AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene057580


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene057580.t1 MTR_7g011390 84.444 135 15 2 45 174 84 217 2.18e-72 217
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCACATGCCAACACAATA+TGG 0.342148 7.2:-85882988 MS.gene057580:CDS
TGAGGATAAAGCTGCTGTTC+AGG 0.399727 7.2:-85882337 MS.gene057580:CDS
GTGAAGCTGTATCATCTTCA+TGG 0.410616 7.2:+85883022 None:intergenic
GGTCCAATATCTAGAGTAGT+TGG 0.437672 7.2:+85882295 None:intergenic
ACCTCCTTGCCATATTGTGT+TGG 0.459988 7.2:+85882979 None:intergenic
CTCTTACTCTAAATTCACTC+TGG 0.470546 7.2:-85883247 MS.gene057580:CDS
ATAAAGCTGCTGTTCAGGAG+GGG 0.477624 7.2:-85882332 MS.gene057580:CDS
TGAAAATGATATGAAGCCCT+TGG 0.478479 7.2:-85882403 MS.gene057580:CDS
GGCATGTGCAGAGGTTGAAT+TGG 0.489875 7.2:+85883000 None:intergenic
GTCCAATATCTAGAGTAGTT+GGG 0.512418 7.2:+85882296 None:intergenic
TAAAGCTGCTGTTCAGGAGG+GGG 0.518520 7.2:-85882331 MS.gene057580:CDS
TCGTTCGTTCCCATGGGTGG+AGG 0.527930 7.2:-85883923 None:intergenic
AGCCTCTTCTGCTAATCGAC+GGG 0.530366 7.2:+85883376 None:intergenic
AGCTCATCCAACGGATCCAA+GGG 0.531382 7.2:+85882387 None:intergenic
GATAAAGCTGCTGTTCAGGA+GGG 0.535418 7.2:-85882333 MS.gene057580:CDS
GAGCTCATCCAACGGATCCA+AGG 0.537088 7.2:+85882386 None:intergenic
ACAGGCCCGCAAAGCAAAAG+AGG 0.538823 7.2:-85883282 MS.gene057580:CDS
AACTCGTTCGTTCCCATGGG+TGG 0.547111 7.2:-85883926 None:intergenic
AGCCCGTCGATTAGCAAAAG+AGG 0.550604 7.2:-85883324 MS.gene057580:CDS
AGCCCGTCGATTAGCAGAAG+AGG 0.554670 7.2:-85883378 MS.gene057580:CDS
CTGTGTTTGTAATGTTTGCA+AGG 0.567137 7.2:+85883159 None:intergenic
TATGAAGCCCTTGGATCCGT+TGG 0.571939 7.2:-85882394 MS.gene057580:CDS
TCGTGTGTGGGCAGTAAAGA+CGG 0.585395 7.2:+85883204 None:intergenic
GAGCCTCTTCTGCTAATCGA+CGG 0.589148 7.2:+85883375 None:intergenic
TATTGTGTTGGCATGTGCAG+AGG 0.593523 7.2:+85882991 None:intergenic
AAAGCTGCTGTTCAGGAGGG+GGG 0.608878 7.2:-85882330 MS.gene057580:CDS
GTGTTTCTCTAGTCGTGTGT+GGG 0.609787 7.2:+85883192 None:intergenic
AGTGTTTCTCTAGTCGTGTG+TGG 0.609826 7.2:+85883191 None:intergenic
GGATAAAGCTGCTGTTCAGG+AGG 0.611925 7.2:-85882334 MS.gene057580:CDS
GAACAGCAGCTTTATCCTCA+AGG 0.621167 7.2:+85882340 None:intergenic
AACACAAAACGTTAGCCTTG+AGG 0.622562 7.2:-85882355 MS.gene057580:CDS
TCTTACTCTAAATTCACTCT+GGG 0.627636 7.2:-85883246 MS.gene057580:CDS
CATGCCAACACAATATGGCA+AGG 0.661413 7.2:-85882983 MS.gene057580:CDS
