AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052947


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052947.t1 MTR_0147s0070 100.000 95 0 0 1 95 1 95 3.99e-65 191
MS.gene052947.t1 MTR_2g101900 96.809 94 3 0 1 94 1 94 1.39e-62 184
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052947.t1 AT1G52300 89.362 94 10 0 1 94 1 94 1.65e-57 172
MS.gene052947.t1 AT3G16080 88.298 94 11 0 1 94 1 94 4.05e-57 171
MS.gene052947.t1 AT1G15250 87.368 95 12 0 1 95 1 95 7.25e-57 170
MS.gene052947.t1 AT1G15250 87.368 95 12 0 1 95 1 95 7.25e-57 170
MS.gene052947.t1 AT3G16080 93.333 45 3 0 1 45 1 45 9.42e-25 89.0

Find 29 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCAGCTGCTCCCTTGTTCC+TGG 0.247813 4.1:+83524856 None:intergenic
ACTGGAGTGAGAAGGCTATT+AGG 0.322324 4.1:-83525919 MS.gene052947:CDS
ATTGTGTGATTTCAGATAAC+TGG 0.324608 4.1:-83525937 MS.gene052947:intron
ATGCTGAGCAGCGACTCTTC+TGG 0.400063 4.1:+83526150 None:intergenic
CATTTCCTGACACGTGCAGC+TGG 0.423824 4.1:+83526119 None:intergenic
AGACCCACACACTCTGTGTT+AGG 0.433282 4.1:-83526196 MS.gene052947:CDS
GCAGCTGCTCCCTTGTTCCT+GGG 0.437974 4.1:+83524857 None:intergenic
GGTAAGGGAACAGGCAGTTT+CGG 0.454393 4.1:-83526233 MS.gene052947:CDS
AGGAGAAAGACCACTGGAAC+TGG 0.467139 4.1:-83525899 MS.gene052947:CDS
CTTACCCAGCTGCACGTGTC+AGG 0.470321 4.1:-83526124 MS.gene052947:CDS
TGAAGCTGCACCCAGGAACA+AGG 0.550050 4.1:-83524867 MS.gene052947:CDS
AGCAGCGACTCTTCTGGAGA+TGG 0.555977 4.1:+83526156 None:intergenic
CACACCTAACACAGAGTGTG+TGG 0.573805 4.1:+83526192 None:intergenic
TTCAAGAGTGGATTCAGAGA+AGG 0.583941 4.1:-83525842 MS.gene052947:intron
TTCAGATAACTGGAGTGAGA+AGG 0.609846 4.1:-83525927 MS.gene052947:intron
ATTTCCTGACACGTGCAGCT+GGG 0.610760 4.1:+83526120 None:intergenic
CAGGCAGTTTCGGTAAGAGA+AGG 0.615161 4.1:-83526223 MS.gene052947:CDS
CCACTGGAACTGGTAGGATG+AGG 0.619264 4.1:-83525889 MS.gene052947:CDS
GCTATTAGGAGAAAGACCAC+TGG 0.627964 4.1:-83525905 MS.gene052947:CDS
CTGGTAGGATGAGGTACTTG+AGG 0.643276 4.1:-83525880 MS.gene052947:CDS
CACACACTCTGTGTTAGGTG+TGG 0.644280 4.1:-83526191 MS.gene052947:CDS
GAAAGACCACTGGAACTGGT+AGG 0.652178 4.1:-83525895 MS.gene052947:CDS
GAAGCTGCACCCAGGAACAA+GGG 0.652652 4.1:-83524866 MS.gene052947:CDS
TCTGGAGATGGAAACTGCGA+CGG 0.655757 4.1:+83526168 None:intergenic
CCTCATCCTACCAGTTCCAG+TGG 0.656605 4.1:+83525889 None:intergenic
CAGGTACTGAAGCTGCACCC+AGG 0.673244 4.1:-83524874 MS.gene052947:CDS
ACACCTAACACAGAGTGTGT+GGG 0.685746 4.1:+83526193 None:intergenic
GTGCCTCGCAGATTCAAGAG+TGG 0.690811 4.1:-83525854 MS.gene052947:CDS
AATCCACTCTTGAATCTGCG+AGG 0.695196 4.1:+83525851 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAATTTGATTTTTGAATTT+CGG - chr4.1:83525235-83525254 MS.gene052947:intron 10.0%
!!! CGTTAAATTATTTTTATATA+TGG - chr4.1:83525854-83525873 MS.gene052947:CDS 10.0%
!! TTGAAAAAACCTAATAAAAA+TGG - chr4.1:83525924-83525943 MS.gene052947:CDS 15.0%
!! TTTGTTGATATGATTATTAT+TGG - chr4.1:83526300-83526319 MS.gene052947:intron 15.0%
!!! ATTTTTGTGTTTTTAGATTT+AGG - chr4.1:83525158-83525177 MS.gene052947:intron 15.0%
!!! TTCTAGAATTATCATTTTTT+TGG - chr4.1:83525553-83525572 MS.gene052947:intron 15.0%
!!! TTTTTGTGTTTTTAGATTTA+GGG - chr4.1:83525159-83525178 MS.gene052947:intron 15.0%
