AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09780.t1 MTR_5g012890 99.296 142 1 0 1 142 1 142 3.09e-101 286
MS.gene09780.t1 MTR_8g093770 94.444 126 7 0 17 142 18 143 2.31e-86 248
MS.gene09780.t1 MTR_4g006830 94.444 126 7 0 17 142 19 144 3.11e-85 246
MS.gene09780.t1 MTR_5g012890 96.262 107 4 0 1 107 1 107 5.85e-71 208
MS.gene09780.t1 MTR_4g073510 70.370 54 14 1 1 52 1 54 6.42e-17 76.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09780.t1 AT2G32060 74.400 125 31 1 18 142 21 144 1.33e-66 199
MS.gene09780.t1 AT2G32060 74.400 125 31 1 18 142 21 144 1.33e-66 199
MS.gene09780.t1 AT2G32060 74.400 125 31 1 18 142 21 144 1.33e-66 199
MS.gene09780.t1 AT1G15930 74.400 125 31 1 18 142 21 144 5.31e-64 192
MS.gene09780.t1 AT1G15930 74.400 125 31 1 18 142 21 144 5.31e-64 192

Find 35 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCACCAATTTGACATAATC+AGG 0.268051 5.3:-6081212 None:intergenic
GTTGTTGCTGCTGCAATTCC+AGG 0.269519 5.3:+6081041 MS.gene09780:CDS
GATGCTCTTGTGTGGTTGTC+AGG 0.354575 5.3:+6081531 MS.gene09780:CDS
ATGCTGCAAAACAACATTGT+AGG 0.363171 5.3:-6081667 None:intergenic
CATAAGCACGAGACTTTCTA+AGG 0.363450 5.3:-6081100 None:intergenic
CCAACCTGATTATGTCAAAT+TGG 0.373462 5.3:+6081208 MS.gene09780:CDS
CTTAGAAAGTCTCGTGCTTA+TGG 0.383982 5.3:+6081101 MS.gene09780:CDS
ATCAGGTTGGTCACAATCTT+CGG 0.412966 5.3:-6081195 None:intergenic
ATGATGTCCATTGGCTCGCC+TGG 0.437864 5.3:-6081059 None:intergenic
TCTCCAAGGGTCTTTGCACT+TGG 0.459795 5.3:-6081275 None:intergenic
TATCAACCAAGAAATATGTC+AGG 0.459989 5.3:+6080166 None:intergenic
GGAATTGCAGCAGCAACAAC+AGG 0.463311 5.3:-6081038 None:intergenic
GGTAAAGCTAGGAAGGTTAC+CGG 0.476827 5.3:+6081509 MS.gene09780:CDS
AACATTGTGCTCTGCGCAGA+GGG 0.503587 5.3:-6081237 None:intergenic
GACAACCACACAAGAGCATC+CGG 0.522597 5.3:-6081528 None:intergenic
TTACGCCAGCCCACTCTCCA+AGG 0.529322 5.3:-6081289 None:intergenic
CCAATTTGACATAATCAGGT+TGG 0.530247 5.3:-6081208 None:intergenic
TGCAAAGACCCTTGGAGAGT+GGG 0.530356 5.3:+6081280 MS.gene09780:CDS
TTTGTTATGCAGTGAAGAAG+AGG 0.537025 5.3:+6081001 MS.gene09780:intron
GTTCCAAGTGCAAAGACCCT+TGG 0.537039 5.3:+6081272 MS.gene09780:CDS
AAGACCCTTGGAGAGTGGGC+TGG 0.538691 5.3:+6081284 MS.gene09780:CDS
TTGATTCAGAAGGTAAAGCT+AGG 0.543764 5.3:+6081498 MS.gene09780:CDS
TTCAGAAGGTAAAGCTAGGA+AGG 0.557714 5.3:+6081502 MS.gene09780:CDS
TGCAATTCCAGGCGAGCCAA+TGG 0.568250 5.3:+6081052 MS.gene09780:CDS
GTGCAAAGACCCTTGGAGAG+TGG 0.569975 5.3:+6081279 MS.gene09780:CDS
ATGCTCTTGTGTGGTTGTCA+GGG 0.586706 5.3:+6081532 MS.gene09780:CDS
