AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene005340

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene005340.t1 MTR_1g084750 87.500 128 10 2 53 180 1 122 1.05e-70 210
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene005340.t1 AT5G26749 40.136 147 69 2 53 180 1 147 2.37e-31 111
MS.gene005340.t1 AT5G26749 35.542 166 69 3 53 180 1 166 5.54e-27 100

Find 64 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCACCTGGCATTCTTGTTAT+TGG 0.169245 1.1:+62631228 None:intergenic
TACCGGCAGAGTGGCGTTTC+CGG 0.248184 1.1:+62631517 None:intergenic
TGTTGCTGCTGTTGTGTATT+GGG 0.274558 1.1:+62631252 None:intergenic
AGAGTGGCGTTTCCGGTCTA+AGG 0.283984 1.1:+62631524 None:intergenic
TTCTTTCTACGCTCACATTA+AGG 0.284952 1.1:-62631795 MS.gene005340:intron
GGGGCGTGGGTGTGGTGAGG+AGG 0.304968 1.1:-62631607 MS.gene005340:CDS
GGAATAGAGTTCTGGTGTTC+GGG 0.348282 1.1:+62631450 None:intergenic
ATCTATCCCCAGTCGAGAAA+TGG 0.349618 1.1:+62631031 None:intergenic
ATGTGAGCGTAGAAAGAAAT+TGG 0.367973 1.1:+62631800 None:intergenic
GGCGTGGGTGTGGTGAGGAG+GGG 0.375901 1.1:-62631605 MS.gene005340:CDS
TGGAATAGAGTTCTGGTGTT+CGG 0.377509 1.1:+62631449 None:intergenic
TTGTTGCTGCTGTTGTGTAT+TGG 0.380624 1.1:+62631251 None:intergenic
GGGCGTGGGTGTGGTGAGGA+GGG 0.389795 1.1:-62631606 MS.gene005340:CDS
TTGTAGTTGGGGCGTGGGTG+TGG 0.411184 1.1:-62631615 MS.gene005340:intron
CAGGCAGAACGGCGGCGTCC+TGG 0.417159 1.1:+62631870 None:intergenic
ATGGTGGTGGAATAGAGTTC+TGG 0.430967 1.1:+62631442 None:intergenic
GGAATCGTACCAACGAGCTT+TGG 0.434321 1.1:+62631479 None:intergenic
CCATATTTGTAGTTGGGGCG+TGG 0.439708 1.1:-62631621 MS.gene005340:intron
GTTCTGGTGTTCGGGTTTGA+AGG 0.464430 1.1:+62631458 None:intergenic
AACGGAGGCGTCGCATAGAA+TGG 0.465306 1.1:+62631841 None:intergenic
ACGCAGAAGGGTTGATTAGA+TGG 0.466779 1.1:+62631423 None:intergenic
CAACCTCCCATTTCTCGACT+GGG 0.475626 1.1:-62631038 MS.gene005340:CDS
TCTATCCCCAGTCGAGAAAT+GGG 0.477681 1.1:+62631032 None:intergenic
GGCTTGTTTGTGTTGAATAC+CGG 0.496651 1.1:+62631500 None:intergenic
CCAACCTCCCATTTCTCGAC+TGG 0.502817 1.1:-62631039 MS.gene005340:CDS
GAGTATCCACCCTCAGGTGG+AGG 0.504269 1.1:+62631061 None:intergenic
GTCACTGCAGCCTCCACCTG+AGG 0.504311 1.1:-62631071 MS.gene005340:CDS
GATACCATGGGAGTGTCATT+CGG 0.508317 1.1:-62631106 MS.gene005340:CDS
TCAGGTGGAGGCTGCAGTGA+CGG 0.508961 1.1:+62631073 None:intergenic
GACCGGAAACGCCACTCTGC+CGG 0.512557 1.1:-62631519 MS.gene005340:CDS