!! ATTTAATTGATTGATCAATC+AGG - chr4.1:83525523-83525542 MS.gene052947:intron 20.0%
!! TTAGTAGATAAGTTCAAATA+AGG - chr4.1:83525982-83526001 MS.gene052947:intron 20.0%
!! TTTAATTGATTGATCAATCA+GGG - chr4.1:83525524-83525543 MS.gene052947:intron 20.0%
!!! ATTATTGAATGATTTTTGCA+GGG - chr4.1:83524949-83524968 MS.gene052947:intron 20.0%
!!! ATTTTGACATGTTTTACTAT+AGG - chr4.1:83526110-83526129 MS.gene052947:intron 20.0%
!!! GTTTTTTGATTTTCGAAAAT+GGG - chr4.1:83525204-83525223 MS.gene052947:intron 20.0%
!!! TGTTTTTTGATTTTCGAAAA+TGG - chr4.1:83525203-83525222 MS.gene052947:intron 20.0%
!!! TTTGTTCGATTTTAGAAAAT+GGG - chr4.1:83525118-83525137 MS.gene052947:intron 20.0%
!!! TTTTGTTCGATTTTAGAAAA+TGG - chr4.1:83525117-83525136 MS.gene052947:intron 20.0%
! ATTCACATAAAACAGAGATT+TGG + chr4.1:83526154-83526173 None:intergenic 25.0%
! TACACCTAAATAAAGAGATT+TGG + chr4.1:83525694-83525713 None:intergenic 25.0%
!! GATTATTGAATGATTTTTGC+AGG - chr4.1:83524948-83524967 MS.gene052947:intron 25.0%
!! TGATTATTATTGGTTAAACC+AGG - chr4.1:83526310-83526329 MS.gene052947:intron 25.0%
!!! AGCTTATGACCATTTTTATT+AGG + chr4.1:83525936-83525955 None:intergenic 25.0%
!!! TTCTGAGTTGTTATTTTTTC+TGG - chr4.1:83526269-83526288 MS.gene052947:intron 25.0%
AATTTAGATCAGTTGGATCT+TGG - chr4.1:83526022-83526041 MS.gene052947:intron 30.0%
ATTGTGTGATTTCAGATAAC+TGG - chr4.1:83525266-83525285 MS.gene052947:intron 30.0%
! AGAGCCAAATCTCTTTATTT+AGG - chr4.1:83525687-83525706 MS.gene052947:intron 30.0%
! AGGTTCTAATTTAGATCAGT+TGG - chr4.1:83526015-83526034 MS.gene052947:intron 30.0%
! CTTTTGTTAGCATGATTGTA+TGG - chr4.1:83526230-83526249 MS.gene052947:CDS 30.0%
! TAGATTTAGGGTTTAAGTTC+AGG - chr4.1:83525171-83525190 MS.gene052947:intron 30.0%
!! GTTACTGAATGAGTTGATTT+AGG - chr4.1:83525664-83525683 MS.gene052947:intron 30.0%
ATAAGCTGAATATCCAATGC+AGG + chr4.1:83525767-83525786 None:intergenic 35.0%
GATCTAAATTAGAACCTGCA+TGG + chr4.1:83526012-83526031 None:intergenic 35.0%
GTGCTAGAAAAACTAAACAC+AGG + chr4.1:83525409-83525428 None:intergenic 35.0%
TAAGCTGAATATCCAATGCA+GGG + chr4.1:83525766-83525785 None:intergenic 35.0%
TCAGACACTGTAATGAAACT+GGG + chr4.1:83524925-83524944 None:intergenic 35.0%
TTAGGTGTAGCAACTTTCTT+GGG - chr4.1:83525705-83525724 MS.gene052947:intron 35.0%
TTCAGACACTGTAATGAAAC+TGG + chr4.1:83524926-83524945 None:intergenic 35.0%
TTTAGGTGTAGCAACTTTCT+TGG - chr4.1:83525704-83525723 MS.gene052947:intron 35.0%
! GAATGATTTTTGCAGGGTAA+GGG - chr4.1:83524955-83524974 MS.gene052947:intron 35.0%
! TAGGGTTTAAGTTCAGGAAA+TGG - chr4.1:83525177-83525196 MS.gene052947:intron 35.0%
! TGAATGATTTTTGCAGGGTA+AGG - chr4.1:83524954-83524973 MS.gene052947:intron 35.0%
!! AGTTGGATCTTGGTTCTTTT+AGG - chr4.1:83526032-83526051 MS.gene052947:intron 35.0%
CAGACACTGTAATGAAACTG+GGG + chr4.1:83524924-83524943 None:intergenic 40.0%
TCAAATAAGGCAATCCATGC+AGG - chr4.1:83525995-83526014 MS.gene052947:intron 40.0%
TTCAGATAACTGGAGTGAGA+AGG - chr4.1:83525276-83525295 MS.gene052947:intron 40.0%
! CTGTAATGAAACTGGGGTTT+TGG + chr4.1:83524918-83524937 None:intergenic 40.0%
! TTCAAGAGTGGATTCAGAGA+AGG - chr4.1:83525361-83525380 MS.gene052947:intron 40.0%
AATCCACTCTTGAATCTGCG+AGG + chr4.1:83525355-83525374 None:intergenic 45.0%
