AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene43284

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43284.t1 MTR_4g106860 71.304 115 1 1 1 83 1 115 4.53e-31 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 13 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTACGCAAGCTTCTTGTCTT+CGG 0.310911 8.4:+20446917 MS.gene43284:CDS
TACGCAAGCTTCTTGTCTTC+GGG 0.326759 8.4:+20446918 MS.gene43284:CDS
CAGACTGTGGAGGGCTATGC+AGG 0.492139 8.4:+20447525 MS.gene43284:intron
CTTGGTCTTGTTACCATGAG+TGG 0.515862 8.4:-20447681 None:intergenic
ATCTGATCATGAGATAGAAA+AGG 0.540603 8.4:+20447208 MS.gene43284:CDS
AATGCATTTAACTGATAAGC+CGG 0.550151 8.4:+20447244 MS.gene43284:CDS
ATAAGGTCTCTAAGGGCACT+TGG 0.552905 8.4:-20447699 None:intergenic
CTTCAGCTTATTGTGCGAGA+CGG 0.558872 8.4:+20447380 MS.gene43284:intron
TACACTGATATGACCACTCA+TGG 0.567522 8.4:+20447668 MS.gene43284:CDS
AGAAGGCTAATGCAAGACAT+AGG 0.585779 8.4:+20447407 MS.gene43284:CDS
GTGGAGGGCTATGCAGGTCA+AGG 0.600120 8.4:+20447531 MS.gene43284:CDS
TTGTGCGAGACGGAAACAGA+AGG 0.605905 8.4:+20447390 MS.gene43284:CDS
TACAAGTTAGTACCTTAGAG+AGG 0.650629 8.4:-20446958 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTATATTTAGTTTTATTTTT+TGG - chr8.4:20447437-20447456 None:intergenic 10.0%
!! ATAAGCATTTAACATATATT+AGG - chr8.4:20447349-20447368 None:intergenic 15.0%
!! GTTCTATTTAAGTATAAAAA+AGG - chr8.4:20447327-20447346 None:intergenic 15.0%
!! AGAAAGTAAAAAATGAATAC+CGG - chr8.4:20447266-20447285 None:intergenic 20.0%
!! TTTCAACCAATAACTTAAAA+TGG - chr8.4:20447066-20447085 None:intergenic 20.0%
!!! TTCATTTTTTACTTTCTTTC+TGG + chr8.4:20447269-20447288 MS.gene43284:intron 20.0%
! AATGTTCAGTATAAGATGAA+AGG - chr8.4:20446988-20447007 None:intergenic 25.0%
!! ATAAAAAAGGTGAAGTACTT+TGG - chr8.4:20447314-20447333 None:intergenic 25.0%
!!! TTTGGACCATTTTAAGTTAT+TGG + chr8.4:20447057-20447076 MS.gene43284:intron 25.0%
AATGCATTTAACTGATAAGC+CGG + chr8.4:20447244-20447263 MS.gene43284:CDS 30.0%
ATCTGATCATGAGATAGAAA+AGG + chr8.4:20447208-20447227 MS.gene43284:CDS 30.0%
GTTCAGTATAAGATGAAAGG+TGG - chr8.4:20446985-20447004 None:intergenic 35.0%
TACAAGTTAGTACCTTAGAG+AGG - chr8.4:20446961-20446980 None:intergenic 35.0%
! GTGTTTTGTCAATATCATGC+AGG + chr8.4:20447181-20447200 MS.gene43284:intron 35.0%
AAGCCCTTGGTTTATGTCAT+GGG + chr8.4:20447030-20447049 MS.gene43284:intron 40.0%
AATTTGTGCAAGTGAGCATG+TGG + chr8.4:20447575-20447594 MS.gene43284:intron 40.0%
AGAAGGCTAATGCAAGACAT+AGG + chr8.4:20447407-20447426 MS.gene43284:CDS 40.0%
ATTTGTGCAAGTGAGCATGT+GGG + chr8.4:20447576-20447595 MS.gene43284:intron 40.0%
CATGCTCACTTGCACAAATT+TGG - chr8.4:20447575-20447594 None:intergenic 40.0%
TACACTGATATGACCACTCA+TGG + chr8.4:20447668-20447687 MS.gene43284:CDS 40.0%
TCCACAAAACTCCCTATTAC+CGG - chr8.4:20447642-20447661 None:intergenic 40.0%
TTACGCAAGCTTCTTGTCTT+CGG + chr8.4:20446917-20446936 MS.gene43284:CDS 40.0%
! AATTTTGTGCAGACTGTGGA+GGG + chr8.4:20447516-20447535 MS.gene43284:intron 40.0%
! GATCAATTTTGTGCAGACTG+TGG + chr8.4:20447512-20447531 MS.gene43284:intron 40.0%
!! GTTTATGTCATGGGGTGTTT+TGG + chr8.4:20447039-20447058 MS.gene43284:intron 40.0%
ACACCCCATGACATAAACCA+AGG - chr8.4:20447037-20447056 None:intergenic 45.0%
AGCCCTTGGTTTATGTCATG+GGG + chr8.4:20447031-20447050 MS.gene43284:intron 45.0%
CAAGCCCTTGGTTTATGTCA+TGG + chr8.4:20447029-20447048 MS.gene43284:intron 45.0%
CACCCCATGACATAAACCAA+GGG - chr8.4:20447036-20447055 None:intergenic 45.0%
CTTCAGCTTATTGTGCGAGA+CGG + chr8.4:20447380-20447399 MS.gene43284:intron 45.0%
TACGCAAGCTTCTTGTCTTC+GGG + chr8.4:20446918-20446937 MS.gene43284:CDS 45.0%
! CAATTTTGTGCAGACTGTGG+AGG + chr8.4:20447515-20447534 MS.gene43284:intron 45.0%
! GCTTTTAGTGTGCCTCTCTA+AGG + chr8.4:20446946-20446965 MS.gene43284:CDS 45.0%
!! CTTGGTCTTGTTACCATGAG+TGG - chr8.4:20447684-20447703 None:intergenic 45.0%
ACCTGGTACTGCCGGTAATA+GGG + chr8.4:20447628-20447647 MS.gene43284:intron 50.0%
ACTGCTCTGTTTCAAGCCCT+TGG + chr8.4:20447017-20447036 MS.gene43284:intron 50.0%
CAAGGTGCAGTGTGCATTCA+AGG + chr8.4:20447549-20447568 MS.gene43284:intron 50.0%
TATTACCGGCAGTACCAGGT+GGG - chr8.4:20447628-20447647 None:intergenic 50.0%
TTGTGCGAGACGGAAACAGA+AGG + chr8.4:20447390-20447409 MS.gene43284:CDS 50.0%
! GCCGGTAATAGGGAGTTTTG+TGG + chr8.4:20447638-20447657 MS.gene43284:intron 50.0%
CACCTGGTACTGCCGGTAAT+AGG + chr8.4:20447627-20447646 MS.gene43284:intron 55.0%
CTATTACCGGCAGTACCAGG+TGG - chr8.4:20447629-20447648 None:intergenic 55.0%
TCCCTATTACCGGCAGTACC+AGG - chr8.4:20447632-20447651 None:intergenic 55.0%
!! CATGTGGGACTTGCTGTGTG+AGG + chr8.4:20447591-20447610 MS.gene43284:intron 55.0%
AGGTGCAAGTGTGTCCCACC+TGG + chr8.4:20447611-20447630 MS.gene43284:intron 60.0%
CAGACTGTGGAGGGCTATGC+AGG + chr8.4:20447525-20447544 MS.gene43284:intron 60.0%
GTGGAGGGCTATGCAGGTCA+AGG + chr8.4:20447531-20447550 MS.gene43284:CDS 60.0%
TGTGTCCCACCTGGTACTGC+CGG + chr8.4:20447620-20447639 MS.gene43284:intron 60.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 20446911 20447712 20446911 ID=MS.gene43284
chr8.4 mRNA 20446911 20447712 20446911 ID=MS.gene43284.t1;Parent=MS.gene43284
chr8.4 exon 20446911 20446967 20446911 ID=MS.gene43284.t1.exon1;Parent=MS.gene43284.t1
chr8.4 CDS 20446911 20446967 20446911 ID=cds.MS.gene43284.t1;Parent=MS.gene43284.t1
chr8.4 exon 20447203 20447265 20447203 ID=MS.gene43284.t1.exon2;Parent=MS.gene43284.t1
chr8.4 CDS 20447203 20447265 20447203 ID=cds.MS.gene43284.t1;Parent=MS.gene43284.t1
chr8.4 exon 20447386 20447428 20447386 ID=MS.gene43284.t1.exon3;Parent=MS.gene43284.t1
chr8.4 CDS 20447386 20447428 20447386 ID=cds.MS.gene43284.t1;Parent=MS.gene43284.t1
chr8.4 exon 20447528 20447552 20447528 ID=MS.gene43284.t1.exon4;Parent=MS.gene43284.t1
chr8.4 CDS 20447528 20447552 20447528 ID=cds.MS.gene43284.t1;Parent=MS.gene43284.t1
chr8.4 exon 20447649 20447712 20447649 ID=MS.gene43284.t1.exon5;Parent=MS.gene43284.t1
chr8.4 CDS 20447649 20447712 20447649 ID=cds.MS.gene43284.t1;Parent=MS.gene43284.t1
Gene Sequence

