AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1248320

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1248320 MtrunA17_Chr2g0309121 90.164 122 11 1 1 122 1 121 9.13e-76 220
Msa1248320 MtrunA17_Chr2g0281511 84.426 122 19 0 1 122 1 122 1.33e-72 212
Msa1248320 MtrunA17_Chr3g0081891 83.750 80 13 0 1 80 1 80 8.78e-44 137
Msa1248320 MtrunA17_Chr7g0276661 32.061 131 69 4 7 119 38 166 3.66e-16 70.5
Msa1248320 MtrunA17_Chr0c01g0489371 42.857 91 50 1 22 110 224 314 8.78e-16 71.6
Msa1248320 MtrunA17_Chr8g0356961 41.573 89 50 1 24 110 77 165 4.30e-15 67.8
Msa1248320 MtrunA17_Chr8g0372431 27.835 97 70 0 24 120 6 102 1.17e-13 62.0
Msa1248320 MtrunA17_Chr5g0434641 36.264 91 56 1 22 110 208 298 1.31e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGGTTATTGCTTCTATTT+TGG 0.132946 8_2:+42042704 Msa1248320:CDS
GAAGTCAATGGTACTGAATT+AGG 0.159497 8_2:+42042645 Msa1248320:CDS
TGTATGCTACCGTCGTTAAC+TGG 0.211996 8_2:+42043064 Msa1248320:CDS
AAAATATCGATGTCCATTAT+TGG 0.234776 8_2:+42042676 Msa1248320:CDS
TACCGGTTTCTTCATCAAAA+AGG 0.272684 8_2:-42042897 None:intergenic
TAACCTTATGCTTCCAATAA+TGG 0.277357 8_2:-42042689 None:intergenic
ATCAAAGTCATAAGATTTAC+CGG 0.326757 8_2:-42042914 None:intergenic
CCTCGATGTGTTGCGGAGAA+TGG 0.338723 8_2:+42042847 Msa1248320:CDS
TTTGGATGGAAACAATGTTT+TGG 0.356448 8_2:+42042722 Msa1248320:CDS
TAAGGAAACATGAATGAGAT+TGG 0.380138 8_2:+42042618 None:intergenic
GTACAACTTTGTTCTTGAAA+AGG 0.417029 8_2:+42042987 Msa1248320:CDS
AAGTCAATGGTACTGAATTA+GGG 0.437113 8_2:+42042646 Msa1248320:CDS
TGTCCATTATTGGAAGCATA+AGG 0.460083 8_2:+42042686 Msa1248320:CDS
CGGTCAATAATCCTCCTAAT+CGG 0.465785 8_2:+42043040 Msa1248320:CDS
ACGGTAGCATACATCCGATT+AGG 0.477261 8_2:-42043054 None:intergenic
CTTGAAAAGGACCTAAAAGT+TGG 0.486000 8_2:+42043000 Msa1248320:CDS
AGAAATACATAGGGAGAGAA+TGG 0.518052 8_2:+42042965 Msa1248320:CDS
GTATGCTACCGTCGTTAACT+GGG 0.522932 8_2:+42043065 Msa1248320:CDS
AACATGCATCAGAAATACAT+AGG 0.535430 8_2:+42042955 Msa1248320:CDS
GAGATTGGAGTTGAAGTCAA+TGG 0.575541 8_2:+42042633 Msa1248320:CDS
ACATGCATCAGAAATACATA+GGG 0.587826 8_2:+42042956 Msa1248320:CDS
GTAGCATACATCCGATTAGG+AGG 0.600441 8_2:-42043051 None:intergenic
CCATTCTCCGCAACACATCG+AGG 0.699602 8_2:-42042847 None:intergenic
GAATCAGTCCCAGTTAACGA+CGG 0.733495 8_2:-42043073 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAATATCGATGTCCATTAT+TGG + chr8_2:42042676-42042695 Msa1248320:CDS 25.0%
!! TAAGGTTATTGCTTCTATTT+TGG + chr8_2:42042704-42042723 Msa1248320:CDS 25.0%
! ATCAAAGTCATAAGATTTAC+CGG - chr8_2:42042917-42042936 None:intergenic 25.0%
! AAGTCAATGGTACTGAATTA+GGG + chr8_2:42042646-42042665 Msa1248320:CDS 30.0%
TAACCTTATGCTTCCAATAA+TGG - chr8_2:42042692-42042711 None:intergenic 30.0%
!! GTTATTGCTTCTATTTTGGA+TGG + chr8_2:42042708-42042727 Msa1248320:CDS 30.0%
