AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09749

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 56 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGAATAATTGATTGGTCTT+TGG 0.254387 5.4:+6651605 None:intergenic
GGAAATGGACGTGGGTGATT+TGG 0.317565 5.4:+6650832 None:intergenic
ATTGGCACTTGCAAAACAAT+TGG 0.337338 5.4:-6651451 MS.gene09749:CDS
GCCCATGGTCCCACAGGAAA+TGG 0.346020 5.4:+6650817 None:intergenic
GTGCTAGACAAGTTGAAGTT+TGG 0.390504 5.4:-6651422 MS.gene09749:CDS
AAGAAGACGCTGAAACTTCA+AGG 0.402562 5.4:-6651644 MS.gene09749:CDS
TCTCTTCTAGAATAATTGAT+TGG 0.421188 5.4:+6651598 None:intergenic
GATGTGAATCGGTTACCTTC+TGG 0.421492 5.4:-6651804 MS.gene09749:CDS
TTTACATGCAGATCGGGATT+CGG 0.433835 5.4:-6651871 None:intergenic
ACACTTGAAACGGTGCTGTT+TGG 0.443597 5.4:+6651747 None:intergenic
TTGGCACTTGCAAAACAATT+GGG 0.452760 5.4:-6651450 MS.gene09749:CDS
GGGCACATGGTAAGAGTTGT+TGG 0.457834 5.4:+6650922 None:intergenic
GTCCATTTCCTGTGGGACCA+TGG 0.458770 5.4:-6650819 MS.gene09749:CDS
TGAAAATAGACGGTTACAAA+AGG 0.474850 5.4:-6651004 MS.gene09749:CDS
TTTACCACTCACACTTGAAA+CGG 0.484021 5.4:+6651737 None:intergenic
TCCATTTCCTGTGGGACCAT+GGG 0.490692 5.4:-6650818 MS.gene09749:CDS
AGAAGCGAAAGAGAAGTTAC+AGG 0.494456 5.4:-6651714 MS.gene09749:CDS
GCAGCATCAACGGCAGATGA+TGG 0.502736 5.4:+6650877 None:intergenic
ATCCGTACAAGTTAAGATCT+AGG 0.515404 5.4:+6650751 None:intergenic
TCATTTGCATGTAGAATTGT+GGG 0.520585 5.4:+6650950 None:intergenic
GTCATTTGCATGTAGAATTG+TGG 0.521859 5.4:+6650949 None:intergenic
TCGATTCCTCGGAGAAGTAA+AGG 0.525636 5.4:+6651825 None:intergenic
TCCGAGGAATCGATGTGAAT+CGG 0.527394 5.4:-6651815 MS.gene09749:CDS
GCTGTGGCCCATGGTCCCAC+AGG 0.538822 5.4:+6650811 None:intergenic
TCAAAGGTCCTATGTTGGAT+AGG 0.542840 5.4:+6650784 None:intergenic
ACGACGCGTGGCAGCATCAA+CGG 0.548952 5.4:+6650867 None:intergenic
ATGGAAAGAGATTGTTCAAG+AGG 0.550270 5.4:-6651678 MS.gene09749:CDS
TGCCACGCGTCGTCATCCTA+TGG 0.554799 5.4:-6650857 MS.gene09749:CDS
ACCGATTCACATCGATTCCT+CGG 0.556594 5.4:+6651814 None:intergenic
CGTGGGTGATTTGGAGCCAT+AGG 0.560215 5.4:+6650841 None:intergenic
CACATGGTAAGAGTTGTTGG+TGG 0.564954 5.4:+6650925 None:intergenic
ATAGGAGCAGCTGTGGCCCA+TGG 0.566808 5.4:+6650802 None:intergenic
GGTCCCACAGGAAATGGACG+TGG 0.582860 5.4:+6650823 None:intergenic
GGTTTCAAAATCGTAGAGCA+AGG 0.583437 5.4:-6651401 MS.gene09749:intron
ACAGCAACACGCTCACAAGA+GGG 0.586849 5.4:+6650901 None:intergenic
ATGTTGGATAGGAGCAGCTG+TGG 0.588541 5.4:+6650795 None:intergenic
CAGCTGCTCCTATCCAACAT+AGG 0.588914 5.4:-6650792 MS.gene09749:CDS
GTGTATCAAAGGTCCTATGT+TGG 0.591308 5.4:+6650779 None:intergenic
CACCCACGTCCATTTCCTGT+GGG 0.600865 5.4:-6650826 MS.gene09749:CDS
AACAGCAACACGCTCACAAG+AGG 0.612400 5.4:+6650900 None:intergenic
