AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071848

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCTTGACCTTGTCATTGA+TGG 0.308981 2.2:-53665343 None:intergenic
ATTAGTATTGTACATCTTGC+TGG 0.366291 2.2:+53664811 MS.gene071848:CDS
ACTAATGAGAATATATGATT+TGG 0.382200 2.2:-53664710 None:intergenic
TTACAGAAGGACAAAGTTCA+TGG 0.422364 2.2:+53665267 MS.gene071848:CDS
GTCTGTGGAGCCAATTGAAT+AGG 0.423617 2.2:+53665057 MS.gene071848:CDS
TAATATATGATATTGCCTTC+AGG 0.427217 2.2:-53665291 None:intergenic
TCCTTGACCTTGTCATTGAT+GGG 0.431246 2.2:-53665342 None:intergenic
TCAAACTCATCCTATTCAAT+TGG 0.437595 2.2:-53665067 None:intergenic
TGTTTAATGTTTCCAAGGAC+AGG 0.452088 2.2:-53665110 None:intergenic
GCGAATGCAGCGTACATGTC+TGG 0.471935 2.2:+53664772 MS.gene071848:CDS
TGGAAACATTAAACAAACAT+TGG 0.481142 2.2:+53665118 MS.gene071848:CDS
GAAGCACATCATCCTGTCCT+TGG 0.484363 2.2:+53665098 MS.gene071848:CDS
GGTCAAGGAATATATATCTC+AGG 0.503625 2.2:+53665356 MS.gene071848:CDS
ATGTTTGTTTAATGTTTCCA+AGG 0.514853 2.2:-53665115 None:intergenic
CTTGCTGAGAGAGCTTCAGA+TGG 0.536183 2.2:+53665318 MS.gene071848:CDS
TGGAACTTCTTGTTCAGCAA+AGG 0.546018 2.2:+53665138 MS.gene071848:CDS
TCTGTGTAGGTATTTACAGA+AGG 0.576215 2.2:+53665254 MS.gene071848:intron
GACAAAGTTCATGGTCCTGA+AGG 0.589939 2.2:+53665276 MS.gene071848:CDS
ACCCATCAATGACAAGGTCA+AGG 0.619915 2.2:+53665341 MS.gene071848:CDS
TGGATATTGCAGAAAGTCTG+TGG 0.628382 2.2:+53665042 MS.gene071848:intron
AGTATTGTACATCTTGCTGG+TGG 0.636060 2.2:+53664814 MS.gene071848:CDS
ACGTGATCTTTCAGGTAGTG+CGG 0.654346 2.2:+53664684 None:intergenic
GCTGGTGGCAAAATTCCAGA+AGG 0.666039 2.2:+53664829 MS.gene071848:CDS
AGATGGACCCATCAATGACA+AGG 0.678422 2.2:+53665335 MS.gene071848:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTTCATATAAATTTGA+AGG - chr2.2:53664742-53664761 None:intergenic 10.0%
!!! TTCTTTTCTTTATATTTATT+GGG + chr2.2:53665465-53665484 MS.gene071848:intron 10.0%
!!! TTTCTTTTCTTTATATTTAT+TGG + chr2.2:53665464-53665483 MS.gene071848:intron 10.0%
!! TTTATATGAAAAATATGTTG+TGG + chr2.2:53664747-53664766 MS.gene071848:CDS 15.0%
!!! TCTGATATTTAAAATATCAA+GGG + chr2.2:53664968-53664987 MS.gene071848:intron 15.0%
!!! TTCTGATATTTAAAATATCA+AGG + chr2.2:53664967-53664986 MS.gene071848:intron 15.0%
!! ACTAATGAGAATATATGATT+TGG - chr2.2:53664713-53664732 None:intergenic 20.0%
!! GAAAGAAAGAAAAAAAAAAC+TGG - chr2.2:53665448-53665467 None:intergenic 20.0%
!! GCAATAAATATAACTATACA+AGG + chr2.2:53664944-53664963 MS.gene071848:intron 20.0%
!!! ATATGAAATTTTAGAACTTC+TGG - chr2.2:53665657-53665676 None:intergenic 20.0%
!!! TCCAATCTTTATTACTTTTA+GGG + chr2.2:53665501-53665520 MS.gene071848:intron 20.0%
!!! TTATGCAAGTTTTGTTTTTT+TGG + chr2.2:53665398-53665417 MS.gene071848:intron 20.0%
! AAGTAATAAAGATTGGACAT+CGG - chr2.2:53665498-53665517 None:intergenic 25.0%
! ACAACTTAAAATATACCTTC+TGG - chr2.2:53664847-53664866 None:intergenic 25.0%
! ATATAACAATCCTGAACATT+TGG - chr2.2:53665628-53665647 None:intergenic 25.0%
! ATGTTTGTTTAATGTTTCCA+AGG - chr2.2:53665118-53665137 None:intergenic 25.0%
! CAAGTTCCATTATGTTAAAA+AGG - chr2.2:53665015-53665034 None:intergenic 25.0%
! TAATATATGATATTGCCTTC+AGG - chr2.2:53665294-53665313 None:intergenic 25.0%
! TATAAAATAAGCAAAACCGA+AGG + chr2.2:53665744-53665763 MS.gene071848:intron 25.0%
! TATAACTTCTGCTAAACTAT+AGG - chr2.2:53665709-53665728 None:intergenic 25.0%
! TGGAAACATTAAACAAACAT+TGG + chr2.2:53665118-53665137 MS.gene071848:CDS 25.0%
!! TAACATAATGGAACTTGATA+TGG + chr2.2:53665018-53665037 MS.gene071848:intron 25.0%
!! TAATTCATCTTTTTCTGTGT+AGG + chr2.2:53665241-53665260 MS.gene071848:intron 25.0%
!!! AATCAAATTTTGCTAGTCTA+AGG + chr2.2:53664908-53664927 MS.gene071848:intron 25.0%