AGGTTGGAGTATCCACCCTC+AGG 0.521427 1.1:+62631055 None:intergenic
AAGGGTTGATTAGATGGTGG+TGG 0.521880 1.1:+62631429 None:intergenic
GTTGGGGCGTGGGTGTGGTG+AGG 0.522044 1.1:-62631610 MS.gene005340:CDS
CATATTTGTAGTTGGGGCGT+GGG 0.528157 1.1:-62631620 MS.gene005340:intron
TTCAAGATACACCCTTAGAC+CGG 0.529755 1.1:-62631536 MS.gene005340:CDS
CCGGCGCGACACCGTTCTCC+AGG 0.530698 1.1:-62631888 MS.gene005340:CDS
TTATGTGTAGGGAATATAGT+AGG 0.533140 1.1:-62631130 MS.gene005340:intron
AACGGCGGCGTCCTGGAGAA+CGG 0.558689 1.1:+62631877 None:intergenic
TCGCATAGAATGGAAGTGGC+AGG 0.559621 1.1:+62631851 None:intergenic
TCACTGCAGCCTCCACCTGA+GGG 0.562993 1.1:-62631070 MS.gene005340:CDS
ATAGTACCGTGTTGACGAAG+TGG 0.572113 1.1:+62631400 None:intergenic
CCAGTCGAGAAATGGGAGGT+TGG 0.572331 1.1:+62631039 None:intergenic
CCTGGAGAACGGTGTCGCGC+CGG 0.577030 1.1:+62631888 None:intergenic
GGCGTCGCATAGAATGGAAG+TGG 0.581345 1.1:+62631847 None:intergenic
GAGTGGCGTTTCCGGTCTAA+GGG 0.584406 1.1:+62631525 None:intergenic
TACAGCGTCGTCGCGCAGAA+CGG 0.586040 1.1:+62631823 None:intergenic
AATGGAAGTGGCAGGCAGAA+CGG 0.586179 1.1:+62631859 None:intergenic
CAACCAATAACAAGAATGCC+AGG 0.589593 1.1:-62631231 MS.gene005340:intron
TTGACGAAGTGGACGCAGAA+GGG 0.593699 1.1:+62631411 None:intergenic
GTTGACGAAGTGGACGCAGA+AGG 0.597332 1.1:+62631410 None:intergenic
CTGCAGCCTCCACCTGAGGG+TGG 0.602600 1.1:-62631067 MS.gene005340:CDS
GAATATAGTAGGAGATACCA+TGG 0.619077 1.1:-62631119 MS.gene005340:CDS
CTGCGTCCACTTCGTCAACA+CGG 0.619782 1.1:-62631406 MS.gene005340:intron
GGTGGAGGCTGCAGTGACGG+AGG 0.622645 1.1:+62631076 None:intergenic
TTGGAGTATCCACCCTCAGG+TGG 0.623820 1.1:+62631058 None:intergenic
AGCGTCGTCGCGCAGAACGG+AGG 0.624495 1.1:+62631826 None:intergenic
ACAAACAAGCCAAAGCTCGT+TGG 0.650557 1.1:-62631488 MS.gene005340:CDS
CAGAAGGGTTGATTAGATGG+TGG 0.659317 1.1:+62631426 None:intergenic
AACCTCCCATTTCTCGACTG+GGG 0.663201 1.1:-62631037 MS.gene005340:CDS
GGAAGTGGCAGGCAGAACGG+CGG 0.688489 1.1:+62631862 None:intergenic
AATATAGTAGGAGATACCAT+GGG 0.697591 1.1:-62631118 MS.gene005340:CDS
ATTGCCGAATGACACTCCCA+TGG 0.703596 1.1:+62631102 None:intergenic
TGTGTTGAATACCGGCAGAG+TGG 0.711189 1.1:+62631508 None:intergenic
ATCCCCAGTCGAGAAATGGG+AGG 0.723699 1.1:+62631035 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATAGTTTCTTTCTTTA+TGG - chr1.1:62631871-62631890 MS.gene005340:CDS 15.0%
!! CTAAGAAATGATAATTAATG+AGG + chr1.1:62631702-62631721 None:intergenic 20.0%
