AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene45098

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 30 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGACTCTCGAGACTCTTAA+AGG 0.300656 5.3:+24062629 MS.gene45098:CDS
GCAAGACTACTCCTAGGATT+TGG 0.338598 5.3:+24063020 MS.gene45098:CDS
TTATATGCTCAACAGGGATT+AGG 0.339322 5.3:+24063171 MS.gene45098:intron
AAAATTGTCGCTACTGAATC+TGG 0.343177 5.3:+24062456 MS.gene45098:CDS
GAGAGCAACATTGCAGTATC+TGG 0.353709 5.3:+24063228 MS.gene45098:CDS
TTAAACTGTAACACTTCTTC+AGG 0.367445 5.3:-24062815 None:intergenic
TACAAAGTCATGGCAGAAAT+TGG 0.369390 5.3:-24062840 None:intergenic
GAGAAGGAATGGACAGCATC+AGG 0.375346 5.3:+24063309 MS.gene45098:CDS
TTCTCTCAATTCACCATGGC+TGG 0.393150 5.3:+24062426 None:intergenic
CCTTCTCCTGAGCCTTTAGC+AGG 0.420476 5.3:-24063293 None:intergenic
ACTGCAATGTTGCTCTCAAA+TGG 0.428409 5.3:-24063222 None:intergenic
ACTGAATCTGGCAGAATAAT+CGG 0.437166 5.3:+24062468 MS.gene45098:CDS
GCTAGCTTCTGCTCTGCAAA+TGG 0.445006 5.3:-24063348 None:intergenic
AATCATGTGCCTCCTGCTAA+AGG 0.476378 5.3:+24063281 MS.gene45098:CDS
TTTAGCAGGAGGCACATGAT+TGG 0.486163 5.3:-24063279 None:intergenic
TACATTTAGGAATTCAAAAG+TGG 0.495920 5.3:+24062939 MS.gene45098:intron
TTGCTGCATTTCCAAATCCT+AGG 0.498301 5.3:-24063031 None:intergenic
TACAGATGAAACAACATAGC+TGG 0.507048 5.3:-24063399 None:intergenic
GTGCCTCCTGCTAAAGGCTC+AGG 0.518275 5.3:+24063287 MS.gene45098:CDS
CTAGCCACATATGTTAATGT+TGG 0.534763 5.3:+24063366 MS.gene45098:CDS
AACAATATCTTACAAAGTCA+TGG 0.541880 5.3:-24062850 None:intergenic
CCTGCTAAAGGCTCAGGAGA+AGG 0.548226 5.3:+24063293 MS.gene45098:CDS
ATAACCAACATTAACATATG+TGG 0.550881 5.3:-24063370 None:intergenic
TCTCCTGAGCCTTTAGCAGG+AGG 0.554544 5.3:-24063290 None:intergenic
AACAAAGCAAGACTACTCCT+AGG 0.581413 5.3:+24063014 MS.gene45098:CDS
TGCTCAACAGGGATTAGGTG+TGG 0.593399 5.3:+24063176 MS.gene45098:intron
TGTAACACTTCTTCAGGTGT+AGG 0.599274 5.3:-24062809 None:intergenic
TAAAGGCTCAGGAGAAGGAA+TGG 0.605102 5.3:+24063298 MS.gene45098:CDS
AGAAGGAATGGACAGCATCA+GGG 0.605879 5.3:+24063310 MS.gene45098:CDS
AGGATTTGGAAATGCAGCAA+AGG 0.628133 5.3:+24063034 MS.gene45098:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACTAATTATTAATACATTT+AGG + chr5.3:24062926-24062945 MS.gene45098:intron 10.0%
!! TGTATAAAATTTACTAATTA+TGG - chr5.3:24062541-24062560 None:intergenic 10.0%
!! GAAATGAGTAAAAAATTAAA+AGG + chr5.3:24062495-24062514 MS.gene45098:CDS 15.0%
!!! TGACAAATATTTTTGATTTA+GGG - chr5.3:24062768-24062787 None:intergenic 15.0%
!!! CTGACAAATATTTTTGATTT+AGG - chr5.3:24062769-24062788 None:intergenic 20.0%
!!! TTTTATTTATATGCTCAACA+GGG + chr5.3:24063165-24063184 MS.gene45098:intron 20.0%
!!! TTTTTATTTATATGCTCAAC+AGG + chr5.3:24063164-24063183 MS.gene45098:intron 20.0%
! AACAATATCTTACAAAGTCA+TGG - chr5.3:24062853-24062872 None:intergenic 25.0%
! ATAACCAACATTAACATATG+TGG - chr5.3:24063373-24063392 None:intergenic 25.0%
! ATCTCACAATGAACTAATTA+CGG - chr5.3:24062664-24062683 None:intergenic 25.0%
! TACATTTAGGAATTCAAAAG+TGG + chr5.3:24062939-24062958 MS.gene45098:intron 25.0%
!! GATTTAGGGTATATTGTAAA+CGG - chr5.3:24062754-24062773 None:intergenic 25.0%
TGTAAACGGAAAAAGTTGTT+AGG - chr5.3:24062740-24062759 None:intergenic 30.0%
TTAAACTGTAACACTTCTTC+AGG - chr5.3:24062818-24062837 None:intergenic 30.0%
AAAATTGTCGCTACTGAATC+TGG + chr5.3:24062456-24062475 MS.gene45098:CDS 35.0%
