AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31651


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:+11889926 None:intergenic
CTTGAAGAAATCAATAATTT+TGG 0.167292 1.1:+11891908 None:intergenic
AATATAGCACGTTTCATTAA+TGG 0.211173 1.1:-11889911 MS.gene31651:CDS
GCATCCCTTGGCGCCATTCC+AGG 0.276840 1.1:+11891133 None:intergenic
CTCCTCTTCAAATCATCATT+TGG 0.347535 1.1:+11891232 None:intergenic
GAGAAAGCGGAGTAGTAGTT+TGG 0.397233 1.1:-11891293 MS.gene31651:CDS
GTTGTTTATGATCCTGTAGA+AGG 0.406850 1.1:-11890191 MS.gene31651:CDS
ACGTTCAAGAACAGGAGAAT+TGG 0.452094 1.1:+11891111 None:intergenic
ATTCCTCCACGTTCAAGAAC+AGG 0.452190 1.1:+11891103 None:intergenic
AAAGCGGAGTAGTAGTTTGG+TGG 0.462327 1.1:-11891290 MS.gene31651:CDS
CGCGTTGACTGCTACTAAAA+CGG 0.476912 1.1:-11891182 MS.gene31651:CDS
CTATATTGCTACGTTTATCT+GGG 0.481139 1.1:+11889927 None:intergenic
ACAATAATAACAGAATATGT+TGG 0.490743 1.1:-11890046 MS.gene31651:CDS
TAACTTGTGCAGAAGTATGA+TGG 0.493269 1.1:-11890240 MS.gene31651:CDS
TTCTAATCCTTCACAGTCAC+TGG 0.505311 1.1:-11889957 MS.gene31651:CDS
GCATCTAAGATTCTGAATCA+TGG 0.512650 1.1:-11891867 MS.gene31651:intron
ATAAGTACTTACCCTTCTAC+AGG 0.515050 1.1:+11890179 None:intergenic
ATTAGAACAGATGGCGTCGT+TGG 0.518768 1.1:-11891209 MS.gene31651:CDS
ATTCAAAGAAGAAGAGAAAG+CGG 0.540362 1.1:-11891306 MS.gene31651:CDS
ACAGGAGAATTGGCATCCCT+TGG 0.541184 1.1:+11891121 None:intergenic
TCTTGAACGTGGAGGAATGC+AGG 0.541405 1.1:-11891098 MS.gene31651:intron
AAGAATCGGGAATATGATGA+TGG 0.544853 1.1:-11890007 MS.gene31651:CDS
AGGAGAATGTCCGCCCCTCA+TGG 0.545962 1.1:-11890213 MS.gene31651:CDS
TGCAGAAGTATGATGGAAAG+AGG 0.546783 1.1:-11890233 MS.gene31651:CDS
AATGAGCTTACATACATGCC+TGG 0.552496 1.1:-11891151 MS.gene31651:CDS
CATGCCTGGAATGGCGCCAA+GGG 0.555292 1.1:-11891137 MS.gene31651:CDS
AATTCTCCTGTTCTTGAACG+TGG 0.561001 1.1:-11891109 MS.gene31651:CDS
ACATGCCTGGAATGGCGCCA+AGG 0.581749 1.1:-11891138 MS.gene31651:CDS
GCTTACATACATGCCTGGAA+TGG 0.584838 1.1:-11891146 MS.gene31651:CDS
CAGAATCTTAGATGCATCAA+CGG 0.589395 1.1:+11891875 None:intergenic
TGCCAAATGATGATTTGAAG+AGG 0.592036 1.1:-11891234 MS.gene31651:CDS
GAAGAGGAGATTAGAACAGA+TGG 0.593117 1.1:-11891218 MS.gene31651:CDS
TTGTTTATGATCCTGTAGAA+GGG 0.614616 1.1:-11890190 MS.gene31651:intron
TCTGCACAAGTTAAGAGTCT+CGG 0.617054 1.1:+11890250 None:intergenic
TCTCCTGTTCTTGAACGTGG+AGG 0.653986 1.1:-11891106 MS.gene31651:CDS
GGATCATAAACAACCATGAG+GGG 0.675550 1.1:+11890200 None:intergenic
AGGATCATAAACAACCATGA+GGG 0.678750 1.1:+11890199 None:intergenic
TCATAAACAACCATGAGGGG+CGG 0.687468 1.1:+11890203 None:intergenic
CAGGATCATAAACAACCATG+AGG 0.703912 1.1:+11890198 None:intergenic
