AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54040


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 40 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTATATTGCTACGTTTATC+TGG 0.121333 1.1:+11907151 None:intergenic
CTTGAAGAAATCAATAATTT+TGG 0.167292 1.1:+11909133 None:intergenic
AATATAGCACGTTTCATTAA+TGG 0.211173 1.1:-11907136 MS.gene54040:CDS
GCATCCCTTGGCGCCATTCC+AGG 0.276840 1.1:+11908358 None:intergenic
CTCCTCTTCAAATCATCATT+TGG 0.347535 1.1:+11908457 None:intergenic
GAGAAAGCGGAGTAGTAGTT+TGG 0.397233 1.1:-11908518 MS.gene54040:CDS
GTTGTTTATGATCCTGTAGA+AGG 0.406850 1.1:-11907416 MS.gene54040:CDS
ACGTTCAAGAACAGGAGAAT+TGG 0.452094 1.1:+11908336 None:intergenic
ATTCCTCCACGTTCAAGAAC+AGG 0.452190 1.1:+11908328 None:intergenic
AAAGCGGAGTAGTAGTTTGG+TGG 0.462327 1.1:-11908515 MS.gene54040:CDS
CGCGTTGACTGCTACTAAAA+CGG 0.476912 1.1:-11908407 MS.gene54040:CDS
CTATATTGCTACGTTTATCT+GGG 0.481139 1.1:+11907152 None:intergenic
ACAATAATAACAGAATATGT+TGG 0.490743 1.1:-11907271 MS.gene54040:CDS
TAACTTGTGCAGAAGTATGA+TGG 0.493269 1.1:-11907465 MS.gene54040:CDS
TTCTAATCCTTCACAGTCAC+TGG 0.505311 1.1:-11907182 MS.gene54040:CDS
GCATCTAAGATTCTGAATCA+TGG 0.512650 1.1:-11909092 MS.gene54040:intron
ATAAGTACTTACCCTTCTAC+AGG 0.515050 1.1:+11907404 None:intergenic
ATTAGAACAGATGGCGTCGT+TGG 0.518768 1.1:-11908434 MS.gene54040:CDS
ATTCAAAGAAGAAGAGAAAG+CGG 0.540362 1.1:-11908531 MS.gene54040:CDS
ACAGGAGAATTGGCATCCCT+TGG 0.541184 1.1:+11908346 None:intergenic
TCTTGAACGTGGAGGAATGC+AGG 0.541405 1.1:-11908323 MS.gene54040:intron
AAGAATCGGGAATATGATGA+TGG 0.544853 1.1:-11907232 MS.gene54040:CDS
AGGAGAATGTCCGCCCCTCA+TGG 0.545962 1.1:-11907438 MS.gene54040:CDS
TGCAGAAGTATGATGGAAAG+AGG 0.546783 1.1:-11907458 MS.gene54040:CDS
AATGAGCTTACATACATGCC+TGG 0.552496 1.1:-11908376 MS.gene54040:CDS
CATGCCTGGAATGGCGCCAA+GGG 0.555292 1.1:-11908362 MS.gene54040:CDS
AATTCTCCTGTTCTTGAACG+TGG 0.561001 1.1:-11908334 MS.gene54040:CDS
ACATGCCTGGAATGGCGCCA+AGG 0.581749 1.1:-11908363 MS.gene54040:CDS
GCTTACATACATGCCTGGAA+TGG 0.584838 1.1:-11908371 MS.gene54040:CDS
CAGAATCTTAGATGCATCAA+CGG 0.589395 1.1:+11909100 None:intergenic
TGCCAAATGATGATTTGAAG+AGG 0.592036 1.1:-11908459 MS.gene54040:CDS
GAAGAGGAGATTAGAACAGA+TGG 0.593117 1.1:-11908443 MS.gene54040:CDS
TTGTTTATGATCCTGTAGAA+GGG 0.614616 1.1:-11907415 MS.gene54040:intron
TCTGCACAAGTTAAGAGTCT+CGG 0.617054 1.1:+11907475 None:intergenic
TCTCCTGTTCTTGAACGTGG+AGG 0.653986 1.1:-11908331 MS.gene54040:CDS
GGATCATAAACAACCATGAG+GGG 0.675550 1.1:+11907425 None:intergenic
AGGATCATAAACAACCATGA+GGG 0.678750 1.1:+11907424 None:intergenic
TCATAAACAACCATGAGGGG+CGG 0.687468 1.1:+11907428 None:intergenic
