTGAGA+AGG 0.517425 2.2:+67432378 MS.gene01564:CDS
TCACCTTCAGCGCAAGATGG+CGG 0.520403 2.2:+67432103 MS.gene01564:CDS
CACCAACAAATCTTCTATAA+CGG 0.521213 2.2:+67432473 MS.gene01564:CDS
CATCGAGAACAGTGCTATGT+TGG 0.527832 2.2:+67432333 MS.gene01564:CDS
ACCTTCAGCGCAAGATGGCG+GGG 0.527946 2.2:+67432105 MS.gene01564:CDS
CCACGTTGAAGATCAGCATC+GGG 0.542465 2.2:-67432154 None:intergenic
TCTTCACCTTCAGCGCAAGA+TGG 0.556088 2.2:+67432100 MS.gene01564:CDS
ACCACGTTGAAGATCAGCAT+CGG 0.572486 2.2:-67432155 None:intergenic
AGTCAGAGAGACAGAAGAAG+AGG 0.589679 2.2:+67432406 MS.gene01564:CDS
TCAGAAATACTCTCCAAATG+AGG 0.591665 2.2:-67432448 None:intergenic
GCGGCGTTGGGAGAGGCATG+AGG 0.597521 2.2:-67432189 None:intergenic
ACAAACAACAGTAGAAGTAA+CGG 0.626432 2.2:+67432295 MS.gene01564:CDS
CGTTGAAGATCAGCATCGGG+AGG 0.643072 2.2:-67432151 None:intergenic
GTTGAAGATCAGCATCGGGA+GGG 0.647155 2.2:-67432150 None:intergenic
GGTCGAGTAGAAGAGATCAG+TGG 0.670260 2.2:+67432019 MS.gene01564:CDS
ATCACATCAAGTGCTCCACA+TGG 0.674792 2.2:-67431977 None:intergenic
ATATCTTGCATTCTACCATG+TGG 0.683335 2.2:+67431962 MS.gene01564:CDS
GAAGAGGACGTGTTGCTGTG+TGG 0.686286 2.2:+67432422 MS.gene01564:CDS
ATCCGTATAGTACACTGCAA+CGG 0.690119 2.2:+67431998 MS.gene01564:CDS
CCCGATGCTGATCTTCAACG+TGG 0.691291 2.2:+67432154 MS.gene01564:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ACAAACAACAGTAGAAGTAA+CGG + chr2.2:67432295-67432314 MS.gene01564:CDS 30.0%
! GTTTCTTGAGAACATGTTTT+GGG - chr2.2:67432078-67432097 None:intergenic 30.0%
!!! TGACGGTGATTATTTTTATC+CGG - chr2.2:67432220-67432239 None:intergenic 30.0%
ATATCTTGCATTCTACCATG+TGG + chr2.2:67431962-67431981 MS.gene01564:CDS 35.0%
TCAGAAATACTCTCCAAATG+AGG - chr2.2:67432451-67432470 None:intergenic 35.0%
! GGTTTCTTGAGAACATGTTT+TGG - chr2.2:67432079-67432098 None:intergenic 35.0%
!!! TGATTATTTTTATCCGGTGG+CGG - chr2.2:67432214-67432233 None:intergenic 35.0%
ATCCGTATAGTACACTGCAA+CGG + chr2.2:67431998-67432017 MS.gene01564:CDS 40.0%
!!! CGGTGATTATTTTTATCCGG+TGG - chr2.2:67432217-67432236 None:intergenic 40.0%
ACCACGTTGAAGATCAGCAT+CGG - chr2.2:67432158-67432177 None:intergenic 45.0%
AGTCAGAGAGACAGAAGAAG+AGG + chr2.2:67432406-67432425 MS.gene01564:CDS 45.0%
ATCACATCAAGTGCTCCACA+TGG - chr2.2:67431980-67431999 None:intergenic 45.0%
CATCGAGAACAGTGCTATGT+TGG + chr2.2:67432333-67432352 MS.gene01564:CDS 45.0%
CCGTCATAGCAAAAACTCGT+CGG + chr2.2:67432234-67432253 MS.gene01564:CDS 45.0%
GACCGTTGCAGTGTACTATA+CGG - chr2.2:67432003-67432022 None:intergenic 45.0%
GACTGAGATTCTGTCTGAGA+AGG + chr2.2:67432378-67432397 MS.gene01564:CDS 45.0%
GGAGGGACAACAACAATCTT+AGG - chr2.2:67432136-67432155 None:intergenic 45.0%
!! CCGACGAGTTTTTGCTATGA+CGG - chr2.2:67432237-67432256 None:intergenic 45.0%
!!! TTATTTTTATCCGGTGGCGG+CGG - chr2.2:67432211-67432230 None:intergenic 45.0%
CCACGTTGAAGATCAGCATC+GGG - chr2.2:67432157-67432176 None:intergenic 50.0%
GGTCGAGTAGAAGAGATCAG+TGG + chr2.2:67432019-67432038 MS.gene01564:CDS 50.0%
TCTTCACCTTCAGCGCAAGA+TGG + chr2.2:67432100-67432119 MS.gene01564:CDS 50.0%
TCTTGCGCTGAAGGTGAAGA+AGG - chr2.2:67432100-67432119 None:intergenic 50.0%
TGCTGTGTGGAGACCTCATT+TGG + chr2.2:67432435-67432454 MS.gene01564:CDS 50.0%
! GTTGAAGATCAGCATCGGGA+GGG - chr2.2:67432153-67432172 None:intergenic 50.0%
CCCGATGCTGATCTTCAACG+TGG + chr2.2:67432154-67432173 MS.gene01564:CDS 55.0%
TCACCTTCAGCGCAAGATGG+CGG + chr2.2:67432103-67432122 MS.gene01564:CDS 55.0%
! CGTTGAAGATCAGCATCGGG+AGG - chr2.2:67432154-67432173 None:intergenic 55.0%
! GAAGAGGACGTGTTGCTGTG+TGG + chr2.2:67432422-67432441 MS.gene01564:CDS 55.0%
ACCTTCAGCGCAAGATGGCG+GGG + chr2.2:67432105-67432124 MS.gene01564:CDS 60.0%
CACCTTCAGCGCAAGATGGC+GGG + chr2.2:67432104-67432123 MS.gene01564:CDS 60.0%
ACCCCGCCATCTTGCGCTGA+AGG - chr2.2:67432109-67432128 None:intergenic 65.0%
! GCGGCGTTGGGAGAGGCATG+AGG - chr2.2:67432192-67432211 None:intergenic 70.0%
! TATCCGGTGGCGGCGGCGTT+GGG - chr2.2:67432204-67432223 None:intergenic 70.0%
! TTATCCGGTGGCGGCGGCGT+TGG - chr2.2:67432205-67432224 None:intergenic 70.0%
TCTCCCAACGCCGCCGCCAC+CGG + chr2.2:67432198-67432217 MS.gene01564:CDS 75.0%
!! GGTGGCGGCGGCGTTGGGAG+AGG - chr2.2:67432199-67432218 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 67431938 67432492 67431938 ID=MS.gene01564
chr2.2 mRNA 67431938 67432492 67431938 ID=MS.gene01564.t1;Parent=MS.gene01564
chr2.2 exon 67431938 67432492 67431938 ID=MS.gene01564.t1.exon1;Parent=MS.gene01564.t1
chr2.2 CDS 67431938 67432492 67431938 ID=cds.MS.gene01564.t1;Parent=MS.gene01564.t1
Gene Sequence

