AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene97800

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene97800.t1 MTR_4g045840 45.794 107 46 2 39 145 68 162 1.14e-19 82.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAGTAACATATTGGATTA+TGG 0.249559 3.4:+17611041 MS.gene97800:CDS
GAAAGAATTTGAAGGTAAAT+TGG 0.261202 3.4:+17611139 MS.gene97800:CDS
CAGATTCCTTCTTCAGAACT+TGG 0.272455 3.4:-17611193 None:intergenic
TTCAACTGTTTGTTTACTTT+CGG 0.296497 3.4:-17611021 None:intergenic
AACAGTTGAAAGTAACATAT+TGG 0.327666 3.4:+17611034 MS.gene97800:CDS
CAACGATAAAACAACCGGTT+TGG 0.369890 3.4:-17610936 None:intergenic
AGCAATTGTTGAAGATGAAT+TGG 0.375324 3.4:+17611073 MS.gene97800:CDS
CTTTCGGTTTCGCATCCAAT+TGG 0.411303 3.4:-17611005 None:intergenic
GTGACAGTAGCATATCTTGT+TGG 0.467127 3.4:-17610874 None:intergenic
ATATTGGATTATGGTTATAA+CGG 0.476994 3.4:+17611050 MS.gene97800:CDS
GCTTGCAACGATAAAACAAC+CGG 0.478709 3.4:-17610941 None:intergenic
ATCCAATTGGTTCACACCAC+CGG 0.482561 3.4:-17610992 None:intergenic
TTCCGGTGGTGTGAACCAAT+TGG 0.492682 3.4:+17610990 MS.gene97800:CDS
AGAGATCCAAGTTCTGAAGA+AGG 0.494494 3.4:+17611187 MS.gene97800:CDS
AGAATTTGAAGGTAAATTGG+TGG 0.509955 3.4:+17611142 MS.gene97800:CDS
ATCTCCAGTGTTGCTTGATG+AGG 0.514040 3.4:-17610829 None:intergenic
TCTGAAGAAGGAATCTGAGA+TGG 0.553310 3.4:+17611199 MS.gene97800:CDS
AATTGTTGAAGATGAATTGG+AGG 0.563278 3.4:+17611076 MS.gene97800:CDS
GCTCTGAAGAAAGAATTTGA+AGG 0.569359 3.4:+17611131 MS.gene97800:CDS
ATGGCCTCATCAAGCAACAC+TGG 0.576409 3.4:+17610825 MS.gene97800:CDS
ACACTGGAGATAGAGTGAGT+TGG 0.634264 3.4:+17610841 MS.gene97800:CDS
GTTGTTAGAAGCTCAAGTGT+AGG 0.634759 3.4:+17611241 MS.gene97800:CDS
CACAAGCCAAACATAAGATG+TGG 0.634831 3.4:+17610963 MS.gene97800:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATTGGATTATGGTTATAA+CGG + chr3.4:17611050-17611069 MS.gene97800:CDS 20.0%
! AAAAAACCACATCTTATGTT+TGG - chr3.4:17610972-17610991 None:intergenic 25.0%
! AACAGTTGAAAGTAACATAT+TGG + chr3.4:17611034-17611053 MS.gene97800:CDS 25.0%
! GAAAGAATTTGAAGGTAAAT+TGG + chr3.4:17611139-17611158 MS.gene97800:CDS 25.0%
! GAAAGTAACATATTGGATTA+TGG + chr3.4:17611041-17611060 MS.gene97800:CDS 25.0%
! TTCAACTGTTTGTTTACTTT+CGG - chr3.4:17611024-17611043 None:intergenic 25.0%
AATTGTTGAAGATGAATTGG+AGG + chr3.4:17611076-17611095 MS.gene97800:CDS 30.0%
AGAATTTGAAGGTAAATTGG+TGG + chr3.4:17611142-17611161 MS.gene97800:CDS 30.0%
AGCAATTGTTGAAGATGAAT+TGG + chr3.4:17611073-17611092 MS.gene97800:CDS 30.0%
!!! ACATAAGATGTGGTTTTTTC+CGG + chr3.4:17610973-17610992 MS.gene97800:CDS 30.0%
GGTGGAGATGAAAAATGTAA+TGG + chr3.4:17611160-17611179 MS.gene97800:CDS 35.0%
!! GCTCTGAAGAAAGAATTTGA+AGG + chr3.4:17611131-17611150 MS.gene97800:CDS 35.0%
!!! AACAACCGGTTTGGATTTTT+CGG - chr3.4:17610930-17610949 None:intergenic 35.0%
CAACGATAAAACAACCGGTT+TGG - chr3.4:17610939-17610958 None:intergenic 40.0%
CACAAGCCAAACATAAGATG+TGG + chr3.4:17610963-17610982 MS.gene97800:CDS 40.0%
CAGATTCCTTCTTCAGAACT+TGG - chr3.4:17611196-17611215 None:intergenic 40.0%
GCTTGCAACGATAAAACAAC+CGG - chr3.4:17610944-17610963 None:intergenic 40.0%
GTGACAGTAGCATATCTTGT+TGG - chr3.4:17610877-17610896 None:intergenic 40.0%
TCTGAAGAAGGAATCTGAGA+TGG + chr3.4:17611199-17611218 MS.gene97800:CDS 40.0%
TGACTCCGAAAAATCCAAAC+CGG + chr3.4:17610922-17610941 MS.gene97800:CDS 40.0%
!! AGAGATCCAAGTTCTGAAGA+AGG + chr3.4:17611187-17611206 MS.gene97800:CDS 40.0%
!!! TAAGATGTGGTTTTTTCCGG+TGG + chr3.4:17610976-17610995 MS.gene97800:CDS 40.0%
ACACTGGAGATAGAGTGAGT+TGG + chr3.4:17610841-17610860 MS.gene97800:CDS 45.0%
CTTTCGGTTTCGCATCCAAT+TGG - chr3.4:17611008-17611027 None:intergenic 45.0%
! ATCCAATTGGTTCACACCAC+CGG - chr3.4:17610995-17611014 None:intergenic 45.0%
!! ATCTCCAGTGTTGCTTGATG+AGG - chr3.4:17610832-17610851 None:intergenic 45.0%
ATGGCCTCATCAAGCAACAC+TGG + chr3.4:17610825-17610844 MS.gene97800:CDS 50.0%
TTCCGGTGGTGTGAACCAAT+TGG + chr3.4:17610990-17611009 MS.gene97800:CDS 50.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 17610825 17611262 17610825 ID=MS.gene97800
chr3.4 mRNA 17610825 17611262 17610825 ID=MS.gene97800.t1;Parent=MS.gene97800
chr3.4 exon 17610825 17611262 17610825 ID=MS.gene97800.t1.exon1;Parent=MS.gene97800.t1
chr3.4 CDS 17610825 17611262 17610825 ID=cds.MS.gene97800.t1;Parent=MS.gene97800.t1
Gene Sequence