!!! CATTGTTCGTTGTTTTTTTA+GGG - chr2.2:53665211-53665230 None:intergenic 25.0%
!!! CCAATCTTTATTACTTTTAG+GGG + chr2.2:53665502-53665521 MS.gene071848:intron 25.0%
!!! GTCCAATCTTTATTACTTTT+AGG + chr2.2:53665500-53665519 MS.gene071848:intron 25.0%
!!! TCATTGTTCGTTGTTTTTTT+AGG - chr2.2:53665212-53665231 None:intergenic 25.0%
AGAAAACATTCATCAATGCT+AGG - chr2.2:53665536-53665555 None:intergenic 30.0%
ATTAGTATTGTACATCTTGC+TGG + chr2.2:53664811-53664830 MS.gene071848:CDS 30.0%
CCCCTAAAAGTAATAAAGAT+TGG - chr2.2:53665505-53665524 None:intergenic 30.0%
TCAAACTCATCCTATTCAAT+TGG - chr2.2:53665070-53665089 None:intergenic 30.0%
! ATAATGGAACTTGATATGGT+TGG + chr2.2:53665022-53665041 MS.gene071848:intron 30.0%
! ATGCTGCCTTTTTAACATAA+TGG + chr2.2:53665006-53665025 MS.gene071848:intron 30.0%
!! ATCTTTATTACTTTTAGGGG+AGG + chr2.2:53665505-53665524 MS.gene071848:intron 30.0%
ACAAGATTCATTGCATTCTG+TGG + chr2.2:53665173-53665192 MS.gene071848:intron 35.0%
CCTTCATAATCTGCAAAAGA+AGG - chr2.2:53665894-53665913 None:intergenic 35.0%
GAATAGAACACCAAATGTTC+AGG + chr2.2:53665615-53665634 MS.gene071848:intron 35.0%
GGTCAAGGAATATATATCTC+AGG + chr2.2:53665356-53665375 MS.gene071848:CDS 35.0%
TCTGTGTAGGTATTTACAGA+AGG + chr2.2:53665254-53665273 MS.gene071848:intron 35.0%
TGTTTAATGTTTCCAAGGAC+AGG - chr2.2:53665113-53665132 None:intergenic 35.0%
TTACAGAAGGACAAAGTTCA+TGG + chr2.2:53665267-53665286 MS.gene071848:CDS 35.0%
! CCTTCTTTTGCAGATTATGA+AGG + chr2.2:53665891-53665910 MS.gene071848:intron 35.0%
AGTATTGTACATCTTGCTGG+TGG + chr2.2:53664814-53664833 MS.gene071848:CDS 40.0%
CGAGTTACGACATATTCCTT+CGG - chr2.2:53665763-53665782 None:intergenic 40.0%
TCCTTGACCTTGTCATTGAT+GGG - chr2.2:53665345-53665364 None:intergenic 40.0%
TGGAACTTCTTGTTCAGCAA+AGG + chr2.2:53665138-53665157 MS.gene071848:CDS 40.0%
TGGATATTGCAGAAAGTCTG+TGG + chr2.2:53665042-53665061 MS.gene071848:intron 40.0%
TTCCTTGACCTTGTCATTGA+TGG - chr2.2:53665346-53665365 None:intergenic 40.0%
! TTGTGCACTTGTTGAACTTG+TGG + chr2.2:53664884-53664903 MS.gene071848:intron 40.0%
ACCCATCAATGACAAGGTCA+AGG + chr2.2:53665341-53665360 MS.gene071848:CDS 45.0%
AGATGGACCCATCAATGACA+AGG + chr2.2:53665335-53665354 MS.gene071848:CDS 45.0%
GACAAAGTTCATGGTCCTGA+AGG + chr2.2:53665276-53665295 MS.gene071848:CDS 45.0%
GTCTGTGGAGCCAATTGAAT+AGG + chr2.2:53665057-53665076 MS.gene071848:CDS 45.0%
CTTGCTGAGAGAGCTTCAGA+TGG + chr2.2:53665318-53665337 MS.gene071848:CDS 50.0%
GAAGCACATCATCCTGTCCT+TGG + chr2.2:53665098-53665117 MS.gene071848:CDS 50.0%
GCTGGTGGCAAAATTCCAGA+AGG + chr2.2:53664829-53664848 MS.gene071848:CDS 50.0%
!! GTACCACTGCAGTGCTACTT+CGG - chr2.2:53665687-53665706 None:intergenic 50.0%
GCGAATGCAGCGTACATGTC+TGG + chr2.2:53664772-53664791 MS.gene071848:CDS 55.0%
TCTCCGAAGTAGCACTGCAG+TGG + chr2.2:53665681-53665700 MS.gene071848:intron 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 53664698 53665924 53664698 ID=MS.gene071848
chr2.2 mRNA 53664698 53665924 53664698 ID=MS.gene071848.t1;Parent=MS.gene071848
chr2.2 exon 53664698 53664850 53664698 ID=MS.gene071848.t1.exon1;Parent=MS.gene071848.t1
chr2.2 CDS 53664698 53664850 53664698 ID=cds.MS.gene071848.t1;Parent=MS.gene071848.t1
chr2.2 exon 53665054 53665159 53665054 ID=MS.gene071848.t1.exon2;Parent=MS.gene071848.t1
chr2.2 CDS 53665054 53665159 53665054 ID=cds.MS.gene071848.t1;Parent=MS.gene071848.t1
chr2.2 exon 53665263 53665377 53665263 ID=MS.gene071848.t1.exon3;Parent=MS.gene071848.t1
chr2.2 CDS 53665263 53665377 53665263 ID=cds.MS.gene071848.t1;Parent=MS.gene071848.t1
chr2.2 exon 53665904 53665924 53665904 ID=MS.gene071848.t1.exon4;Parent=MS.gene071848.t1
chr2.2 CDS 53665904 53665924 53665904 ID=cds.MS.gene071848.t1;Parent=MS.gene071848.t1
Gene Sequence