AAAGCAGTCATGATGTCCAT+TGG 0.589394 5.3:-6081068 None:intergenic
CTTGCACGAGGTCTTCATGA+AGG 0.605005 5.3:+6081128 MS.gene09780:CDS
AGAAAGTCTCGTGCTTATGG+TGG 0.620799 5.3:+6081104 MS.gene09780:CDS
TTGTGCAAGATTGATTCAGA+AGG 0.623879 5.3:+6081488 MS.gene09780:CDS
TACGCCAGCCCACTCTCCAA+GGG 0.624257 5.3:-6081288 None:intergenic
GCTTATGGTGGTCTTGCACG+AGG 0.624672 5.3:+6081116 MS.gene09780:CDS
TAACATTGTGCTCTGCGCAG+AGG 0.632440 5.3:-6081238 None:intergenic
ATCAACCAAGAAATATGTCA+GGG 0.636797 5.3:+6080167 None:intergenic
GGTTACCGGATGCTCTTGTG+TGG 0.638821 5.3:+6081523 MS.gene09780:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGTTCACAATATAAATT+TGG - chr5.3:6081378-6081397 None:intergenic 15.0%
!! AAAGTTCACAATATAAATTT+GGG - chr5.3:6081377-6081396 None:intergenic 15.0%
!!! ATTCTTCTATTTATATGTTT+TGG + chr5.3:6080902-6080921 MS.gene09780:intron 15.0%
!! AAAAATAAGATAAATCCAAC+TGG + chr5.3:6080677-6080696 MS.gene09780:intron 20.0%
!! AAAATAAGATAAATCCAACT+GGG + chr5.3:6080678-6080697 MS.gene09780:intron 20.0%
!! ACAATATAAATTTGGGAATT+GGG - chr5.3:6081370-6081389 None:intergenic 20.0%
!! ATTACTTGTAGTTATTACTA+AGG - chr5.3:6080790-6080809 None:intergenic 20.0%
!! TTCAAATGCAATTGTAATTT+AGG + chr5.3:6080233-6080252 MS.gene09780:intron 20.0%
!!! TAAAGATTTTTAAACTTGCA+AGG - chr5.3:6080955-6080974 None:intergenic 20.0%
! AAAACTAGGTTAAGAATCAA+GGG - chr5.3:6081318-6081337 None:intergenic 25.0%
! AACTTATGAAAACAGCTTAT+GGG - chr5.3:6080351-6080370 None:intergenic 25.0%
! ATCCTGCAAACAAAAAAAAA+AGG - chr5.3:6081628-6081647 None:intergenic 25.0%
! ATCTTAAACGATAAAACTAC+GGG - chr5.3:6080704-6080723 None:intergenic 25.0%
! CACAATATAAATTTGGGAAT+TGG - chr5.3:6081371-6081390 None:intergenic 25.0%
! GATCTTAAACGATAAAACTA+CGG - chr5.3:6080705-6080724 None:intergenic 25.0%
! TAAAACTAGGTTAAGAATCA+AGG - chr5.3:6081319-6081338 None:intergenic 25.0%
! TCCTGCAAACAAAAAAAAAA+GGG - chr5.3:6081627-6081646 None:intergenic 25.0%
! TTAGCATGAAAAAAGACAAT+AGG - chr5.3:6081586-6081605 None:intergenic 25.0%
!! AATGTATAGAACTTTTTACC+AGG - chr5.3:6080885-6080904 None:intergenic 25.0%
!!! CTTTATTTTTTCTTTTGCTG+TGG - chr5.3:6080309-6080328 None:intergenic 25.0%
!!! TTTTTTGTTTGCAGGATTTT+GGG + chr5.3:6081631-6081650 MS.gene09780:intron 25.0%
!!! TTTTTTTGTTTGCAGGATTT+TGG + chr5.3:6081630-6081649 MS.gene09780:intron 25.0%
ACAAGGAATTGGATAAAACT+AGG - chr5.3:6081332-6081351 None:intergenic 30.0%
ACCACTAGATAAGTTCAATT+AGG + chr5.3:6080469-6080488 MS.gene09780:intron 30.0%
