AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060910

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 16 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTGTTGGTGCTGGTGTTGC+TGG 0.278594 1.2:-8561074 MS.gene060910:CDS
CGATGTAGGCGAAGTTAATT+CGG 0.329255 1.2:-8561126 MS.gene060910:intron
TATTGCTCTGGTTGTACTCT+TGG 0.344765 1.2:-8561051 MS.gene060910:CDS
CTCATCAACATATCGGCATC+AGG 0.407565 1.2:-8560609 MS.gene060910:CDS
CTTAAGAAGTGTAATTATGA+AGG 0.426449 1.2:-8561175 MS.gene060910:intron
ATTGCTCTGGTTGTACTCTT+GGG 0.449876 1.2:-8561050 MS.gene060910:CDS
TGGTGTTGCTGGTATTGCTC+TGG 0.454038 1.2:-8561063 MS.gene060910:CDS
AATGTTATCACTGTTGGTGC+TGG 0.466483 1.2:-8561083 MS.gene060910:CDS
CATTTCCCTCATCAACATAT+CGG 0.470848 1.2:-8560616 MS.gene060910:CDS
GCAGTTATCAACATCTTCGT+TGG 0.491361 1.2:-8560653 MS.gene060910:intron
CTCTGGTTGTACTCTTGGGA+AGG 0.498339 1.2:-8561046 MS.gene060910:intron
ATATCGGCATCAGGGCAACT+TGG 0.528755 1.2:-8560600 MS.gene060910:intron
GATGCTAATGTTATCACTGT+TGG 0.589755 1.2:-8561089 MS.gene060910:CDS
TCATCAACATATCGGCATCA+GGG 0.604907 1.2:-8560608 MS.gene060910:CDS
CTGATGCCGATATGTTGATG+AGG 0.666580 1.2:+8560610 None:intergenic
TGATGCCGATATGTTGATGA+GGG 0.679239 1.2:+8560611 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATAGATTGATTTTATATTT+GGG - chr1.2:8561004-8561023 MS.gene060910:intron 10.0%
!!! AAGTTTTGATTTGATTTATT+TGG - chr1.2:8560728-8560747 MS.gene060910:intron 15.0%
!!! CTATAGATTGATTTTATATT+TGG - chr1.2:8561003-8561022 MS.gene060910:intron 15.0%
!! TTACATATAAACAAAACACA+CGG + chr1.2:8560913-8560932 None:intergenic 20.0%
! AAGTGAGAATAATAAAGACA+AGG + chr1.2:8561153-8561172 None:intergenic 25.0%
! AATGAAACAAACAGGAAAAT+AGG + chr1.2:8560889-8560908 None:intergenic 25.0%
! GTTAATTCGGAAAAATTCAA+CGG - chr1.2:8560581-8560600 MS.gene060910:intron 25.0%
! TTGTAATTTAGTCAAACCAT+TGG - chr1.2:8560673-8560692 MS.gene060910:intron 25.0%
!! CTTAAGAAGTGTAATTATGA+AGG - chr1.2:8560519-8560538 MS.gene060910:intron 25.0%
!! GTCTTTATTATTCTCACTTT+TGG - chr1.2:8561154-8561173 MS.gene060910:intron 25.0%
ACAAGCAGCAAATTCAATCA+AGG + chr1.2:8560842-8560861 None:intergenic 35.0%
AGGAATGTGAAAGACAAAAG+TGG + chr1.2:8561133-8561152 None:intergenic 35.0%
ATTGTGACGATTATCGATGT+AGG - chr1.2:8560554-8560573 MS.gene060910:intron 35.0%
CATTTCCCTCATCAACATAT+CGG - chr1.2:8561078-8561097 MS.gene060910:CDS 35.0%
GATGCTAATGTTATCACTGT+TGG - chr1.2:8560605-8560624 MS.gene060910:CDS 35.0%
!! TCTCACTTTTGGTTAAATGC+AGG - chr1.2:8561165-8561184 MS.gene060910:intron 35.0%
AATGTTATCACTGTTGGTGC+TGG - chr1.2:8560611-8560630 MS.gene060910:CDS 40.0%
AGAGATGAACTTGGATCCAA+TGG + chr1.2:8560692-8560711 None:intergenic 40.0%
ATTGCTCTGGTTGTACTCTT+GGG - chr1.2:8560644-8560663 MS.gene060910:CDS 40.0%
CACACGGAAATGAAACAAAC+AGG + chr1.2:8560897-8560916 None:intergenic 40.0%
CATGCAACAAGAGATGAACT+TGG + chr1.2:8560701-8560720 None:intergenic 40.0%
CGATGTAGGCGAAGTTAATT+CGG - chr1.2:8560568-8560587 MS.gene060910:intron 40.0%
GCAGTTATCAACATCTTCGT+TGG - chr1.2:8561041-8561060 MS.gene060910:intron 40.0%
TATTGCTCTGGTTGTACTCT+TGG - chr1.2:8560643-8560662 MS.gene060910:CDS 40.0%
TCATCAACATATCGGCATCA+GGG - chr1.2:8561086-8561105 MS.gene060910:CDS 40.0%
! TGATGCCGATATGTTGATGA+GGG + chr1.2:8561086-8561105 None:intergenic 40.0%
CTCATCAACATATCGGCATC+AGG - chr1.2:8561085-8561104 MS.gene060910:CDS 45.0%
CTGATGCCGATATGTTGATG+AGG + chr1.2:8561087-8561106 None:intergenic 45.0%
ATATCGGCATCAGGGCAACT+TGG - chr1.2:8561094-8561113 MS.gene060910:CDS 50.0%
CTCTGGTTGTACTCTTGGGA+AGG - chr1.2:8560648-8560667 MS.gene060910:CDS 50.0%
!! TGGTGTTGCTGGTATTGCTC+TGG - chr1.2:8560631-8560650 MS.gene060910:CDS 50.0%
!! ACTGTTGGTGCTGGTGTTGC+TGG - chr1.2:8560620-8560639 MS.gene060910:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 8560516 8561200 8560516 ID=MS.gene060910
chr1.2 mRNA 8560516 8561200 8560516 ID=MS.gene060910.t1;Parent=MS.gene060910
chr1.2 exon 8561176 8561200 8561176 ID=MS.gene060910.t1.exon1;Parent=MS.gene060910.t1
chr1.2 CDS 8561176 8561200 8561176 ID=cds.MS.gene060910.t1;Parent=MS.gene060910.t1
chr1.2 exon 8561047 8561140 8561047 ID=MS.gene060910.t1.exon2;Parent=MS.gene060910.t1
chr1.2 CDS 8561047 8561140 8561047 ID=cds.MS.gene060910.t1;Parent=MS.gene060910.t1
chr1.2 exon 8560601 8560671 8560601 ID=MS.gene060910.t1.exon3;Parent=MS.gene060910.t1
chr1.2 CDS 8560601 8560671 8560601 ID=cds.MS.gene060910.t1;Parent=MS.gene060910.t1
chr1.2 exon 8560516 8560529 8560516 ID=MS.gene060910.t1.exon4;Parent=MS.gene060910.t1
chr1.2 CDS 8560516 8560529 8560516 ID=cds.MS.gene060910.t1;Parent=MS.gene060910.t1
Gene Sequence

