AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54297

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54297.t1 MTR_2g016150 96.774 186 4 1 1 184 1 186 5.25e-129 360
MS.gene54297.t1 MTR_3g031140 45.506 178 88 4 1 178 1 169 3.47e-45 147
MS.gene54297.t1 MTR_5g074290 38.798 183 81 5 1 178 1 157 1.21e-32 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54297.t1 AT1G29195 56.915 188 71 3 1 178 1 188 1.42e-67 204
MS.gene54297.t1 AT2G30230 40.642 187 89 6 1 178 1 174 6.73e-36 124
MS.gene54297.t1 AT1G06980 40.761 184 85 4 1 178 1 166 2.61e-35 122

Find 33 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCCGGTGGTGGCGGCGTT+GGG 0.341375 2.3:-69319287 None:intergenic
GGTTTCTTGAGAACATGTTT+TGG 0.350154 2.3:-69319162 None:intergenic
CACCTTCAGCGCAAGATGGC+GGG 0.354822 2.3:+69319190 MS.gene54297:CDS
TGCTGTGTGGAGACCTCATT+TGG 0.366621 2.3:+69319521 MS.gene54297:CDS
GGAGGGACAACAACAATCTT+AGG 0.387106 2.3:-69319219 None:intergenic
AACCGTTATAGAAGATTTGT+TGG 0.403215 2.3:-69319561 None:intergenic
TTATCCGGTGGTGGCGGCGT+TGG 0.422064 2.3:-69319288 None:intergenic
GACCGTTGCAGTGTACTATA+CGG 0.423911 2.3:-69319086 None:intergenic
GGTGGTGGCGGCGTTGGGAG+AGG 0.431618 2.3:-69319282 None:intergenic
ACCCCGCCATCTTGCGCTGA+AGG 0.489813 2.3:-69319192 None:intergenic
TCTTGCGCTGAAGGTGAAGA+AGG 0.505753 2.3:-69319183 None:intergenic
GACTGAGATTCTGTCTGAGA+AGG 0.517425 2.3:+69319464 MS.gene54297:CDS
TCACCTTCAGCGCAAGATGG+CGG 0.520403 2.3:+69319189 MS.gene54297:CDS
CACCAACAAATCTTCTATAA+CGG 0.521213 2.3:+69319559 MS.gene54297:CDS
TCTCCCAACGCCGCCACCAC+CGG 0.524822 2.3:+69319284 MS.gene54297:CDS
CATCGAGAACAGTGCTATGT+TGG 0.527832 2.3:+69319419 MS.gene54297:CDS
ACCTTCAGCGCAAGATGGCG+GGG 0.527946 2.3:+69319191 MS.gene54297:CDS
CCACGTTGAAGATCAGCATC+GGG 0.542465 2.3:-69319240 None:intergenic
TCTTCACCTTCAGCGCAAGA+TGG 0.556088 2.3:+69319186 MS.gene54297:CDS
ACCACGTTGAAGATCAGCAT+CGG 0.572486 2.3:-69319241 None:intergenic
GCGGCGTTGGGAGAGGCATG+AGG 0.582625 2.3:-69319275 None:intergenic
AGTCAGAGAGACAGAAGAAG+AGG 0.589679 2.3:+69319492 MS.gene54297:CDS
TCAGAAATACTCTCCAAATG+AGG 0.591665 2.3:-69319534 None:intergenic
ACAAACAACGGTAGAAGTAA+CGG 0.598405 2.3:+69319381 MS.gene54297:CDS
CGTTGAAGATCAGCATCGGG+AGG 0.643072 2.3:-69319237 None:intergenic
GTTGAAGATCAGCATCGGGA+GGG 0.647155 2.3:-69319236 None:intergenic
GAGAGAATATTAACAAACAA+CGG 0.660955 2.3:+69319369 MS.gene54297:CDS
GGTCGAGTAGAAGAGATCAG+TGG 0.670260 2.3:+69319105 MS.gene54297:CDS
ATCACATCAAGTGCTCCACA+TGG 0.674792 2.3:-69319063 None:intergenic
ATATCTTGCATTCTACCATG+TGG 0.683335 2.3:+69319048 MS.gene54297:CDS
GAAGAGGACGTGTTGCTGTG+TGG 0.686286 2.3:+69319508 MS.gene54297:CDS
ATCCGTATAGTACACTGCAA+CGG 0.690119 2.3:+69319084 MS.gene54297:CDS
CCCGATGCTGATCTTCAACG+TGG 0.691291 2.3:+69319240 MS.gene54297:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GAGAGAATATTAACAAACAA+CGG + chr2.3:69319369-69319388 MS.gene54297:CDS 25.0%
! GTTTCTTGAGAACATGTTTT+GGG - chr2.3:69319164-69319183 None:intergenic 30.0%
!!! TGACGGTGATTATTTTTATC+CGG - chr2.3:69319306-69319325 None:intergenic 30.0%
