AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene070748

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 34 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGAATCTGGCACAAATTC+TGG 0.145064 2.1:-24559895 None:intergenic
AAAGCAGATGTTTATAGTTT+TGG 0.214365 2.1:+24559079 MS.gene070748:CDS
AGGTTCAGATTTCAACAAAA+AGG 0.323029 2.1:+24559765 MS.gene070748:CDS
TTCCTCCTTTGACCGATATA+TGG 0.363263 2.1:-24559140 None:intergenic
TCCATGACTTCACTTGAATC+TGG 0.374902 2.1:-24559907 None:intergenic
TAACCATGCATTGCATGTTC+AGG 0.404880 2.1:-24559046 None:intergenic
GAGCTAGTTGACAGAAGATT+AGG 0.410976 2.1:+24559745 MS.gene070748:CDS
AAGCATTCTATCTTCTAGAA+TGG 0.424346 2.1:+24559161 MS.gene070748:CDS
GAAAGAGAAAGGTGACCTAA+TGG 0.433673 2.1:+24559723 MS.gene070748:CDS
CCCTCTATGTCGTCAGTTGT+AGG 0.439053 2.1:+24559847 MS.gene070748:CDS
TCAATTATGCAGTGGATACA+TGG 0.464209 2.1:+24559021 None:intergenic
TTCTGTCAACTAGCTCCATT+AGG 0.468864 2.1:-24559738 None:intergenic
TGCAATGCATGGTTATTTGA+GGG 0.482423 2.1:+24559054 MS.gene070748:CDS
AGCATTCTATCTTCTAGAAT+GGG 0.484637 2.1:+24559162 MS.gene070748:CDS
GAAAGAGCAACACCATATAT+CGG 0.486359 2.1:+24559128 MS.gene070748:CDS
ATGCAATGCATGGTTATTTG+AGG 0.494795 2.1:+24559053 MS.gene070748:CDS
GCACATATGTTGAAAGAGAA+AGG 0.528089 2.1:+24559712 MS.gene070748:CDS
TTGAAGTGACATTGGTGCAT+AGG 0.530471 2.1:-24559816 None:intergenic
TCAGTTGTAGGCATGCTTGA+AGG 0.534432 2.1:+24559859 MS.gene070748:CDS
AGTCATGGATGAAAAGAAGA+TGG 0.542880 2.1:+24559921 MS.gene070748:CDS
CTGACGACATAGAGGGCCTA+AGG 0.553244 2.1:-24559840 None:intergenic
CCTAAGGTTTGAAGTGACAT+TGG 0.563119 2.1:-24559824 None:intergenic
GCCTACAACTGACGACATAG+AGG 0.589781 2.1:-24559848 None:intergenic
CCAATGTCACTTCAAACCTT+AGG 0.591823 2.1:+24559824 MS.gene070748:CDS
GCCAGATTCAAGTGAAGTCA+TGG 0.594555 2.1:+24559906 MS.gene070748:CDS
CAACACCATATATCGGTCAA+AGG 0.604837 2.1:+24559135 MS.gene070748:CDS
CTTTCCGCTAGCGATTTCCA+AGG 0.613368 2.1:-24559110 None:intergenic
CACCATATATCGGTCAAAGG+AGG 0.641518 2.1:+24559138 MS.gene070748:CDS
GCTCCTGAACATGCAATGCA+TGG 0.644887 2.1:+24559043 MS.gene070748:CDS
GTTGCCTTGGAAATCGCTAG+CGG 0.647484 2.1:+24559106 MS.gene070748:CDS
CCTACAACTGACGACATAGA+GGG 0.661360 2.1:-24559847 None:intergenic
AGCCACATTGATCATCACCA+TGG 0.708704 2.1:-24559791 None:intergenic
CATGCTTGAAGGAAGAACTG+TGG 0.711872 2.1:+24559870 MS.gene070748:CDS
AGCCATGGTGATGATCAATG+TGG 0.845403 2.1:+24559789 MS.gene070748:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTCGATAACAATTTAGA+TGG - chr2.1:24559610-24559629 None:intergenic 20.0%
!! CATATTGAAATTTAGTCATT+AGG + chr2.1:24559188-24559207 MS.gene070748:intron 20.0%
!!! TTCTCTTTTGTAAATTACTT+GGG + chr2.1:24559660-24559679 MS.gene070748:intron 20.0%
! AGTAATTTACAAAAGAGAAG+TGG - chr2.1:24559659-24559678 None:intergenic 25.0%
!! AAACAATTCTTTGTTTCAAC+AGG + chr2.1:24559690-24559709 MS.gene070748:intron 25.0%
!! AAAGCAGATGTTTATAGTTT+TGG + chr2.1:24559079-24559098 MS.gene070748:CDS 25.0%
!! CTTCTCTTTTGTAAATTACT+TGG + chr2.1:24559659-24559678 MS.gene070748:intron 25.0%
!!! TCAACTCTAAAATATGTCAA+AGG + chr2.1:24559303-24559322 MS.gene070748:intron 25.0%
AGGTTCAGATTTCAACAAAA+AGG + chr2.1:24559765-24559784 MS.gene070748:CDS 30.0%
AGTGACGTTCAAACATAATT+GGG + chr2.1:24559455-24559474 MS.gene070748:intron 30.0%
ATAAGTTGTTGTCTTCTTGT+TGG - chr2.1:24559390-24559409 None:intergenic 30.0%
ATGAGGAAAGACATAAGTAA+AGG - chr2.1:24559362-24559381 None:intergenic 30.0%
GGTTAATTGTCTTGAATGAA+TGG + chr2.1:24559520-24559539 MS.gene070748:intron 30.0%
GTTAGTGACGTTCAAAATTA+CGG + chr2.1:24559499-24559518 MS.gene070748:intron 30.0%
GTTCAATTATGTTTAGCAGA+TGG - chr2.1:24559579-24559598 None:intergenic 30.0%