ACGGTGCATTGCATCAGCAG+TGG 0.666153 7.2:+85883223 None:intergenic
GCCAACACAATATGGCAAGG+AGG 0.737684 7.2:-85882980 MS.gene057580:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATACTAAATGTTATAAAAAT+TGG + chr7.2:85882415-85882434 None:intergenic 10.0%
!! AAATACAAATACAAATACAA+TGG + chr7.2:85882734-85882753 None:intergenic 15.0%
!! TATGATATGAATTGTTAATT+TGG - chr7.2:85882620-85882639 MS.gene057580:intron 15.0%
!! TTATAAGAAATTAAGCAAAA+GGG - chr7.2:85883750-85883769 MS.gene057580:intron 15.0%
!! AATTTCTTATAAGTAAGGAA+AGG + chr7.2:85883742-85883761 None:intergenic 20.0%
!! ATAAAATGATACTACTAATC+TGG - chr7.2:85882576-85882595 MS.gene057580:intron 20.0%
!! CTTATAAGAAATTAAGCAAA+AGG - chr7.2:85883749-85883768 MS.gene057580:intron 20.0%
!! GTATTTGTATTTGTATTTGT+AGG - chr7.2:85882736-85882755 MS.gene057580:intron 20.0%
!! TCTATTTATGATCAGATATA+TGG - chr7.2:85882493-85882512 MS.gene057580:intron 20.0%
!! TGCTTAATTTCTTATAAGTA+AGG + chr7.2:85883747-85883766 None:intergenic 20.0%
!!! ACTTAGATTTCTTTTTTGTT+CGG + chr7.2:85882328-85882347 None:intergenic 20.0%
!!! ATGAATTGTTAATTTGGTTA+TGG - chr7.2:85882626-85882645 MS.gene057580:intron 20.0%
!!! CATAGCTTTTCTTTAAAATT+GGG - chr7.2:85883459-85883478 MS.gene057580:intron 20.0%
!!! GTTTTTAATTATGTATTTGC+AGG - chr7.2:85883783-85883802 MS.gene057580:intron 20.0%
!!! TTTTAACTAACTTGTTATGT+TGG - chr7.2:85882530-85882549 MS.gene057580:intron 20.0%
! AAAAATAAAAGTCTCGTAGA+AGG + chr7.2:85883266-85883285 None:intergenic 25.0%
! GTGTATTAGTAAGAAGTAAA+GGG + chr7.2:85883672-85883691 None:intergenic 25.0%
! TAAAAAAAAAGCAGAAGAAG+AGG - chr7.2:85882868-85882887 MS.gene057580:intron 25.0%
!! GTTTTCTTAAAAATTCCTCT+AGG - chr7.2:85883086-85883105 MS.gene057580:intron 25.0%
!!! CCAATTTTAAAGAAAAGCTA+TGG + chr7.2:85883461-85883480 None:intergenic 25.0%
!!! CCATAGCTTTTCTTTAAAAT+TGG - chr7.2:85883458-85883477 MS.gene057580:intron 25.0%
!!! GGAATTTTTAAGAAAACCTA+CGG + chr7.2:85883083-85883102 None:intergenic 25.0%
AATGATACTACTAATCTGGA+TGG - chr7.2:85882580-85882599 MS.gene057580:intron 30.0%
AGATGAAAAGTGAATAGAAG+TGG + chr7.2:85883393-85883412 None:intergenic 30.0%
CTTCTTACTAATACACCAAA+TGG - chr7.2:85883485-85883504 MS.gene057580:intron 30.0%
GAATAGAAGTGGTATACTTA+TGG + chr7.2:85883382-85883401 None:intergenic 30.0%
GGTGTATTAGTAAGAAGTAA+AGG + chr7.2:85883673-85883692 None:intergenic 30.0%
TCTTACTCTAAATTCACTCT+GGG - chr7.2:85882970-85882989 MS.gene057580:intron 30.0%