>MS.gene01564

ATGAGAAACAGCATAAGATGTTGCATATCTTGCATTCTACCATGTGGAGCACTTGATGTGATCCGTATAGTACACTGCAACGGTCGAGTAGAAGAGATCAGTGGCAGCATCAAAGCAAGTGAAATCATGAAAACATACCCAAAACATGTTCTCAAGAAACCTTCTTCACCTTCAGCGCAAGATGGCGGGGTTGTTCCTAAGATTGTTGTTGTCCCTCCCGATGCTGATCTTCAACGTGGTAAGATTTACTTCCTCATGCCTCTCCCAACGCCGCCGCCACCGGATAAAAATAATCACCGTCATAGCAAAAACTCGTCGGTAAGAAAGAAAAGAAAAGAACAGAACGAGAGAATATTAACAAACAACAGTAGAAGTAACGGTAACAGTAACAACAACATCGAGAACAGTGCTATGTTGGTTGTGTCTTCTGATCAGTACTTGACTGAGATTCTGTCTGAGAAGGTTTGTAGTCAGAGAGACAGAAGAAGAGGACGTGTTGCTGTGTGGAGACCTCATTTGGAGAGTATTTCTGAGTCACCAACAAATCTTCTATAA
Protein sequence

>MS.gene01564.t1

MRNSIRCCISCILPCGALDVIRIVHCNGRVEEISGSIKASEIMKTYPKHVLKKPSSPSAQDGGVVPKIVVVPPDADLQRGKIYFLMPLPTPPPPDKNNHRHSKNSSVRKKRKEQNERILTNNSRSNGNSNNNIENSAMLVVSSDQYLTEILSEKVCSQRDRRRGRVAVWRPHLESISESPTNLL