AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0095660

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0095660 MtrunA17_Chr3g0095001 93.220 177 11 1 1 177 1 176 9.27e-110 310
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 62 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAATCCTCGCCAATCGTTTC+TGG 0.178153 1_3:+992046 None:intergenic
GATCCGACGATCGGAGTTAC+TGG 0.318047 1_3:+992068 None:intergenic
GCGCGTGGTGGTTTCGGAAT+TGG 0.324550 1_3:+992314 None:intergenic
GTGAGAGCGCGTGGTGGTTT+CGG 0.347030 1_3:+992308 None:intergenic
TCGGAATTGGATTCGGGTAA+TGG 0.351220 1_3:+992327 None:intergenic
GGTGGTTTCGGAATTGGATT+CGG 0.353642 1_3:+992320 None:intergenic
GTGAGAGAGTGGTAGTAAAA+AGG 0.372256 1_3:+992370 None:intergenic
GTGGTTTCGGAATTGGATTC+GGG 0.381893 1_3:+992321 None:intergenic
CGGAATTGGATTCGGGTAAT+GGG 0.389896 1_3:+992328 None:intergenic
GGATTCACCGTGGTGGGGTC+AGG 0.431073 1_3:-992029 Msa0095660:CDS
GGTGTCGTGTTGTTGGGTTT+TGG 0.431727 1_3:+992278 None:intergenic
AATAGAAGTGACTCTGGTTA+TGG 0.445343 1_3:+992413 None:intergenic
GGGTGGATGTGACGGTTGAT+TGG 0.460462 1_3:+992198 None:intergenic
AGGAAACGGTGTCGTGTTGT+TGG 0.468497 1_3:+992271 None:intergenic
ACCGTGGTGGGGTCAGGTAC+CGG 0.479745 1_3:-992023 Msa0095660:CDS
GGAAACGGTGTCGTGTTGTT+GGG 0.481656 1_3:+992272 None:intergenic
AAGATCATGTCGTTGCCGTA+AGG 0.485439 1_3:+992102 None:intergenic
TGGCGAGGATTCACCGTGGT+GGG 0.487660 1_3:-992035 Msa0095660:CDS
TGGGGTCAGGTACCGGCCGA+TGG 0.490608 1_3:-992016 Msa0095660:CDS
CGGCAACGGCGGTGAGATAA+CGG 0.496678 1_3:+992147 None:intergenic
TCTCACCGCCGTTGCCGTCA+TGG 0.506128 1_3:-992141 Msa0095660:CDS
TTTCATTCGCCGCGATGAGA+AGG 0.508643 1_3:-991977 Msa0095660:CDS
GTCGATGGAGTTGAGATTGA+AGG 0.511417 1_3:+992251 None:intergenic
AACGGCAATATGCGTTGGTG+TGG 0.521157 1_3:+992177 None:intergenic
AAGGAAGAGTAAAACGGTGA+TGG 0.539615 1_3:+992389 None:intergenic
CACCGCCGTCAGATCCCTTA+CGG 0.546747 1_3:-992117 Msa0095660:CDS
TCGTTTCTGGATCCGACGAT+CGG 0.553335 1_3:+992059 None:intergenic
AGTTAACGGAACGTGGTCGA+TGG 0.554931 1_3:+992236 None:intergenic
AGTCTAACGGCAATATGCGT+TGG 0.555667 1_3:+992172 None:intergenic
ATCATCATGATGAGAAGGGT+TGG 0.556355 1_3:-991945 Msa0095660:CDS
ATCGCGGGCGCGTGAGAGAG+TGG 0.558600 1_3:+992359 None:intergenic
GGATGTGACGGTTGATTGGA+CGG 0.559632 1_3:+992202 None:intergenic
CGGAAATCGAGGAAAGTTAA+CGG 0.560543 1_3:+992222 None:intergenic
GGAGTTGAGATTGAAGGAAA+CGG 0.563289 1_3:+992257 None:intergenic
TGAGATAACGGAAAGTCTAA+CGG 0.564277 1_3:+992159 None:intergenic