>MS.gene97800

ATGGCCTCATCAAGCAACACTGGAGATAGAGTGAGTTGGATTAGATATGCCAACAAGATATGCTACTGTCACAATGTAGCAGCAATTAAAGTGTCAATGACTCCGAAAAATCCAAACCGGTTGTTTTATCGTTGCAAGCACAAGCCAAACATAAGATGTGGTTTTTTCCGGTGGTGTGAACCAATTGGATGCGAAACCGAAAGTAAACAAACAGTTGAAAGTAACATATTGGATTATGGTTATAACGGAGCAATTGTTGAAGATGAATTGGAGGTTGTACTATTTGAACAAGCAATGAAGTTTGATGCTCTGAAGAAAGAATTTGAAGGTAAATTGGTGGAGATGAAAAATGTAATGGAGAAAGAGATCCAAGTTCTGAAGAAGGAATCTGAGATGGAGATATCAATCATGAACAAGTTGTTAGAAGCTCAAGTGTAG
Protein sequence

>MS.gene97800.t1

MASSSNTGDRVSWIRYANKICYCHNVAAIKVSMTPKNPNRLFYRCKHKPNIRCGFFRWCEPIGCETESKQTVESNILDYGYNGAIVEDELEVVLFEQAMKFDALKKEFEGKLVEMKNVMEKEIQVLKKESEMEISIMNKLLEAQV