AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059869

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059869.t1 MTR_2g080030 84.694 98 2 2 15 99 13 110 2.17e-51 157
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059869.t1 AT3G15518 64.789 71 22 2 29 96 34 104 7.62e-26 92.8

Find 25 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCTAAGTCCTAAACGTTT+TGG 0.338108 2.2:+15338031 None:intergenic
GAAAGGTTGAAGAAGCGTTT+GGG 0.346922 2.2:-15338091 MS.gene059869:CDS
CAAAACGTTTAGGACTTAGA+TGG 0.365640 2.2:-15338030 MS.gene059869:CDS
ACACCACCACCAAAACGTTT+AGG 0.367788 2.2:-15338040 MS.gene059869:CDS
GTTGTTGTGGTTGATGATGT+TGG 0.368918 2.2:+15338242 None:intergenic
CGTTGAGACATAGACATCTT+TGG 0.375552 2.2:+15338190 None:intergenic
TAGACTCTCTATCATGTCTA+TGG 0.385249 2.2:-15337984 MS.gene059869:CDS
AGAAAGGTTGAAGAAGCGTT+TGG 0.401387 2.2:-15338092 MS.gene059869:CDS
TTGTTGTGGTTGATGATGTT+GGG 0.409137 2.2:+15338243 None:intergenic
ACGAGCACAACGAACCGAAC+CGG 0.435101 2.2:+15338135 None:intergenic
CGCTTCTTCAACCTTTCTCC+TGG 0.435216 2.2:+15338097 None:intergenic
CGGTTCGTTGTGCTCGTCAT+GGG 0.442609 2.2:-15338129 MS.gene059869:CDS
TCGGTTCGTTGTGCTCGTCA+TGG 0.452371 2.2:-15338130 MS.gene059869:CDS
CGTCATGGGTATGTAGTACC+AGG 0.512648 2.2:-15338115 MS.gene059869:CDS
GTGTTTGAACAAACCCGGTT+CGG 0.533431 2.2:-15338149 MS.gene059869:CDS
CGAGCACAACGAACCGAACC+GGG 0.534286 2.2:+15338136 None:intergenic
TGCACGTGTTTGAACAAACC+CGG 0.538386 2.2:-15338154 MS.gene059869:CDS
ATAGAGAGTCTACTAGGTGT+TGG 0.542046 2.2:+15337995 None:intergenic
TGAGACATAGACATCTTTGG+TGG 0.544668 2.2:+15338193 None:intergenic
GGTATGTAGTACCAGGAGAA+AGG 0.554898 2.2:-15338108 MS.gene059869:CDS
TATGTCTCAACGGTTCAGAC+CGG 0.576480 2.2:-15338179 MS.gene059869:CDS
AAAGGTTGAAGAAGCGTTTG+GGG 0.600224 2.2:-15338090 MS.gene059869:CDS
TTGTTCAAACACGTGCAAGC+CGG 0.601812 2.2:+15338160 None:intergenic
GACATGATAGAGAGTCTACT+AGG 0.607741 2.2:+15337989 None:intergenic
CAAAGATGTCTATGTCTCAA+CGG 0.628726 2.2:-15338189 MS.gene059869:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCTTTTGTTTGTTGTTGTTG+TGG + chr2.2:15338003-15338022 None:intergenic 30.0%
CAAAGATGTCTATGTCTCAA+CGG - chr2.2:15338040-15338059 MS.gene059869:CDS 35.0%
TAGACTCTCTATCATGTCTA+TGG - chr2.2:15338245-15338264 MS.gene059869:CDS 35.0%
! CAAAACGTTTAGGACTTAGA+TGG - chr2.2:15338199-15338218 MS.gene059869:CDS 35.0%
! CATCTAAGTCCTAAACGTTT+TGG + chr2.2:15338201-15338220 None:intergenic 35.0%
!! TTGTTGTGGTTGATGATGTT+GGG + chr2.2:15337989-15338008 None:intergenic 35.0%