ATCTAACGGATGAAAATAGA+CGG 0.614300 5.4:-6651014 MS.gene09749:CDS
TCACCCACGTCCATTTCCTG+TGG 0.615645 5.4:-6650827 MS.gene09749:CDS
TCTAGGACGGAGTGTATCAA+AGG 0.615968 5.4:+6650768 None:intergenic
TCTTCACAATCAGCACCAGA+AGG 0.621185 5.4:+6651789 None:intergenic
ACGCTCACAAGAGGGGCACA+TGG 0.624285 5.4:+6650909 None:intergenic
GCTGATTGTGAAGAAGAAGC+AGG 0.645646 5.4:-6651780 MS.gene09749:CDS
GTACAAGTTAAGATCTAGGA+CGG 0.655097 5.4:+6650755 None:intergenic
AGCCATAGGATGACGACGCG+TGG 0.657092 5.4:+6650855 None:intergenic
TACAGGTGAAGATCTTGACA+TGG 0.657130 5.4:-6651697 MS.gene09749:CDS
CAGCAACACGCTCACAAGAG+GGG 0.670133 5.4:+6650902 None:intergenic
AGCACCGTTTCAAGTGTGAG+TGG 0.674395 5.4:-6651741 MS.gene09749:CDS
AGACATGCAGAATCGAAGAA+CGG 0.674956 5.4:-6651848 MS.gene09749:CDS
GAACGGCCTTTACTTCTCCG+AGG 0.691005 5.4:-6651831 MS.gene09749:CDS
GTCCCACAGGAAATGGACGT+GGG 0.703771 5.4:+6650824 None:intergenic
CATTTGCATGTAGAATTGTG+GGG 0.706166 5.4:+6650951 None:intergenic
AAGATGCTGTGAGAATCTAA+CGG 0.718794 5.4:-6651028 MS.gene09749:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAATTATATTTTTTTTT+AGG - chr5.4:6651106-6651125 MS.gene09749:intron 0.0%
!! CAATATTTATTTATTTATGT+TGG - chr5.4:6651508-6651527 MS.gene09749:intron 10.0%
!!! TTATCAATATTTTTTTTTGA+AGG - chr5.4:6651479-6651498 MS.gene09749:intron 10.0%
!! TTACACTTAATTAATACTTA+CGG + chr5.4:6651077-6651096 None:intergenic 15.0%
!! TACACTTAATTAATACTTAC+GGG + chr5.4:6651076-6651095 None:intergenic 20.0%
!! TTGTTTGTAGAAACAAAAAT+TGG - chr5.4:6651153-6651172 MS.gene09749:intron 20.0%
! ACACTTAATTAATACTTACG+GGG + chr5.4:6651075-6651094 None:intergenic 25.0%
! TTAAAACTCAAAGAGATATC+CGG - chr5.4:6651282-6651301 MS.gene09749:intron 25.0%
!! GTTTGTTAAATTGTGATTTC+AGG - chr5.4:6651530-6651549 MS.gene09749:intron 25.0%
!!! TAGAATAATTGATTGGTCTT+TGG + chr5.4:6651020-6651039 None:intergenic 25.0%
!!! TCTCTTCTAGAATAATTGAT+TGG + chr5.4:6651027-6651046 None:intergenic 25.0%
!!! TTGACTAGTCTTTATTTAGT+TGG - chr5.4:6651253-6651272 MS.gene09749:intron 25.0%
TCATTTGCATGTAGAATTGT+GGG + chr5.4:6651675-6651694 None:intergenic 30.0%
TGAAAATAGACGGTTACAAA+AGG - chr5.4:6651618-6651637 MS.gene09749:CDS 30.0%
! ATCTAACGGATGAAAATAGA+CGG - chr5.4:6651608-6651627 MS.gene09749:CDS 30.0%
AAGATGCTGTGAGAATCTAA+CGG - chr5.4:6651594-6651613 MS.gene09749:CDS 35.0%
ATGGAAAGAGATTGTTCAAG+AGG - chr5.4:6650944-6650963 MS.gene09749:CDS 35.0%
ATTGGCACTTGCAAAACAAT+TGG - chr5.4:6651171-6651190 MS.gene09749:intron 35.0%
CATTTGCATGTAGAATTGTG+GGG + chr5.4:6651674-6651693 None:intergenic 35.0%
GTCATTTGCATGTAGAATTG+TGG + chr5.4:6651676-6651695 None:intergenic 35.0%
TTGGCACTTGCAAAACAATT+GGG - chr5.4:6651172-6651191 MS.gene09749:intron 35.0%
TTTACCACTCACACTTGAAA+CGG + chr5.4:6650888-6650907 None:intergenic 35.0%