!! TGATATTAATGTTATGTGTA+GGG - chr1.1:62631909-62631928 MS.gene005340:intron 20.0%
!! TTGATATTAATGTTATGTGT+AGG - chr1.1:62631908-62631927 MS.gene005340:intron 20.0%
! AACTTTCGATCATAAAACAA+AGG + chr1.1:62631054-62631073 None:intergenic 25.0%
! ATCAGTAAATGAACAACTAT+CGG + chr1.1:62631853-62631872 None:intergenic 25.0%
! TAACTCTCTCTGTATATTTA+GGG - chr1.1:62631738-62631757 MS.gene005340:intron 25.0%
! TTAACTCTCTCTGTATATTT+AGG - chr1.1:62631737-62631756 MS.gene005340:intron 25.0%
! TTGAATCCATATTTGTAGTT+GGG - chr1.1:62631423-62631442 MS.gene005340:CDS 25.0%
!!! TCACAATAGTACTTTTTCAT+TGG + chr1.1:62631477-62631496 None:intergenic 25.0%
AATATAGTAGGAGATACCAT+GGG - chr1.1:62631932-62631951 MS.gene005340:intron 30.0%
ATGAAACAAGAGCAAAGTTA+AGG + chr1.1:62631355-62631374 None:intergenic 30.0%
GTTGAATCCATATTTGTAGT+TGG - chr1.1:62631422-62631441 MS.gene005340:CDS 30.0%
TCAGTAAATGAACAACTATC+GGG + chr1.1:62631852-62631871 None:intergenic 30.0%
TGAATCCATATTTGTAGTTG+GGG - chr1.1:62631424-62631443 MS.gene005340:CDS 30.0%
TTATGTGTAGGGAATATAGT+AGG - chr1.1:62631920-62631939 MS.gene005340:intron 30.0%
! ATTTAGGGATTTTGTCGTTA+TGG - chr1.1:62631753-62631772 MS.gene005340:intron 30.0%
AGCAAAGTTAAGGATTGTTC+GGG + chr1.1:62631345-62631364 None:intergenic 35.0%
ATGTGAGCGTAGAAAGAAAT+TGG + chr1.1:62631253-62631272 None:intergenic 35.0%
GAATATAGTAGGAGATACCA+TGG - chr1.1:62631931-62631950 MS.gene005340:intron 35.0%
GAGCAAAGTTAAGGATTGTT+CGG + chr1.1:62631346-62631365 None:intergenic 35.0%
TACAAGTCGTTTGTAATTGG+CGG - chr1.1:62631284-62631303 MS.gene005340:CDS 35.0%
TCGTACAAGTCGTTTGTAAT+TGG - chr1.1:62631281-62631300 MS.gene005340:CDS 35.0%
TTCTTTCTACGCTCACATTA+AGG - chr1.1:62631255-62631274 MS.gene005340:CDS 35.0%
CAACCAATAACAAGAATGCC+AGG - chr1.1:62631819-62631838 MS.gene005340:CDS 40.0%
TGTTGCTGCTGTTGTGTATT+GGG + chr1.1:62631801-62631820 None:intergenic 40.0%
TTCAAGATACACCCTTAGAC+CGG - chr1.1:62631514-62631533 MS.gene005340:CDS 40.0%
TTGTTGCTGCTGTTGTGTAT+TGG + chr1.1:62631802-62631821 None:intergenic 40.0%
! CTCTTGTTTCATGTTCACGT+GGG - chr1.1:62631363-62631382 MS.gene005340:intron 40.0%
! GGCTTGTTTGTGTTGAATAC+CGG + chr1.1:62631553-62631572 None:intergenic 40.0%
! TCACCTGGCATTCTTGTTAT+TGG + chr1.1:62631825-62631844 None:intergenic 40.0%
! TGGAATAGAGTTCTGGTGTT+CGG + chr1.1:62631604-62631623 None:intergenic 40.0%
AACCTCTGTTCTAGTAGGTC+CGG - chr1.1:62631143-62631162 MS.gene005340:intron 45.0%
ACAAACAAGCCAAAGCTCGT+TGG - chr1.1:62631562-62631581 MS.gene005340:CDS 45.0%
