AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073614

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073614.t1 MTR_1g050502 87.624 202 9 2 1 202 1 186 1.60e-123 348
MS.gene073614.t1 MTR_1g050502 87.374 198 9 2 1 198 1 182 3.16e-120 342
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073614.t1 AT1G42990 37.383 214 96 7 6 198 22 218 1.25e-14 71.2

Find 49 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGAGATTCGAAATCGATTT+GGG 0.252626 1.1:-34688530 None:intergenic
AGAGAGATTCGAAATCGATT+TGG 0.334822 1.1:-34688531 None:intergenic
GAAGGCTCTTGAGGAGTTAC+TGG 0.356888 1.1:-34688796 None:intergenic
GGAGTCTGCTGTGCTCTTGT+TGG 0.367032 1.1:+34689266 MS.gene073614:CDS
GGAACCTCTTGAGGAGTTAC+TGG 0.381189 1.1:-34688841 None:intergenic
TTGCAATCGCGTGGTGGCTT+TGG 0.414223 1.1:+34689225 MS.gene073614:CDS
GAATATCTTCGAGAAACTTA+TGG 0.427802 1.1:-34688708 None:intergenic
GAGTCTGCTGTGCTCTTGTT+GGG 0.447976 1.1:+34689267 MS.gene073614:CDS
CCTCGACCCCATCCCTCAAT+CGG 0.450537 1.1:+34688732 MS.gene073614:CDS
TGATCATCCGATTGAGGGAT+GGG 0.451077 1.1:-34688739 None:intergenic
AGCCTTCTTCTGATGAAGCC+AGG 0.459858 1.1:+34688812 MS.gene073614:CDS
TGAAGGGGAATGCAGAAGAC+TGG 0.491226 1.1:+34689152 MS.gene073614:CDS
CCGATTGAGGGATGGGGTCG+AGG 0.492572 1.1:-34688732 None:intergenic
TGGAATTGCGTCGTCATCAT+CGG 0.494775 1.1:+34688675 MS.gene073614:CDS
AGCAGACTCCTGCATGGTCA+TGG 0.499805 1.1:-34689253 None:intergenic
AACCTTGATCATCCGATTGA+GGG 0.504735 1.1:-34688744 None:intergenic
AAACCTTGATCATCCGATTG+AGG 0.512112 1.1:-34688745 None:intergenic
TGGTGCTCCCATGACCATGC+AGG 0.523079 1.1:+34689245 MS.gene073614:CDS
TCATCAGAAGAAGGCTCTTG+AGG 0.530695 1.1:-34688805 None:intergenic
GCCTTCTTCTGATGAAGCCA+GGG 0.533209 1.1:+34688813 MS.gene073614:CDS
AGGAGTTACTGGATCAACTC+TGG 0.544068 1.1:-34688785 None:intergenic
GATTCTCAATCTCTGAGAGA+GGG 0.544535 1.1:-34688633 None:intergenic
TTCGAGAAACTTATGGTAGT+CGG 0.545198 1.1:-34688701 None:intergenic
ATCCCTCAATCGGATGATCA+AGG 0.545906 1.1:+34688742 MS.gene073614:CDS
TCAACTCTGGCTTCATCAGA+AGG 0.547608 1.1:-34688772 None:intergenic
ACCCTGGCTTCATCAGAAGA+AGG 0.549174 1.1:-34688814 None:intergenic
CTTTGTTTGCAATCGCGTGG+TGG 0.550397 1.1:+34689219 MS.gene073614:CDS
TTGATCATCCGATTGAGGGA+TGG 0.552008 1.1:-34688740 None:intergenic
GCAGACTCCTGCATGGTCAT+GGG 0.561161 1.1:-34689252 None:intergenic