ACTGAATCTGGCAGAATAAT+CGG + chr5.3:24062468-24062487 MS.gene45098:CDS 35.0%
AGTTGTTAGGCACTATCATT+AGG - chr5.3:24062727-24062746 None:intergenic 35.0%
CTAGCCACATATGTTAATGT+TGG + chr5.3:24063366-24063385 MS.gene45098:CDS 35.0%
TACAAAGTCATGGCAGAAAT+TGG - chr5.3:24062843-24062862 None:intergenic 35.0%
TACAGATGAAACAACATAGC+TGG - chr5.3:24063402-24063421 None:intergenic 35.0%
TTATATGCTCAACAGGGATT+AGG + chr5.3:24063171-24063190 MS.gene45098:intron 35.0%
! ATCTAGTTGTGCTTCTAGTT+AGG + chr5.3:24062682-24062701 MS.gene45098:intron 35.0%
!!! TGTCAGACTTTTTCGATTCA+AGG + chr5.3:24062783-24062802 MS.gene45098:intron 35.0%
AACAAAGCAAGACTACTCCT+AGG + chr5.3:24063014-24063033 MS.gene45098:CDS 40.0%
AAGACTCTCGAGACTCTTAA+AGG + chr5.3:24062629-24062648 MS.gene45098:CDS 40.0%
ACTGCAATGTTGCTCTCAAA+TGG - chr5.3:24063225-24063244 None:intergenic 40.0%
AGGATTTGGAAATGCAGCAA+AGG + chr5.3:24063034-24063053 MS.gene45098:CDS 40.0%
GGATTAGGTGTGGAAAAACT+AGG + chr5.3:24063186-24063205 MS.gene45098:CDS 40.0%
TGTAACACTTCTTCAGGTGT+AGG - chr5.3:24062812-24062831 None:intergenic 40.0%
TTGCTGCATTTCCAAATCCT+AGG - chr5.3:24063034-24063053 None:intergenic 40.0%
!!! AGGCACATGATTGGTTTTCT+CGG - chr5.3:24063273-24063292 None:intergenic 40.0%
AATCATGTGCCTCCTGCTAA+AGG + chr5.3:24063281-24063300 MS.gene45098:CDS 45.0%
AGAAGGAATGGACAGCATCA+GGG + chr5.3:24063310-24063329 MS.gene45098:CDS 45.0%
GAGAGCAACATTGCAGTATC+TGG + chr5.3:24063228-24063247 MS.gene45098:CDS 45.0%
GCAAGACTACTCCTAGGATT+TGG + chr5.3:24063020-24063039 MS.gene45098:CDS 45.0%
TAAAGGCTCAGGAGAAGGAA+TGG + chr5.3:24063298-24063317 MS.gene45098:CDS 45.0%
! TTTAGCAGGAGGCACATGAT+TGG - chr5.3:24063282-24063301 None:intergenic 45.0%
!!! CATGATTGGTTTTCTCGGAG+TGG - chr5.3:24063268-24063287 None:intergenic 45.0%
GAGAAGGAATGGACAGCATC+AGG + chr5.3:24063309-24063328 MS.gene45098:CDS 50.0%
TGCTCAACAGGGATTAGGTG+TGG + chr5.3:24063176-24063195 MS.gene45098:intron 50.0%
! GCTAGCTTCTGCTCTGCAAA+TGG - chr5.3:24063351-24063370 None:intergenic 50.0%
CCTGCTAAAGGCTCAGGAGA+AGG + chr5.3:24063293-24063312 MS.gene45098:CDS 55.0%
CCTTCTCCTGAGCCTTTAGC+AGG - chr5.3:24063296-24063315 None:intergenic 55.0%
TCTCCTGAGCCTTTAGCAGG+AGG - chr5.3:24063293-24063312 None:intergenic 55.0%
GTGCCTCCTGCTAAAGGCTC+AGG + chr5.3:24063287-24063306 MS.gene45098:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 24062441 24063428 24062441 ID=MS.gene45098
chr5.3 mRNA 24062441 24063428 24062441 ID=MS.gene45098.t1;Parent=MS.gene45098
chr5.3 exon 24062441 24062516 24062441 ID=MS.gene45098.t1.exon1;Parent=MS.gene45098.t1
chr5.3 CDS 24062441 24062516 24062441 ID=cds.MS.gene45098.t1;Parent=MS.gene45098.t1
chr5.3 exon 24062606 24062650 24062606 ID=MS.gene45098.t1.exon2;Parent=MS.gene45098.t1
chr5.3 CDS 24062606 24062650 24062606 ID=cds.MS.gene45098.t1;Parent=MS.gene45098.t1
chr5.3 exon 24062789 24062859 24062789 ID=MS.gene45098.t1.exon3;Parent=MS.gene45098.t1
chr5.3 CDS 24062789 24062859 24062789 ID=cds.MS.gene45098.t1;Parent=MS.gene45098.t1
chr5.3 exon 24062948 24063055 24062948 ID=MS.gene45098.t1.exon4;Parent=MS.gene45098.t1
chr5.3 CDS 24062948 24063055 24062948 ID=cds.MS.gene45098.t1;Parent=MS.gene45098.t1
chr5.3 exon 24063186 24063428 24063186 ID=MS.gene45098.t1.exon5;Parent=MS.gene45098.t1
chr5.3 CDS 24063186 24063428 24063186 ID=cds.MS.gene45098.t1;Parent=MS.gene45098.t1
Gene Sequence

