AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054755

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054755.t1 MTR_5g046230 100.000 118 0 0 1 118 9 126 6.50e-84 244
MS.gene054755.t1 MTR_4g114730 37.037 135 56 4 1 118 6 128 2.17e-23 89.7
MS.gene054755.t1 MTR_2g087740 43.284 134 58 6 1 118 3 134 2.14e-21 84.7
MS.gene054755.t1 MTR_4g050300 36.508 126 68 3 1 118 3 124 9.07e-21 82.4
MS.gene054755.t1 MTR_4g101660 38.806 134 64 3 2 118 12 144 2.21e-17 74.7
MS.gene054755.t1 MTR_4g025900 37.692 130 54 4 11 118 25 149 2.66e-17 74.3
MS.gene054755.t1 MTR_5g034030 35.385 130 55 3 9 118 12 132 3.35e-17 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054755.t1 AT1G69180 64.348 115 36 3 6 118 16 127 2.76e-35 119
MS.gene054755.t1 AT1G08465 42.188 128 55 5 4 118 3 124 1.02e-21 85.1
MS.gene054755.t1 AT2G26580 40.678 118 57 3 7 118 7 117 3.54e-21 83.2
MS.gene054755.t1 AT2G26580 40.678 118 57 3 7 118 7 117 3.54e-21 83.2
MS.gene054755.t1 AT2G45190 40.288 139 59 7 2 118 17 153 5.79e-19 79.0
MS.gene054755.t1 AT1G23420 31.250 128 69 3 10 118 20 147 9.70e-13 62.4
MS.gene054755.t1 AT4G00180 32.237 152 65 5 2 118 17 165 1.35e-12 62.4
MS.gene054755.t1 AT1G23420 31.496 127 68 3 11 118 52 178 1.58e-12 62.4

