AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene72017

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72017.t1 MTR_5g077900 94.318 88 5 0 1 88 137 224 1.00e-57 177
MS.gene72017.t1 MTR_0002s1270 94.318 88 5 0 1 88 311 398 1.39e-56 179
MS.gene72017.t1 MTR_7g046380 94.937 79 4 0 1 79 319 397 2.13e-50 163
MS.gene72017.t1 MTR_0057s0200 93.220 59 4 0 32 90 1 59 1.17e-36 118
MS.gene72017.t1 MTR_4g066320 68.293 82 21 2 14 90 40 121 1.63e-33 112
MS.gene72017.t1 MTR_3g028430 72.222 54 6 1 37 90 15 59 5.54e-20 76.3
MS.gene72017.t1 MTR_0462s0020 39.080 87 51 1 1 85 204 290 1.82e-16 72.0
MS.gene72017.t1 MTR_8g017000 42.697 89 49 1 4 90 601 689 1.83e-16 72.8
MS.gene72017.t1 MTR_2g037270 41.573 89 50 1 4 90 601 689 7.21e-16 71.2
MS.gene72017.t1 MTR_4g066300 88.235 34 4 0 28 61 5 38 1.54e-15 65.1
MS.gene72017.t1 MTR_2g092960 38.372 86 52 1 1 85 1129 1214 2.83e-15 69.7
MS.gene72017.t1 MTR_2g086200 60.000 50 20 0 41 90 185 234 1.56e-14 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCCATTAGGTTGCTTTCT+TGG 0.248489 3.4:+95655333 None:intergenic
GCAATAGAAAGAAGGTTAAA+TGG 0.271188 3.4:-95656163 MS.gene72017:CDS
GTTAACATATAGAGCTTTAG+AGG 0.328169 3.4:-95656204 MS.gene72017:intron
TATAAGTCATCATCAGTTAA+TGG 0.351177 3.4:+95655119 None:intergenic
TCTTTACTTGTATAAGGCTT+AGG 0.388401 3.4:-95655066 None:intergenic
AGAGGTTCATCAACTTGCTC+AGG 0.406730 3.4:-95656186 MS.gene72017:CDS
TATCCACAATCATTGCCATT+AGG 0.411955 3.4:+95655321 None:intergenic
CTGCTAATATTACTAAGTCT+TGG 0.472781 3.4:-95655266 MS.gene72017:CDS
ATATGATTTGCGAAACCAAT+GGG 0.486055 3.4:-95655099 MS.gene72017:CDS
TAGCCAAGAAAGCAACCTAA+TGG 0.495668 3.4:-95655336 MS.gene72017:CDS
CAACCTAATGGCAATGATTG+TGG 0.497368 3.4:-95655324 MS.gene72017:CDS
TCATCATCAGTTAATGGCGT+TGG 0.497730 3.4:+95655125 None:intergenic
AAAGAAAACAAGTTGCCCAT+TGG 0.540408 3.4:+95655084 None:intergenic
TGCTCAGGGCAATAGAAAGA+AGG 0.550095 3.4:-95656171 MS.gene72017:CDS
GAGGTTCATCAACTTGCTCA+GGG 0.558482 3.4:-95656185 MS.gene72017:CDS
TATATGATTTGCGAAACCAA+TGG 0.577102 3.4:-95655100 MS.gene72017:CDS
TAATATTACTAAGTCTTGGA+TGG 0.604101 3.4:-95655262 MS.gene72017:CDS
TATTACTAAGTCTTGGATGG+AGG 0.643493 3.4:-95655259 MS.gene72017:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACTCAAATTATTTAGAAA+GGG - chr3.4:95655713-95655732 MS.gene72017:intron 15.0%