AGATAACTGAATCTGATATC+CGG + chr5.3:6080761-6080780 MS.gene09780:intron 30.0%
CAACTTATGAAAACAGCTTA+TGG - chr5.3:6080352-6080371 None:intergenic 30.0%
TGGAAATGAGTTATGATAAG+TGG - chr5.3:6080289-6080308 None:intergenic 30.0%
TTCACCAATTTGACATAATC+AGG - chr5.3:6081215-6081234 None:intergenic 30.0%
!! GCTGTTTTCATAAGTTGTAT+TGG + chr5.3:6080355-6080374 MS.gene09780:intron 30.0%
!! TTTTTGTTTGCAGGATTTTG+GGG + chr5.3:6081632-6081651 MS.gene09780:intron 30.0%
!!! TCCCTTTTTTTTTTGTTTGC+AGG + chr5.3:6081623-6081642 MS.gene09780:intron 30.0%
AAATAAGCTGAAGACAGCTA+AGG + chr5.3:6080389-6080408 MS.gene09780:intron 35.0%
ACAAATAAGCCAATCCAAAC+AGG - chr5.3:6080502-6080521 None:intergenic 35.0%
AGATAAGTTCAATTAGGCCA+AGG + chr5.3:6080475-6080494 MS.gene09780:intron 35.0%
ATCAATCTTGCACAACTACA+TGG - chr5.3:6081483-6081502 None:intergenic 35.0%
ATCAGATGTTTGTCCAAACA+GGG - chr5.3:6080259-6080278 None:intergenic 35.0%
ATGCTGCAAAACAACATTGT+AGG - chr5.3:6081670-6081689 None:intergenic 35.0%
ATTGTAATTTAGGCCCTGTT+TGG + chr5.3:6080243-6080262 MS.gene09780:intron 35.0%
CCAACCTGATTATGTCAAAT+TGG + chr5.3:6081208-6081227 MS.gene09780:CDS 35.0%
CCAATTTGACATAATCAGGT+TGG - chr5.3:6081211-6081230 None:intergenic 35.0%
GATAAGTTCAATTAGGCCAA+GGG + chr5.3:6080476-6080495 MS.gene09780:intron 35.0%
GCCTAATTGAACTTATCTAG+TGG - chr5.3:6080473-6080492 None:intergenic 35.0%
GTAGTTATTACTAAGGTGAC+CGG - chr5.3:6080783-6080802 None:intergenic 35.0%
TATCAGATGTTTGTCCAAAC+AGG - chr5.3:6080260-6080279 None:intergenic 35.0%
TTGATTCAGAAGGTAAAGCT+AGG + chr5.3:6081498-6081517 MS.gene09780:CDS 35.0%
! TTGTGCAAGATTGATTCAGA+AGG + chr5.3:6081488-6081507 MS.gene09780:CDS 35.0%
! TTTGTTATGCAGTGAAGAAG+AGG + chr5.3:6081001-6081020 MS.gene09780:intron 35.0%
!! AAACTGATTCGAGTTGTTTC+AGG - chr5.3:6080732-6080751 None:intergenic 35.0%
AAAGCAGTCATGATGTCCAT+TGG - chr5.3:6081071-6081090 None:intergenic 40.0%
AATGGATGTGCACAAGGAAT+TGG - chr5.3:6081343-6081362 None:intergenic 40.0%
AGCTATACATGAGACACACA+AGG - chr5.3:6080929-6080948 None:intergenic 40.0%
ATTTGGGAATTGGGAGCAAA+TGG - chr5.3:6081361-6081380 None:intergenic 40.0%
CATAAGCACGAGACTTTCTA+AGG - chr5.3:6081103-6081122 None:intergenic 40.0%
CTTAGAAAGTCTCGTGCTTA+TGG + chr5.3:6081101-6081120 MS.gene09780:CDS 40.0%
TGTCTCAAGATTTATGCTCC+TGG + chr5.3:6080864-6080883 MS.gene09780:intron 40.0%
TTCAGAAGGTAAAGCTAGGA+AGG + chr5.3:6081502-6081521 MS.gene09780:CDS 40.0%
!! ATCAGGTTGGTCACAATCTT+CGG - chr5.3:6081198-6081217 None:intergenic 40.0%