Find 26 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAACAAATGGCGGTGGTCT+AGG 0.360978 5.3:-33559666 None:intergenic
TGCTTACGTTTGACAACAAA+TGG 0.370125 5.3:-33559678 None:intergenic
CAACAAATGGCGGTGGTCTA+GGG 0.442200 5.3:-33559665 None:intergenic
GGAAGACGGTGCTTCTTCTC+AGG 0.456267 5.3:-33559853 None:intergenic
ATTGCACTTACTTCATGAAA+CGG 0.485516 5.3:-33559888 None:intergenic
TGATCACACCCTCAGTCTCC+AGG 0.486490 5.3:+33559356 MS.gene054755:CDS
AGAGAAAGTTACCATGGACT+TGG 0.516644 5.3:+33558886 None:intergenic
TTTGGAACTTGGTGGTCTTG+TGG 0.524145 5.3:-33559322 None:intergenic
ATGAAACGGTTGTATGCAGA+TGG 0.547267 5.3:-33559874 None:intergenic
ATTATTGAACCTGGAGACTG+AGG 0.580682 5.3:-33559365 None:intergenic
TAACAGAGGTGTTGATCAGA+TGG 0.588546 5.3:-33558914 None:intergenic
AGTGACTCAGTTGATGTAGT+TGG 0.590905 5.3:-33559639 None:intergenic
AACAAATGGCGGTGGTCTAG+GGG 0.595027 5.3:-33559664 None:intergenic
GTTGGTGAAGAAGAAGATGA+TGG 0.609575 5.3:-33559621 None:intergenic
CGTTTGACAACAAATGGCGG+TGG 0.615312 5.3:-33559672 None:intergenic
AGATGGTGGAACCAAGTCCA+TGG 0.626957 5.3:-33558897 None:intergenic
GTATCTAGCAGCCTCTTGCA+TGG 0.634316 5.3:-33559255 None:intergenic
GGTTGTATGCAGATGGAAGA+CGG 0.643999 5.3:-33559867 None:intergenic
GTGAAGAAGAAGATGATGGT+TGG 0.655028 5.3:-33559617 None:intergenic
CAGAGGTGTTGATCAGATGG+TGG 0.661444 5.3:-33558911 None:intergenic
AGGTTGGCATACCATGCAAG+AGG 0.666035 5.3:+33559244 MS.gene054755:intron
TTATTGAACCTGGAGACTGA+GGG 0.671255 5.3:-33559364 None:intergenic
TTACGTTTGACAACAAATGG+CGG 0.678472 5.3:-33559675 None:intergenic
GATACTGTGACAGTGAAGTG+TGG 0.709816 5.3:+33559273 MS.gene054755:CDS
AGTTGCAACGAACGTAACAG+AGG 0.710301 5.3:-33558928 None:intergenic
GTCTTGTGGTGAGAAAAGAG+AGG 0.744847 5.3:-33559308 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATTAATTAATTAATAAAA+AGG - chr5.3:33559533-33559552 None:intergenic 0.0%
!! TGATATATGAATAATATTAA+AGG - chr5.3:33558988-33559007 None:intergenic 10.0%
!!! AAATTTTTCTAAAATATGTA+GGG + chr5.3:33559200-33559219 MS.gene054755:intron 10.0%
!!! TAAATTTTTCTAAAATATGT+AGG + chr5.3:33559199-33559218 MS.gene054755:intron 10.0%
!!! TTTTTTATTAGCTACATATA+TGG + chr5.3:33559153-33559172 MS.gene054755:intron 15.0%
!! TTTAATACTGTCTCTAAATT+TGG + chr5.3:33559115-33559134 MS.gene054755:intron 20.0%
!!! ATGATGAGTTTTATATGTAT+TGG + chr5.3:33559506-33559525 MS.gene054755:intron 20.0%
!!! CATCTATATTTTTTGTTTTG+AGG + chr5.3:33559428-33559447 MS.gene054755:intron 20.0%
! CTAAACAAAATTATTGAACC+TGG - chr5.3:33559377-33559396 None:intergenic 25.0%
CTTCGTCTATAATTTCGTAT+AGG - chr5.3:33559088-33559107 None:intergenic 30.0%
GATATTTCCTTAGAGAGTAA+TGG - chr5.3:33559714-33559733 None:intergenic 30.0%
TTAGAGAGTAATGGTGAAAA+GGG - chr5.3:33559705-33559724 None:intergenic 30.0%
! AGTTAACAAGTTGAGAATGA+TGG - chr5.3:33559016-33559035 None:intergenic 30.0%
!! AATACTTTTGTTTGTAGCAG+GGG + chr5.3:33559574-33559593 MS.gene054755:intron 30.0%
!! AGAATACTTTTGTTTGTAGC+AGG + chr5.3:33559572-33559591 MS.gene054755:intron 30.0%
!! GAATACTTTTGTTTGTAGCA+GGG + chr5.3:33559573-33559592 MS.gene054755:intron 30.0%
!! GTGATCAACAGTTTGATTTT+TGG - chr5.3:33559343-33559362 None:intergenic 30.0%
!! GTTTGTTATGTTATGTAGGT+TGG + chr5.3:33559228-33559247 MS.gene054755:intron 30.0%
!! TGTGGTTTGTTATGTTATGT+AGG + chr5.3:33559224-33559243 MS.gene054755:intron 30.0%
!! TTCTAAAATATGTAGGGTTG+TGG + chr5.3:33559206-33559225 MS.gene054755:intron 30.0%
!!! ACAGTTTGATTTTTGGAACT+TGG - chr5.3:33559336-33559355 None:intergenic 30.0%
CTTAGAGAGTAATGGTGAAA+AGG - chr5.3:33559706-33559725 None:intergenic 35.0%
GGGATTTACAGTAGCAAAAA+AGG + chr5.3:33559594-33559613 MS.gene054755:CDS 35.0%
TGCTTACGTTTGACAACAAA+TGG - chr5.3:33559681-33559700 None:intergenic 35.0%
TTACGTTTGACAACAAATGG+CGG - chr5.3:33559678-33559697 None:intergenic 35.0%
! AACAAGTTGAGAATGATGGA+TGG - chr5.3:33559012-33559031 None:intergenic 35.0%
! CTTTTCACCATTACTCTCTA+AGG + chr5.3:33559704-33559723 MS.gene054755:intron 35.0%
!!! GTTTGATTTTTGGAACTTGG+TGG - chr5.3:33559333-33559352 None:intergenic 35.0%
ATGAAACGGTTGTATGCAGA+TGG - chr5.3:33559877-33559896 None:intergenic 40.0%
ATTATTGAACCTGGAGACTG+AGG - chr5.3:33559368-33559387 None:intergenic 40.0%
GGTGAAGTTTACATACAGCT+AGG - chr5.3:33558967-33558986 None:intergenic 40.0%
TTATTGAACCTGGAGACTGA+GGG - chr5.3:33559367-33559386 None:intergenic 40.0%
! AGTGACTCAGTTGATGTAGT+TGG - chr5.3:33559642-33559661 None:intergenic 40.0%
! GTGAAGAAGAAGATGATGGT+TGG - chr5.3:33559620-33559639 None:intergenic 40.0%
! GTTGGTGAAGAAGAAGATGA+TGG - chr5.3:33559624-33559643 None:intergenic 40.0%
!! TAACAGAGGTGTTGATCAGA+TGG - chr5.3:33558917-33558936 None:intergenic 40.0%
AGTTGCAACGAACGTAACAG+AGG - chr5.3:33558931-33558950 None:intergenic 45.0%
GATACTGTGACAGTGAAGTG+TGG + chr5.3:33559273-33559292 MS.gene054755:CDS 45.0%
GGTTGTATGCAGATGGAAGA+CGG - chr5.3:33559870-33559889 None:intergenic 45.0%
GTCTTGTGGTGAGAAAAGAG+AGG - chr5.3:33559311-33559330 None:intergenic 45.0%
! TTTGGAACTTGGTGGTCTTG+TGG - chr5.3:33559325-33559344 None:intergenic 45.0%
AACAAATGGCGGTGGTCTAG+GGG - chr5.3:33559667-33559686 None:intergenic 50.0%
ACAACAAATGGCGGTGGTCT+AGG - chr5.3:33559669-33559688 None:intergenic 50.0%
AGGTTGGCATACCATGCAAG+AGG + chr5.3:33559244-33559263 MS.gene054755:intron 50.0%
CAACAAATGGCGGTGGTCTA+GGG - chr5.3:33559668-33559687 None:intergenic 50.0%
CGTTTGACAACAAATGGCGG+TGG - chr5.3:33559675-33559694 None:intergenic 50.0%
GTATCTAGCAGCCTCTTGCA+TGG - chr5.3:33559258-33559277 None:intergenic 50.0%
!! CAGAGGTGTTGATCAGATGG+TGG - chr5.3:33558914-33558933 None:intergenic 50.0%
GGAAGACGGTGCTTCTTCTC+AGG - chr5.3:33559856-33559875 None:intergenic 55.0%
TGATCACACCCTCAGTCTCC+AGG + chr5.3:33559356-33559375 MS.gene054755:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 33558899 33559903 33558899 ID=MS.gene054755
chr5.3 mRNA 33558899 33559903 33558899 ID=MS.gene054755.t1;Parent=MS.gene054755
chr5.3 exon 33558899 33558970 33558899 ID=MS.gene054755.t1.exon1;Parent=MS.gene054755.t1
chr5.3 CDS 33558899 33558970 33558899 ID=cds.MS.gene054755.t1;Parent=MS.gene054755.t1
chr5.3 exon 33559246 33559377 33559246 ID=MS.gene054755.t1.exon2;Parent=MS.gene054755.t1
chr5.3 CDS 33559246 33559377 33559246 ID=cds.MS.gene054755.t1;Parent=MS.gene054755.t1
chr5.3 exon 33559594 33559693 33559594 ID=MS.gene054755.t1.exon3;Parent=MS.gene054755.t1
chr5.3 CDS 33559594 33559693 33559594 ID=cds.MS.gene054755.t1;Parent=MS.gene054755.t1
chr5.3 exon 33559851 33559903 33559851 ID=MS.gene054755.t1.exon4;Parent=MS.gene054755.t1
chr5.3 CDS 33559851 33559903 33559851 ID=cds.MS.gene054755.t1;Parent=MS.gene054755.t1
Gene Sequence

