AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene064354

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene064354.t1 MTR_3g053510 95.146 103 4 1 1 102 1 103 2.54e-67 197
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACATGCTTTGATAGAATTA+TGG 0.258618 3.1:+40525466 MS.gene064354:intron
AGTGAAGAAGAGTGAGGAAT+TGG 0.296391 3.1:-40524742 None:intergenic
AAAGGAAAGTCATTTGATAA+AGG 0.376794 3.1:+40525504 MS.gene064354:CDS
AAAATTAAATGGTACCTTGA+TGG 0.391314 3.1:-40524816 None:intergenic
TGAAATTCTTCAGCTGTAGA+TGG 0.429413 3.1:-40525535 None:intergenic
GTGAAGAAGAGTGAGGAATT+GGG 0.473632 3.1:-40524741 None:intergenic
TTGTAGAAGAATGGTCTAGA+GGG 0.502419 3.1:-40524791 None:intergenic
TGCTGCTGAAGAAGCTGCTA+AGG 0.518120 3.1:+40525627 MS.gene064354:CDS
AAGCTGCTAAGGGTAATTCA+AGG 0.521770 3.1:+40525638 MS.gene064354:CDS
TGGACAAGAAGTGAAGGAAA+AGG 0.524067 3.1:+40525486 MS.gene064354:CDS
TTGATGGAGTTGTAGAAGAA+TGG 0.525498 3.1:-40524800 None:intergenic
GTTGTAGAAGAATGGTCTAG+AGG 0.544303 3.1:-40524792 None:intergenic
GAGAGTAACCATACCATGGC+TGG 0.545967 3.1:+40524716 None:intergenic
GAGGAATTGGGCACCAGCCA+TGG 0.552723 3.1:-40524729 None:intergenic
AGCTGAAGAATTTCAGAGAG+TGG 0.590235 3.1:+40525543 MS.gene064354:CDS
GTGGCAGAAGAGAAAACCAA+TGG 0.605337 3.1:+40525562 MS.gene064354:CDS
ATTCTTCTACAACTCCATCA+AGG 0.606836 3.1:+40524802 MS.gene064354:CDS
GAATTATGGACAAGAAGTGA+AGG 0.611950 3.1:+40525480 MS.gene064354:intron
AAATGTTAAGAACAAGTACA+AGG 0.627029 3.1:+40525666 MS.gene064354:CDS
AAGATGAGTGAAGAAGAGTG+AGG 0.651606 3.1:-40524748 None:intergenic
GCTGCTGAAGAAGCTGCTAA+GGG 0.655312 3.1:+40525628 MS.gene064354:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTAATTAAAAACATCAA+GGG - chr3.1:40524845-40524864 None:intergenic 10.0%
!!! TTTTAAAAAATCACATAATT+AGG - chr3.1:40525378-40525397 None:intergenic 10.0%
!!! TTTTTTTTCTTTCAATTAAT+TGG + chr3.1:40524873-40524892 MS.gene064354:intron 10.0%
!! CAATTTAATTAAAAACATCA+AGG - chr3.1:40524846-40524865 None:intergenic 15.0%
!!! TTAAATTTTAGTTTGTACTT+TGG + chr3.1:40525003-40525022 MS.gene064354:intron 15.0%
!! AAAAATCTTTACTTTCTTGA+TGG - chr3.1:40525183-40525202 None:intergenic 20.0%
!! AAAATCTTTACTTTCTTGAT+GGG - chr3.1:40525182-40525201 None:intergenic 20.0%
!! ATCAAGGGATAAAAATTAAA+TGG - chr3.1:40524830-40524849 None:intergenic 20.0%
!! CAATAATTAATAGACAACTA+CGG - chr3.1:40525438-40525457 None:intergenic 20.0%
! AAAATTAAATGGTACCTTGA+TGG - chr3.1:40524819-40524838 None:intergenic 25.0%
! AAAGGAAAGTCATTTGATAA+AGG + chr3.1:40525504-40525523 MS.gene064354:CDS 25.0%
! AAATGTTAAGAACAAGTACA+AGG + chr3.1:40525666-40525685 MS.gene064354:CDS 25.0%
! AACATGCTTTGATAGAATTA+TGG + chr3.1:40525466-40525485 MS.gene064354:intron 25.0%
! AACTCTACATGCAATAATTA+AGG - chr3.1:40525074-40525093 None:intergenic 25.0%
! ATTTGACATCTTTACTCAAA+TGG + chr3.1:40525218-40525237 MS.gene064354:intron 25.0%
