AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0052780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0052780 MtrunA17_Chr1g0152341 91.515 165 6 2 1 162 1 160 4.14e-97 277
Msa0052780 MtrunA17_Chr3g0134971 56.707 164 56 5 4 163 6 158 5.92e-50 157
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0052780 AT1G10140.1 46.541 159 76 5 6 156 3 160 2.84e-24 93.2
Msa0052780 AT1G58420.1 43.750 176 81 4 1 159 1 175 3.39e-23 90.5

Find 23 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATCCTCACAAACATGTTT+TGG 0.309120 1_2:+7067877 None:intergenic
CAACAGCAGAAATTGAATAA+AGG 0.334932 1_2:-7067576 Msa0052780:CDS
TGTTCACCAATAAGAGCATT+AGG 0.382819 1_2:-7067852 Msa0052780:CDS
AACAGCAGAAATTGAATAAA+GGG 0.389999 1_2:-7067575 Msa0052780:CDS
TCTAGTGTTGAAGGAAAAGT+TGG 0.393697 1_2:-7067495 Msa0052780:CDS
ACAGCATAACTCTTTGATCT+AGG 0.434486 1_2:+7067453 None:intergenic
AAGATCATCAGCATCATTAG+AGG 0.441233 1_2:-7067688 Msa0052780:CDS
TGTGGTCAAAATATGAGTTA+TGG 0.456641 1_2:-7067792 Msa0052780:CDS
CCTTCAACACTAGAATCAAA+AGG 0.478362 1_2:+7067504 None:intergenic
TTTCTTAATTATGATGAGGA+AGG 0.493881 1_2:-7067907 None:intergenic
TTTAGTTAATAGAATTGATG+TGG 0.523602 1_2:-7067619 Msa0052780:CDS
AATTTACTAGCAGCATCCAT+TGG 0.526181 1_2:+7067762 None:intergenic
TTACCTAAGTCTAGTAGTGT+TGG 0.528478 1_2:-7067552 Msa0052780:CDS
TTCTTAATTATGATGAGGAA+GGG 0.531983 1_2:-7067906 None:intergenic
ATTCCAACACTACTAGACTT+AGG 0.543949 1_2:+7067549 None:intergenic
TAAGTCTAGTAGTGTTGGAA+TGG 0.550381 1_2:-7067547 Msa0052780:CDS
CATCTTTCTTAATTATGATG+AGG 0.579981 1_2:-7067911 None:intergenic
AGATCAAAGAGTTATGCTGT+TGG 0.581741 1_2:-7067450 Msa0052780:CDS
GAGTTATGGAAGTTATCCAA+TGG 0.620886 1_2:-7067778 Msa0052780:CDS
AGATCATCAGCATCATTAGA+GGG 0.626119 1_2:-7067687 Msa0052780:CDS
AGAACCAAAACATGTTTGTG+AGG 0.637515 1_2:-7067881 Msa0052780:CDS
TGGAATGGCTAAGATTGATG+AGG 0.704946 1_2:-7067532 Msa0052780:CDS
GTAAGAAGCATAACAAACTG+TGG 0.710541 1_2:-7067810 Msa0052780:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAGTTAATAGAATTGATG+TGG - chr1_2:7067700-7067719 Msa0052780:CDS 20.0%
! AACAGCAGAAATTGAATAAA+GGG - chr1_2:7067744-7067763 Msa0052780:CDS 25.0%
TGTGGTCAAAATATGAGTTA+TGG - chr1_2:7067527-7067546 Msa0052780:CDS 30.0%
CAACAGCAGAAATTGAATAA+AGG - chr1_2:7067743-7067762 Msa0052780:CDS 30.0%
AGAACCAAAACATGTTTGTG+AGG - chr1_2:7067438-7067457 Msa0052780:CDS 35.0%
! TGATCCTCACAAACATGTTT+TGG + chr1_2:7067445-7067464 None:intergenic 35.0%
!! TGTTCACCAATAAGAGCATT+AGG - chr1_2:7067467-7067486 Msa0052780:CDS 35.0%
! GCTTTTCCTAATGCTCTTAT+TGG + chr1_2:7067476-7067495 None:intergenic 35.0%
! GTAAGAAGCATAACAAACTG+TGG - chr1_2:7067509-7067528 Msa0052780:CDS 35.0%
GAGTTATGGAAGTTATCCAA+TGG - chr1_2:7067541-7067560 Msa0052780:CDS 35.0%
AATTTACTAGCAGCATCCAT+TGG + chr1_2:7067560-7067579 None:intergenic 35.0%
AAGATCATCAGCATCATTAG+AGG - chr1_2:7067631-7067650 Msa0052780:CDS 35.0%
AGATCATCAGCATCATTAGA+GGG - chr1_2:7067632-7067651 Msa0052780:CDS 35.0%
!! AAGATTTTGCTGAGCTTGTT+AGG - chr1_2:7067660-7067679 Msa0052780:CDS 35.0%
!!! AGATTTTGCTGAGCTTGTTA+GGG - chr1_2:7067661-7067680 Msa0052780:CDS 35.0%
TTACCTAAGTCTAGTAGTGT+TGG - chr1_2:7067767-7067786 Msa0052780:CDS 35.0%
ATTCCAACACTACTAGACTT+AGG + chr1_2:7067773-7067792 None:intergenic 35.0%
! TAAGTCTAGTAGTGTTGGAA+TGG - chr1_2:7067772-7067791 Msa0052780:CDS 35.0%
CCTTCAACACTAGAATCAAA+AGG + chr1_2:7067818-7067837 None:intergenic 35.0%
!! CCTTTTGATTCTAGTGTTGA+AGG - chr1_2:7067815-7067834 Msa0052780:CDS 35.0%
! TCTAGTGTTGAAGGAAAAGT+TGG - chr1_2:7067824-7067843 Msa0052780:CDS 35.0%
ACAGCATAACTCTTTGATCT+AGG + chr1_2:7067869-7067888 None:intergenic 35.0%
AGATCAAAGAGTTATGCTGT+TGG - chr1_2:7067869-7067888 Msa0052780:CDS 35.0%
TGGAATGGCTAAGATTGATG+AGG - chr1_2:7067787-7067806 Msa0052780:CDS 40.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 7067422 7067919 7067422 ID=Msa0052780;Name=Msa0052780
chr1_2 mRNA 7067422 7067919 7067422 ID=Msa0052780-mRNA-1;Parent=Msa0052780;Name=Msa0052780-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|165
chr1_2 exon 7067422 7067919 7067422 ID=Msa0052780-mRNA-1:exon:2389;Parent=Msa0052780-mRNA-1
chr1_2 CDS 7067422 7067919 7067422 ID=Msa0052780-mRNA-1:cds;Parent=Msa0052780-mRNA-1
Gene Sequence