>MS.gene054755

ATGGACTTGGTTCCACCATCTGATCAACACCTCTGTTACGTTCGTTGCAACTTCTGTAACACTGTCCTAGCTGTATGTAAACTTCACCTTTAATATTATTCATATATCAACCATCCATCATTCTCAACTTGTTAACTTCTTAGTGATTCATAATCATATTATTCTTTTTAATTTTTAAAATAATATCCTATACGAAATTATAGACGAAGTTTACATTTTAATACTGTCTCTAAATTTGGTCACTAGATCAATTTTTTTTTATTAGCTACATATATGGAGTTTATGAAATATCAAATATTATAAATTTTTCTAAAATATGTAGGGTTGTGGTTTGTTATGTTATGTAGGTTGGCATACCATGCAAGAGGCTGCTAGATACTGTGACAGTGAAGTGTGGTCACTGCAGCAACCTCTCTTTTCTCACCACAAGACCACCAAGTTCCAAAAATCAAACTGTTGATCACACCCTCAGTCTCCAGGTTCAATAATTTTGTTTAGTTTTTTTTTTTAATTATTATTATGAACATAACATCTATATTTTTTGTTTTGAGGAAATAACATCTATATATATTTATTCAATAACTTTATTTAGTTTTTTTTTTTTCATATGATGAGTTTTATATGTATTGGTCCTTTTTATTAATTAATTAATTAATATGTAGAAAGAAAAGTAAGAATACTTTTGTTTGTAGCAGGGGATTTACAGTAGCAAAAAAGGCCAACCATCATCTTCTTCTTCACCAACTACATCAACTGAGTCACTGTCCCCTAGACCACCGCCATTTGTTGTCAAACGTAAGCAACCCTTTTCACCATTACTCTCTAAGGAAATATCAAATTACAATTTTATATATATATATATATATATATATATATATTAAGATGCATTTTTCAACTATAACACACACAAAAAAACTTGTCATAATTTGTTATTTTATTATTTCTTTTGCAGCACCTGAGAAGAAGCACCGTCTTCCATCTGCATACAACCGTTTCATGAAGTAA
Protein sequence

>MS.gene054755.t1

MDLVPPSDQHLCYVRCNFCNTVLAVGIPCKRLLDTVTVKCGHCSNLSFLTTRPPSSKNQTVDHTLSLQGIYSSKKGQPSSSSSPTTSTESLSPRPPPFVVKPPEKKHRLPSAYNRFMK