ATAGAGAGTCTACTAGGTGT+TGG + chr2.2:15338237-15338256 None:intergenic 40.0%
CGTTGAGACATAGACATCTT+TGG + chr2.2:15338042-15338061 None:intergenic 40.0%
GACATGATAGAGAGTCTACT+AGG + chr2.2:15338243-15338262 None:intergenic 40.0%
TGAGACATAGACATCTTTGG+TGG + chr2.2:15338039-15338058 None:intergenic 40.0%
! CTAAGTCCTAAACGTTTTGG+TGG + chr2.2:15338198-15338217 None:intergenic 40.0%
!! AAAGGTTGAAGAAGCGTTTG+GGG - chr2.2:15338139-15338158 MS.gene059869:CDS 40.0%
!! AGAAAGGTTGAAGAAGCGTT+TGG - chr2.2:15338137-15338156 MS.gene059869:CDS 40.0%
!! GAAAGGTTGAAGAAGCGTTT+GGG - chr2.2:15338138-15338157 MS.gene059869:CDS 40.0%
!! GTTGTTGTGGTTGATGATGT+TGG + chr2.2:15337990-15338009 None:intergenic 40.0%
ACACCACCACCAAAACGTTT+AGG - chr2.2:15338189-15338208 MS.gene059869:CDS 45.0%
GGTATGTAGTACCAGGAGAA+AGG - chr2.2:15338121-15338140 MS.gene059869:CDS 45.0%
GTGTTTGAACAAACCCGGTT+CGG - chr2.2:15338080-15338099 MS.gene059869:CDS 45.0%
TATGTCTCAACGGTTCAGAC+CGG - chr2.2:15338050-15338069 MS.gene059869:CDS 45.0%
TGCACGTGTTTGAACAAACC+CGG - chr2.2:15338075-15338094 MS.gene059869:CDS 45.0%
TTGTTCAAACACGTGCAAGC+CGG + chr2.2:15338072-15338091 None:intergenic 45.0%
!! AGTCCTAAACGTTTTGGTGG+TGG + chr2.2:15338195-15338214 None:intergenic 45.0%
CGCTTCTTCAACCTTTCTCC+TGG + chr2.2:15338135-15338154 None:intergenic 50.0%
CGTCATGGGTATGTAGTACC+AGG - chr2.2:15338114-15338133 MS.gene059869:CDS 50.0%
ACGAGCACAACGAACCGAAC+CGG + chr2.2:15338097-15338116 None:intergenic 55.0%
CGGTTCGTTGTGCTCGTCAT+GGG - chr2.2:15338100-15338119 MS.gene059869:CDS 55.0%
! TCGGTTCGTTGTGCTCGTCA+TGG - chr2.2:15338099-15338118 MS.gene059869:CDS 55.0%
CGAGCACAACGAACCGAACC+GGG + chr2.2:15338096-15338115 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 15337976 15338275 15337976 ID=MS.gene059869
chr2.2 mRNA 15337976 15338275 15337976 ID=MS.gene059869.t1;Parent=MS.gene059869
chr2.2 exon 15337976 15338275 15337976 ID=MS.gene059869.t1.exon1;Parent=MS.gene059869.t1
chr2.2 CDS 15337976 15338275 15337976 ID=cds.MS.gene059869.t1;Parent=MS.gene059869.t1
Gene Sequence

>MS.gene059869

ATGCAAGACACCCAACATCATCAACCACAACAACAACAAACAAAAGAAAGTACACAACTTCCACCAAAGATGTCTATGTCTCAACGGTTCAGACCGGCTTGCACGTGTTTGAACAAACCCGGTTCGGTTCGTTGTGCTCGTCATGGGTATGTAGTACCAGGAGAAAGGTTGAAGAAGCGTTTGGGGAGTAAAGAGATTTTGAGAAGAGCTTTAACACCACCACCAAAACGTTTAGGACTTAGATGGTTGAATTTCAAACCAACACCTAGTAGACTCTCTATCATGTCTATGGCTTCATGA
Protein sequence

>MS.gene059869.t1

MQDTQHHQPQQQQTKESTQLPPKMSMSQRFRPACTCLNKPGSVRCARHGYVVPGERLKKRLGSKEILRRALTPPPKRLGLRWLNFKPTPSRLSIMSMAS