AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene002580

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002580.t1 MTR_2g016150 97.312 186 3 1 1 184 1 186 9.07e-130 362
MS.gene002580.t1 MTR_3g031140 44.944 178 89 4 1 178 1 169 2.30e-44 145
MS.gene002580.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.gene002580.t1 AT1G29195 56.915 188 71 3 1 178 1 188 5.55e-68 206
MS.gene002580.t1 AT2G30230 40.642 187 89 6 1 178 1 174 4.37e-36 124
MS.gene002580.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
TATCCGGTGGTGGCGGCGTT+GGG 0.341375 2.1:-69524238 None:intergenic
GGTTTCTTGAGAACATGTTT+TGG 0.350154 2.1:-69524113 None:intergenic
CACCTTCAGCGCAAGATGGC+GGG 0.354822 2.1:+69524141 MS.gene002580:CDS
TGCTGTGTGGAGACCTCATT+TGG 0.366621 2.1:+69524472 MS.gene002580:CDS
GGAGGGACAACAACAATCTT+AGG 0.387106 2.1:-69524170 None:intergenic
AACCGTTATAGAAGATTTGT+TGG 0.403215 2.1:-69524512 None:intergenic
TTATCCGGTGGTGGCGGCGT+TGG 0.422064 2.1:-69524239 None:intergenic
GACCGTTGCAGTGTACTATA+CGG 0.423911 2.1:-69524037 None:intergenic
GGTGGTGGCGGCGTTGGGAG+AGG 0.431618 2.1:-69524233 None:intergenic
ACCCCGCCATCTTGCGCTGA+AGG 0.489813 2.1:-69524143 None:intergenic
TCTTGCGCTGAAGGTGAAGA+AGG 0.505753 2.1:-69524134 None:intergenic
GACTGAGATTCTGTCTGAGA+AGG 0.517425 2.1:+69524415 MS.gene002580:CDS
TCACCTTCAGCGCAAGATGG+CGG 0.520403 2.1:+69524140 MS.gene002580:CDS
CACCAACAAATCTTCTATAA+CGG 0.521213 2.1:+69524510 MS.gene002580:CDS
TCTCCCAACGCCGCCACCAC+CGG 0.524822 2.1:+69524235 MS.gene002580:CDS
CATCGAGAACAGTGCTATGT+TGG 0.527832 2.1:+69524370 MS.gene002580:CDS
ACCTTCAGCGCAAGATGGCG+GGG 0.527946 2.1:+69524142 MS.gene002580:CDS
CCACGTTGAAGATCAGCATC+GGG 0.542465 2.1:-69524191 None:intergenic
TCTTCACCTTCAGCGCAAGA+TGG 0.556088 2.1:+69524137 MS.gene002580:CDS
ACCACGTTGAAGATCAGCAT+CGG 0.572486 2.1:-69524192 None:intergenic
GCGGCGTTGGGAGAGGCATG+AGG 0.582625 2.1:-69524226 None:intergenic
AGTCAGAGAGACAGAAGAAG+AGG 0.589679 2.1:+69524443 MS.gene002580:CDS
TCAGAAATACTCTCCAAATG+AGG 0.591665 2.1:-69524485 None:intergenic
ACAAACAACAGTAGAAGTAA+CGG 0.626432 2.1:+69524332 MS.gene002580:CDS
CGTTGAAGATCAGCATCGGG+AGG 0.643072 2.1:-69524188 None:intergenic
GTTGAAGATCAGCATCGGGA+GGG 0.647155 2.1:-69524187 None:intergenic
GGTCGAGTAGAAGAGATCAG+TGG 0.670260 2.1:+69524056 MS.gene002580:CDS
ATCACATCAAGTGCTCCACA+TGG 0.674792 2.1:-69524014 None:intergenic
ATATCTTGCATTCTACCATG+TGG 0.683335 2.1:+69523999 MS.gene002580:CDS
GAAGAGGACGTGTTGCTGTG+TGG 0.686286 2.1:+69524459 MS.gene002580:CDS
ATCCGTATAGTACACTGCAA+CGG 0.690119 2.1:+69524035 MS.gene002580:CDS
CCCGATGCTGATCTTCAACG+TGG 0.691291 2.1:+69524191 MS.gene002580:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ACAAACAACAGTAGAAGTAA+CGG + chr2.1:69524332-69524351 MS.gene002580:CDS 30.0%
! GTTTCTTGAGAACATGTTTT+GGG - chr2.1:69524115-69524134 None:intergenic 30.0%
!!! TGACGGTGATTATTTTTATC+CGG - chr2.1:69524257-69524276 None:intergenic 30.0%
ATATCTTGCATTCTACCATG+TGG + chr2.1:69523999-69524018 MS.gene002580:CDS 35.0%
TCAGAAATACTCTCCAAATG+AGG - chr2.1:69524488-69524507 None:intergenic 35.0%
! GGTTTCTTGAGAACATGTTT+TGG - chr2.1:69524116-69524135 None:intergenic 35.0%
!!! TGATTATTTTTATCCGGTGG+TGG - chr2.1:69524251-69524270 None:intergenic 35.0%
ATCCGTATAGTACACTGCAA+CGG + chr2.1:69524035-69524054 MS.gene002580:CDS 40.0%
!!! CGGTGATTATTTTTATCCGG+TGG - chr2.1:69524254-69524273 None:intergenic 40.0%
!!! TTATTTTTATCCGGTGGTGG+CGG - chr2.1:69524248-69524267 None:intergenic 40.0%
ACCACGTTGAAGATCAGCAT+CGG - chr2.1:69524195-69524214 None:intergenic 45.0%
AGTCAGAGAGACAGAAGAAG+AGG + chr2.1:69524443-69524462 MS.gene002580:CDS 45.0%
ATCACATCAAGTGCTCCACA+TGG - chr2.1:69524017-69524036 None:intergenic 45.0%
CATCGAGAACAGTGCTATGT+TGG + chr2.1:69524370-69524389 MS.gene002580:CDS 45.0%
CCGTCATAGCAAAAACTCGT+CGG + chr2.1:69524271-69524290 MS.gene002580:CDS 45.0%
GACCGTTGCAGTGTACTATA+CGG - chr2.1:69524040-69524059 None:intergenic 45.0%
GACTGAGATTCTGTCTGAGA+AGG + chr2.1:69524415-69524434 MS.gene002580:CDS 45.0%
GGAGGGACAACAACAATCTT+AGG - chr2.1:69524173-69524192 None:intergenic 45.0%
!! CCGACGAGTTTTTGCTATGA+CGG - chr2.1:69524274-69524293 None:intergenic 45.0%
CCACGTTGAAGATCAGCATC+GGG - chr2.1:69524194-69524213 None:intergenic 50.0%
GGTCGAGTAGAAGAGATCAG+TGG + chr2.1:69524056-69524075 MS.gene002580:CDS 50.0%
TCTTCACCTTCAGCGCAAGA+TGG + chr2.1:69524137-69524156 MS.gene002580:CDS 50.0%
TCTTGCGCTGAAGGTGAAGA+AGG - chr2.1:69524137-69524156 None:intergenic 50.0%
TGCTGTGTGGAGACCTCATT+TGG + chr2.1:69524472-69524491 MS.gene002580:CDS 50.0%
! GTTGAAGATCAGCATCGGGA+GGG - chr2.1:69524190-69524209 None:intergenic 50.0%
CCCGATGCTGATCTTCAACG+TGG + chr2.1:69524191-69524210 MS.gene002580:CDS 55.0%
TCACCTTCAGCGCAAGATGG+CGG + chr2.1:69524140-69524159 MS.gene002580:CDS 55.0%
! CGTTGAAGATCAGCATCGGG+AGG - chr2.1:69524191-69524210 None:intergenic 55.0%
! GAAGAGGACGTGTTGCTGTG+TGG + chr2.1:69524459-69524478 MS.gene002580:CDS 55.0%
ACCTTCAGCGCAAGATGGCG+GGG + chr2.1:69524142-69524161 MS.gene002580:CDS 60.0%
CACCTTCAGCGCAAGATGGC+GGG + chr2.1:69524141-69524160 MS.gene002580:CDS 60.0%
ACCCCGCCATCTTGCGCTGA+AGG - chr2.1:69524146-69524165 None:intergenic 65.0%
!! TATCCGGTGGTGGCGGCGTT+GGG - chr2.1:69524241-69524260 None:intergenic 65.0%
!! TTATCCGGTGGTGGCGGCGT+TGG - chr2.1:69524242-69524261 None:intergenic 65.0%
TCTCCCAACGCCGCCACCAC+CGG + chr2.1:69524235-69524254 MS.gene002580:CDS 70.0%
! GCGGCGTTGGGAGAGGCATG+AGG - chr2.1:69524229-69524248 None:intergenic 70.0%
!! GGTGGTGGCGGCGTTGGGAG+AGG - chr2.1:69524236-69524255 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 69523975 69524529 69523975 ID=MS.gene002580
chr2.1 mRNA 69523975 69524529 69523975 ID=MS.gene002580.t1;Parent=MS.gene002580
chr2.1 exon 69523975 69524529 69523975 ID=MS.gene002580.t1.exon1;Parent=MS.gene002580.t1
chr2.1 CDS 69523975 69524529 69523975 ID=cds.MS.gene002580.t1;Parent=MS.gene002580.t1
Gene Sequence