ACAAACAACGGTAGAAGTAA+CGG + chr2.3:69319381-69319400 MS.gene54297:CDS 35.0%
ATATCTTGCATTCTACCATG+TGG + chr2.3:69319048-69319067 MS.gene54297:CDS 35.0%
TCAGAAATACTCTCCAAATG+AGG - chr2.3:69319537-69319556 None:intergenic 35.0%
! GGTTTCTTGAGAACATGTTT+TGG - chr2.3:69319165-69319184 None:intergenic 35.0%
!!! TGATTATTTTTATCCGGTGG+TGG - chr2.3:69319300-69319319 None:intergenic 35.0%
ATCCGTATAGTACACTGCAA+CGG + chr2.3:69319084-69319103 MS.gene54297:CDS 40.0%
!!! CGGTGATTATTTTTATCCGG+TGG - chr2.3:69319303-69319322 None:intergenic 40.0%
!!! TTATTTTTATCCGGTGGTGG+CGG - chr2.3:69319297-69319316 None:intergenic 40.0%
ACCACGTTGAAGATCAGCAT+CGG - chr2.3:69319244-69319263 None:intergenic 45.0%
AGTCAGAGAGACAGAAGAAG+AGG + chr2.3:69319492-69319511 MS.gene54297:CDS 45.0%
ATCACATCAAGTGCTCCACA+TGG - chr2.3:69319066-69319085 None:intergenic 45.0%
CATCGAGAACAGTGCTATGT+TGG + chr2.3:69319419-69319438 MS.gene54297:CDS 45.0%
CCGTCATAGCAAAAACTCGT+CGG + chr2.3:69319320-69319339 MS.gene54297:CDS 45.0%
GACCGTTGCAGTGTACTATA+CGG - chr2.3:69319089-69319108 None:intergenic 45.0%
GACTGAGATTCTGTCTGAGA+AGG + chr2.3:69319464-69319483 MS.gene54297:CDS 45.0%
GGAGGGACAACAACAATCTT+AGG - chr2.3:69319222-69319241 None:intergenic 45.0%
!! CCGACGAGTTTTTGCTATGA+CGG - chr2.3:69319323-69319342 None:intergenic 45.0%
CCACGTTGAAGATCAGCATC+GGG - chr2.3:69319243-69319262 None:intergenic 50.0%
GGTCGAGTAGAAGAGATCAG+TGG + chr2.3:69319105-69319124 MS.gene54297:CDS 50.0%
TCTTCACCTTCAGCGCAAGA+TGG + chr2.3:69319186-69319205 MS.gene54297:CDS 50.0%
TCTTGCGCTGAAGGTGAAGA+AGG - chr2.3:69319186-69319205 None:intergenic 50.0%
TGCTGTGTGGAGACCTCATT+TGG + chr2.3:69319521-69319540 MS.gene54297:CDS 50.0%
! GTTGAAGATCAGCATCGGGA+GGG - chr2.3:69319239-69319258 None:intergenic 50.0%
CCCGATGCTGATCTTCAACG+TGG + chr2.3:69319240-69319259 MS.gene54297:CDS 55.0%
TCACCTTCAGCGCAAGATGG+CGG + chr2.3:69319189-69319208 MS.gene54297:CDS 55.0%
! CGTTGAAGATCAGCATCGGG+AGG - chr2.3:69319240-69319259 None:intergenic 55.0%
! GAAGAGGACGTGTTGCTGTG+TGG + chr2.3:69319508-69319527 MS.gene54297:CDS 55.0%
ACCTTCAGCGCAAGATGGCG+GGG + chr2.3:69319191-69319210 MS.gene54297:CDS 60.0%
CACCTTCAGCGCAAGATGGC+GGG + chr2.3:69319190-69319209 MS.gene54297:CDS 60.0%
ACCCCGCCATCTTGCGCTGA+AGG - chr2.3:69319195-69319214 None:intergenic 65.0%
!! TATCCGGTGGTGGCGGCGTT+GGG - chr2.3:69319290-69319309 None:intergenic 65.0%
!! TTATCCGGTGGTGGCGGCGT+TGG - chr2.3:69319291-69319310 None:intergenic 65.0%
TCTCCCAACGCCGCCACCAC+CGG + chr2.3:69319284-69319303 MS.gene54297:CDS 70.0%
! GCGGCGTTGGGAGAGGCATG+AGG - chr2.3:69319278-69319297 None:intergenic 70.0%
!! GGTGGTGGCGGCGTTGGGAG+AGG - chr2.3:69319285-69319304 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 69319024 69319578 69319024 ID=MS.gene54297
chr2.3 mRNA 69319024 69319578 69319024 ID=MS.gene54297.t1;Parent=MS.gene54297
chr2.3 exon 69319024 69319578 69319024 ID=MS.gene54297.t1.exon1;Parent=MS.gene54297.t1
chr2.3 CDS 69319024 69319578 69319024 ID=cds.MS.gene54297.t1;Parent=MS.gene54297.t1
Gene Sequence