AGGCAGGCATACAAGGAAAA+TGG + chr1.1:62631082-62631101 None:intergenic 45.0%
CAGAGGTTGTCGAAGCAAAA+CGG + chr1.1:62631131-62631150 None:intergenic 45.0%
CATATTTGTAGTTGGGGCGT+GGG - chr1.1:62631430-62631449 MS.gene005340:CDS 45.0%
GGCAGGCATACAAGGAAAAT+GGG + chr1.1:62631081-62631100 None:intergenic 45.0%
GTTGTCGAAGCAAAACGGAA+GGG + chr1.1:62631126-62631145 None:intergenic 45.0%
TCAGACTCAGACACAACACA+AGG + chr1.1:62631102-62631121 None:intergenic 45.0%
TCGACAACCTCTGTTCTAGT+AGG - chr1.1:62631138-62631157 MS.gene005340:intron 45.0%
TTGCAACTTCAAGCTTCGTG+CGG + chr1.1:62631315-62631334 None:intergenic 45.0%
TTGTCGAAGCAAAACGGAAG+GGG + chr1.1:62631125-62631144 None:intergenic 45.0%
! AAGGGTTGATTAGATGGTGG+TGG + chr1.1:62631624-62631643 None:intergenic 45.0%
! ACGCAGAAGGGTTGATTAGA+TGG + chr1.1:62631630-62631649 None:intergenic 45.0%
! ATAGTACCGTGTTGACGAAG+TGG + chr1.1:62631653-62631672 None:intergenic 45.0%
! CAGAAGGGTTGATTAGATGG+TGG + chr1.1:62631627-62631646 None:intergenic 45.0%
! GCTCTTGTTTCATGTTCACG+TGG - chr1.1:62631362-62631381 MS.gene005340:intron 45.0%
! GGAATAGAGTTCTGGTGTTC+GGG + chr1.1:62631603-62631622 None:intergenic 45.0%
!! ATGGTGGTGGAATAGAGTTC+TGG + chr1.1:62631611-62631630 None:intergenic 45.0%
!! GATACCATGGGAGTGTCATT+CGG - chr1.1:62631944-62631963 MS.gene005340:intron 45.0%
AACCTCCCATTTCTCGACTG+GGG - chr1.1:62632013-62632032 MS.gene005340:intron 50.0%
AATGGAAGTGGCAGGCAGAA+CGG + chr1.1:62631194-62631213 None:intergenic 50.0%
ACTCAGACACAACACAAGGC+AGG + chr1.1:62631098-62631117 None:intergenic 50.0%
ATTGCCGAATGACACTCCCA+TGG + chr1.1:62631951-62631970 None:intergenic 50.0%
CAACACAAGGCAGGCATACA+AGG + chr1.1:62631089-62631108 None:intergenic 50.0%
CAACCTCCCATTTCTCGACT+GGG - chr1.1:62632012-62632031 MS.gene005340:intron 50.0%
CCACGCCCCAACTACAAATA+TGG + chr1.1:62631432-62631451 None:intergenic 50.0%
CCATATTTGTAGTTGGGGCG+TGG - chr1.1:62631429-62631448 MS.gene005340:CDS 50.0%
GGAATCGTACCAACGAGCTT+TGG + chr1.1:62631574-62631593 None:intergenic 50.0%
GGTTGTCGAAGCAAAACGGA+AGG + chr1.1:62631127-62631146 None:intergenic 50.0%
TCGCATAGAATGGAAGTGGC+AGG + chr1.1:62631202-62631221 None:intergenic 50.0%
TGTGTTGAATACCGGCAGAG+TGG + chr1.1:62631545-62631564 None:intergenic 50.0%
TTGACGAAGTGGACGCAGAA+GGG + chr1.1:62631642-62631661 None:intergenic 50.0%
! GTTCTGGTGTTCGGGTTTGA+AGG + chr1.1:62631595-62631614 None:intergenic 50.0%
AGAGTGGCGTTTCCGGTCTA+AGG + chr1.1:62631529-62631548 None:intergenic 55.0%