TCTTGCTCAAAAAAAACTAC+AGG - chr7.2:85882916-85882935 MS.gene057580:intron 30.0%
TTATGATCAGATATATGGTC+AGG - chr7.2:85882498-85882517 MS.gene057580:intron 30.0%
! TAACAAGATGATGATGATCT+TGG - chr7.2:85882662-85882681 MS.gene057580:intron 30.0%
ATAGATAGATAGAGAGAGAG+AGG + chr7.2:85882373-85882392 None:intergenic 35.0%
CAAAAAAGTAGCAGAAGAAG+AGG - chr7.2:85882814-85882833 MS.gene057580:intron 35.0%
CTCTTACTCTAAATTCACTC+TGG - chr7.2:85882969-85882988 MS.gene057580:intron 35.0%
CTGTGTTTGTAATGTTTGCA+AGG + chr7.2:85883060-85883079 None:intergenic 35.0%
GATAAGAAGAAAGTCCTAGA+GGG + chr7.2:85883720-85883739 None:intergenic 35.0%
TAAAGTTGTTGTCATGTGAC+TGG - chr7.2:85883517-85883536 MS.gene057580:intron 35.0%
TCAACTAATATCCAGACACT+AGG + chr7.2:85883334-85883353 None:intergenic 35.0%
TGAAAATGATATGAAGCCCT+TGG - chr7.2:85883813-85883832 MS.gene057580:intron 35.0%
! ATGATCTTGGCTCTCTATAT+AGG - chr7.2:85882675-85882694 MS.gene057580:intron 35.0%
! ATGGATTGACATGAATGTTC+AGG + chr7.2:85883363-85883382 None:intergenic 35.0%
! TTTTGTAATCTGTATGCAGC+TGG - chr7.2:85883170-85883189 MS.gene057580:CDS 35.0%
!! AAGCACGTTGTTTCTTAGTA+AGG + chr7.2:85883127-85883146 None:intergenic 35.0%
!! CGTTGTTTCTTAGTAAGGAA+AGG + chr7.2:85883122-85883141 None:intergenic 35.0%
!!! CTCTTCTTCTGCTACTTTTT+TGG + chr7.2:85882816-85882835 None:intergenic 35.0%
AAAGGACAAGACAATCCTAG+AGG + chr7.2:85883104-85883123 None:intergenic 40.0%
AACAGGAGATAGGTTTATGC+AGG + chr7.2:85883301-85883320 None:intergenic 40.0%
AACATTACAAACACAGCCGT+AGG - chr7.2:85883064-85883083 MS.gene057580:intron 40.0%
AGCCTCTTGTGTAAAAAGCA+GGG - chr7.2:85883567-85883586 MS.gene057580:intron 40.0%
CAGTTTCATGAACAGGAGAT+AGG + chr7.2:85883311-85883330 None:intergenic 40.0%
CGTACAATACACCAAATGGT+GGG - chr7.2:85883598-85883617 MS.gene057580:intron 40.0%
CTTGTGTAAAAAGCAGGGTA+AGG - chr7.2:85883572-85883591 MS.gene057580:intron 40.0%
GGATAAGAAGAAAGTCCTAG+AGG + chr7.2:85883721-85883740 None:intergenic 40.0%
GTGAAGCTGTATCATCTTCA+TGG + chr7.2:85883197-85883216 None:intergenic 40.0%
!! AACACAAAACGTTAGCCTTG+AGG - chr7.2:85883861-85883880 MS.gene057580:intron 40.0%
!! GACTTTTTGAGCTCATCCAA+CGG + chr7.2:85883841-85883860 None:intergenic 40.0%
!!! TACCCTGCTTTTTACACAAG+AGG + chr7.2:85883572-85883591 None:intergenic 40.0%
AATACACCAAATGGCGCAAC+TGG - chr7.2:85883494-85883513 MS.gene057580:intron 45.0%
ACCTCCTTGCCATATTGTGT+TGG + chr7.2:85883240-85883259 None:intergenic 45.0%