>MS.gene54297

ATGAGAAACAGCATAAGATGTTGCATATCTTGCATTCTACCATGTGGAGCACTTGATGTGATCCGTATAGTACACTGCAACGGTCGAGTAGAAGAGATCAGTGGCAGCATCAAAGCAAGTGAAATCATGAAAACATACCCAAAACATGTTCTCAAGAAACCTTCTTCACCTTCAGCGCAAGATGGCGGGGTTGTTCCTAAGATTGTTGTTGTCCCTCCCGATGCTGATCTTCAACGTGGTAAGATTTACTTCCTCATGCCTCTCCCAACGCCGCCACCACCGGATAAAAATAATCACCGTCATAGCAAAAACTCGTCGGTAAGAAAGAAAAGAAAAGAACAGAACGAGAGAATATTAACAAACAACGGTAGAAGTAACGGTAACAGTAACAACAACATCGAGAACAGTGCTATGTTGGTTGTGTCTTCTGATCAGTACTTGACTGAGATTCTGTCTGAGAAGGTTTGTAGTCAGAGAGACAGAAGAAGAGGACGTGTTGCTGTGTGGAGACCTCATTTGGAGAGTATTTCTGAGTCACCAACAAATCTTCTATAA
Protein sequence

>MS.gene54297.t1

MRNSIRCCISCILPCGALDVIRIVHCNGRVEEISGSIKASEIMKTYPKHVLKKPSSPSAQDGGVVPKIVVVPPDADLQRGKIYFLMPLPTPPPPDKNNHRHSKNSSVRKKRKEQNERILTNNGRSNGNSNNNIENSAMLVVSSDQYLTEILSEKVCSQRDRRRGRVAVWRPHLESISESPTNLL