CAGGATCATAAACAACCATG+AGG 0.703912 1.1:+11907423 None:intergenic
CAGATGACCAGTGACTGTGA+AGG 0.718767 1.1:+11907175 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAATTTTCTTTTTTTTGT+AGG - chr1.1:11908939-11908958 MS.gene54040:intron 10.0%
!! AAAAAAGAAAATTAAAAGTC+AGG + chr1.1:11908935-11908954 None:intergenic 15.0%
!!! TATTATTGTCAAATCTTTTA+TGG + chr1.1:11908987-11909006 None:intergenic 15.0%
!! ACAATAATAACAGAATATGT+TGG - chr1.1:11908998-11909017 MS.gene54040:intron 20.0%
!! TAATGTTTAGAGAATTTGAT+TGG - chr1.1:11907239-11907258 MS.gene54040:CDS 20.0%
!! TTAATTGAAAAATTCTACTG+TGG - chr1.1:11908099-11908118 MS.gene54040:intron 20.0%
!!! CTTGAAGAAATCAATAATTT+TGG + chr1.1:11907139-11907158 None:intergenic 20.0%
!!! GTTTGTATATATTTTTTCTC+AGG - chr1.1:11908753-11908772 MS.gene54040:intron 20.0%
!!! TTAGGTATTATATTGTTGTT+AGG - chr1.1:11907998-11908017 MS.gene54040:intron 20.0%
! AAAAAAGAAAAGGAAGTTGT+TGG - chr1.1:11907781-11907800 MS.gene54040:intron 25.0%
! AATATAGCACGTTTCATTAA+TGG - chr1.1:11909133-11909152 MS.gene54040:CDS 25.0%
!! ATAACTTTTGTAAGACTGTT+TGG + chr1.1:11907632-11907651 None:intergenic 25.0%
!!! ATAATTTTGGTTTGTACAAG+AGG + chr1.1:11907126-11907145 None:intergenic 25.0%
!!! ATGTAGACTTTTTGAAGAAT+CGG - chr1.1:11909023-11909042 MS.gene54040:intron 25.0%
!!! CTTAATTGAGTTTGTTAGTT+AGG - chr1.1:11907980-11907999 MS.gene54040:intron 25.0%
ATTCAAAGAAGAAGAGAAAG+CGG - chr1.1:11907738-11907757 MS.gene54040:intron 30.0%
CTATATTGCTACGTTTATCT+GGG + chr1.1:11909120-11909139 None:intergenic 30.0%
GTTTAGAGAATTTGATTGGA+TGG - chr1.1:11907243-11907262 MS.gene54040:CDS 30.0%
TGAGACATTGAATTGATTGT+TGG - chr1.1:11908225-11908244 MS.gene54040:intron 30.0%
TGCAATACTGAAGTATAAAG+TGG - chr1.1:11908580-11908599 MS.gene54040:intron 30.0%
TGGTGGTTTCAAAAAAGAAA+AGG - chr1.1:11907771-11907790 MS.gene54040:intron 30.0%
TGTTGAGTTATGTTTGTATG+AGG - chr1.1:11908071-11908090 MS.gene54040:intron 30.0%
TTGTTTATGATCCTGTAGAA+GGG - chr1.1:11908854-11908873 MS.gene54040:intron 30.0%
! ACTTTGTTGCCTTTATTTCT+AGG + chr1.1:11908559-11908578 None:intergenic 30.0%
! TATTGTTGTTAGGATACGTT+TGG - chr1.1:11908008-11908027 MS.gene54040:intron 30.0%
! TCTGTTTTCACAAGCTATTA+TGG - chr1.1:11907410-11907429 MS.gene54040:intron 30.0%
! TTAGGTTGTCAACACTAATT+AGG - chr1.1:11908336-11908355 MS.gene54040:CDS 30.0%
!! AGTTTATACTTTTTGAGAGC+TGG - chr1.1:11908394-11908413 MS.gene54040:CDS 30.0%
!! CTACAAACTAGTTTGGATTT+TGG - chr1.1:11908608-11908627 MS.gene54040:intron 30.0%
!! CTATTTTTCACAACCTATTG+TGG - chr1.1:11907481-11907500 MS.gene54040:CDS 30.0%
!! GAAGTGTGTGTTTTAAATTG+TGG - chr1.1:11907708-11907727 MS.gene54040:intron 30.0%