ACTTTACCAGTTGCGCCATT+TGG + chr7.2:85883503-85883522 None:intergenic 45.0%
AGTGTTTCTCTAGTCGTGTG+TGG + chr7.2:85883028-85883047 None:intergenic 45.0%
ATAAAGCTGCTGTTCAGGAG+GGG - chr7.2:85883884-85883903 MS.gene057580:CDS 45.0%
CACTAGGCAGTTTCATGAAC+AGG + chr7.2:85883318-85883337 None:intergenic 45.0%
CAGCCTCTTGTGTAAAAAGC+AGG - chr7.2:85883566-85883585 MS.gene057580:intron 45.0%
CATGCCAACACAATATGGCA+AGG - chr7.2:85883233-85883252 MS.gene057580:CDS 45.0%
CTGCACATGCCAACACAATA+TGG - chr7.2:85883228-85883247 MS.gene057580:CDS 45.0%
GATAAAGCTGCTGTTCAGGA+GGG - chr7.2:85883883-85883902 MS.gene057580:CDS 45.0%
GCGTACAATACACCAAATGG+TGG - chr7.2:85883597-85883616 MS.gene057580:intron 45.0%
GCTGCGTACAATACACCAAA+TGG - chr7.2:85883594-85883613 MS.gene057580:intron 45.0%
GTAAGAAGTAAAGGGCAACC+CGG + chr7.2:85883664-85883683 None:intergenic 45.0%
GTGTTTCTCTAGTCGTGTGT+GGG + chr7.2:85883027-85883046 None:intergenic 45.0%
GTTGTTGTCATGTGACTGGA+AGG - chr7.2:85883521-85883540 MS.gene057580:intron 45.0%
TCATGAAACTGCCTAGTGTC+TGG - chr7.2:85883320-85883339 MS.gene057580:CDS 45.0%
TGAGGATAAAGCTGCTGTTC+AGG - chr7.2:85883879-85883898 MS.gene057580:CDS 45.0%
! AGCCTCTTTTGCTAATCGAC+GGG + chr7.2:85882897-85882916 None:intergenic 45.0%
! GAACAGCAGCTTTATCCTCA+AGG + chr7.2:85883879-85883898 None:intergenic 45.0%
! GAGCCTCTTTTGCTAATCGA+CGG + chr7.2:85882898-85882917 None:intergenic 45.0%
! TATTGTGTTGGCATGTGCAG+AGG + chr7.2:85883228-85883247 None:intergenic 45.0%
! TTACACAAGAGGCTGTTTCC+AGG + chr7.2:85883561-85883580 None:intergenic 45.0%
!! TACAAAATAAAAATAAAAAA+TGG + chr7.2:85882455-85882474 None:intergenic 5.0%
AGCCTCTTCTGCTAATCGAC+GGG + chr7.2:85882843-85882862 None:intergenic 50.0%
AGCTCATCCAACGGATCCAA+GGG + chr7.2:85883832-85883851 None:intergenic 50.0%
CACCAAATGGAGAGAGCCTT+AGG - chr7.2:85883689-85883708 MS.gene057580:intron 50.0%
GAGCCTCTTCTGCTAATCGA+CGG + chr7.2:85882844-85882863 None:intergenic 50.0%
GCCAACACAATATGGCAAGG+AGG - chr7.2:85883236-85883255 MS.gene057580:CDS 50.0%
GGATAAAGCTGCTGTTCAGG+AGG - chr7.2:85883882-85883901 MS.gene057580:CDS 50.0%
GGCATGTGCAGAGGTTGAAT+TGG + chr7.2:85883219-85883238 None:intergenic 50.0%
GTCATGTGACTGGAAGGTCA+CGG - chr7.2:85883527-85883546 MS.gene057580:intron 50.0%
TAAAGCTGCTGTTCAGGAGG+GGG - chr7.2:85883885-85883904 MS.gene057580:CDS 50.0%
TATGAAGCCCTTGGATCCGT+TGG - chr7.2:85883822-85883841 MS.gene057580:intron 50.0%
TCATGTGACTGGAAGGTCAC+GGG - chr7.2:85883528-85883547 MS.gene057580:intron 50.0%
