AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene057126

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene057126.t1 MTR_3g491850 93.671 79 4 1 1 78 1 79 1.18e-49 150
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 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAGGTTTCTTTGAATGCTT+TGG 0.177524 3.1:+73719472 None:intergenic
TTCTTTGAATGCTTTGGGTT+GGG 0.313836 3.1:+73719478 None:intergenic
ATTTGTTTACCTGAAGATAA+AGG 0.340472 3.1:+73720031 None:intergenic
CAGGTTTCTTTGAATGCTTT+GGG 0.352628 3.1:+73719473 None:intergenic
AAACCAAGAGGATGGCTAAA+AGG 0.364847 3.1:+73720065 None:intergenic
TTTCTTTGAATGCTTTGGGT+TGG 0.396872 3.1:+73719477 None:intergenic
TTGTAAAGAAAGTTATTAGT+AGG 0.421064 3.1:+73719896 None:intergenic
TACTAATAACTTTCTTTACA+AGG 0.464774 3.1:-73719894 MS.gene057126:intron
GGTGTTTAACGACCCTTGCC+AGG 0.478184 3.1:+73719454 None:intergenic
CCAAAGCATTCAAAGAAACC+TGG 0.549609 3.1:-73719472 MS.gene057126:CDS
ATGAATGAAAACCAAGAGGA+TGG 0.580545 3.1:+73720057 None:intergenic
GTGTTGGATTATGATGAAGC+AGG 0.583814 3.1:-73719502 MS.gene057126:CDS
GCATTCAAAGAAACCTGGCA+AGG 0.596187 3.1:-73719467 MS.gene057126:CDS
CATTCAAAGAAACCTGGCAA+GGG 0.630511 3.1:-73719466 MS.gene057126:CDS
GAAAATGAATGAAAACCAAG+AGG 0.671422 3.1:+73720053 None:intergenic
ATGGTGTAAAGATGAACTCG+AGG 0.686471 3.1:-73719546 MS.gene057126:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGATTACAATTTTTTTTTAT+AGG + chr3.1:73719898-73719917 None:intergenic 10.0%
!!! TTATTTGTAAACATTATTTT+GGG + chr3.1:73719863-73719882 None:intergenic 10.0%
!!! TTTATTTGTAAACATTATTT+TGG + chr3.1:73719864-73719883 None:intergenic 10.0%
!!! TTTTTTCATATAGTTTTAAA+TGG - chr3.1:73719688-73719707 MS.gene057126:intron 10.0%
!!! ATTTATTTTTTTGCTCTTTT+AGG - chr3.1:73719597-73719616 MS.gene057126:intron 15.0%
!! AAAATTAAGATGAATACAGA+TGG - chr3.1:73719772-73719791 MS.gene057126:intron 20.0%
!! AAATTCTTACTTGATATAAG+TGG - chr3.1:73719535-73719554 MS.gene057126:CDS 20.0%
!! CTATATGAAAAAAGATAGTA+AGG + chr3.1:73719681-73719700 None:intergenic 20.0%
!! TACTAATAACTTTCTTTACA+AGG - chr3.1:73719653-73719672 MS.gene057126:intron 20.0%
!! TTGTAAAGAAAGTTATTAGT+AGG + chr3.1:73719654-73719673 None:intergenic 20.0%
!!! AACATTATTTTGGGATTATA+TGG + chr3.1:73719854-73719873 None:intergenic 20.0%
!!! ACATTATTTTGGGATTATAT+GGG + chr3.1:73719853-73719872 None:intergenic 20.0%
!!! TTTTTAACTAACAAGTACTT+TGG - chr3.1:73719965-73719984 MS.gene057126:intron 20.0%
! ATTTGTTTACCTGAAGATAA+AGG + chr3.1:73719519-73719538 None:intergenic 25.0%
!! ATTCATTTTCCTTTATCTTC+AGG - chr3.1:73719507-73719526 MS.gene057126:CDS 25.0%
!! TATGTTCATCTTAAGTATTG+TGG + chr3.1:73719740-73719759 None:intergenic 25.0%
!!! TTTTTTTGCTCTTTTAGGAT+TGG - chr3.1:73719602-73719621 MS.gene057126:intron 25.0%
GAAAATGAATGAAAACCAAG+AGG + chr3.1:73719497-73719516 None:intergenic 30.0%
! AGTACTTTGGTATTGAATGA+AGG - chr3.1:73719978-73719997 MS.gene057126:intron 30.0%
ATGAATGAAAACCAAGAGGA+TGG + chr3.1:73719493-73719512 None:intergenic 35.0%
CAGGTTTCTTTGAATGCTTT+GGG + chr3.1:73720077-73720096 None:intergenic 35.0%
GGCAAATGCTAATATTTGCT+TGG - chr3.1:73719815-73719834 MS.gene057126:intron 35.0%
! ATTGTCTCATGCTTTTGTGT+TGG - chr3.1:73720029-73720048 MS.gene057126:intron 35.0%
! CTTTGGTATTGAATGAAGGA+TGG - chr3.1:73719982-73720001 MS.gene057126:intron 35.0%
! TTCTTTGAATGCTTTGGGTT+GGG + chr3.1:73720072-73720091 None:intergenic 35.0%
! TTTCTTTGAATGCTTTGGGT+TGG + chr3.1:73720073-73720092 None:intergenic 35.0%
AAACCAAGAGGATGGCTAAA+AGG + chr3.1:73719485-73719504 None:intergenic 40.0%
ATGGTGTAAAGATGAACTCG+AGG - chr3.1:73720001-73720020 MS.gene057126:intron 40.0%
CATTCAAAGAAACCTGGCAA+GGG - chr3.1:73720081-73720100 MS.gene057126:CDS 40.0%
CCAGGTTTCTTTGAATGCTT+TGG + chr3.1:73720078-73720097 None:intergenic 40.0%
GAGCTACTACATTCACATTG+AGG - chr3.1:73719794-73719813 MS.gene057126:intron 40.0%
GTGTTGGATTATGATGAAGC+AGG - chr3.1:73720045-73720064 MS.gene057126:CDS 40.0%
! CCAAAGCATTCAAAGAAACC+TGG - chr3.1:73720075-73720094 MS.gene057126:CDS 40.0%
! TTTCCTTTTAGCCATCCTCT+TGG - chr3.1:73719479-73719498 MS.gene057126:CDS 40.0%
GCATTCAAAGAAACCTGGCA+AGG - chr3.1:73720080-73720099 MS.gene057126:CDS 45.0%
!!! GCTCTTTTAGGATTGGCTGA+AGG - chr3.1:73719609-73719628 MS.gene057126:intron 45.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 73719459 73720110 73719459 ID=MS.gene057126
chr3.1 mRNA 73719459 73720110 73719459 ID=MS.gene057126.t1;Parent=MS.gene057126
chr3.1 exon 73720041 73720110 73720041 ID=MS.gene057126.t1.exon1;Parent=MS.gene057126.t1
chr3.1 CDS 73720041 73720110 73720041 ID=cds.MS.gene057126.t1;Parent=MS.gene057126.t1
chr3.1 exon 73719895 73719950 73719895 ID=MS.gene057126.t1.exon2;Parent=MS.gene057126.t1
chr3.1 CDS 73719895 73719950 73719895 ID=cds.MS.gene057126.t1;Parent=MS.gene057126.t1
chr3.1 exon 73719459 73719569 73719459 ID=MS.gene057126.t1.exon3;Parent=MS.gene057126.t1
chr3.1 CDS 73719459 73719569 73719459 ID=cds.MS.gene057126.t1;Parent=MS.gene057126.t1
Gene Sequence