CTTCTCATGTCTGATGCCGA+TGG 0.561993 1.1:+34688655 MS.gene073614:CDS
CGCCTTTGTTTGCAATCGCG+TGG 0.567414 1.1:+34689216 MS.gene073614:CDS
TCAATCTCTGAGAGAGGGGA+GGG 0.571872 1.1:-34688628 None:intergenic
GCAAACAAAGGCGCAAAGCA+TGG 0.573484 1.1:-34689206 None:intergenic
CTCAATCTCTGAGAGAGGGG+AGG 0.584965 1.1:-34688629 None:intergenic
GGTTCAGGAGGAACCTCTTG+AGG 0.589392 1.1:-34688850 None:intergenic
TGATGACGACGCAATTCCAT+CGG 0.590462 1.1:-34688671 None:intergenic
CTGCTGTGAAGTCAAGAGAG+AGG 0.599823 1.1:+34689085 MS.gene073614:CDS
AGATTCTCAATCTCTGAGAG+AGG 0.602579 1.1:-34688634 None:intergenic
AGGAGTTACTGGATCAACCC+TGG 0.607536 1.1:-34688830 None:intergenic
CACCACGCGATTGCAAACAA+AGG 0.612821 1.1:-34689218 None:intergenic
GTGTCTGCGACGGAAACAGA+AGG 0.621465 1.1:-34688604 None:intergenic
ATTCTCAATCTCTGAGAGAG+GGG 0.625653 1.1:-34688632 None:intergenic
GATCATCCGATTGAGGGATG+GGG 0.628861 1.1:-34688738 None:intergenic
AAAATCTTGAGACGAAGAGT+AGG 0.630085 1.1:+34689124 MS.gene073614:CDS
AGGGGAGGGAGTGTCTGCGA+CGG 0.631896 1.1:-34688614 None:intergenic
TGATCCAGTAACTCCTCAAG+AGG 0.636811 1.1:+34688837 MS.gene073614:CDS
AGAGATTCGAAATCGATTTG+GGG 0.646761 1.1:-34688529 None:intergenic
TTTCAGGCAGATGAGGAACA+GGG 0.660559 1.1:+34689059 MS.gene073614:intron
GAGCACAGCAGACTCCTGCA+TGG 0.688063 1.1:-34689259 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTCATTATCATTTTATTTT+AGG + chr1.1:34689336-34689355 MS.gene073614:intron 15.0%
!!! TAATTTGTAATTTGTATTCG+AGG + chr1.1:34688970-34688989 MS.gene073614:intron 20.0%
! GACAATAAAAAAAGAAGCAA+AGG - chr1.1:34689320-34689339 None:intergenic 25.0%
!!! CCTAATTAGCTTTTTTGAAA+CGG - chr1.1:34688875-34688894 None:intergenic 25.0%
!!! CTAATTAGCTTTTTTGAAAC+GGG - chr1.1:34688874-34688893 None:intergenic 25.0%
!!! TTTTTTTTTTTTCAACCTGC+TGG + chr1.1:34688945-34688964 MS.gene073614:intron 25.0%
AAATTACAAATTACTCCAGC+AGG - chr1.1:34688963-34688982 None:intergenic 30.0%
CCGTTTCAAAAAAGCTAATT+AGG + chr1.1:34688872-34688891 MS.gene073614:CDS 30.0%
GAATATCTTCGAGAAACTTA+TGG - chr1.1:34688711-34688730 None:intergenic 30.0%
!!! TGTTTTGGTATCTGATTTTC+AGG + chr1.1:34689043-34689062 MS.gene073614:intron 30.0%
AAAATCTTGAGACGAAGAGT+AGG + chr1.1:34689124-34689143 MS.gene073614:CDS 35.0%
AGAGAGATTCGAAATCGATT+TGG - chr1.1:34688534-34688553 None:intergenic 35.0%