>MS.gene43284

ATGGCATTACGCAAGCTTCTTGTCTTCGGGTTGTTGCTTTTAGTGTGCCTCTCTAAGGTACTAACTTGTAACCACCTTTCATCTTATACTGAACATTTATTCATCAACTGCTCTGTTTCAAGCCCTTGGTTTATGTCATGGGGTGTTTTGGACCATTTTAAGTTATTGGTTGAAAATTTCAATAAACTATTGTTTTTTTCTTTGTTTATATTTTGTTACAATATTTTCTTGAATATGAGAGTGATTTTAATTTTATTTTTATTTTTATTTGTGTTTTGTCAATATCATGCAGGTTTCATCTGATCATGAGATAGAAAAGGAAGAAGATGAAGAAATGCATTTAACTGATAAGCCGGTATTCATTTTTTACTTTCTTTCTGGAATGATAGATATATATATACCAAAGTACTTCACCTTTTTTATACTTAAATAGAACCTAATATATGTTAAATGCTTATGTTGAAATTATCTTCAGCTTATTGTGCGAGACGGAAACAGAAGGCTAATGCAAGACATAGGTAAGCCAAAAAATAAAACTAAATATACTAATTAGTATCTAACAAATTAAGATTTTTTATTAAGACTAAACTTAATTTCTCATGATCAATTTTGTGCAGACTGTGGAGGGCTATGCAGGTCAAGGTGCAGTGTGCATTCAAGGCCAAATTTGTGCAAGTGAGCATGTGGGACTTGCTGTGTGAGGTGCAAGTGTGTCCCACCTGGTACTGCCGGTAATAGGGAGTTTTGTGGAGCTTGTTACACTGATATGACCACTCATGGTAACAAGACCAAGTGCCCTTAG
Protein sequence

>MS.gene43284.t1

MALRKLLVFGLLLLVCLSKVSSDHEIEKEEDEEMHLTDKPLIVRDGNRRLMQDIDCGGLCRSREFCGACYTDMTTHGNKTKCP