ATCCCCAGTCGAGAAATGGG+AGG + chr1.1:62632018-62632037 None:intergenic 55.0%
CAACTTCAAGCTTCGTGCGG+TGG + chr1.1:62631312-62631331 None:intergenic 55.0%
CCAACCTCCCATTTCTCGAC+TGG - chr1.1:62632011-62632030 MS.gene005340:intron 55.0%
CCAGTCGAGAAATGGGAGGT+TGG + chr1.1:62632014-62632033 None:intergenic 55.0%
CTGCGTCCACTTCGTCAACA+CGG - chr1.1:62631644-62631663 MS.gene005340:intron 55.0%
GAGTGGCGTTTCCGGTCTAA+GGG + chr1.1:62631528-62631547 None:intergenic 55.0%
GGCGTCGCATAGAATGGAAG+TGG + chr1.1:62631206-62631225 None:intergenic 55.0%
GTTGACGAAGTGGACGCAGA+AGG + chr1.1:62631643-62631662 None:intergenic 55.0%
! AGGTTGGAGTATCCACCCTC+AGG + chr1.1:62631998-62632017 None:intergenic 55.0%
! TTGGAGTATCCACCCTCAGG+TGG + chr1.1:62631995-62632014 None:intergenic 55.0%
!! AACGGAGGCGTCGCATAGAA+TGG + chr1.1:62631212-62631231 None:intergenic 55.0%
CAACTATCGGGTCGCTCACC+TGG + chr1.1:62631840-62631859 None:intergenic 60.0%
CGCCGGACCTACTAGAACAG+AGG + chr1.1:62631148-62631167 None:intergenic 60.0%
GAGTATCCACCCTCAGGTGG+AGG + chr1.1:62631992-62632011 None:intergenic 60.0%
TACAGCGTCGTCGCGCAGAA+CGG + chr1.1:62631230-62631249 None:intergenic 60.0%
TACCGGCAGAGTGGCGTTTC+CGG + chr1.1:62631536-62631555 None:intergenic 60.0%
TCACTGCAGCCTCCACCTGA+GGG - chr1.1:62631980-62631999 MS.gene005340:intron 60.0%
TCAGGTGGAGGCTGCAGTGA+CGG + chr1.1:62631980-62631999 None:intergenic 60.0%
TTGTAGTTGGGGCGTGGGTG+TGG - chr1.1:62631435-62631454 MS.gene005340:CDS 60.0%
AACGGCGGCGTCCTGGAGAA+CGG + chr1.1:62631176-62631195 None:intergenic 65.0%
GACCGGAAACGCCACTCTGC+CGG - chr1.1:62631531-62631550 MS.gene005340:CDS 65.0%
GGAAGTGGCAGGCAGAACGG+CGG + chr1.1:62631191-62631210 None:intergenic 65.0%
GTCACTGCAGCCTCCACCTG+AGG - chr1.1:62631979-62631998 MS.gene005340:intron 65.0%
AGCGTCGTCGCGCAGAACGG+AGG + chr1.1:62631227-62631246 None:intergenic 70.0%
CTGCAGCCTCCACCTGAGGG+TGG - chr1.1:62631983-62632002 MS.gene005340:intron 70.0%
GGCGTGGGTGTGGTGAGGAG+GGG - chr1.1:62631445-62631464 MS.gene005340:CDS 70.0%
GGGCGTGGGTGTGGTGAGGA+GGG - chr1.1:62631444-62631463 MS.gene005340:CDS 70.0%
GGTGGAGGCTGCAGTGACGG+AGG + chr1.1:62631977-62631996 None:intergenic 70.0%
GTTGGGGCGTGGGTGTGGTG+AGG - chr1.1:62631440-62631459 MS.gene005340:CDS 70.0%
!! CCTGGAGAACGGTGTCGCGC+CGG + chr1.1:62631165-62631184 None:intergenic 70.0%
CAGGCAGAACGGCGGCGTCC+TGG + chr1.1:62631183-62631202 None:intergenic 75.0%
CCGGCGCGACACCGTTCTCC+AGG - chr1.1:62631162-62631181 MS.gene005340:intron 75.0%
