AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06685

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06685.t1 MTR_3g491850 92.405 79 5 1 1 78 1 79 4.32e-49 149
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 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAGGTTTCTTTGAATGCTT+TGG 0.177524 3.3:+76525890 None:intergenic
TTCTTTGAATGCTTTGGGTT+GGG 0.313836 3.3:+76525896 None:intergenic
ATTTGTTTACCTGAAGATAA+AGG 0.340472 3.3:+76526450 None:intergenic
CAGGTTTCTTTGAATGCTTT+GGG 0.352628 3.3:+76525891 None:intergenic
AAACGAAGAGGATGGCTAAA+AGG 0.376625 3.3:+76526484 None:intergenic
TTTCTTTGAATGCTTTGGGT+TGG 0.396872 3.3:+76525895 None:intergenic
TTGTAAAGAAAGTTATTAGT+AGG 0.421064 3.3:+76526315 None:intergenic
TACTAATAACTTTCTTTACA+AGG 0.464774 3.3:-76526313 MS.gene06685:intron
GGTGTTTAACGACCCTTGCC+AGG 0.478184 3.3:+76525872 None:intergenic
CCAAAGCATTCAAAGAAACC+TGG 0.549609 3.3:-76525890 MS.gene06685:CDS
GTGTTGGATTATGATGAAGC+AGG 0.583814 3.3:-76525920 MS.gene06685:CDS
ATGAATGAAAACGAAGAGGA+TGG 0.587075 3.3:+76526476 None:intergenic
GCATTCAAAGAAACCTGGCA+AGG 0.596187 3.3:-76525885 MS.gene06685:CDS
GAAAATGAATGAAAACGAAG+AGG 0.622263 3.3:+76526472 None:intergenic
CATTCAAAGAAACCTGGCAA+GGG 0.630511 3.3:-76525884 MS.gene06685:CDS
ATGGTGTAAAGATGAACTCG+AGG 0.686471 3.3:-76525964 MS.gene06685:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATTACAAATTTTTTTTTAT+AGG + chr3.3:76526316-76526335 None:intergenic 10.0%
!!! TTATTTGTAAACATTATTTT+GGG + chr3.3:76526281-76526300 None:intergenic 10.0%
!!! TTTATTTGTAAACATTATTT+TGG + chr3.3:76526282-76526301 None:intergenic 10.0%
!!! TTTTTTCATATAGTTTTAAA+TGG - chr3.3:76526106-76526125 MS.gene06685:intron 10.0%
!!! ATTTATTTTTTTGCTCTTTT+AGG - chr3.3:76526015-76526034 MS.gene06685:intron 15.0%
!! AAAATTAAGATGAATACAGA+TGG - chr3.3:76526190-76526209 MS.gene06685:intron 20.0%
!! AAATTCTTACTTGATATAAG+TGG - chr3.3:76525953-76525972 MS.gene06685:CDS 20.0%
!! CTATATGAAAAAAGATAGTA+AGG + chr3.3:76526099-76526118 None:intergenic 20.0%
!! TACTAATAACTTTCTTTACA+AGG - chr3.3:76526071-76526090 MS.gene06685:intron 20.0%
!! TTGTAAAGAAAGTTATTAGT+AGG + chr3.3:76526072-76526091 None:intergenic 20.0%
!!! AACATTATTTTGGGATTATA+TGG + chr3.3:76526272-76526291 None:intergenic 20.0%
!!! ACATTATTTTGGGATTATAT+GGG + chr3.3:76526271-76526290 None:intergenic 20.0%
!!! TTTTTAACTAACAAGTACTT+TGG - chr3.3:76526384-76526403 MS.gene06685:intron 20.0%
! ATTTGTTTACCTGAAGATAA+AGG + chr3.3:76525937-76525956 None:intergenic 25.0%
!! ATTCATTTTCCTTTATCTTC+AGG - chr3.3:76525925-76525944 MS.gene06685:CDS 25.0%
!! TATGTTCATCTTAAGTATTG+TGG + chr3.3:76526158-76526177 None:intergenic 25.0%
!!! TTTTTTTGCTCTTTTAGGAT+TGG - chr3.3:76526020-76526039 MS.gene06685:intron 25.0%
GAAAATGAATGAAAACGAAG+AGG + chr3.3:76525915-76525934 None:intergenic 30.0%
! AGTACTTTGGTATTGAATGA+AGG - chr3.3:76526397-76526416 MS.gene06685:intron 30.0%
ATGAATGAAAACGAAGAGGA+TGG + chr3.3:76525911-76525930 None:intergenic 35.0%
CAGGTTTCTTTGAATGCTTT+GGG + chr3.3:76526496-76526515 None:intergenic 35.0%
GGCAAATGCTAATATTTGCT+TGG - chr3.3:76526233-76526252 MS.gene06685:intron 35.0%
! ATTGTCTCATGCTTTTGTGT+TGG - chr3.3:76526448-76526467 MS.gene06685:intron 35.0%
! CTTTGGTATTGAATGAAGGA+TGG - chr3.3:76526401-76526420 MS.gene06685:intron 35.0%
! TTCTTTGAATGCTTTGGGTT+GGG + chr3.3:76526491-76526510 None:intergenic 35.0%
! TTTCTTTGAATGCTTTGGGT+TGG + chr3.3:76526492-76526511 None:intergenic 35.0%
AAACGAAGAGGATGGCTAAA+AGG + chr3.3:76525903-76525922 None:intergenic 40.0%
ATGGTGTAAAGATGAACTCG+AGG - chr3.3:76526420-76526439 MS.gene06685:intron 40.0%
CATTCAAAGAAACCTGGCAA+GGG - chr3.3:76526500-76526519 MS.gene06685:CDS 40.0%
CCAGGTTTCTTTGAATGCTT+TGG + chr3.3:76526497-76526516 None:intergenic 40.0%
GAGCTACTACATTCACATTG+AGG - chr3.3:76526212-76526231 MS.gene06685:intron 40.0%
GTGTTGGATTATGATGAAGC+AGG - chr3.3:76526464-76526483 MS.gene06685:CDS 40.0%
! CCAAAGCATTCAAAGAAACC+TGG - chr3.3:76526494-76526513 MS.gene06685:CDS 40.0%
GCATTCAAAGAAACCTGGCA+AGG - chr3.3:76526499-76526518 MS.gene06685:CDS 45.0%
!!! GCTCTTTTAGGATTGGCTGA+AGG - chr3.3:76526027-76526046 MS.gene06685:intron 45.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 76525877 76526529 76525877 ID=MS.gene06685
chr3.3 mRNA 76525877 76526529 76525877 ID=MS.gene06685.t1;Parent=MS.gene06685
chr3.3 exon 76526460 76526529 76526460 ID=MS.gene06685.t1.exon1;Parent=MS.gene06685.t1
chr3.3 CDS 76526460 76526529 76526460 ID=cds.MS.gene06685.t1;Parent=MS.gene06685.t1
chr3.3 exon 76526314 76526369 76526314 ID=MS.gene06685.t1.exon2;Parent=MS.gene06685.t1
chr3.3 CDS 76526314 76526369 76526314 ID=cds.MS.gene06685.t1;Parent=MS.gene06685.t1
chr3.3 exon 76525877 76525987 76525877 ID=MS.gene06685.t1.exon3;Parent=MS.gene06685.t1
chr3.3 CDS 76525877 76525987 76525877 ID=cds.MS.gene06685.t1;Parent=MS.gene06685.t1
Gene Sequence