! GAAAATTAAAGGTTGAAAAG+TGG + chr3.1:40525133-40525152 MS.gene064354:intron 25.0%
! TTGAGTAAAGATGTCAAATT+TGG - chr3.1:40525217-40525236 None:intergenic 25.0%
! TTTGACATCTTTACTCAAAT+GGG + chr3.1:40525219-40525238 MS.gene064354:intron 25.0%
AAAGTAAGAATGATCCTAGT+AGG + chr3.1:40524949-40524968 MS.gene064354:intron 30.0%
AATTACAAGTGTCTATGTGT+CGG - chr3.1:40525352-40525371 None:intergenic 30.0%
TTAATAGACAACTACGGATA+CGG - chr3.1:40525432-40525451 None:intergenic 30.0%
TTTGTGAGGTGGAAAATTAA+AGG + chr3.1:40525122-40525141 MS.gene064354:intron 30.0%
!! AGATTTGTTAGTTGTGTTTG+AGG + chr3.1:40525042-40525061 MS.gene064354:intron 30.0%
!!! TTTCACTTTTTGTGTTCCAT+TGG - chr3.1:40525581-40525600 None:intergenic 30.0%
ATTCTTCTACAACTCCATCA+AGG + chr3.1:40524802-40524821 MS.gene064354:CDS 35.0%
GAATTATGGACAAGAAGTGA+AGG + chr3.1:40525480-40525499 MS.gene064354:intron 35.0%
TGAAATTCTTCAGCTGTAGA+TGG - chr3.1:40525538-40525557 None:intergenic 35.0%
TTGATGGAGTTGTAGAAGAA+TGG - chr3.1:40524803-40524822 None:intergenic 35.0%
TTGTAGAAGAATGGTCTAGA+GGG - chr3.1:40524794-40524813 None:intergenic 35.0%
! AATTTTCCACCTCACAAAAC+AGG - chr3.1:40525120-40525139 None:intergenic 35.0%
AAGATGAGTGAAGAAGAGTG+AGG - chr3.1:40524751-40524770 None:intergenic 40.0%
AAGCTGCTAAGGGTAATTCA+AGG + chr3.1:40525638-40525657 MS.gene064354:CDS 40.0%
AGCTGAAGAATTTCAGAGAG+TGG + chr3.1:40525543-40525562 MS.gene064354:CDS 40.0%
AGTGAAGAAGAGTGAGGAAT+TGG - chr3.1:40524745-40524764 None:intergenic 40.0%
CTTCAACTCAATCTCCTACT+AGG - chr3.1:40524966-40524985 None:intergenic 40.0%
GTGAAGAAGAGTGAGGAATT+GGG - chr3.1:40524744-40524763 None:intergenic 40.0%
GTTGTAGAAGAATGGTCTAG+AGG - chr3.1:40524795-40524814 None:intergenic 40.0%
TGGACAAGAAGTGAAGGAAA+AGG + chr3.1:40525486-40525505 MS.gene064354:CDS 40.0%
GTGGCAGAAGAGAAAACCAA+TGG + chr3.1:40525562-40525581 MS.gene064354:CDS 45.0%
! CATGATCCTGTTTTGTGAGG+TGG + chr3.1:40525111-40525130 MS.gene064354:intron 45.0%
! CTGCATGATCCTGTTTTGTG+AGG + chr3.1:40525108-40525127 MS.gene064354:intron 45.0%
GCTGCTGAAGAAGCTGCTAA+GGG + chr3.1:40525628-40525647 MS.gene064354:CDS 50.0%
TGCTGCTGAAGAAGCTGCTA+AGG + chr3.1:40525627-40525646 MS.gene064354:CDS 50.0%
ACGGACACGAGACACGACAC+TGG - chr3.1:40525413-40525432 None:intergenic 60.0%
!! GTCTATGTGTCGGTGTCGCG+TGG - chr3.1:40525342-40525361 None:intergenic 60.0%
!! GTGTCGGTGTCGCGTGGTGT+CGG - chr3.1:40525336-40525355 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 40524731 40525696 40524731 ID=MS.gene064354
chr3.1 mRNA 40524731 40525696 40524731 ID=MS.gene064354.t1;Parent=MS.gene064354
chr3.1 exon 40524731 40524823 40524731 ID=MS.gene064354.t1.exon1;Parent=MS.gene064354.t1
chr3.1 CDS 40524731 40524823 40524731 ID=cds.MS.gene064354.t1;Parent=MS.gene064354.t1
chr3.1 exon 40525481 40525696 40525481 ID=MS.gene064354.t1.exon2;Parent=MS.gene064354.t1
chr3.1 CDS 40525481 40525696 40525481 ID=cds.MS.gene064354.t1;Parent=MS.gene064354.t1
Gene Sequence

