AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004251

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004251.t1 MTR_2g016150 96.774 186 4 1 1 184 1 186 1.13e-128 359
MS.gene004251.t1 MTR_3g031140 44.382 178 90 4 1 178 1 169 7.23e-43 141
MS.gene004251.t1 MTR_5g074290 38.251 183 82 5 1 178 1 157 1.79e-31 112
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004251.t1 AT1G29195 56.383 188 72 3 1 178 1 188 1.18e-66 202
MS.gene004251.t1 AT2G30230 40.107 187 90 6 1 178 1 174 8.38e-35 120
MS.gene004251.t1 AT1G06980 40.217 184 86 4 1 178 1 166 5.83e-34 118

Find 31 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCCGGTGGTGGCGGCGTT+GGG 0.341375 2.4:-68864964 None:intergenic
GGTTTCTTGAGAACATGTTT+TGG 0.350154 2.4:-68864839 None:intergenic
GAAGGGACAACAACAATCTT+AGG 0.351160 2.4:-68864896 None:intergenic
CACCTTCAGCGCAAGATGGC+GGG 0.354822 2.4:+68864867 MS.gene004251:CDS
TGCTGTGTGGAGACCTCATT+TGG 0.366621 2.4:+68865198 MS.gene004251:CDS
AACCGTTATAGAAGATTTGT+TGG 0.403215 2.4:-68865238 None:intergenic
TTATCCGGTGGTGGCGGCGT+TGG 0.422064 2.4:-68864965 None:intergenic
GACCGTTGCAGTGTACTATA+CGG 0.423911 2.4:-68864763 None:intergenic
GGTGGTGGCGGCGTTGGGAG+AGG 0.431618 2.4:-68864959 None:intergenic
ACCCCGCCATCTTGCGCTGA+AGG 0.489813 2.4:-68864869 None:intergenic
TCTTGCGCTGAAGGTGAAGA+AGG 0.505753 2.4:-68864860 None:intergenic
GACTGAGATTCTGTCTGAGA+AGG 0.517425 2.4:+68865141 MS.gene004251:CDS
TCACCTTCAGCGCAAGATGG+CGG 0.520403 2.4:+68864866 MS.gene004251:CDS
CACCAACAAATCTTCTATAA+CGG 0.521213 2.4:+68865236 MS.gene004251:CDS
TCTCCCAACGCCGCCACCAC+CGG 0.524822 2.4:+68864961 MS.gene004251:CDS
CATCGAGAACAGTGCTATGT+TGG 0.527832 2.4:+68865096 MS.gene004251:CDS
ACCTTCAGCGCAAGATGGCG+GGG 0.527946 2.4:+68864868 MS.gene004251:CDS
TCTTCACCTTCAGCGCAAGA+TGG 0.556088 2.4:+68864863 MS.gene004251:CDS
GCGGCGTTGGGAGAGGCATG+AGG 0.582625 2.4:-68864952 None:intergenic
AGTCAGAGAGACAGAAGAAG+AGG 0.589679 2.4:+68865169 MS.gene004251:CDS
TCAGAAATACTCTCCAAATG+AGG 0.591665 2.4:-68865211 None:intergenic
CGTTGAAGATCAGCATCGGA+AGG 0.596656 2.4:-68864914 None:intergenic
ACCACGTTGAAGATCAGCAT+CGG 0.623623 2.4:-68864918 None:intergenic
ACAAACAACAGTAGAAGTAA+CGG 0.626432 2.4:+68865058 MS.gene004251:CDS
GTTGAAGATCAGCATCGGAA+GGG 0.641800 2.4:-68864913 None:intergenic
GGTCGAGTAGAAGAGATCAG+TGG 0.670260 2.4:+68864782 MS.gene004251:CDS
ATCACATCAAGTGCTCCACA+TGG 0.674792 2.4:-68864740 None:intergenic
ATATCTTGCATTCTACCATG+TGG 0.683335 2.4:+68864725 MS.gene004251:CDS
GAAGAGGACGTGTTGCTGTG+TGG 0.686286 2.4:+68865185 MS.gene004251:CDS
ATCCGTATAGTACACTGCAA+CGG 0.690119 2.4:+68864761 MS.gene004251:CDS
TCCGATGCTGATCTTCAACG+TGG 0.747704 2.4:+68864917 MS.gene004251:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ACAAACAACAGTAGAAGTAA+CGG + chr2.4:68865058-68865077 MS.gene004251:CDS 30.0%
! GTTTCTTGAGAACATGTTTT+GGG - chr2.4:68864841-68864860 None:intergenic 30.0%
!!! TGACGGTGATTATTTTTATC+CGG - chr2.4:68864983-68865002 None:intergenic 30.0%
ATATCTTGCATTCTACCATG+TGG + chr2.4:68864725-68864744 MS.gene004251:CDS 35.0%
TCAGAAATACTCTCCAAATG+AGG - chr2.4:68865214-68865233 None:intergenic 35.0%
! GGTTTCTTGAGAACATGTTT+TGG - chr2.4:68864842-68864861 None:intergenic 35.0%
!!! TGATTATTTTTATCCGGTGG+TGG - chr2.4:68864977-68864996 None:intergenic 35.0%
ATCCGTATAGTACACTGCAA+CGG + chr2.4:68864761-68864780 MS.gene004251:CDS 40.0%
GAAGGGACAACAACAATCTT+AGG - chr2.4:68864899-68864918 None:intergenic 40.0%
!!! CGGTGATTATTTTTATCCGG+TGG - chr2.4:68864980-68864999 None:intergenic 40.0%
!!! TTATTTTTATCCGGTGGTGG+CGG - chr2.4:68864974-68864993 None:intergenic 40.0%
ACCACGTTGAAGATCAGCAT+CGG - chr2.4:68864921-68864940 None:intergenic 45.0%
AGTCAGAGAGACAGAAGAAG+AGG + chr2.4:68865169-68865188 MS.gene004251:CDS 45.0%
ATCACATCAAGTGCTCCACA+TGG - chr2.4:68864743-68864762 None:intergenic 45.0%
CATCGAGAACAGTGCTATGT+TGG + chr2.4:68865096-68865115 MS.gene004251:CDS 45.0%
CCGTCATAGCAAAAACTCGT+CGG + chr2.4:68864997-68865016 MS.gene004251:CDS 45.0%
GACCGTTGCAGTGTACTATA+CGG - chr2.4:68864766-68864785 None:intergenic 45.0%
GACTGAGATTCTGTCTGAGA+AGG + chr2.4:68865141-68865160 MS.gene004251:CDS 45.0%
! GTTGAAGATCAGCATCGGAA+GGG - chr2.4:68864916-68864935 None:intergenic 45.0%
!! CCGACGAGTTTTTGCTATGA+CGG - chr2.4:68865000-68865019 None:intergenic 45.0%
GGTCGAGTAGAAGAGATCAG+TGG + chr2.4:68864782-68864801 MS.gene004251:CDS 50.0%
TCCGATGCTGATCTTCAACG+TGG + chr2.4:68864917-68864936 MS.gene004251:CDS 50.0%
TCTTCACCTTCAGCGCAAGA+TGG + chr2.4:68864863-68864882 MS.gene004251:CDS 50.0%
TCTTGCGCTGAAGGTGAAGA+AGG - chr2.4:68864863-68864882 None:intergenic 50.0%
TGCTGTGTGGAGACCTCATT+TGG + chr2.4:68865198-68865217 MS.gene004251:CDS 50.0%
! CGTTGAAGATCAGCATCGGA+AGG - chr2.4:68864917-68864936 None:intergenic 50.0%
TCACCTTCAGCGCAAGATGG+CGG + chr2.4:68864866-68864885 MS.gene004251:CDS 55.0%
! GAAGAGGACGTGTTGCTGTG+TGG + chr2.4:68865185-68865204 MS.gene004251:CDS 55.0%
ACCTTCAGCGCAAGATGGCG+GGG + chr2.4:68864868-68864887 MS.gene004251:CDS 60.0%
CACCTTCAGCGCAAGATGGC+GGG + chr2.4:68864867-68864886 MS.gene004251:CDS 60.0%
ACCCCGCCATCTTGCGCTGA+AGG - chr2.4:68864872-68864891 None:intergenic 65.0%
!! TATCCGGTGGTGGCGGCGTT+GGG - chr2.4:68864967-68864986 None:intergenic 65.0%
!! TTATCCGGTGGTGGCGGCGT+TGG - chr2.4:68864968-68864987 None:intergenic 65.0%
TCTCCCAACGCCGCCACCAC+CGG + chr2.4:68864961-68864980 MS.gene004251:CDS 70.0%
! GCGGCGTTGGGAGAGGCATG+AGG - chr2.4:68864955-68864974 None:intergenic 70.0%
!! GGTGGTGGCGGCGTTGGGAG+AGG - chr2.4:68864962-68864981 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 68864701 68865255 68864701 ID=MS.gene004251
chr2.4 mRNA 68864701 68865255 68864701 ID=MS.gene004251.t1;Parent=MS.gene004251
chr2.4 exon 68864701 68865255 68864701 ID=MS.gene004251.t1.exon1;Parent=MS.gene004251.t1
chr2.4 CDS 68864701 68865255 68864701 ID=cds.MS.gene004251.t1;Parent=MS.gene004251.t1
Gene Sequence