TCGTCATCATCATGATGAGA+AGG 0.564544 1_3:-991950 Msa0095660:CDS
GGTTGATTGGACGGAAATCG+AGG 0.564608 1_3:+992211 None:intergenic
GGCGAGGATTCACCGTGGTG+GGG 0.570494 1_3:-992034 Msa0095660:CDS
GGCGGTGACCATGACGGCAA+CGG 0.573371 1_3:+992133 None:intergenic
GATGGAAATAGAAGTGACTC+TGG 0.580506 1_3:+992407 None:intergenic
GTTGGTGTGGGTGGATGTGA+CGG 0.586166 1_3:+992190 None:intergenic
GCAATATGCGTTGGTGTGGG+TGG 0.597606 1_3:+992181 None:intergenic
AGTGACTCTGGTTATGGCCA+TGG 0.597966 1_3:+992419 None:intergenic
AGATCATGTCGTTGCCGTAA+GGG 0.599013 1_3:+992103 None:intergenic
CGTCATCATCATGATGAGAA+GGG 0.603183 1_3:-991949 Msa0095660:CDS
CGTTGCCGTAAGGGATCTGA+CGG 0.605253 1_3:+992112 None:intergenic
ATGCCAGTAACTCCGATCGT+CGG 0.606961 1_3:-992071 Msa0095660:CDS
CGAGGAAAGTTAACGGAACG+TGG 0.607466 1_3:+992229 None:intergenic
TTGGCGAGGATTCACCGTGG+TGG 0.615362 1_3:-992036 Msa0095660:CDS
TCTGACGGCGGTGACCATGA+CGG 0.619366 1_3:+992127 None:intergenic
TCGTCGGATCCAGAAACGAT+TGG 0.624574 1_3:-992055 Msa0095660:CDS
GGTGACCATGACGGCAACGG+CGG 0.633427 1_3:+992136 None:intergenic
TCGTTATAAGTCATCACCAT+CGG 0.635222 1_3:+992000 None:intergenic
TATAAGTCATCACCATCGGC+CGG 0.644387 1_3:+992004 None:intergenic
GGAAGAACTGTGAGAGCGCG+TGG 0.644400 1_3:+992299 None:intergenic
ACGGCAATATGCGTTGGTGT+GGG 0.646745 1_3:+992178 None:intergenic
TGCCGTAAGGGATCTGACGG+CGG 0.663675 1_3:+992115 None:intergenic
GCCGGTACCTGACCCCACCA+CGG 0.667549 1_3:+992022 None:intergenic
GGATCCAGAAACGATTGGCG+AGG 0.676844 1_3:-992050 Msa0095660:CDS
AGAACTGTGAGAGCGCGTGG+TGG 0.748898 1_3:+992302 None:intergenic
GACGACGATCCTTCTCATCG+CGG 0.765053 1_3:+991968 None:intergenic
CGATTGGCGAGGATTCACCG+TGG 0.837550 1_3:-992039 Msa0095660:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGTAAAAAGGAAGAGTAAAA+CGG + chr1_3:991943-991962 None:intergenic 25.0%
AATAGAAGTGACTCTGGTTA+TGG + chr1_3:991913-991932 None:intergenic 35.0%
!! TGAGATAACGGAAAGTCTAA+CGG + chr1_3:992167-992186 None:intergenic 35.0%
TCGTTATAAGTCATCACCAT+CGG + chr1_3:992326-992345 None:intergenic 35.0%
GATGGAAATAGAAGTGACTC+TGG + chr1_3:991919-991938 None:intergenic 40.0%
AAGGAAGAGTAAAACGGTGA+TGG + chr1_3:991937-991956 None:intergenic 40.0%
GTGAGAGAGTGGTAGTAAAA+AGG + chr1_3:991956-991975 None:intergenic 40.0%
!!! TAATGGGTTTTGAAGATCGC+GGG + chr1_3:991982-992001 None:intergenic 40.0%
!!! GTAATGGGTTTTGAAGATCG+CGG + chr1_3:991983-992002 None:intergenic 40.0%
GGAGTTGAGATTGAAGGAAA+CGG + chr1_3:992069-992088 None:intergenic 40.0%
CGGAAATCGAGGAAAGTTAA+CGG + chr1_3:992104-992123 None:intergenic 40.0%