TTCGAGAAACTTATGGTAGT+CGG - chr1.1:34688704-34688723 None:intergenic 35.0%
! GAGAGATTCGAAATCGATTT+GGG - chr1.1:34688533-34688552 None:intergenic 35.0%
!! ACGAAGAGTAGGTATTTTGA+AGG + chr1.1:34689135-34689154 MS.gene073614:CDS 35.0%
!! AGAGATTCGAAATCGATTTG+GGG - chr1.1:34688532-34688551 None:intergenic 35.0%
!! CGAAGAGTAGGTATTTTGAA+GGG + chr1.1:34689136-34689155 MS.gene073614:CDS 35.0%
!! GAAGAGTAGGTATTTTGAAG+GGG + chr1.1:34689137-34689156 MS.gene073614:CDS 35.0%
!!! GGTTCTAATGAGAAGTGTTT+TGG + chr1.1:34689028-34689047 MS.gene073614:intron 35.0%
AAACCTTGATCATCCGATTG+AGG - chr1.1:34688748-34688767 None:intergenic 40.0%
AACCTTGATCATCCGATTGA+GGG - chr1.1:34688747-34688766 None:intergenic 40.0%
CCATAAGACCCCATCAAATT+CGG - chr1.1:34688999-34689018 None:intergenic 40.0%
CTCATCCTCCTGCAAAAAAT+CGG - chr1.1:34688575-34688594 None:intergenic 40.0%
TCGAGGTTACCGAATTTGAT+GGG + chr1.1:34688987-34689006 MS.gene073614:intron 40.0%
TTCGAGGTTACCGAATTTGA+TGG + chr1.1:34688986-34689005 MS.gene073614:intron 40.0%
! AGATTCTCAATCTCTGAGAG+AGG - chr1.1:34688637-34688656 None:intergenic 40.0%
! ATTCTCAATCTCTGAGAGAG+GGG - chr1.1:34688635-34688654 None:intergenic 40.0%
! CGAATTTGATGGGGTCTTAT+GGG + chr1.1:34688997-34689016 MS.gene073614:intron 40.0%
! GATTCTCAATCTCTGAGAGA+GGG - chr1.1:34688636-34688655 None:intergenic 40.0%
!! ATCTGATTTTCAGGCAGATG+AGG + chr1.1:34689052-34689071 MS.gene073614:intron 40.0%
!!! AGCTTTTTTGAAACGGGTTC+AGG - chr1.1:34688868-34688887 None:intergenic 40.0%
!!! TTTTTTGAAACGGGTTCAGG+AGG - chr1.1:34688865-34688884 None:intergenic 40.0%
AGGAGTTACTGGATCAACTC+TGG - chr1.1:34688788-34688807 None:intergenic 45.0%
ATCCCTCAATCGGATGATCA+AGG + chr1.1:34688742-34688761 MS.gene073614:CDS 45.0%
CCGAATTTGATGGGGTCTTA+TGG + chr1.1:34688996-34689015 MS.gene073614:intron 45.0%
CGAGGTTACCGAATTTGATG+GGG + chr1.1:34688988-34689007 MS.gene073614:intron 45.0%
TCATCAGAAGAAGGCTCTTG+AGG - chr1.1:34688808-34688827 None:intergenic 45.0%
TGATCATCCGATTGAGGGAT+GGG - chr1.1:34688742-34688761 None:intergenic 45.0%
TGATCCAGTAACTCCTCAAG+AGG + chr1.1:34688792-34688811 MS.gene073614:CDS 45.0%
TGGAATTGCGTCGTCATCAT+CGG + chr1.1:34688675-34688694 MS.gene073614:CDS 45.0%
TTGATCATCCGATTGAGGGA+TGG - chr1.1:34688743-34688762 None:intergenic 45.0%
TTTCAGGCAGATGAGGAACA+GGG + chr1.1:34689059-34689078 MS.gene073614:intron 45.0%
