AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0369210

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0369210 MtrunA17_Chr3g0113431 99.167 120 1 0 1 120 11 130 1.17e-86 248
Msa0369210 MtrunA17_Chr2g0300391 46.250 80 43 0 26 105 6 85 3.78e-22 84.0
Msa0369210 MtrunA17_Chr4g0070681 52.857 70 33 0 36 105 17 86 4.43e-22 84.0
Msa0369210 MtrunA17_Chr8g0343731 42.500 80 46 0 26 105 6 85 3.07e-19 76.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0369210 AT2G40080.1 68.293 82 25 1 29 109 14 95 7.98e-35 116
Msa0369210 AT2G29950.1 50.549 91 44 1 24 113 21 111 1.46e-23 88.6
Msa0369210 AT2G06255.1 52.857 70 33 0 36 105 17 86 8.87e-22 83.6
Msa0369210 AT1G17455.2 47.500 80 42 0 26 105 6 85 1.22e-20 80.5
Msa0369210 AT1G17455.1 47.500 80 42 0 26 105 6 85 1.22e-20 80.5
Msa0369210 AT1G72630.1 46.250 80 43 0 26 105 10 89 4.61e-19 76.6

Find 37 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCGGCGGCGTTGATTCTTCT+TGG 0.236721 3_1:-66309905 None:intergenic
ATCTAGAATGCCTGATAATA+TGG 0.270265 3_1:+66310089 Msa0369210:CDS
TTAAGGGTCTGCCATGCTTC+GGG 0.352696 3_1:-66309991 None:intergenic
GTTAAGGGTCTGCCATGCTT+CGG 0.360927 3_1:-66309992 None:intergenic
ACGTTCTTCACCATATTATC+AGG 0.362205 3_1:-66310099 None:intergenic
AGTCGGTGCTTGACAGGAAC+AGG 0.378549 3_1:+66310034 Msa0369210:CDS
GGTTTGATTCAAGAGCTTAA+TGG 0.403333 3_1:+66310123 Msa0369210:CDS
TCGGAGTAGTCGTTGTTTGT+TGG 0.405287 3_1:-66309943 None:intergenic
TTGCCTGAAGCTCTTGTTAA+GGG 0.405821 3_1:-66310007 None:intergenic
CTTGCCTGAAGCTCTTGTTA+AGG 0.452710 3_1:-66310008 None:intergenic
TATGAGAAGAACGTTGTTGC+TGG 0.466787 3_1:-66310209 None:intergenic
GAACAGGGCAATTATTCAAC+AGG 0.467993 3_1:+66310050 Msa0369210:CDS
GTTGTTTGTTGGAGTGGCGG+AGG 0.471753 3_1:-66309932 None:intergenic
GGCGTTGATTCTTCTTGGAA+CGG 0.478309 3_1:-66309900 None:intergenic
TTGTTGGAGTGGCGGAGGGA+CGG 0.484279 3_1:-66309927 None:intergenic
ACGGTGGTTGGTGTCTTCCA+TGG 0.485355 3_1:-66309881 None:intergenic
AAGTTCAGTCGGTGCTTGAC+AGG 0.488761 3_1:+66310028 Msa0369210:CDS
ATTCTTCTTGGAACGGTGGT+TGG 0.500480 3_1:-66309893 None:intergenic
GAGTGGCGGAGGGACGGCGG+CGG 0.507547 3_1:-66309921 None:intergenic
GTAGTCGTTGTTTGTTGGAG+TGG 0.524126 3_1:-66309938 None:intergenic
AGACCCTTAACAAGAGCTTC+AGG 0.525177 3_1:+66310004 Msa0369210:CDS
TTGTTTGTTGGAGTGGCGGA+GGG 0.536933 3_1:-66309931 None:intergenic