! TTTGGATGGAAACAATGTTT+TGG + chr8_2:42042722-42042741 Msa1248320:CDS 30.0%
AACATGCATCAGAAATACAT+AGG + chr8_2:42042955-42042974 Msa1248320:CDS 30.0%
ACATGCATCAGAAATACATA+GGG + chr8_2:42042956-42042975 Msa1248320:CDS 30.0%
GTACAACTTTGTTCTTGAAA+AGG + chr8_2:42042987-42043006 Msa1248320:CDS 30.0%
! AAATAACGTCACCAACTTTT+AGG - chr8_2:42043014-42043033 None:intergenic 30.0%
! GAAGTCAATGGTACTGAATT+AGG + chr8_2:42042645-42042664 Msa1248320:CDS 35.0%
! TGTCCATTATTGGAAGCATA+AGG + chr8_2:42042686-42042705 Msa1248320:CDS 35.0%
!!! GGAAACAATGTTTTGGTTAG+TGG + chr8_2:42042729-42042748 Msa1248320:intron 35.0%
! CTCCTTTTTGATGAAGAAAC+CGG + chr8_2:42042895-42042914 Msa1248320:CDS 35.0%
!! TACCGGTTTCTTCATCAAAA+AGG - chr8_2:42042900-42042919 None:intergenic 35.0%
AGAAATACATAGGGAGAGAA+TGG + chr8_2:42042965-42042984 Msa1248320:CDS 35.0%
CTTGAAAAGGACCTAAAAGT+TGG + chr8_2:42043000-42043019 Msa1248320:CDS 35.0%
!! TGGTGACGTTATTTTGTTCA+CGG + chr8_2:42043020-42043039 Msa1248320:CDS 35.0%
GAGATTGGAGTTGAAGTCAA+TGG + chr8_2:42042633-42042652 Msa1248320:CDS 40.0%
CGGTCAATAATCCTCCTAAT+CGG + chr8_2:42043040-42043059 Msa1248320:CDS 40.0%
! GCATTTTCCTCGATGTGTTG+CGG + chr8_2:42042840-42042859 Msa1248320:intron 45.0%
GTAGCATACATCCGATTAGG+AGG - chr8_2:42043054-42043073 None:intergenic 45.0%
ACGGTAGCATACATCCGATT+AGG - chr8_2:42043057-42043076 None:intergenic 45.0%
TGTATGCTACCGTCGTTAAC+TGG + chr8_2:42043064-42043083 Msa1248320:CDS 45.0%
GTATGCTACCGTCGTTAACT+GGG + chr8_2:42043065-42043084 Msa1248320:CDS 45.0%
CCATTCTCCGCAACACATCG+AGG - chr8_2:42042850-42042869 None:intergenic 55.0%
CCTCGATGTGTTGCGGAGAA+TGG + chr8_2:42042847-42042866 Msa1248320:CDS 55.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 42042627 42043092 42042627 ID=Msa1248320;Name=Msa1248320
chr8_2 mRNA 42042627 42043092 42042627 ID=Msa1248320-mRNA-1;Parent=Msa1248320;Name=Msa1248320-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|122
chr8_2 exon 42042627 42042743 42042627 ID=Msa1248320-mRNA-1:exon:12779;Parent=Msa1248320-mRNA-1
chr8_2 exon 42042841 42043092 42042841 ID=Msa1248320-mRNA-1:exon:12780;Parent=Msa1248320-mRNA-1
chr8_2 CDS 42042627 42042743 42042627 ID=Msa1248320-mRNA-1:cds;Parent=Msa1248320-mRNA-1
chr8_2 CDS 42042841 42043092 42042841 ID=Msa1248320-mRNA-1:cds;Parent=Msa1248320-mRNA-1
Gene Sequence

>Msa1248320

ATGAATGAGATTGGAGTTGAAGTCAATGGTACTGAATTAGGGAATGTTCAAAATATCGATGTCCATTATTGGAAGCATAAGGTTATTGCTTCTATTTTGGATGGAAACAATGTTTTGCATTTTCCTCGATGTGTTGCGGAGAATGGTTTGTTTATCAATCAATCTAAAATTCTCCTTTTTGATGAAGAAACCGGTAAATCTTATGACTTTGATGTTCACACTACGTCAAAAAACATGCATCAGAAATACATAGGGAGAGAATGGTACAACTTTGTTCTTGAAAAGGACCTAAAAGTTGGTGACGTTATTTTGTTCACGGTCAATAATCCTCCTAATCGGATGTATGCTACCGTCGTTAACTGGGACTGA
Protein sequence

>Msa1248320

MNEIGVEVNGTELGNVQNIDVHYWKHKVIASILDGNNVLHFPRCVAENGLFINQSKILLFDEETGKSYDFDVHTTSKNMHQKYIGREWYNFVLEKDLKVGDVILFTVNNPPNRMYATVVNWD*