TCGTGTGTGGGCAGTAAAGA+CGG + chr7.2:85883015-85883034 None:intergenic 50.0%
TGCCTAAGGCTCTCTCCATT+TGG + chr7.2:85883694-85883713 None:intergenic 50.0%
! AGCCCGTCGATTAGCAAAAG+AGG - chr7.2:85882892-85882911 MS.gene057580:intron 50.0%
! CTGCTGCCTCTTTTGCTTTG+CGG + chr7.2:85882943-85882962 None:intergenic 50.0%
! TGCTGCCTCTTTTGCTTTGC+GGG + chr7.2:85882942-85882961 None:intergenic 50.0%
AAAGCTGCTGTTCAGGAGGG+GGG - chr7.2:85883886-85883905 MS.gene057580:CDS 55.0%
AAGGTCACGGGTTCAAGTCC+TGG - chr7.2:85883540-85883559 MS.gene057580:intron 55.0%
ACAGGCCCGCAAAGCAAAAG+AGG - chr7.2:85882934-85882953 MS.gene057580:intron 55.0%
ACGGTGCATTGCATCAGCAG+TGG + chr7.2:85882996-85883015 None:intergenic 55.0%
ACTAAAGCTCCCGCATACGC+AGG + chr7.2:85883638-85883657 None:intergenic 55.0%
AGCCTTAGGCAATGCCCTCT+AGG - chr7.2:85883703-85883722 MS.gene057580:intron 55.0%
CTAAAGCTCCCGCATACGCA+GGG + chr7.2:85883637-85883656 None:intergenic 55.0%
GAGCTCATCCAACGGATCCA+AGG + chr7.2:85883833-85883852 None:intergenic 55.0%
! AGCCCGTCGATTAGCAGAAG+AGG - chr7.2:85882838-85882857 MS.gene057580:intron 55.0%
! ATGCGGGAGCTTTAGTGCAC+CGG - chr7.2:85883642-85883661 MS.gene057580:intron 55.0%
!! GTCCTAGAGGGCATTGCCTA+AGG + chr7.2:85883708-85883727 None:intergenic 55.0%
! CAAATGGTGGGACCCCTTCC+CGG - chr7.2:85883610-85883629 MS.gene057580:intron 60.0%
! GCTGTTCAGGAGGGGGGTAT+TGG - chr7.2:85883892-85883911 MS.gene057580:CDS 60.0%
! TGCGGGAGCTTTAGTGCACC+GGG - chr7.2:85883643-85883662 MS.gene057580:intron 60.0%
CATACGCAGGGTCCGGGAAG+GGG + chr7.2:85883625-85883644 None:intergenic 65.0%
CGGGAAGGGGTCCCACCATT+TGG + chr7.2:85883612-85883631 None:intergenic 65.0%
CTTCCCGGACCCTGCGTATG+CGG - chr7.2:85883625-85883644 MS.gene057580:intron 65.0%
GCATACGCAGGGTCCGGGAA+GGG + chr7.2:85883626-85883645 None:intergenic 65.0%
TTCCCGGACCCTGCGTATGC+GGG - chr7.2:85883626-85883645 MS.gene057580:intron 65.0%
CGCATACGCAGGGTCCGGGA+AGG + chr7.2:85883627-85883646 None:intergenic 70.0%
CTCCCGCATACGCAGGGTCC+GGG + chr7.2:85883631-85883650 None:intergenic 70.0%
GCTCCCGCATACGCAGGGTC+CGG + chr7.2:85883632-85883651 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 85882305 85883933 85882305 ID=MS.gene057580
chr7.2 mRNA 85882305 85883933 85882305 ID=MS.gene057580.t1;Parent=MS.gene057580
chr7.2 exon 85883876 85883933 85883876 ID=MS.gene057580.t1.exon1;Parent=MS.gene057580.t1
chr7.2 CDS 85883876 85883933 85883876 ID=cds.MS.gene057580.t1;Parent=MS.gene057580.t1