GCTTAATGGCAATATTTCAA+AGG 0.542695 3_1:+66310137 Msa0369210:CDS
GTCGTTGTTTGTTGGAGTGG+CGG 0.547841 3_1:-66309935 None:intergenic
GCTAAAATCAGAATTAAGAT+CGG 0.560174 3_1:-66310175 None:intergenic
TTGGAGTGGCGGAGGGACGG+CGG 0.562226 3_1:-66309924 None:intergenic
GACGTGGAGGATGCTGAAGA+CGG 0.583878 3_1:+66309964 Msa0369210:CDS
AAGACGGCGATCCCGAAGCA+TGG 0.588795 3_1:+66309980 Msa0369210:CDS
GAGCTTCAGGCAAGTTCAGT+CGG 0.593643 3_1:+66310017 Msa0369210:CDS
GTTGATTCTTCTTGGAACGG+TGG 0.599566 3_1:-66309897 None:intergenic
TGATAATATGGTGAAGAACG+TGG 0.629062 3_1:+66310101 Msa0369210:CDS
GTCGGTGCTTGACAGGAACA+GGG 0.640394 3_1:+66310035 Msa0369210:CDS
GATAATATGGTGAAGAACGT+GGG 0.654854 3_1:+66310102 Msa0369210:CDS
CAACGACTACTCCGACGTGG+AGG 0.676846 3_1:+66309951 Msa0369210:CDS
GTCTTCAGCATCCTCCACGT+CGG 0.689723 3_1:-66309962 None:intergenic
CAACGTTCTTCTCATAACCG+TGG 0.719410 3_1:+66310216 Msa0369210:CDS
AAACAACGACTACTCCGACG+TGG 0.738856 3_1:+66309948 Msa0369210:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GCTAAAATCAGAATTAAGAT+CGG - chr3_1:66310178-66310197 None:intergenic 25.0%
! ATCTAGAATGCCTGATAATA+TGG + chr3_1:66310089-66310108 Msa0369210:CDS 30.0%
GCTTAATGGCAATATTTCAA+AGG + chr3_1:66310137-66310156 Msa0369210:CDS 30.0%
ACGTTCTTCACCATATTATC+AGG - chr3_1:66310102-66310121 None:intergenic 35.0%
TGATAATATGGTGAAGAACG+TGG + chr3_1:66310101-66310120 Msa0369210:CDS 35.0%
GATAATATGGTGAAGAACGT+GGG + chr3_1:66310102-66310121 Msa0369210:CDS 35.0%
GGTTTGATTCAAGAGCTTAA+TGG + chr3_1:66310123-66310142 Msa0369210:CDS 35.0%
TTGCCTGAAGCTCTTGTTAA+GGG - chr3_1:66310010-66310029 None:intergenic 40.0%
GAACAGGGCAATTATTCAAC+AGG + chr3_1:66310050-66310069 Msa0369210:CDS 40.0%
TATGAGAAGAACGTTGTTGC+TGG - chr3_1:66310212-66310231 None:intergenic 40.0%
ATTCTTCTTGGAACGGTGGT+TGG - chr3_1:66309896-66309915 None:intergenic 45.0%
! GTTGATTCTTCTTGGAACGG+TGG - chr3_1:66309900-66309919 None:intergenic 45.0%
!! GGCGTTGATTCTTCTTGGAA+CGG - chr3_1:66309903-66309922 None:intergenic 45.0%
! GTAGTCGTTGTTTGTTGGAG+TGG - chr3_1:66309941-66309960 None:intergenic 45.0%
TCGGAGTAGTCGTTGTTTGT+TGG - chr3_1:66309946-66309965 None:intergenic 45.0%
AGACCCTTAACAAGAGCTTC+AGG + chr3_1:66310004-66310023 Msa0369210:CDS 45.0%
CTTGCCTGAAGCTCTTGTTA+AGG - chr3_1:66310011-66310030 None:intergenic 45.0%
CAACGTTCTTCTCATAACCG+TGG + chr3_1:66310216-66310235 Msa0369210:CDS 45.0%
