AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene46341

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCCCCTTATCAGTTATT+AGG 0.253021 8.4:+24463672 MS.gene46341:CDS
ATGCTACTTATGTATCAATA+TGG 0.369271 8.4:+24464091 MS.gene46341:CDS
AGAGACCTAATAACTGATAA+GGG 0.388207 8.4:-24463677 None:intergenic
TAGAGACCTAATAACTGATA+AGG 0.414618 8.4:-24463678 None:intergenic
GGATGTACATGAGTAGAGTA+TGG 0.464213 8.4:-24463835 None:intergenic
CATACAGAAGTGGCTCCAAC+TGG 0.466065 8.4:-24463594 None:intergenic
GTCACGGCAGTTCCACCTCC+TGG 0.467816 8.4:+24463636 MS.gene46341:CDS
GAAATGGCTCAGTTAGTTTG+TGG 0.475051 8.4:+24463806 MS.gene46341:intron
TCACACAGTCAATCTAGCTC+TGG 0.518089 8.4:+24463889 MS.gene46341:CDS
AACCTTCTTATGTATCCAGT+TGG 0.523909 8.4:+24463579 None:intergenic
TGCTGTTTGCAATGCTGTCA+CGG 0.534366 8.4:+24463620 MS.gene46341:CDS
TATTGCATCATACCAGGAGG+TGG 0.571555 8.4:-24463648 None:intergenic
AACAGCACAGCATACAGAAG+TGG 0.604154 8.4:-24463604 None:intergenic
GAAGAATATTGCATCATACC+AGG 0.620839 8.4:-24463654 None:intergenic
ATGGCTCAGTTAGTTTGTGG+AGG 0.620989 8.4:+24463809 MS.gene46341:intron
GAGACCTAATAACTGATAAG+GGG 0.634823 8.4:-24463676 None:intergenic
ACAGTCAATCTAGCTCTGGA+AGG 0.636792 8.4:+24463893 MS.gene46341:CDS
ATGTCAACTGTGGTAACTGC+AGG 0.637282 8.4:+24464068 MS.gene46341:CDS
ATTGAACACTCGTCGCTCCG+CGG 0.692743 8.4:-24463856 None:intergenic
ACTCTACTCATGTACATCCG+CGG 0.707343 8.4:+24463839 MS.gene46341:CDS
CAGGTGGCACATGTCAACTG+TGG 0.714575 8.4:+24464058 MS.gene46341:intron
GAATATTGCATCATACCAGG+AGG 0.733807 8.4:-24463651 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTCTTAAAACTACAAAGTA+CGG - chr8.4:24464014-24464033 None:intergenic 20.0%
! TGAGTTAAATTGTTGTGATT+CGG + chr8.4:24463985-24464004 MS.gene46341:intron 25.0%
!! ATGCTACTTATGTATCAATA+TGG + chr8.4:24464091-24464110 MS.gene46341:CDS 25.0%
AGAGACCTAATAACTGATAA+GGG - chr8.4:24463680-24463699 None:intergenic 30.0%
GTTCAGTTGACTAATAAATG+TGG - chr8.4:24463743-24463762 None:intergenic 30.0%
TAGAGACCTAATAACTGATA+AGG - chr8.4:24463681-24463700 None:intergenic 30.0%
GAAGAATATTGCATCATACC+AGG - chr8.4:24463657-24463676 None:intergenic 35.0%
GAGACCTAATAACTGATAAG+GGG - chr8.4:24463679-24463698 None:intergenic 35.0%
TCTTCCCCTTATCAGTTATT+AGG + chr8.4:24463672-24463691 MS.gene46341:CDS 35.0%
!! ACAAGCATTGATGTATTCAC+AGG + chr8.4:24463779-24463798 MS.gene46341:intron 35.0%
GAATATTGCATCATACCAGG+AGG - chr8.4:24463654-24463673 None:intergenic 40.0%
GGATGTACATGAGTAGAGTA+TGG - chr8.4:24463838-24463857 None:intergenic 40.0%
GTGTATTGTGACAGCAAATC+AGG + chr8.4:24464039-24464058 MS.gene46341:intron 40.0%
TATTGTGACAGCAAATCAGG+TGG + chr8.4:24464042-24464061 MS.gene46341:intron 40.0%
TGTATTCACAGGCACAGAAA+TGG + chr8.4:24463790-24463809 MS.gene46341:intron 40.0%
! GAAATGGCTCAGTTAGTTTG+TGG + chr8.4:24463806-24463825 MS.gene46341:intron 40.0%
AACAGCACAGCATACAGAAG+TGG - chr8.4:24463607-24463626 None:intergenic 45.0%
ACTCTACTCATGTACATCCG+CGG + chr8.4:24463839-24463858 MS.gene46341:CDS 45.0%
ATGTCAACTGTGGTAACTGC+AGG + chr8.4:24464068-24464087 MS.gene46341:CDS 45.0%
TATTGCATCATACCAGGAGG+TGG - chr8.4:24463651-24463670 None:intergenic 45.0%
! TCACACAGTCAATCTAGCTC+TGG + chr8.4:24463889-24463908 MS.gene46341:CDS 45.0%
! TGCTGTTTGCAATGCTGTCA+CGG + chr8.4:24463620-24463639 MS.gene46341:CDS 45.0%
!! ACAGTCAATCTAGCTCTGGA+AGG + chr8.4:24463893-24463912 MS.gene46341:CDS 45.0%
!! ATGGCTCAGTTAGTTTGTGG+AGG + chr8.4:24463809-24463828 MS.gene46341:intron 45.0%
CATACAGAAGTGGCTCCAAC+TGG - chr8.4:24463597-24463616 None:intergenic 50.0%
ATTGAACACTCGTCGCTCCG+CGG - chr8.4:24463859-24463878 None:intergenic 55.0%
CAGGTGGCACATGTCAACTG+TGG + chr8.4:24464058-24464077 MS.gene46341:intron 55.0%
GTCACGGCAGTTCCACCTCC+TGG + chr8.4:24463636-24463655 MS.gene46341:CDS 65.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 24463588 24464127 24463588 ID=MS.gene46341
chr8.4 mRNA 24463588 24464127 24463588 ID=MS.gene46341.t1;Parent=MS.gene46341
chr8.4 exon 24463588 24463693 24463588 ID=MS.gene46341.t1.exon1;Parent=MS.gene46341.t1
chr8.4 CDS 24463588 24463693 24463588 ID=cds.MS.gene46341.t1;Parent=MS.gene46341.t1
chr8.4 exon 24463818 24463914 24463818 ID=MS.gene46341.t1.exon2;Parent=MS.gene46341.t1
chr8.4 CDS 24463818 24463914 24463818 ID=cds.MS.gene46341.t1;Parent=MS.gene46341.t1
chr8.4 exon 24464061 24464127 24464061 ID=MS.gene46341.t1.exon3;Parent=MS.gene46341.t1
chr8.4 CDS 24464061 24464127 24464061 ID=cds.MS.gene46341.t1;Parent=MS.gene46341.t1
Gene Sequence