GGGGCGTGGGTGTGGTGAGG+AGG - chr1.1:62631443-62631462 MS.gene005340:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 62631033 62632039 62631033 ID=MS.gene005340
chr1.1 mRNA 62631033 62632039 62631033 ID=MS.gene005340.t1;Parent=MS.gene005340
chr1.1 exon 62632031 62632039 62632031 ID=MS.gene005340.t1.exon1;Parent=MS.gene005340.t1
chr1.1 CDS 62632031 62632039 62632031 ID=cds.MS.gene005340.t1;Parent=MS.gene005340.t1
chr1.1 exon 62631796 62631912 62631796 ID=MS.gene005340.t1.exon2;Parent=MS.gene005340.t1
chr1.1 CDS 62631796 62631912 62631796 ID=cds.MS.gene005340.t1;Parent=MS.gene005340.t1
chr1.1 exon 62631407 62631631 62631407 ID=MS.gene005340.t1.exon3;Parent=MS.gene005340.t1
chr1.1 CDS 62631407 62631631 62631407 ID=cds.MS.gene005340.t1;Parent=MS.gene005340.t1
chr1.1 exon 62631232 62631313 62631232 ID=MS.gene005340.t1.exon4;Parent=MS.gene005340.t1
chr1.1 CDS 62631232 62631313 62631232 ID=cds.MS.gene005340.t1;Parent=MS.gene005340.t1
chr1.1 exon 62631033 62631142 62631033 ID=MS.gene005340.t1.exon5;Parent=MS.gene005340.t1
chr1.1 CDS 62631033 62631142 62631033 ID=cds.MS.gene005340.t1;Parent=MS.gene005340.t1
Gene Sequence

>MS.gene005340

ATGCATGATGTAGTTTAGCCTTTGTTTTATGATCGAAAGTTGAAACCCATTTTCCTTGTATGCCTGCCTTGTGTTGTGTCTGAGTCTGACCCCTTCCGTTTTGCTTCGACAACCTCTGTTCTAGTAGGTCCGGCGCGACACCGTTCTCCAGGACGCCGCCGTTCTGCCTGCCACTTCCATTCTATGCGACGCCTCCGTTCTGCGCGACGACGCTGTACCAATTTCTTTCTACGCTCACATTAAGGTAATCGTACAAGTCGTTTGTAATTGGCGGTGCCACCGCACGAAGCTTGAAGTTGCAATCTTTGTCCCGAACAATCCTTAACTTTGCTCTTGTTTCATGTTCACGTGGGTTCTTTCATTTTTGTTTCTTATGCAGATTATATATTGTTGAATCCATATTTGTAGTTGGGGCGTGGGTGTGGTGAGGAGGGGAAAATGCCAATGAAAAAGTACTATTGTGAGTATTGCGATAAGCAATTTCAAGATACACCCTTAGACCGGAAACGCCACTCTGCCGGTATTCAACACAAACAAGCCAAAGCTCGTTGGTACGATTCCTTCAAACCCGAACACCAGAACTCTATTCCACCACCATCTAATCAACCCTTCTGCGTCCACTTCGTCAACACGGTACTATCAATTTATATTTAAATTTATTTGCATCCTCATTAATTATCATTTCTTAGTGCTCTATAAGTCGATTAACTCTCTCTGTATATTTAGGGATTTTGTCGTTATGGCGATTCTTGCAAATATTTTCATCCCAATACACAACAGCAGCAACAACCAATAACAAGAATGCCAGGTGAGCGACCCGATAGTTGTTCATTTACTGATTTATAGTTTCTTTCTTTATGGTGTTGAATTCATGATTGATATTAATGTTATGTGTAGGGAATATAGTAGGAGATACCATGGGAGTGTCATTCGGCAATTTGCCTCCGTCACTGCAGCCTCCACCTGAGGGTGGATACTCCAACCTCCCATTTCTCGACTGGGGATAG
Protein sequence

>MS.gene005340.t1

MHDVRRDTVLQDAAVLPATSILCDASVLRDDAVPISFYAHIKLGRGCGEEGKMPMKKYYCEYCDKQFQDTPLDRKRHSAGIQHKQAKARWYDSFKPEHQNSIPPPSNQPFCVHFVNTGFCRYGDSCKYFHPNTQQQQQPITRMPGNIVGDTMGVSFGNLPPSLQPPPEGGYSNLPFLDWG