TTTCATGTTTGGTATCACGT+TGG - chr5.4:6651404-6651423 MS.gene09749:CDS 35.0%
! GAGATGCATGTTTTCATGTT+TGG - chr5.4:6651393-6651412 MS.gene09749:intron 35.0%
AAGAAGACGCTGAAACTTCA+AGG - chr5.4:6650978-6650997 MS.gene09749:CDS 40.0%
AGAAGCGAAAGAGAAGTTAC+AGG - chr5.4:6650908-6650927 MS.gene09749:CDS 40.0%
AGACATGCAGAATCGAAGAA+CGG - chr5.4:6650774-6650793 MS.gene09749:CDS 40.0%
GGTTTCAAAATCGTAGAGCA+AGG - chr5.4:6651221-6651240 MS.gene09749:intron 40.0%
GTGTATCAAAGGTCCTATGT+TGG + chr5.4:6651846-6651865 None:intergenic 40.0%
TACAGGTGAAGATCTTGACA+TGG - chr5.4:6650925-6650944 MS.gene09749:CDS 40.0%
TCAAAGGTCCTATGTTGGAT+AGG + chr5.4:6651841-6651860 None:intergenic 40.0%
! GTGCTAGACAAGTTGAAGTT+TGG - chr5.4:6651200-6651219 MS.gene09749:intron 40.0%
CACATGGTAAGAGTTGTTGG+TGG + chr5.4:6651700-6651719 None:intergenic 45.0%
GATGTGAATCGGTTACCTTC+TGG - chr5.4:6650818-6650837 MS.gene09749:CDS 45.0%
GCTGATTGTGAAGAAGAAGC+AGG - chr5.4:6650842-6650861 MS.gene09749:CDS 45.0%
TCCGAGGAATCGATGTGAAT+CGG - chr5.4:6650807-6650826 MS.gene09749:CDS 45.0%
TCGATTCCTCGGAGAAGTAA+AGG + chr5.4:6650800-6650819 None:intergenic 45.0%
TCTTCACAATCAGCACCAGA+AGG + chr5.4:6650836-6650855 None:intergenic 45.0%
! TCTAGGACGGAGTGTATCAA+AGG + chr5.4:6651857-6651876 None:intergenic 45.0%
!! ACACTTGAAACGGTGCTGTT+TGG + chr5.4:6650878-6650897 None:intergenic 45.0%
!! ACCGATTCACATCGATTCCT+CGG + chr5.4:6650811-6650830 None:intergenic 45.0%
AACAGCAACACGCTCACAAG+AGG + chr5.4:6651725-6651744 None:intergenic 50.0%
ACAGCAACACGCTCACAAGA+GGG + chr5.4:6651724-6651743 None:intergenic 50.0%
AGAGATATCCGGTGCATGTC+TGG - chr5.4:6651293-6651312 MS.gene09749:intron 50.0%
ATGTTGGATAGGAGCAGCTG+TGG + chr5.4:6651830-6651849 None:intergenic 50.0%
CAGCTGCTCCTATCCAACAT+AGG - chr5.4:6651830-6651849 MS.gene09749:CDS 50.0%
CTGTGATACCAGACATGCAC+CGG + chr5.4:6651304-6651323 None:intergenic 50.0%
GGAAATGGACGTGGGTGATT+TGG + chr5.4:6651793-6651812 None:intergenic 50.0%
GGGCACATGGTAAGAGTTGT+TGG + chr5.4:6651703-6651722 None:intergenic 50.0%
TCCATTTCCTGTGGGACCAT+GGG - chr5.4:6651804-6651823 MS.gene09749:CDS 50.0%
! AGCACCGTTTCAAGTGTGAG+TGG - chr5.4:6650881-6650900 MS.gene09749:CDS 50.0%
CACCCACGTCCATTTCCTGT+GGG - chr5.4:6651796-6651815 MS.gene09749:CDS 55.0%
CAGCAACACGCTCACAAGAG+GGG + chr5.4:6651723-6651742 None:intergenic 55.0%
GAACGGCCTTTACTTCTCCG+AGG - chr5.4:6650791-6650810 MS.gene09749:CDS 55.0%
GCAGCATCAACGGCAGATGA+TGG + chr5.4:6651748-6651767 None:intergenic 55.0%
GTCCATTTCCTGTGGGACCA+TGG - chr5.4:6651803-6651822 MS.gene09749:CDS 55.0%
GTCCCACAGGAAATGGACGT+GGG + chr5.4:6651801-6651820 None:intergenic 55.0%
TCACCCACGTCCATTTCCTG+TGG - chr5.4:6651795-6651814 MS.gene09749:CDS 55.0%