CAGATGACCAGTGACTGTGA+AGG 0.718767 1.1:+11889950 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAATTTTCTTTTTTTTGT+AGG - chr1.1:11891714-11891733 MS.gene31651:intron 10.0%
!! AAAAAAGAAAATTAAAAGTC+AGG + chr1.1:11891710-11891729 None:intergenic 15.0%
!!! TATTATTGTCAAATCTTTTA+TGG + chr1.1:11891762-11891781 None:intergenic 15.0%
!! ACAATAATAACAGAATATGT+TGG - chr1.1:11891773-11891792 MS.gene31651:intron 20.0%
!! TAATGTTTAGAGAATTTGAT+TGG - chr1.1:11890014-11890033 MS.gene31651:CDS 20.0%
!! TTAATTGAAAAATTCTACTG+TGG - chr1.1:11890874-11890893 MS.gene31651:intron 20.0%
!!! CTTGAAGAAATCAATAATTT+TGG + chr1.1:11889914-11889933 None:intergenic 20.0%
!!! GTTTGTATATATTTTTTCTC+AGG - chr1.1:11891528-11891547 MS.gene31651:intron 20.0%
!!! TTAGGTATTATATTGTTGTT+AGG - chr1.1:11890773-11890792 MS.gene31651:intron 20.0%
! AAAAAAGAAAAGGAAGTTGT+TGG - chr1.1:11890556-11890575 MS.gene31651:intron 25.0%
! AATATAGCACGTTTCATTAA+TGG - chr1.1:11891908-11891927 MS.gene31651:CDS 25.0%
!! ATAACTTTTGTAAGACTGTT+TGG + chr1.1:11890407-11890426 None:intergenic 25.0%
!!! ATAATTTTGGTTTGTACAAG+AGG + chr1.1:11889901-11889920 None:intergenic 25.0%
!!! ATGTAGACTTTTTGAAGAAT+CGG - chr1.1:11891798-11891817 MS.gene31651:intron 25.0%
!!! CTTAATTGAGTTTGTTAGTT+AGG - chr1.1:11890755-11890774 MS.gene31651:intron 25.0%
ATTCAAAGAAGAAGAGAAAG+CGG - chr1.1:11890513-11890532 MS.gene31651:intron 30.0%
CTATATTGCTACGTTTATCT+GGG + chr1.1:11891895-11891914 None:intergenic 30.0%
GTTTAGAGAATTTGATTGGA+TGG - chr1.1:11890018-11890037 MS.gene31651:CDS 30.0%
TGAGACATTGAATTGATTGT+TGG - chr1.1:11891000-11891019 MS.gene31651:intron 30.0%
TGCAATACTGAAGTATAAAG+TGG - chr1.1:11891355-11891374 MS.gene31651:intron 30.0%
TGGTGGTTTCAAAAAAGAAA+AGG - chr1.1:11890546-11890565 MS.gene31651:intron 30.0%
TGTTGAGTTATGTTTGTATG+AGG - chr1.1:11890846-11890865 MS.gene31651:intron 30.0%
TTGTTTATGATCCTGTAGAA+GGG - chr1.1:11891629-11891648 MS.gene31651:intron 30.0%
! ACTTTGTTGCCTTTATTTCT+AGG + chr1.1:11891334-11891353 None:intergenic 30.0%
! TATTGTTGTTAGGATACGTT+TGG - chr1.1:11890783-11890802 MS.gene31651:intron 30.0%
! TCTGTTTTCACAAGCTATTA+TGG - chr1.1:11890185-11890204 MS.gene31651:intron 30.0%
! TTAGGTTGTCAACACTAATT+AGG - chr1.1:11891111-11891130 MS.gene31651:CDS 30.0%
!! AGTTTATACTTTTTGAGAGC+TGG - chr1.1:11891169-11891188 MS.gene31651:CDS 30.0%
!! CTACAAACTAGTTTGGATTT+TGG - chr1.1:11891383-11891402 MS.gene31651:intron 30.0%
!! CTATTTTTCACAACCTATTG+TGG - chr1.1:11890256-11890275 MS.gene31651:CDS 30.0%
!! GAAGTGTGTGTTTTAAATTG+TGG - chr1.1:11890483-11890502 MS.gene31651:intron 30.0%
!! TGTAGACTTTTTGAAGAATC+GGG - chr1.1:11891799-11891818 MS.gene31651:intron 30.0%