!! TGTAGACTTTTTGAAGAATC+GGG - chr1.1:11909024-11909043 MS.gene54040:intron 30.0%
!! TTGTTTTGTTGAACTGATAC+TGG - chr1.1:11908313-11908332 MS.gene54040:intron 30.0%
!!! GCTGTTTTTACAAGTTATTG+TGG - chr1.1:11907301-11907320 MS.gene54040:CDS 30.0%
AAGAATCGGGAATATGATGA+TGG - chr1.1:11909037-11909056 MS.gene54040:intron 35.0%
AGGATCATAAACAACCATGA+GGG + chr1.1:11908848-11908867 None:intergenic 35.0%
ATAAGTACTTACCCTTCTAC+AGG + chr1.1:11908868-11908887 None:intergenic 35.0%
CAGAATCTTAGATGCATCAA+CGG + chr1.1:11907172-11907191 None:intergenic 35.0%
CTCCTCTTCAAATCATCATT+TGG + chr1.1:11907815-11907834 None:intergenic 35.0%
CTGCACTATTTGTCATGATT+TGG - chr1.1:11908635-11908654 MS.gene54040:intron 35.0%
GACATTGAATTGATTGTTGG+TGG - chr1.1:11908228-11908247 MS.gene54040:intron 35.0%
GAGAATTTGATTGGATGGAT+TGG - chr1.1:11907248-11907267 MS.gene54040:CDS 35.0%
GCAGTGTTACCTAGAAATAA+AGG - chr1.1:11908547-11908566 MS.gene54040:intron 35.0%
GCTATATTGCTACGTTTATC+TGG + chr1.1:11909121-11909140 None:intergenic 35.0%
GCTCTGATAATCTGATTAAG+TGG + chr1.1:11908685-11908704 None:intergenic 35.0%
GTTGTTTATGATCCTGTAGA+AGG - chr1.1:11908853-11908872 MS.gene54040:intron 35.0%
TAATACAAGCGCAATGTCTT+TGG - chr1.1:11908447-11908466 MS.gene54040:CDS 35.0%
TCGTCTTCATTTGTACAACT+AGG + chr1.1:11908369-11908388 None:intergenic 35.0%
TCTCAACTTATGCTCAATGT+AGG - chr1.1:11908472-11908491 MS.gene54040:CDS 35.0%
TGCCAAATGATGATTTGAAG+AGG - chr1.1:11907810-11907829 MS.gene54040:intron 35.0%
! GCATCTAAGATTCTGAATCA+TGG - chr1.1:11907177-11907196 MS.gene54040:CDS 35.0%
! TAACTTGTGCAGAAGTATGA+TGG - chr1.1:11908804-11908823 MS.gene54040:intron 35.0%
! TAGCTTGTGAAAACAGTTGA+TGG + chr1.1:11907537-11907556 None:intergenic 35.0%
! TGGTTTGTACAAGAGGAAAA+GGG + chr1.1:11907119-11907138 None:intergenic 35.0%
! TTGTTGAACTGATACTGGTT+AGG - chr1.1:11908318-11908337 MS.gene54040:intron 35.0%
!! GCTGTTTTCATAAGCTAATG+TGG - chr1.1:11907370-11907389 MS.gene54040:intron 35.0%
!! TTATACTTTTTGAGAGCTGG+TGG - chr1.1:11908397-11908416 MS.gene54040:CDS 35.0%
!! TTGATTGGATGGATTGGTTT+GGG - chr1.1:11907254-11907273 MS.gene54040:CDS 35.0%
!! TTGGTTTGTACAAGAGGAAA+AGG + chr1.1:11907120-11907139 None:intergenic 35.0%
!! TTTGATTGGATGGATTGGTT+TGG - chr1.1:11907253-11907272 MS.gene54040:CDS 35.0%
AATGAGCTTACATACATGCC+TGG - chr1.1:11907893-11907912 MS.gene54040:intron 40.0%
AATTCTCCTGTTCTTGAACG+TGG - chr1.1:11907935-11907954 MS.gene54040:intron 40.0%
ACGTTCAAGAACAGGAGAAT+TGG + chr1.1:11907936-11907955 None:intergenic 40.0%
CAGGATCATAAACAACCATG+AGG + chr1.1:11908849-11908868 None:intergenic 40.0%
GAAGAGGAGATTAGAACAGA+TGG - chr1.1:11907826-11907845 MS.gene54040:intron 40.0%
