AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90494

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90494.t1 MTR_4g123470 86.207 87 12 0 9 95 139 225 5.76e-52 162
MS.gene90494.t1 MTR_7g113060 86.486 37 5 0 57 93 3 39 3.03e-17 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGAATTTGCCGAAAGTATC+AGG 0.335653 8.3:-23608868 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.341127 8.3:-23608888 None:intergenic
TAGGAACTACCTGATACTTT+CGG 0.409962 8.3:+23608859 MS.gene90494:intron
TCCGAACATCACATTTGGTA+TGG 0.417548 8.3:-23608974 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.451435 8.3:-23608973 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 8.3:+23608979 MS.gene90494:CDS
TTGTGCTGCCAATGGTATTG+AGG 0.475840 8.3:+23609014 MS.gene90494:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 8.3:+23608973 MS.gene90494:CDS
GTCATGCGTTTATCAACGCT+TGG 0.494559 8.3:-23609097 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 8.3:+23609015 MS.gene90494:CDS
ACAGAAATGATATTGTCATA+AGG 0.528831 8.3:-23608928 None:intergenic
GGCCATTGTTGACAGATGGT+TGG 0.532036 8.3:+23608536 None:intergenic
CGAACATCACATTTGGTATG+GGG 0.552019 8.3:-23608972 None:intergenic
CACGATTACGTCACGTTGTG+CGG 0.563420 8.3:+23608904 MS.gene90494:CDS
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 8.3:+23609053 MS.gene90494:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 8.3:-23609022 None:intergenic
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 8.3:+23608983 MS.gene90494:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 8.3:+23609018 MS.gene90494:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATATATGCTATAATAA+AGG + chr8.3:23608799-23608818 MS.gene90494:intron 10.0%
!!! CAATTTTTTTTTCTTTTTGT+AGG + chr8.3:23608840-23608859 MS.gene90494:intron 15.0%
! ACAGAAATGATATTGTCATA+AGG - chr8.3:23608931-23608950 None:intergenic 25.0%
AATCGTGATGTTTCACTCTA+AGG - chr8.3:23608891-23608910 None:intergenic 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr8.3:23608598-23608617 MS.gene90494:intron 35.0%
TAGGAACTACCTGATACTTT+CGG + chr8.3:23608859-23608878 MS.gene90494:intron 35.0%
TATCCAGATAGGAACTTCAA+AGG - chr8.3:23608722-23608741 None:intergenic 35.0%
TTGAAGTTCCTATCTGGATA+TGG + chr8.3:23608722-23608741 MS.gene90494:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr8.3:23608618-23608637 None:intergenic 35.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr8.3:23608983-23609002 MS.gene90494:CDS 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr8.3:23608979-23608998 MS.gene90494:CDS 40.0%
CCCATACCAAATGTGATGTT+CGG + chr8.3:23608973-23608992 MS.gene90494:CDS 40.0%
CCGAACATCACATTTGGTAT+GGG - chr8.3:23608976-23608995 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr8.3:23608975-23608994 None:intergenic 40.0%
TCATCGATCCATATCCAGAT+AGG - chr8.3:23608733-23608752 None:intergenic 40.0%
TCCGAACATCACATTTGGTA+TGG - chr8.3:23608977-23608996 None:intergenic 40.0%
TGATAGGGTGGATAATCAAC+TGG - chr8.3:23608667-23608686 None:intergenic 40.0%
TGGATCGATGAAATCACTGA+AGG + chr8.3:23608742-23608761 MS.gene90494:intron 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr8.3:23608982-23609001 None:intergenic 40.0%
!! AGGAATTTGCCGAAAGTATC+AGG - chr8.3:23608871-23608890 None:intergenic 40.0%
!! GTACCTTTGAAGTTCCTATC+TGG + chr8.3:23608716-23608735 MS.gene90494:intron 40.0%
!!! ACGATTTTTTGTGCTGCCAA+TGG + chr8.3:23609006-23609025 MS.gene90494:CDS 40.0%
ACCCTATCATTCCATGAGTG+CGG + chr8.3:23608678-23608697 MS.gene90494:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr8.3:23608612-23608631 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr8.3:23608601-23608620 MS.gene90494:intron 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr8.3:23609014-23609033 MS.gene90494:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr8.3:23609015-23609034 MS.gene90494:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr8.3:23609053-23609072 MS.gene90494:CDS 45.0%
CACGATTACGTCACGTTGTG+CGG + chr8.3:23608904-23608923 MS.gene90494:CDS 50.0%
GCACTCATGGAATGATAGGG+TGG - chr8.3:23608679-23608698 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr8.3:23608682-23608701 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr8.3:23608683-23608702 None:intergenic 50.0%
GTCTCCGCCCTCAATACCAT+TGG - chr8.3:23609025-23609044 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr8.3:23609018-23609037 MS.gene90494:CDS 55.0%
ACACGATGCTGCCGCACTCA+TGG - chr8.3:23608692-23608711 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 23608551 23609107 23608551 ID=MS.gene90494
chr8.3 mRNA 23608551 23609107 23608551 ID=MS.gene90494.t1;Parent=MS.gene90494
chr8.3 exon 23608551 23608592 23608551 ID=MS.gene90494.t1.exon1;Parent=MS.gene90494.t1
chr8.3 CDS 23608551 23608592 23608551 ID=cds.MS.gene90494.t1;Parent=MS.gene90494.t1
chr8.3 exon 23608862 23609107 23608862 ID=MS.gene90494.t1.exon2;Parent=MS.gene90494.t1
chr8.3 CDS 23608862 23609107 23608862 ID=cds.MS.gene90494.t1;Parent=MS.gene90494.t1
Gene Sequence

>MS.gene90494

ATGGTTGGAATGCATTGCGATTATTCTACGAGTTTAGTGAAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTTATAACATTACTCCAGTTGATTATCCACCCTATCATTCCATGAGTGCGGCAGCATCGTGTTATTGTACCTTTGAAGTTCCTATCTGGATATGGATCGATGAAATCACTGAAGGTTGTTTATTGTTTTTTGATGCTATTCATTTAGAGATTTATATATGCTATAATAAAGGATTTATGTATGTCATTAACAATTTTTTTTTCTTTTTGTAGGAACTACCTGATACTTTCGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCACGTTGTGCGGACCTTATGACAATATCATTTCTGTGAGACTCAAATATGCAAACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGATTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>MS.gene90494.t1

MVGMHCDYSTSLVKELPDTFGKFLRVKHHDYVTLCGPYDNIISVRLKYANDPIPNVMFGKGWTIFCAANGIEGGDVLIFKCKCVMDKKYVIVSKR