>MS.gene071848

GTAGTGCGGATGCCAAATCATATATTCTCATTAGTCGACTTCCTTCAAATTTATATGAAAAATATGTTGTGGATGCGAATGCAGCGTACATGTCTGGTTTCACGTTTGTCATAATTAGTATTGTACATCTTGCTGGTGGCAAAATTCCAGAAGGTATATTTTAAGTTGTATACAGCTATAATTATCTTGTGCACTTGTTGAACTTGTGGAAATCAAATTTTGCTAGTCTAAGGTCTCTAGATGAATGCAATAAATATAACTATACAAGGTTCTGATATTTAAAATATCAAGGGTAATTGAGATCTGTGATGCTGCCTTTTTAACATAATGGAACTTGATATGGTTGGATATTGCAGAAAGTCTGTGGAGCCAATTGAATAGGATGAGTTTGAGTGACACTGAAGCACATCATCCTGTCCTTGGAAACATTAAACAAACATTGGAACTTCTTGTTCAGCAAAGGTGAAATTAAATTACAAGATTCATTGCATTCTGTGGCACATATAGTTTCCCTAAAAAAACAACGAACAATGAAGTAATTCATAATTCATCTTTTTCTGTGTAGGTATTTACAGAAGGACAAAGTTCATGGTCCTGAAGGCAATATCATATATTATGAGCTTGCTGAGAGAGCTTCAGATGGACCCATCAATGACAAGGTCAAGGAATATATATCTCAGGTAGTGTTTTGAAAAGTAAATTATGCAAGTTTTGTTTTTTTGGTAGACAATTATGCACGTTTTGTGTCCAGTTTTTTTTTTCTTTCTTTCTTTTCTTTATATTTATTGGGATAAATGCCGATGTCCAATCTTTATTACTTTTAGGGGAGGTCTAACCTAGCATTGATGAATGTTTTCTATTTAGTTTATTAAATTGTTGCTGAACACTGTTGTCTGTATTGAAAAAATAGCTGAAGCGAATAGAACACCAAATGTTCAGGATTGTTATATAATACACCAGAAGTTCTAAAATTTCATATAGTATCTCCGAAGTAGCACTGCAGTGGTACCTATAGTTTAGCAGAAGTTATAAAATTTGATTTATAGTATAAAATAAGCAAAACCGAAGGAATATGTCGTAACTCGTGTTGTGTTGAATGATGATGTTACTATAACTTACTCTTCATTAATAAAAATACTGACATGTGTTTTGAAGTTTAATACTATTGTTACTTATATTTTTTCTGAAATATTCCTTCTTTTGCAGATTATGAAGGACACTGCCTAA
Protein sequence

>MS.gene071848.t1

VVRMPNHIFSLVDFLQIYMKNMLWMRMQRTCLVSRLSULVLYILLVAKFQKKVCGANUIGUVUVTLKHIILSLETLNKHWNFLFSKGIYRRTKFMVLKAISYIMSLLRELQMDPSMTRSRNIYLRLURTLP