GGATCATAAACAACCATGAG+GGG + chr1.1:11908847-11908866 None:intergenic 40.0%
GGTCTGTCTACAAACTAGTT+TGG - chr1.1:11908601-11908620 MS.gene54040:intron 40.0%
TCTGCACAAGTTAAGAGTCT+CGG + chr1.1:11908797-11908816 None:intergenic 40.0%
TTCTAATCCTTCACAGTCAC+TGG - chr1.1:11909087-11909106 MS.gene54040:intron 40.0%
TTGCATCTCAATGTGCATGT+TGG - chr1.1:11908040-11908059 MS.gene54040:intron 40.0%
TTTCACATGCTCTCCACAAT+AGG + chr1.1:11907497-11907516 None:intergenic 40.0%
! CAATGTGCATGTTGGTTGTT+TGG - chr1.1:11908048-11908067 MS.gene54040:intron 40.0%
! TGCAGAAGTATGATGGAAAG+AGG - chr1.1:11908811-11908830 MS.gene54040:intron 40.0%
AAAGCGGAGTAGTAGTTTGG+TGG - chr1.1:11907754-11907773 MS.gene54040:intron 45.0%
ATGTTGCCTCTTTGTCGTCA+TGG - chr1.1:11908193-11908212 MS.gene54040:intron 45.0%
ATTAGAACAGATGGCGTCGT+TGG - chr1.1:11907835-11907854 MS.gene54040:intron 45.0%
ATTCCTCCACGTTCAAGAAC+AGG + chr1.1:11907944-11907963 None:intergenic 45.0%
GAGAAAGCGGAGTAGTAGTT+TGG - chr1.1:11907751-11907770 MS.gene54040:intron 45.0%
GCTTACATACATGCCTGGAA+TGG - chr1.1:11907898-11907917 MS.gene54040:intron 45.0%
TCATAAACAACCATGAGGGG+CGG + chr1.1:11908844-11908863 None:intergenic 45.0%
TCTAGGTAACACTGCGTACT+AGG + chr1.1:11908542-11908561 None:intergenic 45.0%
TCTTAGCCATGACGACAAAG+AGG + chr1.1:11908202-11908221 None:intergenic 45.0%
!! CGCGTTGACTGCTACTAAAA+CGG - chr1.1:11907862-11907881 MS.gene54040:intron 45.0%
!! CGTTTTAGTAGCAGTCAACG+CGG + chr1.1:11907864-11907883 None:intergenic 45.0%
ACAGGAGAATTGGCATCCCT+TGG + chr1.1:11907926-11907945 None:intergenic 50.0%
CAGATGACCAGTGACTGTGA+AGG + chr1.1:11909097-11909116 None:intergenic 50.0%
TCTCCTGTTCTTGAACGTGG+AGG - chr1.1:11907938-11907957 MS.gene54040:intron 50.0%
TCTTGAACGTGGAGGAATGC+AGG - chr1.1:11907946-11907965 MS.gene54040:intron 50.0%
ACATGCCTGGAATGGCGCCA+AGG - chr1.1:11907906-11907925 MS.gene54040:intron 60.0%
AGGAGAATGTCCGCCCCTCA+TGG - chr1.1:11908831-11908850 MS.gene54040:intron 60.0%
CATGCCTGGAATGGCGCCAA+GGG - chr1.1:11907907-11907926 MS.gene54040:intron 60.0%
GCATCCCTTGGCGCCATTCC+AGG + chr1.1:11907914-11907933 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 11907118 11909173 11907118 ID=MS.gene54040
chr1.1 mRNA 11907118 11909173 11907118 ID=MS.gene54040.t1;Parent=MS.gene54040
chr1.1 exon 11909093 11909173 11909093 ID=MS.gene54040.t1.exon1;Parent=MS.gene54040.t1
chr1.1 CDS 11909093 11909173 11909093 ID=cds.MS.gene54040.t1;Parent=MS.gene54040.t1
chr1.1 exon 11908324 11908553 11908324 ID=MS.gene54040.t1.exon2;Parent=MS.gene54040.t1
chr1.1 CDS 11908324 11908553 11908324 ID=cds.MS.gene54040.t1;Parent=MS.gene54040.t1
chr1.1 exon 11907416 11907516 11907416 ID=MS.gene54040.t1.exon3;Parent=MS.gene54040.t1