>MS.gene46341

ATGTATCCAGTTGGAGCCACTTCTGTATGCTGTGCTGTTTGCAATGCTGTCACGGCAGTTCCACCTCCTGGTATGATGCAATATTCTTCCCCTTATCAGTTATTAGGTCTCTATCTTTGAAGCTTTGTATGTTCTTCAATTTGTGATATTTACCACATTTATTAGTCAACTGAACATGAATCAGATAAATTACAAGCATTGATGTATTCACAGGCACAGAAATGGCTCAGTTAGTTTGTGGAGGATGCCATACTCTACTCATGTACATCCGCGGAGCGACGAGTGTTCAATGCTCTTGTTGTCACACAGTCAATCTAGCTCTGGAAGGTATTGATTTTTTTTGTTAATAATCTCATGAGCTTTGCATAATGACAGCTTCAAAAACATGTTTCATTTTTGAGTTAAATTGTTGTGATTCGGAGTCCGTACTTTGTAGTTTTAAGAATGAAATGTGTATTGTGACAGCAAATCAGGTGGCACATGTCAACTGTGGTAACTGCAGGATGCTACTTATGTATCAATATGGAGCAAGATCCGTGA
Protein sequence

>MS.gene46341.t1

MYPVGATSVCCAVCNAVTAVPPPGMMQYSSPYQLLVSLWRMPYSTHVHPRSDECSMLLLSHSQSSSGRWHMSTVVTAGCYLCINMEQDP