chr7.2 exon 85883157 85883425 85883157 ID=MS.gene057580.t1.exon2;Parent=MS.gene057580.t1
chr7.2 CDS 85883157 85883425 85883157 ID=cds.MS.gene057580.t1;Parent=MS.gene057580.t1
chr7.2 exon 85882981 85883049 85882981 ID=MS.gene057580.t1.exon3;Parent=MS.gene057580.t1
chr7.2 CDS 85882981 85883049 85882981 ID=cds.MS.gene057580.t1;Parent=MS.gene057580.t1
chr7.2 exon 85882305 85882433 85882305 ID=MS.gene057580.t1.exon4;Parent=MS.gene057580.t1
chr7.2 CDS 85882305 85882433 85882305 ID=cds.MS.gene057580.t1;Parent=MS.gene057580.t1
Gene Sequence

>MS.gene057580

ATGGGTGGAGGCAGCAAAAGCCGAACAAAAAAGAAATCTAAGTCTAAGAAGAAACTGAGTCTGTTCCTCTCTCTCTCTATCTATCTATCTATCACAAGTTATCTTTTCCAATTTTTATAACATTTAGTATTTATCTTTCAACTAATTCCATTTTTTATTTTTATTTTGTAGCATCTTCTGAACGTCAATCTATTTATGATCAGATATATGGTCAGGTGTGTTTAATTTTAACTAACTTGTTATGTTGGTTCATGATCTGTTCTGTACTGATATAAAATGATACTACTAATCTGGATGGATAAAACTCACATATGATATGATATGAATTGTTAATTTGGTTATGGTAACAAAAACTTATAACAAGATGATGATGATCTTGGCTCTCTATATAGGTTTCTGTCTCTCTTACTTTCATTATATCATCTTCCATTGTATTTGTATTTGTATTTGTATTTGTATTTGTATTTGTATTTGTATTTGTATTTGTAGGTACTATCTGATATACAAGCCAAAAAAGTAGCAGAAGAAGAGGAAGCCCGTCGATTAGCAGAAGAGGCTCTTGCTAAAAAAAAAGCAGAAGAAGAGGAAGCCCGTCGATTAGCAAAAGAGGCTCTTGCTCAAAAAAAACTACAGGCCCGCAAAGCAAAAGAGGCAGCAGAAAAGACTCTTACTCTAAATTCACTCTGGGCCACTGCTGATGCAATGCACCGTCTTTACTGCCCACACACGACTAGAGAAACACTTTTTCGAAACCTTGCAAACATTACAAACACAGCCGTAGGTTTTCTTAAAAATTCCTCTAGGATTGTCTTGTCCTTTCCTTACTAAGAAACAACGTGCTTGAATTTTGAATTTATTCATGAAATTTTGTAATCTGTATGCAGCTGGACCATGAAGATGATACAGCTTCACCAATTCAACCTCTGCACATGCCAACACAATATGGCAAGGAGGTGAGCCTTCTACGAGACTTTTATTTTTATTTTTATATGACCTGCATAAACCTATCTCCTGTTCATGAAACTGCCTAGTGTCTGGATATTAGTTGAATGCAACCTGAACATTCATGTCAATCCATAAGTATACCACTTCTATTCACTTTTCATCTTGAAGTCAGTCTTAACTTACTTTGTACTCAGTGATTCAAACATAGCCATAGCTTTTCTTTAAAATTGGGATACTTCTTACTAATACACCAAATGGCGCAACTGGTAAAGTTGTTGTCATGTGACTGGAAGGTCACGGGTTCAAGTCCTGGAAACAGCCTCTTGTGTAAAAAGCAGGGTAAGGCTGCGTACAATACACCAAATGGTGGGACCCCTTCCCGGACCCTGCGTATGCGGGAGCTTTAGTGCACCGGGTTGCCCTTTACTTCTTACTAATACACCAAATGGAGAGAGCCTTAGGCAATGCCCTCTAGGACTTTCTTCTTATCCTTTCCTTACTTATAAGAAATTAAGCAAAAGGGACGTGCTTCAGTTTTTAATTATGTATTTGCAGGTCAACTATGAAAATGATATGAAGCCCTTGGATCCGTTGGATGAGCTCAAAAAGTCAACACAAAACGTTAGCCTTGAGGATAAAGCTGCTGTTCAGGAGGGGGGTATTGGTAGCGCCCAACTACTCTAG

Protein sequence

>MS.gene057580.t1

MGGGSKSRTKKKSKSKKKLTKKVAEEEEARRLAEEALAKKKAEEEEARRLAKEALAQKKLQARKAKEAAEKTLTLNSLWATADAMHRLYCPHTTRETLFRNLANITNTALDHEDDTASPIQPLHMPTQYGKEVNYENDMKPLDPLDELKKSTQNVSLEDKAAVQEGGIGSAQLL