AATGATGCAACAAGACTGCG+CGG - chr5.3:6081427-6081446 None:intergenic 45.0%
AGAAAGTCTCGTGCTTATGG+TGG + chr5.3:6081104-6081123 MS.gene09780:CDS 45.0%
ATGCTCTTGTGTGGTTGTCA+GGG + chr5.3:6081532-6081551 MS.gene09780:CDS 45.0%
GGTAAAGCTAGGAAGGTTAC+CGG + chr5.3:6081509-6081528 MS.gene09780:CDS 45.0%
!! TTGTTTGCAGGATTTTGGGG+AGG + chr5.3:6081635-6081654 MS.gene09780:intron 45.0%
!!! TATTTATTTTATTGATTTTT+GGG + chr5.3:6081448-6081467 MS.gene09780:intron 5.0%
!!! TTATTTATTTTATTGATTTT+TGG + chr5.3:6081447-6081466 MS.gene09780:intron 5.0%
AACATTGTGCTCTGCGCAGA+GGG - chr5.3:6081240-6081259 None:intergenic 50.0%
AATTAGGCCAAGGGCCTGTT+TGG + chr5.3:6080485-6080504 MS.gene09780:intron 50.0%
ATGATGCAACAAGACTGCGC+GGG - chr5.3:6081426-6081445 None:intergenic 50.0%
CTTGCACGAGGTCTTCATGA+AGG + chr5.3:6081128-6081147 MS.gene09780:CDS 50.0%
CTTGTGTGGTTGTCAGGGTA+TGG + chr5.3:6081537-6081556 MS.gene09780:intron 50.0%
GATAAAACTACGGGCCCAGT+TGG - chr5.3:6080695-6080714 None:intergenic 50.0%
GATGCTCTTGTGTGGTTGTC+AGG + chr5.3:6081531-6081550 MS.gene09780:CDS 50.0%
GGAATTGCAGCAGCAACAAC+AGG - chr5.3:6081041-6081060 None:intergenic 50.0%
GGAGCAAATGGATGTGCACA+AGG - chr5.3:6081349-6081368 None:intergenic 50.0%
GTTCCAAGTGCAAAGACCCT+TGG + chr5.3:6081272-6081291 MS.gene09780:CDS 50.0%
GTTGTTGCTGCTGCAATTCC+AGG + chr5.3:6081041-6081060 MS.gene09780:CDS 50.0%
TAACATTGTGCTCTGCGCAG+AGG - chr5.3:6081241-6081260 None:intergenic 50.0%
TCTCCAAGGGTCTTTGCACT+TGG - chr5.3:6081278-6081297 None:intergenic 50.0%
TGCAAAGACCCTTGGAGAGT+GGG + chr5.3:6081280-6081299 MS.gene09780:CDS 50.0%
!! GACAACCACACAAGAGCATC+CGG - chr5.3:6081531-6081550 None:intergenic 50.0%
AGCCAATCCAAACAGGCCCT+TGG - chr5.3:6080495-6080514 None:intergenic 55.0%
GGTTACCGGATGCTCTTGTG+TGG + chr5.3:6081523-6081542 MS.gene09780:CDS 55.0%
GTGCAAAGACCCTTGGAGAG+TGG + chr5.3:6081279-6081298 MS.gene09780:CDS 55.0%
TGCAATTCCAGGCGAGCCAA+TGG + chr5.3:6081052-6081071 MS.gene09780:CDS 55.0%
! GCTTATGGTGGTCTTGCACG+AGG + chr5.3:6081116-6081135 MS.gene09780:CDS 55.0%
!! ATGATGTCCATTGGCTCGCC+TGG - chr5.3:6081062-6081081 None:intergenic 55.0%
AAGACCCTTGGAGAGTGGGC+TGG + chr5.3:6081284-6081303 MS.gene09780:CDS 60.0%
GGCCAAGGGCCTGTTTGGAT+TGG + chr5.3:6080490-6080509 MS.gene09780:intron 60.0%
TACGCCAGCCCACTCTCCAA+GGG - chr5.3:6081291-6081310 None:intergenic 60.0%
TTACGCCAGCCCACTCTCCA+AGG - chr5.3:6081292-6081311 None:intergenic 60.0%
GCAACAAGACTGCGCGGGCA+TGG - chr5.3:6081421-6081440 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 6080181 6081704 6080181 ID=MS.gene09780