!! TTGTTTTGTTGAACTGATAC+TGG - chr1.1:11891088-11891107 MS.gene31651:intron 30.0%
!!! GCTGTTTTTACAAGTTATTG+TGG - chr1.1:11890076-11890095 MS.gene31651:CDS 30.0%
AAGAATCGGGAATATGATGA+TGG - chr1.1:11891812-11891831 MS.gene31651:intron 35.0%
AGGATCATAAACAACCATGA+GGG + chr1.1:11891623-11891642 None:intergenic 35.0%
ATAAGTACTTACCCTTCTAC+AGG + chr1.1:11891643-11891662 None:intergenic 35.0%
CAGAATCTTAGATGCATCAA+CGG + chr1.1:11889947-11889966 None:intergenic 35.0%
CTCCTCTTCAAATCATCATT+TGG + chr1.1:11890590-11890609 None:intergenic 35.0%
CTGCACTATTTGTCATGATT+TGG - chr1.1:11891410-11891429 MS.gene31651:intron 35.0%
GACATTGAATTGATTGTTGG+TGG - chr1.1:11891003-11891022 MS.gene31651:intron 35.0%
GAGAATTTGATTGGATGGAT+TGG - chr1.1:11890023-11890042 MS.gene31651:CDS 35.0%
GCAGTGTTACCTAGAAATAA+AGG - chr1.1:11891322-11891341 MS.gene31651:intron 35.0%
GCTATATTGCTACGTTTATC+TGG + chr1.1:11891896-11891915 None:intergenic 35.0%
GCTCTGATAATCTGATTAAG+TGG + chr1.1:11891460-11891479 None:intergenic 35.0%
GTTGTTTATGATCCTGTAGA+AGG - chr1.1:11891628-11891647 MS.gene31651:intron 35.0%
TAATACAAGCGCAATGTCTT+TGG - chr1.1:11891222-11891241 MS.gene31651:CDS 35.0%
TCGTCTTCATTTGTACAACT+AGG + chr1.1:11891144-11891163 None:intergenic 35.0%
TCTCAACTTATGCTCAATGT+AGG - chr1.1:11891247-11891266 MS.gene31651:CDS 35.0%
TGCCAAATGATGATTTGAAG+AGG - chr1.1:11890585-11890604 MS.gene31651:intron 35.0%
! GCATCTAAGATTCTGAATCA+TGG - chr1.1:11889952-11889971 MS.gene31651:CDS 35.0%
! TAACTTGTGCAGAAGTATGA+TGG - chr1.1:11891579-11891598 MS.gene31651:intron 35.0%
! TAGCTTGTGAAAACAGTTGA+TGG + chr1.1:11890312-11890331 None:intergenic 35.0%
! TGGTTTGTACAAGAGGAAAA+GGG + chr1.1:11889894-11889913 None:intergenic 35.0%
! TTGTTGAACTGATACTGGTT+AGG - chr1.1:11891093-11891112 MS.gene31651:intron 35.0%
!! GCTGTTTTCATAAGCTAATG+TGG - chr1.1:11890145-11890164 MS.gene31651:intron 35.0%
!! TTATACTTTTTGAGAGCTGG+TGG - chr1.1:11891172-11891191 MS.gene31651:CDS 35.0%
!! TTGATTGGATGGATTGGTTT+GGG - chr1.1:11890029-11890048 MS.gene31651:CDS 35.0%
!! TTGGTTTGTACAAGAGGAAA+AGG + chr1.1:11889895-11889914 None:intergenic 35.0%
!! TTTGATTGGATGGATTGGTT+TGG - chr1.1:11890028-11890047 MS.gene31651:CDS 35.0%
AATGAGCTTACATACATGCC+TGG - chr1.1:11890668-11890687 MS.gene31651:intron 40.0%
AATTCTCCTGTTCTTGAACG+TGG - chr1.1:11890710-11890729 MS.gene31651:intron 40.0%
ACGTTCAAGAACAGGAGAAT+TGG + chr1.1:11890711-11890730 None:intergenic 40.0%
CAGGATCATAAACAACCATG+AGG + chr1.1:11891624-11891643 None:intergenic 40.0%
GAAGAGGAGATTAGAACAGA+TGG - chr1.1:11890601-11890620 MS.gene31651:intron 40.0%
GGATCATAAACAACCATGAG+GGG + chr1.1:11891622-11891641 None:intergenic 40.0%