!! AACTAATCACTTTATAAAAA+TGG - chr3.4:95656003-95656022 MS.gene72017:intron 15.0%
!! GTATTATACAAAAGAATTAT+TGG + chr3.4:95655911-95655930 None:intergenic 15.0%
!! TAAACTCAAATTATTTAGAA+AGG - chr3.4:95655712-95655731 MS.gene72017:intron 15.0%
!!! AGAAGATTGTAAATTTTTTA+TGG + chr3.4:95655486-95655505 None:intergenic 15.0%
!!! CTTTGATGATTTTTTTAATT+TGG - chr3.4:95655147-95655166 MS.gene72017:intron 15.0%
!! AATTGAAAACATATAGGTTT+AGG - chr3.4:95655545-95655564 MS.gene72017:intron 20.0%
!! ATTGAAAACATATAGGTTTA+GGG - chr3.4:95655546-95655565 MS.gene72017:intron 20.0%
!! TAAAGTAAAAAAATTCACTG+AGG - chr3.4:95655744-95655763 MS.gene72017:intron 20.0%
!! TAATACAAGAAACAATCATA+CGG + chr3.4:95655293-95655312 None:intergenic 20.0%
!!! AGATTGTAAATTTTTTATGG+AGG + chr3.4:95655483-95655502 None:intergenic 20.0%
!!! ATTGTTTCTTGTATTAAAAG+TGG - chr3.4:95655297-95655316 MS.gene72017:CDS 20.0%
!!! TAAACCTATATGTTTTCAAT+TGG + chr3.4:95655546-95655565 None:intergenic 20.0%
!!! TTGTTTTCTTTACTTGTATA+AGG - chr3.4:95656301-95656320 MS.gene72017:intron 20.0%
! AAATATACAGGGAACAATTA+AGG + chr3.4:95655269-95655288 None:intergenic 25.0%
! AATCATACGGAAAATATACA+GGG + chr3.4:95655280-95655299 None:intergenic 25.0%
! TAAAAAAATTCACTGAGGTA+CGG - chr3.4:95655749-95655768 MS.gene72017:intron 25.0%
! TAATATTACTAAGTCTTGGA+TGG - chr3.4:95656111-95656130 MS.gene72017:intron 25.0%
! TATAAGTCATCATCAGTTAA+TGG + chr3.4:95656257-95656276 None:intergenic 25.0%
! TATATTAACCTACACATTGT+AGG - chr3.4:95656214-95656233 MS.gene72017:intron 25.0%
! TTGGTTAAGTAGTGTAAAAA+AGG + chr3.4:95655892-95655911 None:intergenic 25.0%
!! TAGCTTAATTGATTTAGTAG+TGG + chr3.4:95655618-95655637 None:intergenic 25.0%
!!! GTTATACATTTTAGTGTTGT+AGG + chr3.4:95655128-95655147 None:intergenic 25.0%
AAGAAGAACCATACTTACTT+TGG + chr3.4:95655243-95655262 None:intergenic 30.0%
ACAACAGTATCTATTCATGA+AGG + chr3.4:95655933-95655952 None:intergenic 30.0%
AGAAGAACCATACTTACTTT+GGG + chr3.4:95655242-95655261 None:intergenic 30.0%
ATTATTTAGAAAGGGTAGTC+TGG - chr3.4:95655721-95655740 MS.gene72017:intron 30.0%
CAATCATACGGAAAATATAC+AGG + chr3.4:95655281-95655300 None:intergenic 30.0%
CTGCTAATATTACTAAGTCT+TGG - chr3.4:95656107-95656126 MS.gene72017:intron 30.0%
GCAATAGAAAGAAGGTTAAA+TGG - chr3.4:95655210-95655229 MS.gene72017:intron 30.0%
GCAGTGAAACAATATAATCT+TGG - chr3.4:95655399-95655418 MS.gene72017:intron 30.0%
