AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0112750


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0112750 MtrunA17_Chr2g0279161 63.415 123 6 2 1 84 209 331 3.71e-37 126
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0112750 AT2G37990.1 56.897 58 21 1 1 54 208 265 9.38e-13 62.0

Find 14 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATCAAAATTACTGTGCTTT+TGG 0.169446 1_3:-28264416 None:intergenic
TGATTCTTTCCTTTATGTTT+TGG 0.213955 1_3:-28263930 None:intergenic
TGGGAAGTTTGACAAGAAAT+TGG 0.321610 1_3:+28263893 Msa0112750:CDS
CCTTCGATTTATCATTCCTT+CGG 0.409239 1_3:-28264325 None:intergenic
GAAAAGCCTCCAAAACATAA+AGG 0.470960 1_3:+28263921 Msa0112750:CDS
GATGAGTTAGGCAGTGTAGC+AGG 0.486950 1_3:+28263843 Msa0112750:CDS
CACAGTGACCAATGTGAAGA+AGG 0.507110 1_3:+28264295 Msa0112750:CDS
TGAGTAACAAAGGATGAGTT+AGG 0.530881 1_3:+28263831 None:intergenic
ACCGCTAGCTGTAGCAGTTG+AGG 0.564063 1_3:-28263871 None:intergenic
ACATAAAGGAAAGAATCAAA+AGG 0.566037 1_3:+28263935 Msa0112750:CDS
GCCTCAACTGCTACAGCTAG+CGG 0.592484 1_3:+28263870 Msa0112750:CDS
CCGAAGGAATGATAAATCGA+AGG 0.616796 1_3:+28264325 Msa0112750:CDS
TCAACTGCTACAGCTAGCGG+TGG 0.622135 1_3:+28263873 Msa0112750:CDS
CAACTGCTACAGCTAGCGGT+GGG 0.666293 1_3:+28263874 Msa0112750:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGATTCTTTCCTTTATGTTT+TGG - chr1_3:28263933-28263952 None:intergenic 25.0%
! ACATAAAGGAAAGAATCAAA+AGG + chr1_3:28263935-28263954 Msa0112750:CDS 25.0%
! TCGACAAATGATTATTTACA+AGG - chr1_3:28263998-28264017 None:intergenic 25.0%
! GCAGTTAACTTTCATTTAAT+TGG + chr1_3:28264019-28264038 Msa0112750:intron 25.0%
! TGTTAACATTGAGTATATCA+TGG - chr1_3:28264165-28264184 None:intergenic 25.0%
! TGATATACTCAATGTTAACA+AGG + chr1_3:28264165-28264184 Msa0112750:intron 25.0%
!! TTCTTTCCTTTATGTTTTGG+AGG - chr1_3:28263930-28263949 None:intergenic 30.0%
GAGTATATCATGGTTATTCT+TGG - chr1_3:28264155-28264174 None:intergenic 30.0%
!! TCAGAAGAAGCCTTTTAAAA+AGG + chr1_3:28264376-28264395 Msa0112750:CDS 30.0%
!! CAGAAGAAGCCTTTTAAAAA+GGG + chr1_3:28264377-28264396 Msa0112750:CDS 30.0%
TGGGAAGTTTGACAAGAAAT+TGG + chr1_3:28263893-28263912 Msa0112750:CDS 35.0%
GAAAAGCCTCCAAAACATAA+AGG + chr1_3:28263921-28263940 Msa0112750:CDS 35.0%
ACTAGACGAAGAGATAACAA+AGG - chr1_3:28264056-28264075 None:intergenic 35.0%
AATTGTACTCTCTGCATTCT+AGG + chr1_3:28264268-28264287 Msa0112750:intron 35.0%
! GTTTTTCTCCTTCTTCACAT+TGG - chr1_3:28264306-28264325 None:intergenic 35.0%
CCTTCGATTTATCATTCCTT+CGG - chr1_3:28264328-28264347 None:intergenic 35.0%
! TTCTTGGCACCCTTTTTAAA+AGG - chr1_3:28264389-28264408 None:intergenic 35.0%