TCGTCATCATCATGATGAGA+AGG - chr1_3:992373-992392 Msa0095660:CDS 40.0%
CGTCATCATCATGATGAGAA+GGG - chr1_3:992374-992393 Msa0095660:CDS 40.0%
ATCATCATGATGAGAAGGGT+TGG - chr1_3:992378-992397 Msa0095660:CDS 40.0%
CGGAATTGGATTCGGGTAAT+GGG + chr1_3:991998-992017 None:intergenic 45.0%
TCGGAATTGGATTCGGGTAA+TGG + chr1_3:991999-992018 None:intergenic 45.0%
GTGGTTTCGGAATTGGATTC+GGG + chr1_3:992005-992024 None:intergenic 45.0%
GGTGGTTTCGGAATTGGATT+CGG + chr1_3:992006-992025 None:intergenic 45.0%
GTCGATGGAGTTGAGATTGA+AGG + chr1_3:992075-992094 None:intergenic 45.0%
AGTCTAACGGCAATATGCGT+TGG + chr1_3:992154-992173 None:intergenic 45.0%
AGATCATGTCGTTGCCGTAA+GGG + chr1_3:992223-992242 None:intergenic 45.0%
AAGATCATGTCGTTGCCGTA+AGG + chr1_3:992224-992243 None:intergenic 45.0%
TATAAGTCATCACCATCGGC+CGG + chr1_3:992322-992341 None:intergenic 45.0%
!! GGTGTCGTGTTGTTGGGTTT+TGG + chr1_3:992048-992067 None:intergenic 50.0%
!! GGAAACGGTGTCGTGTTGTT+GGG + chr1_3:992054-992073 None:intergenic 50.0%
!! AGGAAACGGTGTCGTGTTGT+TGG + chr1_3:992055-992074 None:intergenic 50.0%
AGTTAACGGAACGTGGTCGA+TGG + chr1_3:992090-992109 None:intergenic 50.0%
CGAGGAAAGTTAACGGAACG+TGG + chr1_3:992097-992116 None:intergenic 50.0%
GGTTGATTGGACGGAAATCG+AGG + chr1_3:992115-992134 None:intergenic 50.0%
GGATGTGACGGTTGATTGGA+CGG + chr1_3:992124-992143 None:intergenic 50.0%
! ACGGCAATATGCGTTGGTGT+GGG + chr1_3:992148-992167 None:intergenic 50.0%
! AACGGCAATATGCGTTGGTG+TGG + chr1_3:992149-992168 None:intergenic 50.0%
ATGCCAGTAACTCCGATCGT+CGG - chr1_3:992252-992271 Msa0095660:CDS 50.0%
! TCGTTTCTGGATCCGACGAT+CGG + chr1_3:992267-992286 None:intergenic 50.0%
TCGTCGGATCCAGAAACGAT+TGG - chr1_3:992268-992287 Msa0095660:CDS 50.0%
GAATCCTCGCCAATCGTTTC+TGG + chr1_3:992280-992299 None:intergenic 50.0%
TTTCATTCGCCGCGATGAGA+AGG - chr1_3:992346-992365 Msa0095660:CDS 50.0%
GGGTGGATGTGACGGTTGAT+TGG + chr1_3:992128-992147 None:intergenic 55.0%
GTTGGTGTGGGTGGATGTGA+CGG + chr1_3:992136-992155 None:intergenic 55.0%
! GCAATATGCGTTGGTGTGGG+TGG + chr1_3:992145-992164 None:intergenic 55.0%
CGTTGCCGTAAGGGATCTGA+CGG + chr1_3:992214-992233 None:intergenic 55.0%
GATCCGACGATCGGAGTTAC+TGG + chr1_3:992258-992277 None:intergenic 55.0%
GGATCCAGAAACGATTGGCG+AGG - chr1_3:992273-992292 Msa0095660:CDS 55.0%
GACGACGATCCTTCTCATCG+CGG + chr1_3:992358-992377 None:intergenic 55.0%
GCGCGTGGTGGTTTCGGAAT+TGG + chr1_3:992012-992031 None:intergenic 60.0%
! GTGAGAGCGCGTGGTGGTTT+CGG + chr1_3:992018-992037 None:intergenic 60.0%