TAGTGACGTTCAAACATAAT+TGG + chr2.1:24559454-24559473 MS.gene070748:intron 30.0%
TGAGGAAAGACATAAGTAAA+GGG - chr2.1:24559361-24559380 None:intergenic 30.0%
! AAGCATTCTATCTTCTAGAA+TGG + chr2.1:24559161-24559180 MS.gene070748:CDS 30.0%
!! ACTCTAAAATATGTCAAAGG+AGG + chr2.1:24559306-24559325 MS.gene070748:intron 30.0%
!! AGCATTCTATCTTCTAGAAT+GGG + chr2.1:24559162-24559181 MS.gene070748:CDS 30.0%
AGTCATGGATGAAAAGAAGA+TGG + chr2.1:24559921-24559940 MS.gene070748:CDS 35.0%
ATGCAATGCATGGTTATTTG+AGG + chr2.1:24559053-24559072 MS.gene070748:CDS 35.0%
GAAAGAGCAACACCATATAT+CGG + chr2.1:24559128-24559147 MS.gene070748:CDS 35.0%
GAGGAAAGACATAAGTAAAG+GGG - chr2.1:24559360-24559379 None:intergenic 35.0%
GCACATATGTTGAAAGAGAA+AGG + chr2.1:24559712-24559731 MS.gene070748:CDS 35.0%
TGCAATGCATGGTTATTTGA+GGG + chr2.1:24559054-24559073 MS.gene070748:CDS 35.0%
TGGATGAAAAGAAGATGGAA+TGG + chr2.1:24559926-24559945 MS.gene070748:CDS 35.0%
TTTCAACAAAAAGGAAGCCA+TGG + chr2.1:24559774-24559793 MS.gene070748:CDS 35.0%
!!! TAGTTTTGGAATTGTTGCCT+TGG + chr2.1:24559093-24559112 MS.gene070748:CDS 35.0%
CAACACCATATATCGGTCAA+AGG + chr2.1:24559135-24559154 MS.gene070748:CDS 40.0%
CTTGAATCTGGCACAAATTC+TGG - chr2.1:24559898-24559917 None:intergenic 40.0%
GAAAGAGAAAGGTGACCTAA+TGG + chr2.1:24559723-24559742 MS.gene070748:CDS 40.0%
GAGCTAGTTGACAGAAGATT+AGG + chr2.1:24559745-24559764 MS.gene070748:CDS 40.0%
TAACCATGCATTGCATGTTC+AGG - chr2.1:24559049-24559068 None:intergenic 40.0%
TCCATGACTTCACTTGAATC+TGG - chr2.1:24559910-24559929 None:intergenic 40.0%
TTCCTCCTTTGACCGATATA+TGG - chr2.1:24559143-24559162 None:intergenic 40.0%
TTCTGTCAACTAGCTCCATT+AGG - chr2.1:24559741-24559760 None:intergenic 40.0%
TTGAAGTGACATTGGTGCAT+AGG - chr2.1:24559819-24559838 None:intergenic 40.0%
TTGTTGTCTTCTTGTTGGTC+AGG - chr2.1:24559385-24559404 None:intergenic 40.0%
! CCAATGTCACTTCAAACCTT+AGG + chr2.1:24559824-24559843 MS.gene070748:CDS 40.0%
! CCTAAGGTTTGAAGTGACAT+TGG - chr2.1:24559827-24559846 None:intergenic 40.0%
AGCCACATTGATCATCACCA+TGG - chr2.1:24559794-24559813 None:intergenic 45.0%
CACCATATATCGGTCAAAGG+AGG + chr2.1:24559138-24559157 MS.gene070748:CDS 45.0%
CATGCTTGAAGGAAGAACTG+TGG + chr2.1:24559870-24559889 MS.gene070748:CDS 45.0%
CCTACAACTGACGACATAGA+GGG - chr2.1:24559850-24559869 None:intergenic 45.0%
GCCAGATTCAAGTGAAGTCA+TGG + chr2.1:24559906-24559925 MS.gene070748:CDS 45.0%
TCAGTTGTAGGCATGCTTGA+AGG + chr2.1:24559859-24559878 MS.gene070748:CDS 45.0%
TCTTCTTGTTGGTCAGGATG+AGG - chr2.1:24559379-24559398 None:intergenic 45.0%
! AGCCATGGTGATGATCAATG+TGG + chr2.1:24559789-24559808 MS.gene070748:CDS 45.0%
CCCTCTATGTCGTCAGTTGT+AGG + chr2.1:24559847-24559866 MS.gene070748:CDS 50.0%
CTTTCCGCTAGCGATTTCCA+AGG - chr2.1:24559113-24559132 None:intergenic 50.0%
GCCTACAACTGACGACATAG+AGG - chr2.1:24559851-24559870 None:intergenic 50.0%
GCTCCTGAACATGCAATGCA+TGG + chr2.1:24559043-24559062 MS.gene070748:CDS 50.0%
GTTGCCTTGGAAATCGCTAG+CGG + chr2.1:24559106-24559125 MS.gene070748:CDS 50.0%
CTGACGACATAGAGGGCCTA+AGG - chr2.1:24559843-24559862 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 24559033 24559945 24559033 ID=MS.gene070748
chr2.1 mRNA 24559033 24559945 24559033 ID=MS.gene070748.t1;Parent=MS.gene070748
chr2.1 exon 24559033 24559183 24559033 ID=MS.gene070748.t1.exon1;Parent=MS.gene070748.t1
chr2.1 CDS 24559033 24559183 24559033 ID=cds.MS.gene070748.t1;Parent=MS.gene070748.t1
chr2.1 exon 24559712 24559945 24559712 ID=MS.gene070748.t1.exon2;Parent=MS.gene070748.t1
chr2.1 CDS 24559712 24559945 24559712 ID=cds.MS.gene070748.t1;Parent=MS.gene070748.t1
Gene Sequence