! CGTGGGTGATTTGGAGCCAT+AGG + chr5.4:6651784-6651803 None:intergenic 55.0%
ACGACGCGTGGCAGCATCAA+CGG + chr5.4:6651758-6651777 None:intergenic 60.0%
AGCCATAGGATGACGACGCG+TGG + chr5.4:6651770-6651789 None:intergenic 60.0%
ATAGGAGCAGCTGTGGCCCA+TGG + chr5.4:6651823-6651842 None:intergenic 60.0%
GCCCATGGTCCCACAGGAAA+TGG + chr5.4:6651808-6651827 None:intergenic 60.0%
GGTCCCACAGGAAATGGACG+TGG + chr5.4:6651802-6651821 None:intergenic 60.0%
TGCCACGCGTCGTCATCCTA+TGG - chr5.4:6651765-6651784 MS.gene09749:CDS 60.0%
! ACGCTCACAAGAGGGGCACA+TGG + chr5.4:6651716-6651735 None:intergenic 60.0%
GCTGTGGCCCATGGTCCCAC+AGG + chr5.4:6651814-6651833 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 6650762 6651882 6650762 ID=MS.gene09749
chr5.4 mRNA 6650762 6651882 6650762 ID=MS.gene09749.t1;Parent=MS.gene09749
chr5.4 exon 6651569 6651882 6651569 ID=MS.gene09749.t1.exon1;Parent=MS.gene09749.t1
chr5.4 CDS 6651569 6651882 6651569 ID=cds.MS.gene09749.t1;Parent=MS.gene09749.t1
chr5.4 exon 6651402 6651481 6651402 ID=MS.gene09749.t1.exon2;Parent=MS.gene09749.t1
chr5.4 CDS 6651402 6651481 6651402 ID=cds.MS.gene09749.t1;Parent=MS.gene09749.t1
chr5.4 exon 6650762 6651092 6650762 ID=MS.gene09749.t1.exon3;Parent=MS.gene09749.t1
chr5.4 CDS 6650762 6651092 6650762 ID=cds.MS.gene09749.t1;Parent=MS.gene09749.t1
Gene Sequence

>MS.gene09749

ATCGGGATTCGGAGACATGCAGAATCGAAGAACGGCCTTTACTTCTCCGAGGAATCGATGTGAATCGGTTACCTTCTGGTGCTGATTGTGAAGAAGAAGCAGGAGTTTCATCACCAAACAGCACCGTTTCAAGTGTGAGTGGTAAAAGAAGCGAAAGAGAAGTTACAGGTGAAGATCTTGACATGGAAAGAGATTGTTCAAGAGGAATCAGTGATGAAGAAGACGCTGAAACTTCAAGGAAAAAACTTAGACTCACCAAAGACCAATCAATTATTCTAGAAGAGAGTTTCAAAGAACACAACACTCTTAACCCCGTAAGTATTAATTAAGTGTAATTAAGCTCTTTTAAATTATATTTTTTTTTAGGTGATTAACTTTTTTTTGATTTGTTTTGTTTGTAGAAACAAAAATTGGCACTTGCAAAACAATTGGGACTTCGTGCTAGACAAGTTGAAGTTTGGTTTCAAAATCGTAGAGCAAGGTTTGTTCATTTGACTAGTCTTTATTTAGTTGGCAATATTTAAAACTCAAAGAGATATCCGGTGCATGTCTGGTATCACAGTTGATTTGTCAAAATCACTATGATCTAATGATATTCACTGTGATTTCGACAAATTCATCGCACACATACGAGATGCATGTTTTCATGTTTGGTATCACGTTGGATTTGACTAAGATCTGTTAACTTAAATTGATTTTTAAAAACATAAGTGTCATTTATCAATATTTTTTTTTGAAGGATTTATCAATATTTATTTATTTATGTTGGTTTGTTAAATTGTGATTTCAGGACTAAGTTGAAGCAAACAGAAGTAGATTGTGAGTTTTTGAAAAGATGCTGTGAGAATCTAACGGATGAAAATAGACGGTTACAAAAGGAAGTGCAAGAGTTAAGAGCATTGAAACTTTCCCCACAATTCTACATGCAAATGACACCACCAACAACTCTTACCATGTGCCCCTCTTGTGAGCGTGTTGCTGTTCCATCATCTGCCGTTGATGCTGCCACGCGTCGTCATCCTATGGCTCCAAATCACCCACGTCCATTTCCTGTGGGACCATGGGCCACAGCTGCTCCTATCCAACATAGGACCTTTGATACACTCCGTCCTAGATCTTAA
Protein sequence

>MS.gene09749.t1

IGIRRHAESKNGLYFSEESMUIGYLLVLIVKKKQEFHHQTAPFQVUVVKEAKEKLQVKILTWKEIVQEESVMKKTLKLQGKNLDSPKTNQLFUKRVSKNTTLLTPNKNWHLQNNWDFVLDKLKFGFKIVEQGLSUSKQKUIVSFUKDAVRIURMKIDGYKRKCKSUEHUNFPHNSTCKUHHQQLLPCAPLVSVLLFHHLPLMLPRVVILWLQITHVHFLWDHGPQLLLSNIGPLIHSVLDL