>MS.gene060910

ATGCTTAAGAAGTGTAATTATGAAGGTTTGTTTCTTAAATTGTGACGATTATCGATGTAGGCGAAGTTAATTCGGAAAAATTCAACGGTGATGCTAATGTTATCACTGTTGGTGCTGGTGTTGCTGGTATTGCTCTGGTTGTACTCTTGGGAAGGTATTGTAATTTAGTCAAACCATTGGATCCAAGTTCATCTCTTGTTGCATGTGTTTAGAAGTTTTGATTTGATTTATTTGGTGATTGAACTAGATAAATTTTGAATTAATAAGTGTTAGTTAGTTGCTGCTTGTGAATTCAGTTTCAATTGATTTGTGTTTTTAACAATCCTTGATTGAATTTGCTGCTTGTAATTTGATTTGATTAGCTTGCTGACCTATTTTCCTGTTTGTTTCATTTCCGTGTGTTTTGTTTATATGTAAAATTTGAGTTTTTTTTTTAGATCTCTGCTAGTTAATTTTCTGTTAACACTCAAAATTATTTGATTGTTTTCTATAGATTGATTTTATATTTGGGTAATTGTAATTTATGCAGTTATCAACATCTTCGTTGGCATTTGTTTATCTGCATTTCCCTCATCAACATATCGGCATCAGGGCAACTTGGTAACACATTTTCGCCACTTTTGTCTTTCACATTCCTTGTCTTTATTATTCTCACTTTTGGTTAAATGCAGGTGAACAAGCTTAA
Protein sequence

>MS.gene060910.t1

MLKKCNYEGEVNSEKFNGDANVITVGAGVAGIALVVLLGSYQHLRWHLFICISLINISASGQLGEQA