GGAGGATAAACAAGAATAAA+AGG + chr3.4:95655465-95655484 None:intergenic 30.0%
GTAGCCAATTGAAAACATAT+AGG - chr3.4:95655539-95655558 MS.gene72017:intron 30.0%
! ATATGATTTGCGAAACCAAT+GGG - chr3.4:95656274-95656293 MS.gene72017:intron 30.0%
! GTTAACATATAGAGCTTTAG+AGG - chr3.4:95655169-95655188 MS.gene72017:intron 30.0%
! TAGACTTAGCTTGATTACAT+TGG - chr3.4:95655776-95655795 MS.gene72017:intron 30.0%
! TATATGATTTGCGAAACCAA+TGG - chr3.4:95656273-95656292 MS.gene72017:intron 30.0%
AAAGAAAACAAGTTGCCCAT+TGG + chr3.4:95656292-95656311 None:intergenic 35.0%
AAAGCAAATTGTTGTCACCA+AGG - chr3.4:95655570-95655589 MS.gene72017:intron 35.0%
AAGCAAATTGTTGTCACCAA+GGG - chr3.4:95655571-95655590 MS.gene72017:intron 35.0%
AGATCTAACTCTGTTCTGTA+TGG + chr3.4:95655812-95655831 None:intergenic 35.0%
ATTGAAGACCTACAATGTGT+AGG + chr3.4:95656225-95656244 None:intergenic 35.0%
CCATGTGAATGTACAGTAAA+AGG + chr3.4:95655380-95655399 None:intergenic 35.0%
CTTTCTTGGCTACATATGAA+TGG + chr3.4:95656029-95656048 None:intergenic 35.0%
GATCTAACTCTGTTCTGTAT+GGG + chr3.4:95655811-95655830 None:intergenic 35.0%
TACAGAACAGAGTTAGATCT+AGG - chr3.4:95655812-95655831 MS.gene72017:intron 35.0%
TATCCACAATCATTGCCATT+AGG + chr3.4:95656055-95656074 None:intergenic 35.0%
TATTACTAAGTCTTGGATGG+AGG - chr3.4:95656114-95656133 MS.gene72017:intron 35.0%
TGCTTCTGCTTATAAAAAGC+TGG - chr3.4:95655856-95655875 MS.gene72017:intron 35.0%
! AGATCTAGGATTCCATTACA+TGG - chr3.4:95655826-95655845 MS.gene72017:intron 35.0%
! CCTTTTACTGTACATTCACA+TGG - chr3.4:95655377-95655396 MS.gene72017:intron 35.0%
AAGCATGTGAGTCCATGTAA+TGG + chr3.4:95655841-95655860 None:intergenic 40.0%
CAACCTAATGGCAATGATTG+TGG - chr3.4:95656049-95656068 MS.gene72017:intron 40.0%
GTTTCGTCCCAAAGTAAGTA+TGG - chr3.4:95655232-95655251 MS.gene72017:intron 40.0%
TAGCCAAGAAAGCAACCTAA+TGG - chr3.4:95656037-95656056 MS.gene72017:intron 40.0%
TCATCATCAGTTAATGGCGT+TGG + chr3.4:95656251-95656270 None:intergenic 40.0%
! TTGCCATTAGGTTGCTTTCT+TGG + chr3.4:95656043-95656062 None:intergenic 40.0%
CTAAGAAACGAACACACCCT+TGG + chr3.4:95655590-95655609 None:intergenic 45.0%
TGCTCAGGGCAATAGAAAGA+AGG - chr3.4:95655202-95655221 MS.gene72017:intron 45.0%
! AGAGGTTCATCAACTTGCTC+AGG - chr3.4:95655187-95655206 MS.gene72017:intron 45.0%
! GAGGTTCATCAACTTGCTCA+GGG - chr3.4:95655188-95655207 MS.gene72017:intron 45.0%