>MS.gene06685

ATGGAACACAAAGTCAAAACTTTCCTTTTAGCCATCCTCTTCGTTTTCATTCATTTTCCTTTATCTTCAGGTAAACAAATTCTTACTTGATATAAGTGGTTTAAGTTTTGTAGAGATTAATTCAACTCATGTAACATAATTTATTTTTTTGCTCTTTTAGGATTGGCTGAAGGATTCAGAGAAAATATGCATCCTACTAATAACTTTCTTTACAAGGTACCTTACTATCTTTTTTCATATAGTTTTAAATGGTAAACATTAATGAAGCTAATTGCATGCCACAATACTTAAGATGAACATAAAAAAGAAATAAAAAATTAAGATGAATACAGATGGAGCTACTACATTCACATTGAGGCAAATGCTAATATTTGCTTGGATTTACTAATCTCCCATATAATCCCAAAATAATGTTTACAAATAAATTAAAAATTGTCCTATAAAAAAAAATTTGTAATCTTTTTGTGAATTATTTCAATTTAGTATTTGATGATTAGATGTTAATTTTTTTTAACTAACAAGTACTTTGGTATTGAATGAAGGATGGTGTAAAGATGAACTCGAGGAAGCTATTGTCTCATGCTTTTGTGTTGGATTATGATGAAGCAGGACCCAACCCAAAGCATTCAAAGAAACCTGGCAAGGGTCGTTAA
Protein sequence

>MS.gene06685.t1

MEHKVKTFLLAILFVFIHFPLSSGLAEGFRENMHPTNNFLYKDGVKMNSRKLLSHAFVLDYDEAGPNPKHSKKPGKGR