AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053846

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053846.t1 MTR_4g123470 87.037 108 14 0 2 109 118 225 1.48e-67 202
MS.gene053846.t1 MTR_7g113060 89.189 37 4 0 71 107 3 39 3.67e-18 75.9
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 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGTTCCTATCGTTGGATA+TGG 0.258835 5.3:-44409856 MS.gene053846:CDS
CATAGTGCATGAACAAAATC+AGG 0.339133 5.3:-44410000 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.341127 5.3:+44409695 None:intergenic
AGGAATTTGCCAAAAGTATC+AGG 0.344083 5.3:+44409715 None:intergenic
TAGGAACTACCTGATACTTT+TGG 0.356273 5.3:-44409724 MS.gene053846:CDS
TCCGAACATCACATTTGGTA+TGG 0.417548 5.3:+44409609 None:intergenic
ACCTTTGAAGTTCCTATCGT+TGG 0.439777 5.3:-44409862 MS.gene053846:CDS
CCGAACATCACATTTGGTAT+GGG 0.451435 5.3:+44409610 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 5.3:-44409604 MS.gene053846:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 5.3:-44409610 MS.gene053846:CDS
GTCATGTGTTTATCAACGCT+TGG 0.483566 5.3:+44409486 None:intergenic
CACGATTACGTCATGTTGTA+CGG 0.501494 5.3:-44409679 MS.gene053846:CDS
ACAGGAATTATATTGTCATA+AGG 0.502590 5.3:+44409655 None:intergenic
TTGTGCTGCTAATGGTATTG+AGG 0.529169 5.3:-44409569 MS.gene053846:CDS
CGAACATCACATTTGGTATG+GGG 0.552019 5.3:+44409611 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 5.3:+44409637 None:intergenic
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 5.3:-44409530 MS.gene053846:CDS
GTCGATCCATATCCAACGAT+AGG 0.588698 5.3:+44409850 None:intergenic
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 5.3:-44409600 MS.gene053846:CDS
TCCAACGATAGGAACTTCAA+AGG 0.611311 5.3:+44409861 None:intergenic
TGGATCGACAAAATCACCGA+AGG 0.660770 5.3:-44409836 MS.gene053846:intron
GCTGCTAATGGTATTGAGGA+CGG 0.706139 5.3:-44409565 MS.gene053846:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTATTTAAATAAAATGAA+CGG - chr5.3:44409540-44409559 MS.gene053846:CDS 10.0%
!!! CAGTTTTTTTTCTTTTTTTT+AGG - chr5.3:44409747-44409766 MS.gene053846:intron 15.0%
!! AAAAAACAATAAACAACCTT+CGG + chr5.3:44409673-44409692 None:intergenic 20.0%
!! AAATTTACGGAATAAGTTTA+CGG + chr5.3:44409569-44409588 None:intergenic 20.0%
! ACAGGAATTATATTGTCATA+AGG + chr5.3:44409838-44409857 None:intergenic 25.0%
! AGTTAGGCAGAAAAAATTTA+CGG + chr5.3:44409582-44409601 None:intergenic 25.0%
AATCGTGATGTTTCACTCTA+AGG + chr5.3:44409798-44409817 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + chr5.3:44409856-44409875 None:intergenic 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr5.3:44409766-44409785 MS.gene053846:intron 35.0%
! TTTTCTGCCTAACTTTAGTG+CGG - chr5.3:44409588-44409607 MS.gene053846:CDS 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr5.3:44409778-44409797 None:intergenic 35.0%
ATGTGATGTTCGGAAAAGGT+TGG - chr5.3:44409890-44409909 MS.gene053846:intron 40.0%
CACGATTACGTCATGTTGTA+CGG - chr5.3:44409811-44409830 MS.gene053846:intron 40.0%
CCAAATGTGATGTTCGGAAA+AGG - chr5.3:44409886-44409905 MS.gene053846:CDS 40.0%
CCCATACCAAATGTGATGTT+CGG - chr5.3:44409880-44409899 MS.gene053846:CDS 40.0%
CCGAACATCACATTTGGTAT+GGG + chr5.3:44409883-44409902 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG + chr5.3:44409882-44409901 None:intergenic 40.0%
GAAGTTCCTATCGTTGGATA+TGG - chr5.3:44409634-44409653 MS.gene053846:CDS 40.0%
TCCAACGATAGGAACTTCAA+AGG + chr5.3:44409632-44409651 None:intergenic 40.0%
TCCGAACATCACATTTGGTA+TGG + chr5.3:44409884-44409903 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG + chr5.3:44409889-44409908 None:intergenic 40.0%
! TTGTGCTGCTAATGGTATTG+AGG - chr5.3:44409921-44409940 MS.gene053846:intron 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG - chr5.3:44409628-44409647 MS.gene053846:CDS 40.0%
!! ACGAGTTTTTGTGCTGCTAA+TGG - chr5.3:44409913-44409932 MS.gene053846:intron 40.0%
GATGTTGCCGCACTAAAGTT+AGG + chr5.3:44409598-44409617 None:intergenic 45.0%
GTCGATCCATATCCAACGAT+AGG + chr5.3:44409643-44409662 None:intergenic 45.0%
TGGATCGACAAAATCACCGA+AGG - chr5.3:44409654-44409673 MS.gene053846:CDS 45.0%
! GCTGCTAATGGTATTGAGGA+CGG - chr5.3:44409925-44409944 MS.gene053846:intron 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG - chr5.3:44409960-44409979 MS.gene053846:intron 45.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 44409498 44410014 44409498 ID=MS.gene053846
chr5.3 mRNA 44409498 44410014 44409498 ID=MS.gene053846.t1;Parent=MS.gene053846
chr5.3 exon 44410001 44410014 44410001 ID=MS.gene053846.t1.exon1;Parent=MS.gene053846.t1
chr5.3 CDS 44410001 44410014 44410001 ID=cds.MS.gene053846.t1;Parent=MS.gene053846.t1
chr5.3 exon 44409837 44409906 44409837 ID=MS.gene053846.t1.exon2;Parent=MS.gene053846.t1
chr5.3 CDS 44409837 44409906 44409837 ID=cds.MS.gene053846.t1;Parent=MS.gene053846.t1
chr5.3 exon 44409498 44409743 44409498 ID=MS.gene053846.t1.exon3;Parent=MS.gene053846.t1
chr5.3 CDS 44409498 44409743 44409498 ID=cds.MS.gene053846.t1;Parent=MS.gene053846.t1
Gene Sequence

>MS.gene053846

ATGAACAAAATCAGGTTTGTTTCACTTGATGATTTAATCTTTTTCTATTTAAATAAAATGAACGGATTCCGTAAACTTATTCCGTAAATTTTTTCTGCCTAACTTTAGTGCGGCAACATCATGTTATTGTACCTTTGAAGTTCCTATCGTTGGATATGGATCGACAAAATCACCGAAGGTTGTTTATTGTTTTTTTGTTGCTATTTAATTAGATATATACTATAATAAACGATTTGTGTCTGTCATTAACAGTTTTTTTTCTTTTTTTTAGGAACTACCTGATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCATGTTGTACGGACCTTATGACAATATAATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCTAATGGTATTGAGGACGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>MS.gene053846.t1

MNKISAATSCYCTFEVPIVGYGSTKSPKELPDTFGKFLRVKHHDYVMLYGPYDNIIPVRLKYTDDPIPNVMFGKGWTSFCAANGIEDGDVLIFKCKCVMDKKYVIVSKR