ACACCTAACACAGAGTGTGT+GGG + chr4.1:83525013-83525032 None:intergenic 45.0%
ACTGGAGTGAGAAGGCTATT+AGG - chr4.1:83525284-83525303 MS.gene052947:intron 45.0%
CAATGATCAAGTCCCTGCAT+TGG - chr4.1:83525751-83525770 MS.gene052947:intron 45.0%
GCTATTAGGAGAAAGACCAC+TGG - chr4.1:83525298-83525317 MS.gene052947:intron 45.0%
! TTTTTGCAGGGTAAGGGAAC+AGG - chr4.1:83524961-83524980 MS.gene052947:intron 45.0%
!!! AAACTGGGGTTTTGGATCGA+AGG + chr4.1:83524910-83524929 None:intergenic 45.0%
AGACCCACACACTCTGTGTT+AGG - chr4.1:83525007-83525026 MS.gene052947:intron 50.0%
AGAGAGAGAGAGAGAGAGAG+AGG + chr4.1:83524867-83524886 None:intergenic 50.0%
AGGAGAAAGACCACTGGAAC+TGG - chr4.1:83525304-83525323 MS.gene052947:intron 50.0%
ATTTCCTGACACGTGCAGCT+GGG + chr4.1:83525086-83525105 None:intergenic 50.0%
CACACACTCTGTGTTAGGTG+TGG - chr4.1:83525012-83525031 MS.gene052947:intron 50.0%
CACACCTAACACAGAGTGTG+TGG + chr4.1:83525014-83525033 None:intergenic 50.0%
CAGGCAGTTTCGGTAAGAGA+AGG - chr4.1:83524980-83524999 MS.gene052947:intron 50.0%
GAAAGACCACTGGAACTGGT+AGG - chr4.1:83525308-83525327 MS.gene052947:intron 50.0%
GGTAAGGGAACAGGCAGTTT+CGG - chr4.1:83524970-83524989 MS.gene052947:intron 50.0%
TCTGGAGATGGAAACTGCGA+CGG + chr4.1:83525038-83525057 None:intergenic 50.0%
! CTGGTAGGATGAGGTACTTG+AGG - chr4.1:83525323-83525342 MS.gene052947:intron 50.0%
ATGCTGAGCAGCGACTCTTC+TGG + chr4.1:83525056-83525075 None:intergenic 55.0%
CATTTCCTGACACGTGCAGC+TGG + chr4.1:83525087-83525106 None:intergenic 55.0%
CCACTGGAACTGGTAGGATG+AGG - chr4.1:83525314-83525333 MS.gene052947:intron 55.0%
CCTCATCCTACCAGTTCCAG+TGG + chr4.1:83525317-83525336 None:intergenic 55.0%
GAAGCTGCACCCAGGAACAA+GGG - chr4.1:83526337-83526356 MS.gene052947:intron 55.0%
GTGCCTCGCAGATTCAAGAG+TGG - chr4.1:83525349-83525368 MS.gene052947:intron 55.0%
TGAAGCTGCACCCAGGAACA+AGG - chr4.1:83526336-83526355 MS.gene052947:intron 55.0%
! AGCAGCGACTCTTCTGGAGA+TGG + chr4.1:83525050-83525069 None:intergenic 55.0%
AGCAGCTGCTCCCTTGTTCC+TGG + chr4.1:83526350-83526369 None:intergenic 60.0%
CTGGGTGCAGCTTCAGTACC+TGG + chr4.1:83526331-83526350 None:intergenic 60.0%
CTTACCCAGCTGCACGTGTC+AGG - chr4.1:83525079-83525098 MS.gene052947:intron 60.0%
GCAGCTGCTCCCTTGTTCCT+GGG + chr4.1:83526349-83526368 None:intergenic 60.0%
!! CAGGTACTGAAGCTGCACCC+AGG - chr4.1:83526329-83526348 MS.gene052947:intron 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 83524847 83526378 83524847 ID=MS.gene052947
chr4.1 mRNA 83524847 83526378 83524847 ID=MS.gene052947.t1;Parent=MS.gene052947
chr4.1 exon 83526376 83526378 83526376 ID=MS.gene052947.t1.exon1;Parent=MS.gene052947.t1
chr4.1 CDS 83526376 83526378 83526376 ID=cds.MS.gene052947.t1;Parent=MS.gene052947.t1
chr4.1 exon 83526120 83526255 83526120 ID=MS.gene052947.t1.exon2;Parent=MS.gene052947.t1
chr4.1 CDS 83526120 83526255 83526120 ID=cds.MS.gene052947.t1;Parent=MS.gene052947.t1
chr4.1 exon 83525843 83525944 83525843 ID=MS.gene052947.t1.exon3;Parent=MS.gene052947.t1
chr4.1 CDS 83525843 83525944 83525843 ID=cds.MS.gene052947.t1;Parent=MS.gene052947.t1
chr4.1 exon 83524847 83524893 83524847 ID=MS.gene052947.t1.exon4;Parent=MS.gene052947.t1
chr4.1 CDS 83524847 83524893 83524847 ID=cds.MS.gene052947.t1;Parent=MS.gene052947.t1
Gene Sequence