>MS.gene004251

ATGAGAAACAGCATAAGATGTTGCATATCTTGCATTCTACCATGTGGAGCACTTGATGTGATCCGTATAGTACACTGCAACGGTCGAGTAGAAGAGATCAGTGGCAGCATCAAAGCAAGTGAAATCATGAAAACATACCCAAAACATGTTCTCAAGAAACCTTCTTCACCTTCAGCGCAAGATGGCGGGGTTGTTCCTAAGATTGTTGTTGTCCCTTCCGATGCTGATCTTCAACGTGGTAAGATTTACTTCCTCATGCCTCTCCCAACGCCGCCACCACCGGATAAAAATAATCACCGTCATAGCAAAAACTCGTCGGTAAGAAAGAAAAGAAAAGAACAGAACGAGAGAATATTAACAAACAACAGTAGAAGTAACGGTAACAGTAACAACAACATCGAGAACAGTGCTATGTTGGTTGTGTCTTCTGATCAGTACTTGACTGAGATTCTGTCTGAGAAGGTTTGTAGTCAGAGAGACAGAAGAAGAGGACGTGTTGCTGTGTGGAGACCTCATTTGGAGAGTATTTCTGAGTCACCAACAAATCTTCTATAA
Protein sequence

>MS.gene004251.t1

MRNSIRCCISCILPCGALDVIRIVHCNGRVEEISGSIKASEIMKTYPKHVLKKPSSPSAQDGGVVPKIVVVPSDADLQRGKIYFLMPLPTPPPPDKNNHRHSKNSSVRKKRKEQNERILTNNSRSNGNSNNNIENSAMLVVSSDQYLTEILSEKVCSQRDRRRGRVAVWRPHLESISESPTNLL