AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene050218

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 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTATGATATTTATAATCT+TGG 0.237785 1.2:+67711954 MS.gene050218:CDS
TCGTCCTTCTCAACTTCTTC+AGG 0.297180 1.2:+67711675 MS.gene050218:CDS
CAACATGTGAACGCAATCTA+TGG 0.375038 1.2:+67711638 MS.gene050218:CDS
TTGCTTTATCAATGATTTGT+TGG 0.412400 1.2:-67712028 None:intergenic
TTACCTCTTTGAAGAAGCTT+AGG 0.413182 1.2:-67712097 None:intergenic
AAAATTGATGCAAGAATTGC+CGG 0.420339 1.2:-67712246 None:intergenic
ATTGATAAAGCAACATTAGC+AGG 0.485264 1.2:+67712038 MS.gene050218:CDS
CAAAGTGAGCTCCGAGGCTG+CGG 0.496681 1.2:-67712334 None:intergenic
GAGGCTGCGGATTATGTAGA+TGG 0.504063 1.2:-67712321 None:intergenic
TTGAAGAAGCTTAGGTGTTG+AGG 0.516308 1.2:-67712089 None:intergenic
CGCAATCTATGGTGGATTGG+TGG 0.541391 1.2:+67711649 MS.gene050218:CDS
ATCTACATAATCCGCAGCCT+CGG 0.542523 1.2:+67712323 MS.gene050218:CDS
AAGCTTGTTCTGTTCTTCAG+AGG 0.544937 1.2:-67711470 None:intergenic
TAGATTGCGTTCACATGTTG+TGG 0.545132 1.2:-67711635 None:intergenic
TTTATGATGATGACAAGCTA+CGG 0.576647 1.2:+67711536 MS.gene050218:CDS
TACAGGCTGATAATCTTCGC+CGG 0.591845 1.2:+67712227 MS.gene050218:intron
GTGCACAAATGTTTCAGTTG+AGG 0.592785 1.2:-67711921 None:intergenic
ACACCTAAGCTTCTTCAAAG+AGG 0.598796 1.2:+67712094 MS.gene050218:CDS
CATGTGAACGCAATCTATGG+TGG 0.599889 1.2:+67711641 MS.gene050218:CDS
GAACGCAATCTATGGTGGAT+TGG 0.599907 1.2:+67711646 MS.gene050218:CDS
GCTGAATATGCTCTTGCACA+AGG 0.606518 1.2:+67711993 MS.gene050218:CDS
TGAGCTCGTAGTTACTCTGA+AGG 0.607552 1.2:+67712297 MS.gene050218:CDS
ATTACCTGAAGAAGTTGAGA+AGG 0.659326 1.2:-67711679 None:intergenic
AATTCTCAAAGTGAGCTCCG+AGG 0.740720 1.2:-67712340 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTTTATGATATTTATAATCT+TGG + chr1.2:67711954-67711973 MS.gene050218:CDS 15.0%
!! TAAGAAAACATAATTCAAAT+TGG - chr1.2:67711858-67711877 None:intergenic 15.0%
!! AAGTACTATGTGATTTAATA+TGG + chr1.2:67711879-67711898 MS.gene050218:intron 20.0%
!! GATTTAATATGGATATACAT+AGG + chr1.2:67711890-67711909 MS.gene050218:intron 20.0%
!! TAGGGTTAAAACTTAAAAAT+AGG - chr1.2:67712125-67712144 None:intergenic 20.0%
!! TTGCTTTATCAATGATTTGT+TGG - chr1.2:67712031-67712050 None:intergenic 25.0%
AAAATTGATGCAAGAATTGC+CGG - chr1.2:67712249-67712268 None:intergenic 30.0%
AACTAATTCTACCCCTAATT+AGG - chr1.2:67711820-67711839 None:intergenic 30.0%
ATTGATAAAGCAACATTAGC+AGG + chr1.2:67712038-67712057 MS.gene050218:CDS 30.0%
ATTGATGTGATGTCCTAATT+AGG + chr1.2:67711804-67711823 MS.gene050218:intron 30.0%
CATCATATAGAAAACTGACT+TGG + chr1.2:67712193-67712212 MS.gene050218:intron 30.0%
TTGATGTGATGTCCTAATTA+GGG + chr1.2:67711805-67711824 MS.gene050218:intron 30.0%
! TTTATGATGATGACAAGCTA+CGG + chr1.2:67711536-67711555 MS.gene050218:CDS 30.0%
!!! GAAGCACTGTTTTGAATTAT+TGG + chr1.2:67711579-67711598 MS.gene050218:CDS 30.0%
ACTTGGTTTCTTGTAACTAC+AGG + chr1.2:67712210-67712229 MS.gene050218:intron 35.0%
ATTACCTGAAGAAGTTGAGA+AGG - chr1.2:67711682-67711701 None:intergenic 35.0%
TGATGTGATGTCCTAATTAG+GGG + chr1.2:67711806-67711825 MS.gene050218:intron 35.0%
! TTACCTCTTTGAAGAAGCTT+AGG - chr1.2:67712100-67712119 None:intergenic 35.0%
ACACCTAAGCTTCTTCAAAG+AGG + chr1.2:67712094-67712113 MS.gene050218:CDS 40.0%
CAACATGTGAACGCAATCTA+TGG + chr1.2:67711638-67711657 MS.gene050218:CDS 40.0%
GTGCACAAATGTTTCAGTTG+AGG - chr1.2:67711924-67711943 None:intergenic 40.0%
TAGATTGCGTTCACATGTTG+TGG - chr1.2:67711638-67711657 None:intergenic 40.0%
! AAGCTTGTTCTGTTCTTCAG+AGG - chr1.2:67711473-67711492 None:intergenic 40.0%
! TTGAAGAAGCTTAGGTGTTG+AGG - chr1.2:67712092-67712111 None:intergenic 40.0%
ACCCTACACACTCTCTAACA+CGG + chr1.2:67712139-67712158 MS.gene050218:intron 45.0%
ATCTACATAATCCGCAGCCT+CGG + chr1.2:67712323-67712342 MS.gene050218:CDS 45.0%
CATGTGAACGCAATCTATGG+TGG + chr1.2:67711641-67711660 MS.gene050218:CDS 45.0%
GCTGAATATGCTCTTGCACA+AGG + chr1.2:67711993-67712012 MS.gene050218:CDS 45.0%
TACAGGCTGATAATCTTCGC+CGG + chr1.2:67712227-67712246 MS.gene050218:intron 45.0%
TCGTCCTTCTCAACTTCTTC+AGG + chr1.2:67711675-67711694 MS.gene050218:CDS 45.0%
TGAGCTCGTAGTTACTCTGA+AGG + chr1.2:67712297-67712316 MS.gene050218:CDS 45.0%
!! GAACGCAATCTATGGTGGAT+TGG + chr1.2:67711646-67711665 MS.gene050218:CDS 45.0%
! AGCCGTGTTAGAGAGTGTGT+AGG - chr1.2:67712144-67712163 None:intergenic 50.0%
! GAGGCTGCGGATTATGTAGA+TGG - chr1.2:67712324-67712343 None:intergenic 50.0%
! GCCGTGTTAGAGAGTGTGTA+GGG - chr1.2:67712143-67712162 None:intergenic 50.0%
!! CGCAATCTATGGTGGATTGG+TGG + chr1.2:67711649-67711668 MS.gene050218:CDS 50.0%
CAAAGTGAGCTCCGAGGCTG+CGG - chr1.2:67712337-67712356 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 67711437 67712357 67711437 ID=MS.gene050218
chr1.2 mRNA 67711437 67712357 67711437 ID=MS.gene050218.t1;Parent=MS.gene050218
chr1.2 exon 67711437 67711696 67711437 ID=MS.gene050218.t1.exon1;Parent=MS.gene050218.t1
chr1.2 CDS 67711437 67711696 67711437 ID=cds.MS.gene050218.t1;Parent=MS.gene050218.t1
chr1.2 exon 67711912 67712115 67711912 ID=MS.gene050218.t1.exon2;Parent=MS.gene050218.t1
chr1.2 CDS 67711912 67712115 67711912 ID=cds.MS.gene050218.t1;Parent=MS.gene050218.t1
chr1.2 exon 67712232 67712357 67712232 ID=MS.gene050218.t1.exon3;Parent=MS.gene050218.t1
chr1.2 CDS 67712232 67712357 67712232 ID=cds.MS.gene050218.t1;Parent=MS.gene050218.t1
Gene Sequence