GGTCTGTCTACAAACTAGTT+TGG - chr1.1:11891376-11891395 MS.gene31651:intron 40.0%
TCTGCACAAGTTAAGAGTCT+CGG + chr1.1:11891572-11891591 None:intergenic 40.0%
TTCTAATCCTTCACAGTCAC+TGG - chr1.1:11891862-11891881 MS.gene31651:intron 40.0%
TTGCATCTCAATGTGCATGT+TGG - chr1.1:11890815-11890834 MS.gene31651:intron 40.0%
TTTCACATGCTCTCCACAAT+AGG + chr1.1:11890272-11890291 None:intergenic 40.0%
! CAATGTGCATGTTGGTTGTT+TGG - chr1.1:11890823-11890842 MS.gene31651:intron 40.0%
! TGCAGAAGTATGATGGAAAG+AGG - chr1.1:11891586-11891605 MS.gene31651:intron 40.0%
AAAGCGGAGTAGTAGTTTGG+TGG - chr1.1:11890529-11890548 MS.gene31651:intron 45.0%
ATGTTGCCTCTTTGTCGTCA+TGG - chr1.1:11890968-11890987 MS.gene31651:intron 45.0%
ATTAGAACAGATGGCGTCGT+TGG - chr1.1:11890610-11890629 MS.gene31651:intron 45.0%
ATTCCTCCACGTTCAAGAAC+AGG + chr1.1:11890719-11890738 None:intergenic 45.0%
GAGAAAGCGGAGTAGTAGTT+TGG - chr1.1:11890526-11890545 MS.gene31651:intron 45.0%
GCTTACATACATGCCTGGAA+TGG - chr1.1:11890673-11890692 MS.gene31651:intron 45.0%
TCATAAACAACCATGAGGGG+CGG + chr1.1:11891619-11891638 None:intergenic 45.0%
TCTAGGTAACACTGCGTACT+AGG + chr1.1:11891317-11891336 None:intergenic 45.0%
TCTTAGCCATGACGACAAAG+AGG + chr1.1:11890977-11890996 None:intergenic 45.0%
!! CGCGTTGACTGCTACTAAAA+CGG - chr1.1:11890637-11890656 MS.gene31651:intron 45.0%
!! CGTTTTAGTAGCAGTCAACG+CGG + chr1.1:11890639-11890658 None:intergenic 45.0%
ACAGGAGAATTGGCATCCCT+TGG + chr1.1:11890701-11890720 None:intergenic 50.0%
CAGATGACCAGTGACTGTGA+AGG + chr1.1:11891872-11891891 None:intergenic 50.0%
TCTCCTGTTCTTGAACGTGG+AGG - chr1.1:11890713-11890732 MS.gene31651:intron 50.0%
TCTTGAACGTGGAGGAATGC+AGG - chr1.1:11890721-11890740 MS.gene31651:intron 50.0%
ACATGCCTGGAATGGCGCCA+AGG - chr1.1:11890681-11890700 MS.gene31651:intron 60.0%
AGGAGAATGTCCGCCCCTCA+TGG - chr1.1:11891606-11891625 MS.gene31651:intron 60.0%
CATGCCTGGAATGGCGCCAA+GGG - chr1.1:11890682-11890701 MS.gene31651:intron 60.0%
GCATCCCTTGGCGCCATTCC+AGG + chr1.1:11890689-11890708 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 11889893 11891948 11889893 ID=MS.gene31651
chr1.1 mRNA 11889893 11891948 11889893 ID=MS.gene31651.t1;Parent=MS.gene31651
chr1.1 exon 11891868 11891948 11891868 ID=MS.gene31651.t1.exon1;Parent=MS.gene31651.t1
chr1.1 CDS 11891868 11891948 11891868 ID=cds.MS.gene31651.t1;Parent=MS.gene31651.t1
chr1.1 exon 11891099 11891328 11891099 ID=MS.gene31651.t1.exon2;Parent=MS.gene31651.t1
chr1.1 CDS 11891099 11891328 11891099 ID=cds.MS.gene31651.t1;Parent=MS.gene31651.t1
chr1.1 exon 11890191 11890291 11890191 ID=MS.gene31651.t1.exon3;Parent=MS.gene31651.t1