! TTGTTTGTTGGAGTGGCGGA+GGG - chr3_1:66309934-66309953 None:intergenic 50.0%
! GTCGTTGTTTGTTGGAGTGG+CGG - chr3_1:66309938-66309957 None:intergenic 50.0%
AAACAACGACTACTCCGACG+TGG + chr3_1:66309948-66309967 Msa0369210:CDS 50.0%
TTAAGGGTCTGCCATGCTTC+GGG - chr3_1:66309994-66310013 None:intergenic 50.0%
GTTAAGGGTCTGCCATGCTT+CGG - chr3_1:66309995-66310014 None:intergenic 50.0%
GAGCTTCAGGCAAGTTCAGT+CGG + chr3_1:66310017-66310036 Msa0369210:CDS 50.0%
! AAGTTCAGTCGGTGCTTGAC+AGG + chr3_1:66310028-66310047 Msa0369210:CDS 50.0%
! GTTGTTTGTTGGAGTGGCGG+AGG - chr3_1:66309935-66309954 None:intergenic 55.0%
GTCTTCAGCATCCTCCACGT+CGG - chr3_1:66309965-66309984 None:intergenic 55.0%
GACGTGGAGGATGCTGAAGA+CGG + chr3_1:66309964-66309983 Msa0369210:CDS 55.0%
! AGTCGGTGCTTGACAGGAAC+AGG + chr3_1:66310034-66310053 Msa0369210:CDS 55.0%
! GTCGGTGCTTGACAGGAACA+GGG + chr3_1:66310035-66310054 Msa0369210:CDS 55.0%
!! GCGGCGGCGTTGATTCTTCT+TGG - chr3_1:66309908-66309927 None:intergenic 60.0%
! TTGTTGGAGTGGCGGAGGGA+CGG - chr3_1:66309930-66309949 None:intergenic 60.0%
CAACGACTACTCCGACGTGG+AGG + chr3_1:66309951-66309970 Msa0369210:CDS 60.0%
AAGACGGCGATCCCGAAGCA+TGG + chr3_1:66309980-66309999 Msa0369210:CDS 60.0%
! TTGGAGTGGCGGAGGGACGG+CGG - chr3_1:66309927-66309946 None:intergenic 70.0%
!! GAGTGGCGGAGGGACGGCGG+CGG - chr3_1:66309924-66309943 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 66309883 66310245 66309883 ID=Msa0369210;Name=Msa0369210
chr3_1 mRNA 66309883 66310245 66309883 ID=Msa0369210-mRNA-1;Parent=Msa0369210;Name=Msa0369210-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|-1|0|1|-1|1|1|0|120
chr3_1 exon 66309883 66310245 66309883 ID=Msa0369210-mRNA-1:exon:13465;Parent=Msa0369210-mRNA-1
chr3_1 CDS 66309883 66310245 66309883 ID=Msa0369210-mRNA-1:cds;Parent=Msa0369210-mRNA-1
Gene Sequence

>Msa0369210

ATGGAAGACACCAACCACCGTTCCAAGAAGAATCAACGCCGCCGCCGTCCCTCCGCCACTCCAACAAACAACGACTACTCCGACGTGGAGGATGCTGAAGACGGCGATCCCGAAGCATGGCAGACCCTTAACAAGAGCTTCAGGCAAGTTCAGTCGGTGCTTGACAGGAACAGGGCAATTATTCAACAGGTGAATGAGAATCAACAATCTAGAATGCCTGATAATATGGTGAAGAACGTGGGTTTGATTCAAGAGCTTAATGGCAATATTTCAAAGGTTGCTTCTCTTTATTCCGATCTTAATTCTGATTTTAGCAATATTTGTCACCAGCAACAACGTTCTTCTCATAACCGTGGCAAGTGA
Protein sequence

>Msa0369210

MEDTNHRSKKNQRRRRPSATPTNNDYSDVEDAEDGDPEAWQTLNKSFRQVQSVLDRNRAIIQQVNENQQSRMPDNMVKNVGLIQELNGNISKVASLYSDLNSDFSNICHQQQRSSHNRGK*