>Msa0052780

ATGATGAGGAAGGGACAGAACCAAAACATGTTTGTGAGGATCATGTGTTCACCAATAAGAGCATTAGGAAAAGCAAGAGATGCATACGTAAGAAGCATAACAAACTGTGGTCAAAATATGAGTTATGGAAGTTATCCAATGGATGCTGCTAGTAAATTTTCTTTATCAAGAAGTCAAAGTGCAGCAACATCAAGAAGATCATCATCAAGAAGATCATCAGCATCATTAGAGGGTAATGAAGATTTTGCTGAGCTTGTTAGGGCTGCTTCTGCTAGAACTTTAGTTAATAGAATTGATGTGGATTTAGTTCTCAAGCAACAACAACAGCAGAAATTGAATAAAGGGTTACCTAAGTCTAGTAGTGTTGGAATGGCTAAGATTGATGAGGATATGCCTTTTGATTCTAGTGTTGAAGGAAAAGTTGGTTTTGTTGCTGATTCTTATCCTAGATCAAAGAGTTATGCTGTTGGACATAGAAGAAATGTTGTTGCTTTCTGA

Protein sequence

>Msa0052780

MMRKGQNQNMFVRIMCSPIRALGKARDAYVRSITNCGQNMSYGSYPMDAASKFSLSRSQSAATSRRSSSRRSSASLEGNEDFAELVRAASARTLVNRIDVDLVLKQQQQQKLNKGLPKSSSVGMAKIDEDMPFDSSVEGKVGFVADSYPRSKSYAVGHRRNVVAF*