>MS.gene002580

ATGAGAAACAGCATAAGATGTTGCATATCTTGCATTCTACCATGTGGAGCACTTGATGTGATCCGTATAGTACACTGCAACGGTCGAGTAGAAGAGATCAGTGGCAGCATCAAAGCAAGTGAAATCATGAAAACATACCCAAAACATGTTCTCAAGAAACCTTCTTCACCTTCAGCGCAAGATGGCGGGGTTGTTCCTAAGATTGTTGTTGTCCCTCCCGATGCTGATCTTCAACGTGGTAAGATTTACTTCCTCATGCCTCTCCCAACGCCGCCACCACCGGATAAAAATAATCACCGTCATAGCAAAAACTCGTCGGTAAGAAAGAAAAGAAAAGAACAGAACGAGAGAATATTAACAAACAACAGTAGAAGTAACGGTAACAGTAACAACAACATCGAGAACAGTGCTATGTTGGTTGTGTCTTCTGATCAGTACTTGACTGAGATTCTGTCTGAGAAGGTTTGTAGTCAGAGAGACAGAAGAAGAGGACGTGTTGCTGTGTGGAGACCTCATTTGGAGAGTATTTCTGAGTCACCAACAAATCTTCTATAA
Protein sequence

>MS.gene002580.t1

MRNSIRCCISCILPCGALDVIRIVHCNGRVEEISGSIKASEIMKTYPKHVLKKPSSPSAQDGGVVPKIVVVPPDADLQRGKIYFLMPLPTPPPPDKNNHRHSKNSSVRKKRKEQNERILTNNSRSNGNSNNNIENSAMLVVSSDQYLTEILSEKVCSQRDRRRGRVAVWRPHLESISESPTNLL