>MS.gene057126

ATGGAACACAAAGTCAAAACTTTCCTTTTAGCCATCCTCTTGGTTTTCATTCATTTTCCTTTATCTTCAGGTAAACAAATTCTTACTTGATATAAGTGGTTTAAGTTTTGTAGAGATTAATTCAACTCATGTAACATAATTTATTTTTTTGCTCTTTTAGGATTGGCTGAAGGATTCAGAGAAAATATGCATCCTACTAATAACTTTCTTTACAAGGTACCTTACTATCTTTTTTCATATAGTTTTAAATGGTAAACATTAATGAAGCTAATTGCATGCCACAATACTTAAGATGAACATAAAAAAGAAATAAAAAATTAAGATGAATACAGATGGAGCTACTACATTCACATTGAGGCAAATGCTAATATTTGCTTGGATTTACTAATCTCCCATATAATCCCAAAATAATGTTTACAAATAAATTAAAAATTGTCCTATAAAAAAAAATTGTAATCTTTTTGTGAATTATTTCAATTTAGTATTTGATGATTAGATGTTAATTTTTTTTAACTAACAAGTACTTTGGTATTGAATGAAGGATGGTGTAAAGATGAACTCGAGGAAGCTATTGTCTCATGCTTTTGTGTTGGATTATGATGAAGCAGGACCCAACCCAAAGCATTCAAAGAAACCTGGCAAGGGTCGTTAA
Protein sequence

>MS.gene057126.t1

MEHKVKTFLLAILLVFIHFPLSSGLAEGFRENMHPTNNFLYKDGVKMNSRKLLSHAFVLDYDEAGPNPKHSKKPGKGR