>MS.gene064354

ATGGCTGGTGCCCAATTCCTCACTCTTCTTCACTCATCTTCAAGATCTTCTTTGCTCAAACCCTCTAGACCATTCTTCTACAACTCCATCAAGGTACCATTTAATTTTTATCCCTTGATGTTTTTAATTAAATTGTATAATATTTTTTTTCTTTCAATTAATTGGTGTTACAAAAACTATATAAAATTGTTTAATTTAATTTTAATTTTTTTTTTTTGAAAGTAAGAATGATCCTAGTAGGAGATTGAGTTGAAGAAAGAAAATGTTGAATTTTAAATTTTAGTTTGTACTTTGGTTGAAATTAAAGAGTTAGATTTGTTAGTTGTGTTTGAGGAAGAAACCTTAATTATTGCATGTAGAGTTAATGAAGAATTGTTCTGCATGATCCTGTTTTGTGAGGTGGAAAATTAAAGGTTGAAAAGTGGATCAAAAGATTCATAAATCAAAACCCATCAAGAAAGTAAAGATTTTTCATTGTTGAATCCAAATTTGACATCTTTACTCAAATGGGTTTGCTTTAAAATTGTCAAATTGATCAAAAAGTTTGATTTTTAGTGTTATGATTTTGTGACTTTGAAACTGTTCGATTTAGCTTGTCGCGTCCGACACCACGCGACACCGACACATAGACACTTGTAATTACACCTAATTATGTGATTTTTTAAAATTATTAGCTGTGCCAGTGTCGTGTCTCGTGTCCGTATCCGTAGTTGTCTATTAATTATTGAATGAATGAACATGCTTTGATAGAATTATGGACAAGAAGTGAAGGAAAAGGAAAGTCATTTGATAAAGGAGAGAGCACCATCTACAGCTGAAGAATTTCAGAGAGTGGCAGAAGAGAAAACCAATGGAACACAAAAAGTGAAAAGTCAAACAGTTGATAAAGCAATTGATGCTGCTGAAGAAGCTGCTAAGGGTAATTCAAGGATTGAAAATGTTAAGAACAAGTACAAGGAGCATTGA
Protein sequence

>MS.gene064354.t1

MAGAQFLTLLHSSSRSSLLKPSRPFFYNSIKNYGQEVKEKESHLIKERAPSTAEEFQRVAEEKTNGTQKVKSQTVDKAIDAAEEAAKGNSRIENVKNKYKEH