>MS.gene050218

GAAAAACAATTTCTGTGAAAAACTATGCACTTTCCTCTGAAGAACAGAACAAGCTTATTTCTGAGATACATAATGCTCTAAATGATCACAATCACGTTATTTATGATGATGACAAGCTACGGTTAGTTATAAACACAATCATGAAGCACTGTTTTGAATTATTGGAGATAAAAACACGTTCTGCAAATGTAGATTCTGCCACAACATGTGAACGCAATCTATGGTGGATTGGTGGCTTTCGTCCTTCTCAACTTCTTCAGGTAATGCATGTTGATATTTTGTAAATATGAGTCAGACTCAATTTCAACACTATATATTGTCACTTACGCATTCATTTTGTTCTTTATATTTTTTTAGTGCTAAAAAGATTGATGTGATGTCCTAATTAGGGGTAGAATTAGTTAGAAACATATACACACCAATTTGAATTATGTTTTCTTACAAGTACTATGTGATTTAATATGGATATACATAGGTTATTCTGCCTCAACTGAAACATTTGTGCACTCAACAACAACTTTATGATATTTATAATCTTGGACAATCATGTCAACAAGCTGAATATGCTCTTGCACAAGGCATGATAGAACTCCAACAAATCATTGATAAAGCAACATTAGCAGGTGACAAAGAGTTTCAGCAGACGTGTGTACCTCAACACCTAAGCTTCTTCAAAGAGGTAATACCTATTTTTAAGTTTTAACCCTACACACTCTCTAACACGGCTCGATTATAAGTTGAAATTCATGCGAGTCTCATCATATAGAAAACTGACTTGGTTTCTTGTAACTACAGGCTGATAATCTTCGCCGGCAATTCTTGCATCAATTTTCTCGTCTCTTTACAATTTCTCAGCAAGCTGAGCTCGTAGTTACTCTGAAGGACCATCTACATAATCCGCAGCCTCGGAGCTCACTTTGA
Protein sequence

>MS.gene050218.t1

EKQFLUKTMHFPLKNRTSLFLRYIMLUMITITLFMMMTSYGULUTQSUSTVLNYWRUKHVLQMUILPQHVNAIYGGLVAFVLLNFFRLFCLNUNICALNNNFMIFIILDNHVNKLNMLLHKAUUNSNKSLIKQHUQVTKSFSRRVYLNTUASSKRLIIFAGNSCINFLVSLQFLSKLSSULLURTIYIIRSLGAHF