chr1.1 CDS 11890191 11890291 11890191 ID=cds.MS.gene31651.t1;Parent=MS.gene31651.t1
chr1.1 exon 11889893 11890105 11889893 ID=MS.gene31651.t1.exon4;Parent=MS.gene31651.t1
chr1.1 CDS 11889893 11890105 11889893 ID=cds.MS.gene31651.t1;Parent=MS.gene31651.t1
Gene Sequence

>MS.gene31651

CTTTTCCTCTTGTACAAACCAAAATTATTGATTTCTTCAAGATTCAAAGATCCGTTGATGCATCTAAGATTCTGAATCATGGTAAGCTGAATCTTATTAAATTGATAATTGATTGTGATATTAATGTTTAGAGAATTTGATTGGATGGATTGGTTTGGGTATTATCTTCTTTTTAAGTTATAAGCTGTTTTTACAAGTTATTGTGGAGAGCTTGTGATAAAAGCTGAAAACAGCTTATGAATAATGTCATAAGCTGTTTTCATAAGCTAATGTGGTCAACTTGTAAAAATAATCTGTTTTCACAAGCTATTATGGATAGCTTGTAAAAATAAGCTGAAAACAGCTTATGAACAAAGTCATTAGCTATTTTTCACAACCTATTGTGGAGAGCATGTGAAAACAGCTTATGAACAATGCCATCAACTGTTTTCACAAGCTATTGTGCAGAACTTGTGAAAATAAGCTGAAGACAGCTTATGAGCAATGTCATAAGTAGTTTTCATAAGTTTTTCCAAACAGTCTTACAAAAGTTATGTTAGTAGATAATCTCAAATAAGTCGATACAAATAGACTCTTGATTTTTAATAATTGAAGTGTGTGTTTTAAATTGTGGTTTTTAGATTCAAAGAAGAAGAGAAAGCGGAGTAGTAGTTTGGTGGTTTCAAAAAAGAAAAGGAAGTTGTTGGTATTTGTGCCAAATGATGATTTGAAGAGGAGATTAGAACAGATGGCGTCGTTGGCAACCGCGTTGACTGCTACTAAAACGGAGTTCAGTAATGAGCTTACATACATGCCTGGAATGGCGCCAAGGGATGCCAATTCTCCTGTTCTTGAACGTGGAGGAATGCAGGTAACTATTTAACTTAATTGAGTTTGTTAGTTAGGTATTATATTGTTGTTAGGATACGTTTGGTTAATAAGCTTGCATCTCAATGTGCATGTTGGTTGTTTGGTGTTGAGTTATGTTTGTATGAGGAACAGTTAATTGAAAAATTCTACTGTGGACTAGTTTGATAGTATATTAGTCTATTGTTGATTAATATTTGAAAATTGTTTAAAACTTTAACAACAACAGATGTTGCCTCTTTGTCGTCATGGCTAAGAGTTTGAGACATTGAATTGATTGTTGGTGGTTCAACAAAAACAAGATAAAACGATTATGCATTTCTCAAAACTCAATCATATTCATTTTTCTTTGTTTTGTTGAACTGATACTGGTTAGGTTGTCAACACTAATTAGGTTACTGTCCTAGTTGTACAAATGAAGACGACTATGAGTTTATACTTTTTGAGAGCTGGTGGCATTTGTGCTATTAGATGATTATCTCTTAATACAAGCGCAATGTCTTTGGCTTCTCAACTTATGCTCAATGTAGGACTTGTCTAGTTAAGCTGTCTGCAGAAAACTATAACAGCAATAGCCTAGTACGCAGTGTTACCTAGAAATAAAGGCAACAAAGTTTGCAATACTGAAGTATAAAGTGGTCTGTCTACAAACTAGTTTGGATTTTGGCACACTGCACTATTTGTCATGATTTGGATTAACTTTTTTGTATTATGCACACCACTTAATCAGATTATCAGAGCACAGATGTTTATAACTACTGTTGTTATATGCATTAAGATTTGATGCATGTTTGTATATATTTTTTCTCAGGTCTTATCAAAAGAAGACACCGAGACTCTTAACTTGTGCAGAAGTATGATGGAAAGAGGAGAATGTCCGCCCCTCATGGTTGTTTATGATCCTGTAGAAGGGTAAGTACTTATGCAACACAATCTGAAATCAATTTTTTCATCTTTTGCAATTCATTCCTGACTTTTAATTTTCTTTTTTTTGTAGGTTCACTGTTGAAGCAGACAAGTCCATAAAAGATTTGACAATAATAACAGAATATGTTGGAGATGTAGACTTTTTGAAGAATCGGGAATATGATGATGGAGATAGCATTATGACACTTCTTTCTGCTTCTAATCCTTCACAGTCACTGGTCATCTGCCCAGATAAACGTAGCAATATAGCACGTTTCATTAATGGAATCAACAATCACACACC

Protein sequence

>MS.gene31651.t1

LFLLYKPKLLISSRFKDPLMHLRFUIMIQRRRESGVVVWWFQKRKGSCWYLCQMMIURGDUNRWRRWQPRULLLKRSSVMSLHTCLEWRQGMPILLFLNVEECRSYQKKTPRLLTCAEVUWKEENVRPSWLFMILUKGSLLKQTSPUKIUQUUQNMLEMUTFURIGNMMMEIALUHFFLLLILHSHWSSAQINVAIUHVSLMESTITH