>MS.gene45098

ATGGCTGGTTTCTTCAAAATTGTCGCTACTGAATCTGGCAGAATAATCGGTGACGAAATGAGTAAAAAATTAAAAGGTTATCTCTAATGTCAGAAATCCATAATTAGTAAATTTTATACACATTTTTAATTTGTGTGATGTTTAACGTTTGATCTTCTATTTCAGATCTTCAACTTAGCGATATCGTCAAGACTCTCGAGACTCTTAAAGGTAATCGCTACCGTAATTAGTTCATTGTGAGATCTAGTTGTGCTTCTAGTTAGGTTTCAGATCTAGTTTTGTTCCTAATGATAGTGCCTAACAACTTTTTCCGTTTACAATATACCCTAAATCAAAAATATTTGTCAGACTTTTTCGATTCAAGGAGACCTACACCTGAAGAAGTGTTACAGTTTAAGACCAATTTCTGCCATGACTTTGTAAGATATTGTTACAATGAGTTAATTTAATTTATTATAATTTTTATTATAATTTGATTTTTTACTAACTAATTATTAATACATTTAGGAATTCAAAAGTGGCTTAGAGACTAAAAGAATCACTACTGCAGCTGTTGATTCAACTATCTGCTTAAACAAAGCAAGACTACTCCTAGGATTTGGAAATGCAGCAAAGGTAGTATCTATATATGTTAACACTAAAAAAATCAATTGCATACTAAAACTTGAAAATTACATTATATTTTCATATGCTATATAATAACTAGCAAAATGCTATATATATTTTTTATTTATATGCTCAACAGGGATTAGGTGTGGAAAAACTAGGAGTTGAATATTTTCCATTTGAGAGCAACATTGCAGTATCTGGTCTTGTGAATTTTGCCACTCCGAGAAAACCAATCATGTGCCTCCTGCTAAAGGCTCAGGAGAAGGAATGGACAGCATCAGGGCAACTTGTCTACAAACCATTTGCAGAGCAGAAGCTAGCCACATATGTTAATGTTGGTTATGTCACTCCAGCTATGTTGTTTCATCTGTACAAGTAA
Protein sequence

>MS.gene45098.t1

MAGFFKIVATESGRIIGDEMSKKLKDLQLSDIVKTLETLKDFFDSRRPTPEEVLQFKTNFCHDFEFKSGLETKRITTAAVDSTICLNKARLLLGFGNAAKGLGVEKLGVEYFPFESNIAVSGLVNFATPRKPIMCLLLKAQEKEWTASGQLVYKPFAEQKLATYVNVGYVTPAMLFHLYK