! GGGGTCTTATGGGATGATTA+TGG + chr1.1:34689007-34689026 MS.gene073614:intron 45.0%
! TCAACTCTGGCTTCATCAGA+AGG - chr1.1:34688775-34688794 None:intergenic 45.0%
! TGATGACGACGCAATTCCAT+CGG - chr1.1:34688674-34688693 None:intergenic 45.0%
!! TTTTCAGGCAGATGAGGAAC+AGG + chr1.1:34689058-34689077 MS.gene073614:intron 45.0%
!!! CGATTTTTTGCAGGAGGATG+AGG + chr1.1:34688573-34688592 MS.gene073614:CDS 45.0%
ACCCTGGCTTCATCAGAAGA+AGG - chr1.1:34688817-34688836 None:intergenic 50.0%
AGCCTTCTTCTGATGAAGCC+AGG + chr1.1:34688812-34688831 MS.gene073614:CDS 50.0%
AGGAGTTACTGGATCAACCC+TGG - chr1.1:34688833-34688852 None:intergenic 50.0%
CACCACGCGATTGCAAACAA+AGG - chr1.1:34689221-34689240 None:intergenic 50.0%
CTGCTGTGAAGTCAAGAGAG+AGG + chr1.1:34689085-34689104 MS.gene073614:CDS 50.0%
CTTCTCATGTCTGATGCCGA+TGG + chr1.1:34688655-34688674 MS.gene073614:CDS 50.0%
GAAGGCTCTTGAGGAGTTAC+TGG - chr1.1:34688799-34688818 None:intergenic 50.0%
GAGTCTGCTGTGCTCTTGTT+GGG + chr1.1:34689267-34689286 MS.gene073614:CDS 50.0%
GATCATCCGATTGAGGGATG+GGG - chr1.1:34688741-34688760 None:intergenic 50.0%
GCCTTCTTCTGATGAAGCCA+GGG + chr1.1:34688813-34688832 MS.gene073614:CDS 50.0%
GGAACCTCTTGAGGAGTTAC+TGG - chr1.1:34688844-34688863 None:intergenic 50.0%
TGAAGGGGAATGCAGAAGAC+TGG + chr1.1:34689152-34689171 MS.gene073614:CDS 50.0%
TGCTGTGCTCTTGTTGGGTA+AGG + chr1.1:34689272-34689291 MS.gene073614:intron 50.0%
! CTTTGTTTGCAATCGCGTGG+TGG + chr1.1:34689219-34689238 MS.gene073614:CDS 50.0%
! GCAAACAAAGGCGCAAAGCA+TGG - chr1.1:34689209-34689228 None:intergenic 50.0%
! TCAATCTCTGAGAGAGGGGA+GGG - chr1.1:34688631-34688650 None:intergenic 50.0%
!!! AGTCGCCGATTTTTTGCAGG+AGG + chr1.1:34688567-34688586 MS.gene073614:CDS 50.0%
!!! CGAAGTCGCCGATTTTTTGC+AGG + chr1.1:34688564-34688583 MS.gene073614:CDS 50.0%
AGCAGACTCCTGCATGGTCA+TGG - chr1.1:34689256-34689275 None:intergenic 55.0%
GCAGACTCCTGCATGGTCAT+GGG - chr1.1:34689255-34689274 None:intergenic 55.0%
GGAGTCTGCTGTGCTCTTGT+TGG + chr1.1:34689266-34689285 MS.gene073614:CDS 55.0%
GGTTCAGGAGGAACCTCTTG+AGG - chr1.1:34688853-34688872 None:intergenic 55.0%
GTGTCTGCGACGGAAACAGA+AGG - chr1.1:34688607-34688626 None:intergenic 55.0%
TTGCAATCGCGTGGTGGCTT+TGG + chr1.1:34689225-34689244 MS.gene073614:CDS 55.0%
! CGCCTTTGTTTGCAATCGCG+TGG + chr1.1:34689216-34689235 MS.gene073614:CDS 55.0%