!! ATAAGTAATTAATATTAATA+AGG + chr3.4:95656197-95656216 None:intergenic 5.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 95655067 95656328 95655067 ID=MS.gene72017
chr3.4 mRNA 95655067 95656328 95655067 ID=MS.gene72017.t1;Parent=MS.gene72017
chr3.4 exon 95656309 95656328 95656309 ID=MS.gene72017.t1.exon1;Parent=MS.gene72017.t1
chr3.4 CDS 95656309 95656328 95656309 ID=cds.MS.gene72017.t1;Parent=MS.gene72017.t1
chr3.4 exon 95656151 95656214 95656151 ID=MS.gene72017.t1.exon2;Parent=MS.gene72017.t1
chr3.4 CDS 95656151 95656214 95656151 ID=cds.MS.gene72017.t1;Parent=MS.gene72017.t1
chr3.4 exon 95655260 95655355 95655260 ID=MS.gene72017.t1.exon3;Parent=MS.gene72017.t1
chr3.4 CDS 95655260 95655355 95655260 ID=cds.MS.gene72017.t1;Parent=MS.gene72017.t1
chr3.4 exon 95655067 95655159 95655067 ID=MS.gene72017.t1.exon4;Parent=MS.gene72017.t1
chr3.4 CDS 95655067 95655159 95655067 ID=cds.MS.gene72017.t1;Parent=MS.gene72017.t1
Gene Sequence

>MS.gene72017

ATGATTAAGATTGTTTCAAAGTAAGTGTATATGTTACGTTGCATTTGATATATTACTTCCTACAACACTAAAATGTATAACTTTGATGATTTTTTTAATTTGGTTAACATATAGAGCTTTAGAGGTTCATCAACTTGCTCAGGGCAATAGAAAGAAGGTTAAATGGTTTCGTCCCAAAGTAAGTATGGTTCTTCTTTATCCTTAATTGTTCCCTGTATATTTTCCGTATGATTGTTTCTTGTATTAAAAGTGGAATGTGTTTGTCTGTTGAACTCTGTTGAACATGATTAAGATATGAATTCTTGTTTATCCTTTTACTGTACATTCACATGGCAGTGAAACAATATAATCTTGGAACTCTGTTGAGCATGATTAAGATATGAATTCTTGTTTATCCTTTTATTCTTGTTTATCCTCCATAAAAAATTTACAATCTTCTCTCTCACTCAGTAGCTTAACATAGTTAAAAATAGTAGCCAATTGAAAACATATAGGTTTAGGGAAAAGCAAATTGTTGTCACCAAGGGTGTGTTCGTTTCTTAGCTGCTCCACTACTAAATCAATTAAGCTAGCATGTCTAATGCTAATTATAATGTGATGATATTATATGCTTATATAACAACATCTAAACTTTGAAAACAAGACTAAACTCAAATTATTTAGAAAGGGTAGTCTGGTAAAGTAAAAAAATTCACTGAGGTACGGTAGCTAGACTTAGCTTGATTACATTGGAACAGTTGTCCCATACAGAACAGAGTTAGATCTAGGATTCCATTACATGGACTCACATGCTTCTGCTTATAAAAAGCTGGAGAATATGTGCCTTTTTTACACTACTTAACCAATAATTCTTTTGTATAATACCTTCATGAATAGATACTGTTGTAAACTCAAGTCATTATAGAATGATAGATAATAAACTATTTTTTTTATATGAACTAATCACTTTATAAAAATGGCCATTCATATGTAGCCAAGAAAGCAACCTAATGGCAATGATTGTGGATACTATGTGATGAAGAATATGCTAGATATCATCTCTGCTAATATTACTAAGTCTTGGATGGAGGTATTTTAATTTTATGATAACATGTTTATACTATATGTATTGTCAAATATAAACATATCCTTATTAATATTAATTACTTATATTAACCTACACATTGTAGGTCTTCAATGATCCAACGCCATTAACTGATGATGACTTATATGATTTGCGAAACCAATGGGCAACTTGTTTTCTTTACTTGTATAAGGCTTAG
Protein sequence

>MS.gene72017.t1

MIKIVSKALEVHQLAQGNRKKVKWFRPKPRKQPNGNDCGYYVMKNMLDIISANITKSWMEVFNDPTPLTDDDLYDLRNQWATCFLYLYKA