chr1.1 CDS 11907416 11907516 11907416 ID=cds.MS.gene54040.t1;Parent=MS.gene54040.t1
chr1.1 exon 11907118 11907330 11907118 ID=MS.gene54040.t1.exon4;Parent=MS.gene54040.t1
chr1.1 CDS 11907118 11907330 11907118 ID=cds.MS.gene54040.t1;Parent=MS.gene54040.t1
Gene Sequence

>MS.gene54040

CTTTTCCTCTTGTACAAACCAAAATTATTGATTTCTTCAAGATTCAAAGATCCGTTGATGCATCTAAGATTCTGAATCATGGTAAGCTGAATCTTATTAAATTGATAATTGATTGTGATATTAATGTTTAGAGAATTTGATTGGATGGATTGGTTTGGGTATTATCTTCTTTTTAAGTTATAAGCTGTTTTTACAAGTTATTGTGGAGAGCTTGTGATAAAAGCTGAAAACAGCTTATGAATAATGTCATAAGCTGTTTTCATAAGCTAATGTGGTCAACTTGTAAAAATAATCTGTTTTCACAAGCTATTATGGATAGCTTGTAAAAATAAGCTGAAAACAGCTTATGAACAAAGTCATTAGCTATTTTTCACAACCTATTGTGGAGAGCATGTGAAAACAGCTTATGAACAATGCCATCAACTGTTTTCACAAGCTATTGTGCAGAACTTGTGAAAATAAGCTGAAGACAGCTTATGAGCAATGTCATAAGTAGTTTTCATAAGTTTTTCCAAACAGTCTTACAAAAGTTATGTTAGTAGATAATCTCAAATAAGTCGATACAAATAGACTCTTGATTTTTAATAATTGAAGTGTGTGTTTTAAATTGTGGTTTTTAGATTCAAAGAAGAAGAGAAAGCGGAGTAGTAGTTTGGTGGTTTCAAAAAAGAAAAGGAAGTTGTTGGTATTTGTGCCAAATGATGATTTGAAGAGGAGATTAGAACAGATGGCGTCGTTGGCAACCGCGTTGACTGCTACTAAAACGGAGTTCAGTAATGAGCTTACATACATGCCTGGAATGGCGCCAAGGGATGCCAATTCTCCTGTTCTTGAACGTGGAGGAATGCAGGTAACTATTTAACTTAATTGAGTTTGTTAGTTAGGTATTATATTGTTGTTAGGATACGTTTGGTTAATAAGCTTGCATCTCAATGTGCATGTTGGTTGTTTGGTGTTGAGTTATGTTTGTATGAGGAACAGTTAATTGAAAAATTCTACTGTGGACTAGTTTGATAGTATATTAGTCTATTGTTGATTAATATTTGAAAATTGTTTAAAACTTTAACAACAACAGATGTTGCCTCTTTGTCGTCATGGCTAAGAGTTTGAGACATTGAATTGATTGTTGGTGGTTCAACAAAAACAAGATAAAACGATTATGCATTTCTCAAAACTCAATCATATTCATTTTTCTTTGTTTTGTTGAACTGATACTGGTTAGGTTGTCAACACTAATTAGGTTACTGTCCTAGTTGTACAAATGAAGACGACTATGAGTTTATACTTTTTGAGAGCTGGTGGCATTTGTGCTATTAGATGATTATCTCTTAATACAAGCGCAATGTCTTTGGCTTCTCAACTTATGCTCAATGTAGGACTTGTCTAGTTAAGCTGTCTGCAGAAAACTATAACAGCAATAGCCTAGTACGCAGTGTTACCTAGAAATAAAGGCAACAAAGTTTGCAATACTGAAGTATAAAGTGGTCTGTCTACAAACTAGTTTGGATTTTGGCACACTGCACTATTTGTCATGATTTGGATTAACTTTTTTGTATTATGCACACCACTTAATCAGATTATCAGAGCACAGATGTTTATAACTACTGTTGTTATATGCATTAAGATTTGATGCATGTTTGTATATATTTTTTCTCAGGTCTTATCAAAAGAAGACACCGAGACTCTTAACTTGTGCAGAAGTATGATGGAAAGAGGAGAATGTCCGCCCCTCATGGTTGTTTATGATCCTGTAGAAGGGTAAGTACTTATGCAACACAATCTGAAATCAATTTTTTCATCTTTTGCAATTCATTCCTGACTTTTAATTTTCTTTTTTTTGTAGGTTCACTGTTGAAGCAGACAAGTCCATAAAAGATTTGACAATAATAACAGAATATGTTGGAGATGTAGACTTTTTGAAGAATCGGGAATATGATGATGGAGATAGCATTATGACACTTCTTTCTGCTTCTAATCCTTCACAGTCACTGGTCATCTGCCCAGATAAACGTAGCAATATAGCACGTTTCATTAATGGAATCAACAATCACACACC

Protein sequence

>MS.gene54040.t1

LFLLYKPKLLISSRFKDPLMHLRFUIMIQRRRESGVVVWWFQKRKGSCWYLCQMMIURGDUNRWRRWQPRULLLKRSSVMSLHTCLEWRQGMPILLFLNVEECRSYQKKTPRLLTCAEVUWKEENVRPSWLFMILUKGSLLKQTSPUKIUQUUQNMLEMUTFURIGNMMMEIALUHFFLLLILHSHWSSAQINVAIUHVSLMESTITH