! CTCAATCTCTGAGAGAGGGG+AGG - chr1.1:34688632-34688651 None:intergenic 55.0%
CCTCGACCCCATCCCTCAAT+CGG + chr1.1:34688732-34688751 MS.gene073614:CDS 60.0%
GAGCACAGCAGACTCCTGCA+TGG - chr1.1:34689262-34689281 None:intergenic 60.0%
TGGTGCTCCCATGACCATGC+AGG + chr1.1:34689245-34689264 MS.gene073614:CDS 60.0%
CCGATTGAGGGATGGGGTCG+AGG - chr1.1:34688735-34688754 None:intergenic 65.0%
!! AGGGGAGGGAGTGTCTGCGA+CGG - chr1.1:34688617-34688636 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 34688514 34689371 34688514 ID=MS.gene073614
chr1.1 mRNA 34688514 34689371 34688514 ID=MS.gene073614.t1;Parent=MS.gene073614
chr1.1 exon 34688514 34688893 34688514 ID=MS.gene073614.t1.exon1;Parent=MS.gene073614.t1
chr1.1 CDS 34688514 34688893 34688514 ID=cds.MS.gene073614.t1;Parent=MS.gene073614.t1
chr1.1 exon 34689065 34689288 34689065 ID=MS.gene073614.t1.exon2;Parent=MS.gene073614.t1
chr1.1 CDS 34689065 34689288 34689065 ID=cds.MS.gene073614.t1;Parent=MS.gene073614.t1
chr1.1 exon 34689358 34689371 34689358 ID=MS.gene073614.t1.exon3;Parent=MS.gene073614.t1
chr1.1 CDS 34689358 34689371 34689358 ID=cds.MS.gene073614.t1;Parent=MS.gene073614.t1
Gene Sequence

>MS.gene073614

ATGGACACTTTAGAACCCCAAATCGATTTCGAATCTCTCTTCGCAGAATACGAAGTCGCCGATTTTTTGCAGGAGGATGAGGATATCAATCCTTCTGTTTCCGTCGCAGACACTCCCTCCCCTCTCTCAGAGATTGAGAATCTTCTCATGTCTGATGCCGATGGAATTGCGTCGTCATCATCGGATTCCGACTACCATAAGTTTCTCGAAGATATTCTCCTCGACCCCATCCCTCAATCGGATGATCAAGGTTTCGTTCCTTCTGATGAAGCCAGAGTTGATCCAGTAACTCCTCAAGAGCCTTCTTCTGATGAAGCCAGGGTTGATCCAGTAACTCCTCAAGAGGTTCCTCCTGAACCCGTTTCAAAAAAGCTAATTAGGTAAAACACACATAAGTATTAATTAGTCTATAAGAATCATGATTTTTTTTTTTTTTTTTTTTTCAACCTGCTGGAGTAATTTGTAATTTGTATTCGAGGTTACCGAATTTGATGGGGTCTTATGGGATGATTATGGTTCTAATGAGAAGTGTTTTGGTATCTGATTTTCAGGCAGATGAGGAACAGGGATGCTGCTGTGAAGTCAAGAGAGAGGAAGAAGATGTACGTGAAAAATCTTGAGACGAAGAGTAGGTATTTTGAAGGGGAATGCAGAAGACTGGAGCATTTGCTTCAGTGCTGCTATGCTGAGAACCATGCTTTGCGCCTTTGTTTGCAATCGCGTGGTGGCTTTGGTGCTCCCATGACCATGCAGGAGTCTGCTGTGCTCTTGTTGGGTAAGGCTTGTGATTGCAAATCATATTTCCTTTGCTTCTTTTTTTATTGTCATTATCATTTTATTTTAGGTATTTTAGTTTAA
Protein sequence

>MS.gene073614.t1

MDTLEPQIDFESLFAEYEVADFLQEDEDINPSVSVADTPSPLSEIENLLMSDADGIASSSSDSDYHKFLEDILLDPIPQSDDQGFVPSDEARVDPVTPQEPSSDEARVDPVTPQEVPPEPVSKKLIRQMRNRDAAVKSRERKKMYVKNLETKSRYFEGECRRLEHLLQCCYAENHALRLCLQSRGGFGAPMTMQESAVLLLGILV