! AGAACTGTGAGAGCGCGTGG+TGG + chr1_3:992024-992043 None:intergenic 60.0%
! GGAAGAACTGTGAGAGCGCG+TGG + chr1_3:992027-992046 None:intergenic 60.0%
CGGCAACGGCGGTGAGATAA+CGG + chr1_3:992179-992198 None:intergenic 60.0%
TCTGACGGCGGTGACCATGA+CGG + chr1_3:992199-992218 None:intergenic 60.0%
CACCGCCGTCAGATCCCTTA+CGG - chr1_3:992206-992225 Msa0095660:CDS 60.0%
TGCCGTAAGGGATCTGACGG+CGG + chr1_3:992211-992230 None:intergenic 60.0%
CGATTGGCGAGGATTCACCG+TGG - chr1_3:992284-992303 Msa0095660:CDS 60.0%
TTGGCGAGGATTCACCGTGG+TGG - chr1_3:992287-992306 Msa0095660:CDS 60.0%
TGGCGAGGATTCACCGTGGT+GGG - chr1_3:992288-992307 Msa0095660:CDS 60.0%
TCTCACCGCCGTTGCCGTCA+TGG - chr1_3:992182-992201 Msa0095660:CDS 65.0%
GGTGACCATGACGGCAACGG+CGG + chr1_3:992190-992209 None:intergenic 65.0%
GGCGGTGACCATGACGGCAA+CGG + chr1_3:992193-992212 None:intergenic 65.0%
GGCGAGGATTCACCGTGGTG+GGG - chr1_3:992289-992308 Msa0095660:CDS 65.0%
! GGATTCACCGTGGTGGGGTC+AGG - chr1_3:992294-992313 Msa0095660:CDS 65.0%
! ACCGTGGTGGGGTCAGGTAC+CGG - chr1_3:992300-992319 Msa0095660:CDS 65.0%
ATCGCGGGCGCGTGAGAGAG+TGG + chr1_3:991967-991986 None:intergenic 70.0%
GCCGGTACCTGACCCCACCA+CGG + chr1_3:992304-992323 None:intergenic 70.0%
!! TGGGGTCAGGTACCGGCCGA+TGG - chr1_3:992307-992326 Msa0095660:CDS 70.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 991906 992439 991906 ID=Msa0095660;Name=Msa0095660
chr1_3 mRNA 991906 992439 991906 ID=Msa0095660-mRNA-1;Parent=Msa0095660;Name=Msa0095660-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|177
chr1_3 exon 991906 992439 991906 ID=Msa0095660-mRNA-1:exon:127;Parent=Msa0095660-mRNA-1
chr1_3 CDS 991906 992439 991906 ID=Msa0095660-mRNA-1:cds;Parent=Msa0095660-mRNA-1
Gene Sequence

>Msa0095660

ATGGCCATAACCAGAGTCACTTCTATTTCCATCACCGTTTTACTCTTCCTTTTTACTACCACTCTCTCACGCGCCCGCGATCTTCAAAACCCATTACCCGAATCCAATTCCGAAACCACCACGCGCTCTCACAGTTCTTCCAAAACCCAACAACACGACACCGTTTCCTTCAATCTCAACTCCATCGACCACGTTCCGTTAACTTTCCTCGATTTCCGTCCAATCAACCGTCACATCCACCCACACCAACGCATATTGCCGTTAGACTTTCCGTTATCTCACCGCCGTTGCCGTCATGGTCACCGCCGTCAGATCCCTTACGGCAACGACATGATCTTGTCGAAAGATGCCAGTAACTCCGATCGTCGGATCCAGAAACGATTGGCGAGGATTCACCGTGGTGGGGTCAGGTACCGGCCGATGGTGATGACTTATAACGATTTCATTCGCCGCGATGAGAAGGATCGTCGTCATCATCATGATGAGAAGGGTTGGTTTGAGAAGAAGATTCATGAGTTGTTGAACTTGTTCTAA
Protein sequence

>Msa0095660

MAITRVTSISITVLLFLFTTTLSRARDLQNPLPESNSETTTRSHSSSKTQQHDTVSFNLNSIDHVPLTFLDFRPINRHIHPHQRILPLDFPLSHRRCRHGHRRQIPYGNDMILSKDASNSDRRIQKRLARIHRGGVRYRPMVMTYNDFIRRDEKDRRHHHDEKGWFEKKIHELLNLF*