!! TTTAAAAAGGGTGCCAAGAA+AGG + chr1_3:28264389-28264408 Msa0112750:CDS 35.0%
TGAAGAAGGAGAAAAACCGA+AGG + chr1_3:28264309-28264328 Msa0112750:CDS 40.0%
CCGAAGGAATGATAAATCGA+AGG + chr1_3:28264325-28264344 Msa0112750:CDS 40.0%
!!! ATGTTTTGGAGGCTTTTCGC+AGG - chr1_3:28263919-28263938 None:intergenic 45.0%
CACAGTGACCAATGTGAAGA+AGG + chr1_3:28264295-28264314 Msa0112750:CDS 45.0%
!!! TGCTTTTGGGTTGCCTTTCT+TGG - chr1_3:28264405-28264424 None:intergenic 45.0%
GATGAGTTAGGCAGTGTAGC+AGG + chr1_3:28263843-28263862 Msa0112750:CDS 50.0%
! TCTCTTCGTCTAGTTCCTGC+CGG + chr1_3:28264062-28264081 Msa0112750:intron 50.0%
GAAGGAACGGGTAGGATCAA+AGG + chr1_3:28264090-28264109 Msa0112750:intron 50.0%
AACGGGTAGGATCAAAGGAG+AGG + chr1_3:28264095-28264114 Msa0112750:intron 50.0%
ACGGGTAGGATCAAAGGAGA+GGG + chr1_3:28264096-28264115 Msa0112750:intron 50.0%
GCCTCAACTGCTACAGCTAG+CGG + chr1_3:28263870-28263889 Msa0112750:CDS 55.0%
ACCGCTAGCTGTAGCAGTTG+AGG - chr1_3:28263874-28263893 None:intergenic 55.0%
TCAACTGCTACAGCTAGCGG+TGG + chr1_3:28263873-28263892 Msa0112750:CDS 55.0%
CAACTGCTACAGCTAGCGGT+GGG + chr1_3:28263874-28263893 Msa0112750:CDS 55.0%
TAGTTCCTGCCGGTAGCAGA+AGG + chr1_3:28264072-28264091 Msa0112750:intron 55.0%
CTACCCGTTCCTTCTGCTAC+CGG - chr1_3:28264084-28264103 None:intergenic 55.0%
CCTGCCGGTAGCAGAAGGAA+CGG + chr1_3:28264077-28264096 Msa0112750:intron 60.0%
CTGCCGGTAGCAGAAGGAAC+GGG + chr1_3:28264078-28264097 Msa0112750:intron 60.0%
CGGTAGCAGAAGGAACGGGT+AGG + chr1_3:28264082-28264101 Msa0112750:intron 60.0%
CCGTTCCTTCTGCTACCGGC+AGG - chr1_3:28264080-28264099 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 28263843 28264430 28263843 ID=Msa0112750;Name=Msa0112750
chr1_3 mRNA 28263843 28264430 28263843 ID=Msa0112750-mRNA-1;Parent=Msa0112750;Name=Msa0112750-mRNA-1;_AED=0.32;_eAED=0.32;_QI=0|0|0|1|1|1|2|0|84
chr1_3 exon 28263843 28263956 28263843 ID=Msa0112750-mRNA-1:exon:9303;Parent=Msa0112750-mRNA-1
chr1_3 exon 28264290 28264430 28264290 ID=Msa0112750-mRNA-1:exon:9304;Parent=Msa0112750-mRNA-1
chr1_3 CDS 28263843 28263956 28263843 ID=Msa0112750-mRNA-1:cds;Parent=Msa0112750-mRNA-1
chr1_3 CDS 28264290 28264430 28264290 ID=Msa0112750-mRNA-1:cds;Parent=Msa0112750-mRNA-1
Gene Sequence

>Msa0112750

GATGAGTTAGGCAGTGTAGCAGGATTTGCCTCAACTGCTACAGCTAGCGGTGGGAAGTTTGACAAGAAATTGGCCTGCGAAAAGCCTCCAAAACATAAAGGAAAGAATCAAAAGGCTGTCACAGTGACCAATGTGAAGAAGGAGAAAAACCGAAGGAATGATAAATCGAAGGCTTCAGCAACTAACAGCAAATTGAAAACTCAGAAGAAGCCTTTTAAAAAGGGTGCCAAGAAAGGCAACCCAAAAGCACAGTAA

Protein sequence

>Msa0112750

DELGSVAGFASTATASGGKFDKKLACEKPPKHKGKNQKAVTVTNVKKEKNRRNDKSKASATNSKLKTQKKPFKKGAKKGNPKAQ*