chr5.3 mRNA 6080181 6081704 6080181 ID=MS.gene09780.t1;Parent=MS.gene09780
chr5.3 exon 6080181 6080188 6080181 ID=MS.gene09780.t1.exon1;Parent=MS.gene09780.t1
chr5.3 CDS 6080181 6080188 6080181 ID=cds.MS.gene09780.t1;Parent=MS.gene09780.t1
chr5.3 exon 6081013 6081307 6081013 ID=MS.gene09780.t1.exon2;Parent=MS.gene09780.t1
chr5.3 CDS 6081013 6081307 6081013 ID=cds.MS.gene09780.t1;Parent=MS.gene09780.t1
chr5.3 exon 6081488 6081553 6081488 ID=MS.gene09780.t1.exon3;Parent=MS.gene09780.t1
chr5.3 CDS 6081488 6081553 6081488 ID=cds.MS.gene09780.t1;Parent=MS.gene09780.t1
chr5.3 exon 6081645 6081704 6081645 ID=MS.gene09780.t1.exon4;Parent=MS.gene09780.t1
chr5.3 CDS 6081645 6081704 6081645 ID=cds.MS.gene09780.t1;Parent=MS.gene09780.t1
Gene Sequence

>MS.gene09780

ATGTCAGGGTATGTATGCTAATTTATTCTATCATATGAACTATATTCAAAGTTTCAAATGCAATTGTAATTTAGGCCCTGTTTGGACAAACATCTGATAGCTTAACCACTTATCATAACTCATTTCCACAGCAAAAGAAAAAATAAAGTCAAACTGTTTTTGTATAACCCATAAGCTGTTTTCATAAGTTGTATTGGAGAAATTATGAAAATAAGCTGAAGACAGCTAAGGAACATGTCATAAGCTGTTTTCATAAGTTTTTTTTGAACAATCTCACAAGTGTTTTTTACCACTAGATAAGTTCAATTAGGCCAAGGGCCTGTTTGGATTGGCTTATTTGTTTAGCTTATGCAAATGAATAAGCTTTTGTGTATTATTCATAAGCTTGTCAAGATAGTTTATGAGAAAACAGCTTATGCATCTAATTTTTGTTAGTGAGAACTTATGAATTAATATAAAAGCTTATTTATTTGCATAAGCTGTTTTTAATAAGCTCAAAAATAAGATAAATCCAACTGGGCCCGTAGTTTTATCGTTTAAGATCTGATCCTGAAACAACTCGAATCAGTTTAACTTGACTAGATAACTGAATCTGATATCCGGTCACCTTAGTAATAACTACAAGTAATTAAGAAAACAACTGAATTAATCATATGCATTGCGTTTTCAGTGTGAAAATTATTTGTCTCAAGATTTATGCTCCTGGTAAAAAGTTCTATACATTCTTCTATTTATATGTTTTGGTCCTTGTGTGTCTCATGTATAGCTTTTCCTTGCAAGTTTAAAAATCTTTAATAAGTTGCTCACTAGTGAAAAAATCTTTGTTATGCAGTGAAGAAGAGGTTGTTGCAGTTGAGCCTGTTGTTGCTGCTGCAATTCCAGGCGAGCCAATGGACATCATGACTGCTTTACAGCTTGTCCTTAGAAAGTCTCGTGCTTATGGTGGTCTTGCACGAGGTCTTCATGAAGGTGCAAAAGTGATTGAGAAGCATGCTGCACAGCTTTGTGTTCTAGCCGAAGATTGTGACCAACCTGATTATGTCAAATTGGTGAAAGCCCTCTGCGCAGAGCACAATGTTAGCTTGTTGACAGTTCCAAGTGCAAAGACCCTTGGAGAGTGGGCTGGCGTAAGTGCCCTTGATTCTTAACCTAGTTTTATCCAATTCCTTGTGCACATCCATTTGCTCCCAATTCCCAAATTTATATTGTGAACTTTTATTCTTATACTGTTCTTTATCCATGCCCGCGCAGTCTTGTTGCATCATTTTATTTATTTTATTGATTTTTGGGTATACTTTTCCATGTAGTTGTGCAAGATTGATTCAGAAGGTAAAGCTAGGAAGGTTACCGGATGCTCTTGTGTGGTTGTCAGGGTATGGTTTATACTTGAAATGCAAATGTTCCTATTGTCTTTTTTCATGCTAAATGTAAATTGAAGTATTTCCCTTTTTTTTTTGTTTGCAGGATTTTGGGGAGGAACACGAAGCCTACAATGTTGTTTTGCAGCATGTAAAAGCTAACTAA

Protein sequence

>MS.gene09780.t1

MSGEEEVVAVEPVVAAAIPGEPMDIMTALQLVLRKSRAYGGLARGLHEGAKVIEKHAAQLCVLAEDCDQPDYVKLVKALCAEHNVSLLTVPSAKTLGEWAGLCKIDSEGKARKVTGCSCVVVRDFGEEHEAYNVVLQHVKAN