>MS.gene052947

ATGGTACTTTGCATTCTCTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTTCGATCCAAAACCCCAGTTTCATTACAGTGTCTGAATCGATTATTGAATGATTTTTGCAGGGTAAGGGAACAGGCAGTTTCGGTAAGAGAAGGAACAAGACCCACACACTCTGTGTTAGGTGTGGCCGTCGCAGTTTCCATCTCCAGAAGAGTCGCTGCTCAGCATGTGCTTACCCAGCTGCACGTGTCAGGAAATGTAAGTTTTTTTTTTGTTCGATTTTAGAAAATGGGTTTAGTGTCAAAATTCGATTTTTGTGTTTTTAGATTTAGGGTTTAAGTTCAGGAAATGGAAGTGTTTTTTGATTTTCGAAAATGGGTTTTTGTCAAAATTTGATTTTTGAATTTCGGCGTTTTGTATTGTGTGATTTCAGATAACTGGAGTGAGAAGGCTATTAGGAGAAAGACCACTGGAACTGGTAGGATGAGGTACTTGAGGAACGTGCCTCGCAGATTCAAGAGTGGATTCAGAGAAGGTAATTTTTTCTTTAATCAATTTCCTGTGTTTAGTTTTTCTAGCACGTGCAATGCTTTAAATGTATAATGATTAAGCAATAATTTATGAATCAATAGATGAATAACTGTTAAGTTCATAAAGTAAAATGTTTTGTATTTGATTTAATTGATTGATCAATCAGGGTGATTTTTCTAGAATTATCATTTTTTTGGTACGCTAGAATGAGCAACTTTACAATATGATTTAATTGATAATATCATTATCAATAGATGAATGACTGTTAAGCTTAAACTTCTGTGTGTTACTGAATGAGTTGATTTAGGAGAGCCAAATCTCTTTATTTAGGTGTAGCAACTTTCTTGGGTTTGTGTTTTGTTAAAATGATTACAATGATCAAGTCCCTGCATTGGATATTCAGCTTATTTGCACAATAACTGCTGCTCATGCATAAGCTTGCATACGCTATTTTTAACAGCAAAAGAAAAAGTAACGTTAAATTATTTTTATATATGGTATAAGTTGTTTTATAAGCTATATTTAAGAAACTTGTGAAAAATAAGTTGAAAAAACCTAATAAAAATGGTCATAAGCTGTTTTCATAAGTTCTCACAATTTATGTTAGTAGATAAGTTCAAATAAGGCAATCCATGCAGGTTCTAATTTAGATCAGTTGGATCTTGGTTCTTTTAGGTGTGTTATTCTGTTTGTATTGAAACATTATTATGATTATAATACGTTAAATGTTAATTTTGACATGTTTTACTATAGGTATGTTATTTTATAAGCGCCAAATCTCTGTTTTATGTGAATTATTTGTTTGTTTGTGTATTTTGCTAATGTGAGCTCTTTTAGTTCTGTTTTTTTAGCTTTTGTTAGCATGATTGTATGGAAGTAGTTAAATCACTTTCTGAGTTGTTATTTTTTCTGGATTATTTTTTTGTTGATATGATTATTATTGGTTAAACCAGGTACTGAAGCTGCACCCAGGAACAAGGGAGCAGCTGCTTCTACCTAA

Protein sequence

>MS.gene052947.t1

MGKGTGSFGKRRNKTHTLCVRCGRRSFHLQKSRCSACAYPAARVRKYNWSEKAIRRKTTGTGRMRYLRNVPRRFKSGFREGTEAAPRNKGAAAST