>MS.gene070748

TGGATACATGGCTCCTGAACATGCAATGCATGGTTATTTGAGGGACAAAGCAGATGTTTATAGTTTTGGAATTGTTGCCTTGGAAATCGCTAGCGGAAAGAGCAACACCATATATCGGTCAAAGGAGGAAGCATTCTATCTTCTAGAATGGGTAACATATTGAAATTTAGTCATTAGGTCATGCAAATCTGATTATTGATGCTACTATCTACTGACACTTCATTTTTGTGTCTTACATATACTGTTGTTGTTCACTGTTAATCTAATAATTCAACTCTAAAATATGTCAAAGGAGGAAGCATTCTATCTTCATATATCATGTTTCCCCTTTACTTATGTCTTTCCTCATCCTGACCAACAAGAAGACAACAACTTATCAAAAATATTAAGAATTAAGATACAATCTGCTAAACGTAATTGCTAGTGACGTTCAAACATAATTGGGTTTAAAAATTTGAAAATCATTGTTAGTGACGTTCAAAATTACGGTTAATTGTCTTGAATGAATGGTTAATTAGTTGTGACACTTGTTATATTCATTAACCATCTGCTAAACATAATTGAACTACAATAACCATCTAAATTGTTATCGAATTTTGATGTCAAATTTGTGTATCATAATACCACTTCTCTTTTGTAAATTACTTGGGTTTCACAAAACAATTCTTTGTTTCAACAGGCACATATGTTGAAAGAGAAAGGTGACCTAATGGAGCTAGTTGACAGAAGATTAGGTTCAGATTTCAACAAAAAGGAAGCCATGGTGATGATCAATGTGGCTCTCCTATGCACCAATGTCACTTCAAACCTTAGGCCCTCTATGTCGTCAGTTGTAGGCATGCTTGAAGGAAGAACTGTGGTTCCAGAATTTGTGCCAGATTCAAGTGAAGTCATGGATGAAAAGAAGATGGAA
Protein sequence

>MS.gene070748.t1

WIHGSUTCNAWLFEGQSRCLUFWNCCLGNRURKEQHHISVKGGSILSSRMGTYVERERUPNGASUQKIRFRFQQKGSHGDDQCGSPMHQCHFKPUALYVVSCRHAURKNCGSRICARFKUSHGUKEDG